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Role of epigenetics in unicellular to multicellular transition in Dictyostelium
Genome Biology volume 22, Article number: 134 (2021)
The evolution of multicellularity is a critical event that remains incompletely understood. We use the social amoeba, Dictyostelium discoideum, one of the rare organisms that readily transits back and forth between both unicellular and multicellular stages, to examine the role of epigenetics in regulating multicellularity.
While transitioning to multicellular states, patterns of H3K4 methylation and H3K27 acetylation significantly change. By combining transcriptomics, epigenomics, chromatin accessibility, and orthologous gene analyses with other unicellular and multicellular organisms, we identify 52 conserved genes, which are specifically accessible and expressed during multicellular states. We validated that four of these genes, including the H3K27 deacetylase hdaD, are necessary and that an SMC-like gene, smcl1, is sufficient for multicellularity in Dictyostelium.
These results highlight the importance of epigenetics in reorganizing chromatin architecture to facilitate multicellularity in Dictyostelium discoideum and raise exciting possibilities about the role of epigenetics in the evolution of multicellularity more broadly.
A critical evolutionary event, the transition from unicellularity to multicellularity, requires the acquisition of cell-cell adhesion and cooperation, and frees the organism for growth and specialization . However, the molecular adaptations that facilitated this transition remain incompletely understood. Multicellularity is believed to have evolved due to both aggregation of non-clonal single cells cooperating to form a multicellular organism  and to clonal development where the individual cells never dissociate [3, 4]. However, how this evolution from primitive amoeba or fungal unicellular organisms occurred ~ 900 million years ago is still incompletely understood . Earlier studies proposed that the acquisition of new genes or new transcription factor networks drove the evolution of multicellularity . However, the emergence of multicellularity does not appear to be explained exclusively by the appearance of new genes as unicellular ancestors contain complex gene repertoires required for multicellular functions [7, 8]. Likewise, the acquisition of new transcription factor networks does not always correlate with multicellularity . These observations suggest a potential role for chromatin regulation in the transition to multicellularity. Indeed, recent work in the unicellular Capsaspora owczarzaki suggested that cellular state changes in this organism were due to non-genetic factors rather than the conserved transcription factor networks present in this unicellular eukaryote . Although many of the individual components for modern epigenetic regulatory systems are present in more ancient ancestors, their integration into a coherent system of gene regulation did not occur until eukaryotes. Moreover, epigenetic diversity expanded rapidly upon the transition to multicellularity [11,12,13,14]. However, whether the increased complexity of epigenetic regulation may have helped to drive the transition to multicellularity is unknown.
We sought to examine multicellularity using Dictyostelium discoideum because it is one of the rare organisms that readily transforms back and forth through both unicellular and multicellular states. When bacterial food is plentiful, Dictyostelium are single-celled amoebae. However, when the food supply is exhausted, Dictyostelium produce a chemoattractant, which signals to neighboring cells to aggregate into a multicellular organism of ~ 215,000 cells [15, 16]. Within 6–8 h, unicellular Dictyostelium aggregate into a multicellular mound that develops to a migrating facultative slug state . After locating an appropriate environment, the slug will subsequently develop into a mature fruiting body, complete with both a stalk and spores that disseminate to distant locations (Fig. 1a). Once food becomes available, spores quickly germinate into single-celled amoebae . The rapidity with which this organism undergoes such dramatic and plastic physiological changes, while maintaining the same DNA code, makes it an ideal model organism for studying the role of epigenetics in multicellularity. Epigenetic changes have been extensively cataloged as totipotent zygotes unidirectionally develop into multicellular organisms [19, 20]. Dictyostelium represents an inherently epigenetic model organism, as Dictyostelium transitions from unicellular to multicellular states and back again and therefore do not represent a developmental progression but rather an adaptive cellularity transition. Additionally, Dictyostelium has a relatively small genome (34 megabases ), is easy to culture in a lab and to manipulate genetically [22,23,24], and can be induced to develop using simple environmental manipulations . Importantly, Dictyostelium contain the conserved epigenetic regulating systems of other eukaryotes , including histone modifications and modifying enzymes that regulate gene expression [26,27,28].
Here we provide the first comprehensive map of epigenetic states (RNA expression, histone modifications, and chromatin accessibility) across four life cycle stages of Dictyostelium. By comparing 2473 orthologues gene expression patterns and chromatin accessibility between unicellular and multicellular Dictyostelium with that of fission yeast S. pombe and C. elegans, we identify candidate genes that could play important roles in the transition to multicellularity. We take advantage of the epigenetic plasticity of Dictyostelium to examine how epigenetic modifications can regulate transitions from unicellular to multicellular states. Furthermore, knockout of four multicellular genes caused delays in multicellularity while overexpression of one of these multicellular genes increased multicellularity. Our findings identify critical, novel regulators of multicellularity, and reveal that epigenomic changes correlate with the transition from unicellularity to multicellularity in Dictyostelium.
Dictyostelium display unicellular and multicellular specific chromatin patterns
To begin to determine whether chromatin modifications might contribute to D. discoideum life cycle changes, overall histone methylation and acetylation levels were assessed by western blots at different cellularity stages. These analyses revealed that histone H3 lysine 4 trimethylation (H3K4me3) levels decreased and H3K4me1 increased significantly upon the transition to multicellularity suggesting that chromatin modification might help regulate the transition to multicellularity in Dictyostelium (Additional file 1: Figure S1A). To examine, in a more unbiased manner, how histone modifications change during different cellularity stages we performed comparative quantitative mass spectrometry at 4 different stages. This analysis confirmed an increase in H3K4me1 upon the transition to multicellularity, as well as identified increases in H2Ax9me2 which was often accompanied by an increase in H2AxS1 acetylation (H2AxS1ac), H2AxK17ac, and H2AxK18me1 (Additional file 1: Figure S1B). This transition to multicellularity was also correlated with an increase in H3K14ac, H4K9ac, and H4K13acK17me1K21ac triply modified histone tails (Additional file 1: Figure S1B). Some of these changes in histone modifications were previously found in Dictyostelium  while others were identified for the first time here (Additional file 1: Figure S1C and S1D). These methods of quantifying histone modification changes are by no means comprehensive, but do reveal that many different chromatin modifications change in overall abundance upon the transition from unicellular to multicellular Dictyostelium discoideum raising the possibility that these changes in chromatin modifications could help to drive multicellularity in Dictyostelium. To more precisely ascertain where within the genome specific changes in chromatin state occur during this transition, we performed Assay for Transposase-Accessible Chromatin using sequencing (ATACseq) , which broadly identifies which regions of the chromatin are open and accessible for transcription and which regions are closed and quiescent at four stages of D. discoideum life cycle: the vegetative, streaming, mound, and fruiting stages. We performed ATACseq on both frozen and fresh samples with highly reproducible results (Additional file 1: Figure S2). Similar to most eukaryotes , the chromatin is compacted directly preceding the transcriptional start sites (TSS) (Fig. 1b). By performing a metagene analysis of the ATACseq data, we found that there was a reduction in the number of genes with accessible promoters immediately after the TSS and an increase in the number of genes with accessible gene bodies as Dictyostelium transition from the unicellular to multicellular forms (Fig. 1c and Additional file 1: Figure S3A). A principal component analysis (PCA) and clustering analyses of the ATACseq datasets clearly separated the vegetative unicellular stage from the multicellular stages, indicating that the accessible chromatin might reveal genomic patterns unique to unicellular and multicellular states of D. discoideum (Fig. 1d, e, and Additional file 2: Table S1). This was accompanied by a progressive increase of accessibility at more gene promoters and a progressive increase of compaction at more gene exons as Dictyostelium proceed from vegetative toward fruiting body stage (Additional file 1: Figure S3B). A motif analysis of accessible regions revealed a motif, CCATATATGG, that was enriched in all multicellular stages but was absent in the unicellular stage (Additional file 1: Figure S4). This motif provides a binding site for MADS-box transcription factors , which, interestingly, have been implicated in the evolution of multicellularity . Deletion of two Dictyostelium MADS-box transcription factors, mef2A and srfA, has been shown to slow progression to multicellular states [33,34,35]. These results raise the possibility that to transition to multicellularity, Dictyostelium reorganizes its chromatin structure to make binding sites for multicellular specific transcription factors mef2A and srfA accessible for binding, likely to facilitate the transcription of their target genes. Alternatively, these transcription factors could act as pioneering transcription factors, opening up the chromatin to facilitate their binding and transcriptional activity. Together these data reveal unicellular and multicellular D. discoideum have different patterns of chromatin accessibility regions throughout the genome, which could expose different transcription factor binding sites at specific stages.
To characterize chromatin modifications, which might explain these alterations in chromatin accessibility, ChIP-seq was performed in duplicate at the four stages analyzed by ATACseq using antibodies that recognize Histone H3, Histone H3 lysine 4 monomethylation (H3K4me1), H3K4 trimethylation (H3K4me3), H3K9me3, H3K27me3, H3K36me3, or H3K27 acetylation (H3K27ac) (Fig. 1f, g and Additional file 1: Figures S5 and S6). A high correlation in ChIPseq peaks was observed across biological replicates indicating good specificity and reproducibility (Additional file 1: Figure S5). A principal component analysis (PCA) of observed ChIPseq patterns revealed that certain chromatin modifications accurately distinguished between the life cycle stages of Dictyostelium. For instance, H3K4me3 and H3K27ac marks clearly separated the unicellular and multicellular stages from each other (Fig. 1f, g). H3K4me1 modifications were able to separate the unicellular stage from the multicellular stages but were not as powerful at distinguishing the different multicellular stages (Fig. 1f, g). H3K36me3 had some capacity to distinguish stages at the 2nd principal component, but H3K27me3, H3K9me3, and Histone H3 did not discern distinct stages even by the 3rd principal component (Additional file 1: Figure S6B, Additional file 3: Tables S2, and Additional file 4: Table S3), suggesting that these marks may not change consistently with life cycle stage and that histone occupancy is not sufficient to distinguish different stages. The chromatin modifications that were capable of distinguishing unicellular from multicellular stages were similar to those marks that we observed to have different overall levels across the life cycle of Dictyostelium (Additional file 1: Figure S1). Additionally, chromatin marks with the capacity to distinguish stages correlate with gene activation, while marks that correlate with gene repression are unable to distinguish Dictyostelium stages. This observation suggests that activating chromatin marks may be more important for determining cellular states than repressive marks. Together, these data demonstrate that chromatin modifications change as D. discoideum transitions through different life cycle stages and that the most dramatic chromatin modification changes occur in H3K4 methylation and H3K27 acetylation upon the transition from unicellular to multicellular states raising the possibility that regulation of these specific chromatin marks could play a critical role in the transition to multicellularity in Dictyostelium.
Histone deacetylation and methylation inhibitors delay multicellularity
To begin to test whether changes in H3K4 methylation and H3K27 acetylation affect the transition to multicellularity, we treated vegetative D. discoideum with chemical inhibitors of histone deacetylation and methylation enzymes and then induced multicellularity by starvation. The histone deacetylation inhibitor Trichostatin A (TSA), the histone methylation enzyme inhibitors sinefungin and BIX 01294 all caused a concentration-dependent delay in the initiation of multicellularity, defined by the amount of time required to achieve the mound stage, as well as a delay in the completion of multicellularity transition, defined by the time required to produce fruiting bodies (Additional file 1: Figure S7). We confirmed that TSA caused an increase in H3K27ac while sinefungin caused a decrease in H3K4me3 and H3K9me3. BIX01294, although reported to be an H3K9me3 inhibitor, led to a decrease in H3K4me3 and H3K27ac without any measurable effects on H3K9me3 in 293 T cells (Additional file 1: Figure S7A). These inhibitors delayed the initiation of multicellularity from ~ 12 h in control conditions to ~ 17 h in 5 μM sinefungin (p=0.001), ~ 15 h in 10 μM BIX 01294 (p=0.047), and ~ 17 h in 1 μM TSA (p=0.0024) (Additional file 1: Figure S7B and S7C). Histone modification chemical inhibition similarly delayed the completion of multicellularity transition (Additional file 1: Figure S7B and S7C). While D. discoideum took ~ 22 h to reach the fruiting body stage under basal conditions, 10 μM BIX 01294, 5 μM sinefungin, and 1 μM TSA significantly increased this time to 27, 37, and 29 h, respectively (Additional file 1: Figure S7B and S7C, BIX 01294 p=0.0126; sinefungin p < 0.0001; TSA p=0.0009). Treatment with sinefungin also caused a reduction in the number of cells making up the multicellular D. discoideum (Additional file 1: Figure S7D). The diameter of the fruiting body, which correlates with the number of cells composing the multicellular form [15, 16], was ~ 9 μm without treatment and ~ 6 um after 5 μM sinefungin treatment (p < 0.05). To determine whether these inhibitors specifically delayed multicellularity or were more generally toxic, the effects of the lowest concentrations of TSA, sinefungin, and BIX 01294 that delayed multicellularity were measured for effects on chemotaxis and cell viability. Although 1 μM TSA and 5 μM sinefungin significantly reduced chemotaxis towards folate (Additional file 1: Figure. S8A and S8B, p < 0.0001 and p=007, respectively), 10 μM BIX 01294 had no significant effect on chemotaxis (Additional file 1: Figure S8A and S8B, p=0.9978). Additionally, 10 μM BIX 01294 and 5 μM sinefungin had no effect on cell viability as assessed by trypan blue staining (Additional file 1: Figure S8C), propidium iodide (PI) staining (Additional file 1: Figure S8D), or annexin V staining (Additional file 1: Figure S8E) while 1 μM TSA caused a modest decrease in cell viability when assessed by annexin V staining (Additional file 1: Figure S8E). Thus, chemicals which regulate histone methylation inhibit multicellularity without having dramatic effects on other properties of D. discoideum. Interestingly, while both sinefungin and BIX 01294 affected other histone methylation marks, they both caused a decrease in H3K4me3. Confirming the importance of H3K4 methylation in multicellularity, previous work has demonstrated that deletion of the H3K4me3 methyltransferase set1, causes unusually rapid multicellularity . Taken together, these results suggest that changes to the amounts or locations of chromatin modifications might regulate multicellularity.
Stage-specific gene expression patterns highlight important transcription factors and chromatin modifiers
To begin to investigate whether the chromatin changes we observed correlate with gene expression changes, we performed RNA-seq analysis on vegetative, streaming, mound, and fruiting stages of D. discoideum. Biological replicates were reproducible (Additional file 1: Figure S9A), individual stages were readily distinguished from each other by correlation analysis in a heatmap and Bland-Altman plots (Additional file 1: Figure S9B-F), and our results correlated well with previously generated RNAseq data (Additional file 1: Figure S9G-J) . As expected, the expression of some genes remained constant, some declined, and others increased at each transition (Fig. 2a and Additional file 5: Table S4). A principal component analysis (PCA) readily distinguished individual stages. The similar mound and streaming stages clustered close to each other, while the unicellular vegetative and the final fruiting body stage clustered far from each other (Fig. 2b). Importantly, this approach recapitulates previously reported stage-specific patterns of gene expression , (Fig. 2c). We confirmed by qRT-PCR the stage-specific gene expression patterns of 5 multicellular and 1 unicellular enriched genes (Fig. 2d). Together, these data suggest that the RNAseq analysis is reliable. Gene ontology (GO) analysis revealed stage-specific enrichment of gene expression in distinct processes and pathways (Fig. 2e). Using a threshold FDR of < 0.05, 1216 genes were enriched in the unicellular state and 1649 genes were enriched in the multicellular states (Fig. 2f). By GO analysis, unicellular genes were enriched for genes involved in protein synthesis (Fig. 2g, upper panel and Additional file 5: Table S4). Conversely, multicellular enriched genes were selectively involved in cell differentiation, development, and adhesion and cellular components required for extracellular elements, such as the cell surface and the plasma membrane (Fig. 2g, lower panel and Additional file 5: Table S4). These changes reflect the shifting cellular priorities during multicellular stages.
As transcription factors play an important role in the transition to multicellularity [37, 38], we next identified transcription factors that had stage-specific expression (Additional file 1: Figure S10A). Ten transcription factors were expressed predominantly in multicellular stages, but none was found to be predominant in the vegetative stage (Fig. 2h). Two of these transcription factors were the MADS-box transcription factors srfA and mef2A, which were previously shown to play a role in D. discoideum progression to multicellular states [33,34,35]. We found that genes which were upregulated in multicellular states were enriched for MADS-box transcription factor binding motifs (Additional file 1: Figure S10C p = 4.08e−25). These results suggest that not only does the chromatin reorganize to expose srfA and mef2A binding sites (Additional file 1: Figure S4), but srfA and mef2A expression is coordinately upregulated (Fig. 2d, h) to facilitate the transcription of SrfA and Mef2A targets.
We also examined stage-specific expression of all putative chromatin modifying and binding proteins, identified based on homology (Additional file 1: Figure S10B). Seventeen chromatin-modifying enzymes or binding proteins displayed unicellular or multicellular specific expression patterns (Fig. 2i). More transcription factors whose expression varied with cellularity stages were upregulated in the multicellular stages, whereas more chromatin-modifying enzymes were upregulated in the unicellular stage (Additional file 1: Figure S10A and S10B, p < 0.05). Notably, one of the chromatin regulating enzymes, the putative histone deacetylase hdaD, was selectively enriched in multicellular states (Fig. 2d,i), raising the possibility that hdaD could be activated in multicellular states to deacetylate histones and reorganize chromatin to facilitate the transition to multicellularity.
Comparative epigenomic analysis of S. pombe, unicellular and multicellular D. discoideum, and C. elegans identifies unicellular and multicellular signatures
To begin to determine whether chromatin modifications or accessibility could be used to identify critical regions whose chromatin changed upon multicellularity, we first investigated whether chromatin modifications in D. discoideum are interpreted in a similar manner as they are in other eukaryotes. We therefore characterized how gene expression correlated with the ChIP-seq and ATACseq data we generated in D. discoideum. As has previously been demonstrated in mammalian cell lines [39, 40], chromatin accessibility correlated with gene expression in Dictyostelium; the top 1000 most lowly and highly expressed genes displayed lower and higher chromatin accessibility, respectively (Fig. 3a and Additional file 6: Table S5). Similarly, the 1216 unicellular enriched genes, based on the RNAseq analysis, were significantly enriched for increased chromatin accessibility at the unicellular stage while the 1649 multicellular enriched genes, were significantly enriched for increased chromatin accessibility at the multicellular stages (Additional file 1: Figure S11A, χ2 = 511.56, p < 0.00001). Histone modifications of specific genes also correlated with their expression in similar ways in D. discoideum as they do in other eukaryotic organisms. H3K4me3, which typically correlates with active transcription [41, 42], displayed increased occurrence on unicellular enriched genes while largely being absent from multicellular enriched genes at the unicellular stage and increased occurrence on multicellular enriched genes while largely being absent from unicellular enriched genes at the multicellular stage (Additional file 1: Figure S11B, χ2 = 391.33, p < 0.00001). For instance, srfA, which turns on during multicellular stages (Fig. 2d), exhibited increased H3K4me3, decreased H3K27me3, and increased chromatin accessibility at its promoter at multicellular stages relative to the unicellular stage, which is when it is more highly expressed (Fig. 3b).
To investigate further whether epigenomic changes could correlate with unicellular or multicellular states, we compared the epigenomic signatures of unicellular and multicellular D. discoideum to two other eukaryotes whose epigenomes are well defined, the unicellular Schizosaccharomyces pombe and the multicellular Caenorhabditis elegans, which are both ~ 1480 million years evolutionarily separated from D. discoideum [43, 44] (Additional file 1: Figure S12A). We identified 2473 conserved regions by predicting orthology and paralogy relationships in all three species by metaphors using pre-computed phylogenetic trees  (Fig. 3c and Additional file 7: Table S6). The majority of these highly conserved genes (79.1%) were evenly expressed across all Dictyostelium stages while 15.6% were unicellular enriched and 5% were multicellular enriched (Additional file 1: Figure S12B). Interestingly, a PCA analysis of the orthologous genes showed that by principal component 3 the expression patterns of unicellular Dictyostelium genes were more similar to that of S. pombe than to multicellular Dictyostelium genes (Fig. 3d).
To determine whether epigenetic features could underlie these unicellular and multicellular gene expression signatures, we examined whether accessible chromatin regions correlated with unicellular or multicellular signatures. We examined the ATACseq profiles of C. elegans  and S. pombe  at the 2473 evolutionarily conserved regions of the genome and found that of the conserved genes, 1352 and 804 were accessible, respectively. Of the D. discoideum conserved genes, 922 were accessible in the unicellular stage while 720 were accessible in the multicellular stages. Among those 922 accessible regions in unicellular D. discoideum, 132 were accessible in multicellular Dictyostelium or C. elegans (14.3%), but 289 sites were exclusively accessible in S. pombe (31.3%). Similarly, among the 720 accessible regions in multicellular D. discoideum, 94 were accessible in unicellular Dictyostelium or S. pombe (13.1%), but 333 sites were exclusively accessible in C. elegans (46.3%). We further reduced these lists of 289 unicellular accessible and 333 multicellular accessible regions to genes which were expressed exclusively in unicellular or multicellular stages. This analysis left us with 67 genes which were accessible and expressed in unicellular state or organisms and inaccessible and not expressed in multicellular state or organisms and 52 genes which were accessible and expressed in multicellular state or organisms and inaccessible and not expressed in unicellular state or organisms (Additional file 8: Table S7), suggesting that these accessible chromatin regions correlate with unicellularity or multicellularity, respectively across evolution. Interestingly, srfA, the MADS-box transcription factor that had previously been shown to play a role in progression to multicellularity in D. discoideum , was one of the genes present in the multicellular list suggesting that our method of identifying critical genes involved in multicellularity based on their chromatin states was successful.
Because bulk RNAseq experiments may mask the gene expression of specific cell types that are critical for transition states, we performed single-cell RNAseq experiments. This analysis clearly distinguished the unicellular state from the multicellular stages (Fig. 3e). We found that the expression of the 67 unicellular genes and 52 multicellular genes, identified based on the orthologous gene analysis of their expression in bulk RNAseq and ATACseq experiments, correlated well with the single-cell RNAseq experiments (Fig. 3f). We next used the single-cell RNAseq data to examine which genes’ expression signatures could account for the progression of D. discoideum from vegetative through slug to fruiting body stages. This lineage tracing analysis revealed that of the top 100 genes whose expression changes helped determine this temporal progression, 54 of them are ribosomal genes (Fig. 3g). This finding demonstrates that the ribosomal heterogeneity that was initially discovered and reported in Dictyostelium  is predominantly driven by gene expression changes in ribosomal protein genes. Interestingly, 13 of these ribosomal protein genes were identified as part of our unicellular signature (Fig. 3f and Additional file 8: Table S7), indicating that changes in chromatin accessibility at ribosomal protein genes could be a critical driver of the evolution of multicellularity. We further confirmed that 4 genes that were accessible and expressed in C. elegans and multicellular Dictyostelium and quiescent in unicellular state or S. pombe were highly enriched or only expressed in multicellular cells while a gene that was accessible and expressed in S. pombe and unicellular Dictyostelium and quiescent in multicellular state or C. elegans was highly enriched in the unicellular stage (Fig. 3h).
Deletion of epigenomically identified multicellular genes delays or prevents multicellularity in D. discoideum
Together, these approaches identified a total of 67 “unicellular” genes, which were accessible and expressed in unicellular state or organisms and inaccessible and not expressed in multicellular state or organisms and 52 “multicellular” genes, which were accessible and expressed in multicellular state or organisms and inaccessible and not expressed in unicellular state or organisms. To begin to test whether these identified genes contribute to the transition between unicellularity and multicellularity, we analyzed knockouts of a subset of these genes. We obtained a previously generated knock-out strain of srfA  and attempted to delete 4 additional “multicellular” genes and 3 “unicellular” genes individually to generate single mutation knockouts, and examined their effects on rates of multicellularity. Despite repeated attempts, one “multicellular” gene (DDB_G0274899) and two “unicellular” gene (DDB_G0267824 and DDB_G0277333) knock-outs were inviable, suggesting that these genes are essential for D. discoideum survival. Successful knock-outs of the remaining 4 genes were validated by sequencing (Additional file 1: Figure S13).
Individual deletion of each of the four “multicellular” genes: srfA; hdaD; DDB_G0283437, a gene which we renamed ammr1 based on its homology to the uncharacterized Alport syndrome gene Ammerc1; and DDB_G0288013; a gene which we renamed smcl1 based on its similarity to a structural maintenance of chromatin (SMC) gene, delayed the transition to multicellularity and extended the entire progression to multicellular state (Fig. 4a,b: srfA p=0.0014 and p < 0.0001; hdaD p=0.0165 and p=0.0011; ammr1 p < 0.0001 and p < 0.0001; smcl1 p < 0.0001 and p < 0.0001, respectively). For instance, knock-out of hdaD caused the initiation of multicellularity to be delayed from 10.75 h in control cells to 13.6 h and the time required to achieve a fruiting body to be delayed from 22.11 h to 29.88 h (Fig. 4a, b). Similarly, srfA knock-out caused a delay of the initiation of multicellularity (16.96 h, p=0.0022) and a delay in complete transition to fruiting body stage (38.83 h, p < 0.0001) and a reduction in the number of cells in the multicellular state to 45% of the wildtype Dictyostelium (Fig. 4c, p=0.0405). Likewise, deletion of ammr1 dramatically slowed multicellularity to 45.8 h (p < 0.0001) and caused complete transition to fruiting body stage to take 87.33 h (p < 0.0001), while deletion of smcl1 caused a complete blockage in the progression past the aggregation stage to any multicellular stages (Fig. 4a, b). By contrast, knock-out of the “unicellular” gene DDB_G0293674, a gene which we renamed hspH2 based on its homology to the heat shock protein hsc70-3, had no effect on the transition to multicellularity or the transition to fruiting body stage (Fig. 4a, b, p=0.5166 and p=0.2585, respectively) but did cause an increase in the fruiting body diameter (Fig. 4c, p < 0.01).
To determine whether deletion of these “multicellular” genes was simply reducing overall fitness, or was more specifically affecting D. discoideum multicellularity, we examined the effect of gene knock-outs on chemotaxis and cell viability. While the “unicellular” gene hspH2 displayed no effect on D. discoideum transition to multicellularity, it did result in chemotaxis delay (Fig. 4d, p < 0.0001), suggesting that this gene is essential for unicellular phenotypes. Of the “multicellular” genes only srfA displayed a decrease in chemotaxis (p=0.0144 by one-way ANOVA) while hdaD, ammr1, and smcl1 were indistinguishable from control cells (Fig. 4d, p=0.7128, p=0.06836, and p=0.1199, respectively). Additionally, knock-outs of all “multicellular” genes had no effect on cell viability under basal conditions or in response to a 95 °C heat shock as assessed by PI staining (Fig. 4d), suggesting that these deletions are not simply making the Dictyostelium sick and are more specifically affecting the transition to multicellularity.
To begin to determine whether the function of the genes that we identified as being necessary for multicellularity was also sufficient to induce a multicellular state in Dictyostelium, we overexpressed two of them, hdaD and smcl1, in WT Dictyostelium. We confirmed the overexpression of these genes by real-time RT PCR (Additional file 1: Figure S14A). While overexpression of neither hdaD nor smcl1 accelerated the timing of multicellularity (in fact smcl1 overexpression caused a slowing of multicellularity timing) (Fig. 5a, b, and Additional file 1: Figure S14B and S14C), overexpression of smcl1 but not hdaD, did cause a ~ 3 fold increase in the number of cells which make up a multicellular Dictyostelium organism (Fig. 5c–e and Additional file 1: Figure S14D), suggesting that smcl1 enhances multicellularity. We found that overexpression of smcl1 had no effect on chemotaxis (Additional file 1: Figure S14E, p=0.1207). Together, these findings suggest that a gene which we identified based on its epigenomic status, the SMC-like gene smcl1, was both necessary and sufficient to regulate multicellularity.
Together, these experiments identified four genes that regulate the transition from unicellularity to multicellularity. To begin to investigate the mechanisms by which these genes control multicellularity, we focused on hdaD, which sequence alignment suggested might encode a histone deacetylase. HDACs are attractive candidates to mediate these processes because of their capacity to deacetylate histones and therefore cause a reorganization of the chromatin. Western blotting of hdaD knockouts revealed an increase in H3K27ac when compared to wild type Dictyostelium (Fig. 5f and Additional file 1: Figure S14F), suggesting that HdaD is a H3K27 deacetylase in D. discoideum. Consistent with this hypothesis, overexpression of hdaD caused a decrease in H3K27 acetylation (Fig. 5g and Additional file 1: Figure S14G). To determine whether HdaD is a direct H3K27 deacetylase we expressed a polyhistidine (His)-tagged catalytic domain of HdaD in bacteria, purified His-HdaDcatalytic domain to a single band, and analyzed its ability to deacetylate histones purified from D. discoideum. We found that His-HdaDcatalytic domain, but not control proteins, was able to deacetylate H3K27 in purified histones (Fig. 5h and Additional file 1: Figure S14H and I), suggesting that HdaD is an H3K27 deacetylase in vitro and in vivo. Reinforcing the hypothesis that HdaD is regulating multicellularity through an alteration in chromatin, we found that hdaD knockouts, similar to the deacetylase inhibitor TSA, had decreased heterochromatin as assessed by electron microscopy (Fig. 5i, j and Additional file 1: Figure S15).
The finding that hdaD deletion inhibits multicellularity highlights the importance of H3K27 acetylation regulation that we had observed correlating on a global level with multicellularity in our ChIPseq experiments (Fig. 1f, g). Together these results indicate that the epigenomic status of genes can be used to identify critical genes necessary for multicellularity. Interestingly histone deacetylases of the hdaD family have been shown to bind to MADS box transcription factors on DNA [50, 51], raising the possibility of a coordinated evolution of transcription factor networks and epigenetic machinery for regulating multicellularity.
Dictyostelium: a new epigenetic model organism for studying the evolution of multicellularity
By comparing the chromatin accessibility at orthologous genes of Dictyostelium to S. pombe and C. elegans, we were able to identify a set of candidate genes whose chromatin status correlated with unicellularity or multicellularity. This analysis identified one gene, srfA, which had previously been shown to play a role in timing of progression to multicellular states [33, 34], as well as several uncharacterized genes. We found that knocking out three novel “multicellular” genes delayed or inhibited multicellularity without making the Dictyostelium less fit. Similarly, the overexpression of one of these “multicellular” genes was sufficient to triple the number of cells integrated into a multicellular state. Together the approaches employed in this study have identified several genes, based on their epigenetic status, which are necessary and sufficient for the transition to multicellularity. This analysis also suggests that a deeper comparison of not only the chromatin accessibility at promoters, as was performed in this study, but also the chromatin accessibility in the gene body or further upstream of the TSS along with specific chromatin modifications across different unicellular and multicellular organisms and Dictyostelium stages could reveal additional genes essential for multicellularity. Additionally, a similar epigenetic comparative analysis of more closely related Amoebozoa, those which can and cannot transition to multicellular forms , could help to further refine this multicellular epigenetic signature. It will be important, in future experiments, to also examine whether changing the epigenome at these critical genes is sufficient to induce multicellularity.
It is interesting to note that the uncharacterized genes which we identified as being important for determining multicellularity elicited unique cellular responses in addition to their effect on multicellularity. This highlights how several independent characteristics, including cell to cell communication, adhesion, cellular specialization, cooperation, and cellular altruism all had to develop for multicellularity to have evolved . It will be interesting, in future studies, to examine how altering one of these characteristics elicits a trade-off in other cellular traits. While increasing the amount of cells which create a multicellular Dictyostelium could provide advantages in facilitating increased cellular specialization, this would have to come at the expense of either a shortening of or increased cell number of the stalk to accommodate the larger sorocarp. This would elicit either a decrease in the distance from the immediate environment which lacks sufficient food that spores would be able to travel or an increase in the number of cells which sacrifice themselves for the survival of the remaining cells in the organism.
Since Dictyostelium rapidly transitions between physiologically and morphologically distinct states, this organism is ideally situated to be utilized as an epigenetic model organism for examining some of the critical outstanding questions in the field of epigenetics. Here we have displayed the ease and capacity to not only perform comparative observational science but also to manipulate the genome and epigenome of Dictyostelium to test theories. Therefore, we feel this will be a useful organism to study a host of epigenetic questions beyond the role of epigenetics in the evolution of multicellularity. Our study has provided a comprehensive epigenomic sequencing of critical stages of Dictyostelium. It also demonstrates how this comprehensive dataset can be used to study the role of epigenetics in multicellularity. This comprehensive dataset opens the possibility of identifying additional processes that epigenetic modifications and drugs can regulate.
Proof-of-principle that epigenetics plays a role in regulating multicellularity (genetic vs epigenetic)
In this study, we used Dictyostelium discoiduem as a model organism to investigate the role of epigenetics in the evolution of multicellularity. Through a combination of chemical, comparative genomic, and epigenomic approaches, we identified several key components of multicellular progression. The histone deacetylase inhibitor, TSA, had previously been demonstrated to delay multicellularity in Dictyostelium , suggesting that histone acetylation could play a critical role in the transition to multicellularity. We confirmed these findings and found that chemical inhibitors of histone methylation, Sinefungin and BIX 01294, also delayed induction of multicellularity, suggesting that chromatin regulation is important for multicellularity. We also examined the distribution of several histone modifications; H3K4me3, H3K4me1, H3K27ac, H3K36me3, H3K27me3, and H3K9me3. Principal component analysis (PCA) demonstrated that specific histone modifications, such as H3K4me3 and H3K27ac, were sufficient to distinguish unicellular from multicellular forms of Dictyostelium. Because our ChIPseq experiments did not include an exogenous spike-in, we can only assess the relative changes in abundance rather than identify the absolute quantifications of histone modification changes. The importance of H3K4me3 in regulating multicellularity in Dictyostelium is reinforced by the demonstration that deletion of the H3K4me3 methyltransferase set1, causes an unusually rapid progression to multicellular states . Our results further demonstrated the importance of H3K27ac by our unbiased identification that the histone deacetylase hdaD, which we demonstrate is an H3K27 deacetylase (Fig. 5f–h), increases expression upon transition to multicellularity (Fig. 2d) and is necessary for an appropriately timed induction of multicellularity (Fig. 4a, b). Together these results suggest that chromatin modifications are important and could help to drive multicellularity in Dictyostelium.
To gain a global view of chromatin accessibility of Dictyostelium, we performed ATAC-seq at specific life cycle stages. We found dramatic differences in chromatin accessibility in the unicellular versus multicellular stages, suggesting that chromatin reorganization during this transition to multicellularity is critical. This analysis revealed that MADS-box transcription factor motifs become accessible upon transition to multicellularity (Additional file 1: Figure S4). The importance of these binding sites becoming accessible is reinforced by previously published work demonstrating that two MADS-box transcription factors, mef2A and srfA, are necessary for appropriate multicellularity timing [33,34,35]. These results suggest that to transition to multicellularity, Dictyostelium reorganizes its chromatin structure to make binding sites for multicellular specific transcription factors mef2A and srfA accessible for binding, to facilitate the transcription of their target genes. Excitingly, class II histone deacetylases, of which hdaD is a member, have been shown to bind to MADS box transcription factors on DNA [50, 51], raising the possibility of a coordinated evolution of transcription factor networks and epigenetic machinery for regulating multicellularity. It will be interesting, in future studies, to examine whether the “multicellular” genes that we identified here, functionally evolved during the transition to multicellularity or whether it is simply a question of when these genes are activated that facilitates multicellularity. While our work, and the work of many other labs, has demonstrated that genetic changes helped contribute to the evolution of multicellularity, this study adds to this work and suggests that these genetic changes were accompanied by contemporaneous epigenetic changes and suggests that the co-evolution of new transcription factor networks and chromatin remodeling coalesced to facilitate multicellularity.
The Axenic strain (AX2) of Dictyostelium discoideum was generously given by Peter Devreotes at Johns Hopkins University. This stain was used as the main material for RNA-seq, ChIP-seq and ATAC-seq experiments. The other axenic strain (AX4) and the srfA knock out mutant was obtained from Dicty Stock Center. We cultured the strain at 22 °C shaken in the incubator at 180 rpm in HL5 medium with 300 μg/ml streptomycin.
Antibodies used for histone chromatin immunoprecipitation and western blots were: rabbit anti-H3 (Abcam Ab1791), rabbit anti-H3K27ac (Abcam Ab4729), rabbit anti-H3K4me3 (Abcam Ab8580), rabbit anti-H3K9me3 (Abcam Ab8898), rabbit anti-H3K27me3 (Abcam Ab6002), rabbit anti-H3K36me3 (Abcam Ab 9050), and rabbit anti-H3K4me1 (Abcam Ab8895). These antibodies have demonstrated specificity in eukaryotes [53,54,55,56,57,58,59].
Quantitative mass spectrometry
Histone chemical derivatization and peptide preparation for mass spectrometry
Histones were propionylated as previously described . Briefly, proteins were diluted with acetonitrile and neutralized with ammonium hydroxide. Chemical derivatization of lysines was performed with propionic anhydride twice, proteins were digested with trypsin, then two additional rounds of derivatization were performed. Propionylated peptides were desalted using an MCX protocol (Oasis MCX cartridge 1 cc/30 mg LP, Waters Corporation).
Orbitrap liquid chromatography-mass spectrometry
Peptides were analyzed with a Thermo Dionex UPLC coupled with a Thermo Q-Exactive HF tandem mass spectrometer. We used an in-house pulled column created from 75 μm inner diameter fused silica capillary packed with 3 μm ReproSil-Pur C18 beads (Dr. Maisch) to 30 cm. Solvent A was 0.1% formic acid in water, while solvent B was 0.1% formic acid in 80% acetonitrile. For each injection, we loaded approximately 1 μg peptides and separated them using a 47-min gradient from 2 to 35% B, followed by a 13 min washing gradient.
For data dependent acquisition (DDA) analysis, a top 20 method was used (default charge state 2, minimum AGC target 5e4, charge exclusion 1 and > 6, and dynamic exclusion 4 s) with full MS (resolution 120,000; AGC 3e6, maximum IT 50 ms) and data dependent-MS2 (resolution 15,000; AGC 1e6, max IT 40 ms, isolation window 2.0 m/z, NCE 27)).
For data-independent acquisition (DIA) analysis, the Thermo Q-Exactive HF was configured to acquire 25 × 24 m/z (covering 300–900 m/z) precursor isolation window DIA spectra (30,000 resolution, AGC target 1e6, maximum inject time 60 ms, 27 NCE) using an optimized staggered window pattern. Precursor spectra (target range ± 15 m/z at 60,000 resolution, AGC target 1e6, maximum inject time 60 ms) were interspersed every 51 MS/MS spectra. The isolation window scheme is detailed on the PanoramaWeb project folder, https://panoramaweb.org/dictyostelium_histones.url
For parallel reaction monitoring (PRM), a Thermo Fusion tribrid mass spectrometer was configured to acquire target m/z using Orbitrap tMS2 (30,000 resolution, AGC target Standard, maximum inject time 60 ms, 30% CID CE) with precursor spectra (target range 290–910 m/z at 60,000 resolution, AGC target 1e6, maximum inject time 60 ms) interspersed every 50 MS/MS spectra. The isolation list is detailed on the PanoramaWeb project folder, https://panoramaweb.org/dictyostelium_histones.url
DDA data analysis
RAW files were converted to MZML using MSConvert (version 3.0.18). Byonic (version 3.10.2) was used to search a focused Dictyostelium FASTA with histone proteins and contaminants (on the PanoramaWeb project folder, https://panoramaweb.org/dictyostelium_histones.url) within Proteome Discoverer (version 2.4) using the following parameters: arg-c digestion, 2 max missed cleavages, minimum peptide length 7; 8 maximum modifications; fixed carbamidomethyl on C and U, variable oxidation on M, variable acetylation on protein N-terminus and K, methylation on R, dimethylation on K and R, trimethylation on protein N-terminal A and K, phosphorylation on S, T, and Y, propionylation on peptide N-terminus and K, propionyl-methylation on K, and GG-propionylation on K; precursor mass tolerance 10 ppm, product mass tolerance 20 ppm; HCD fragmentation.
DIA data analysis
Mass spectrometry data files were demultiplexed and converted to MZML using MSConvert (version 3.0.18). Database search results from DDA data analysis were built into a spectral library using Bibliospec  in Skyline-daily (version 20.1) . DIA files were imported into Skyline using MS/MS IDs in the spectral library (all settings default except Peptide Settings: digestion enzyme ArgC [R|P], background proteome from Uniprot Dictyostelium FASTA (accessed 21 Dec 2020, 12742 entries); Transition Settings: Filter for precursor charges 1–3, ion charges 1–2, ion types y, b, p; from ion 1 to last ion; Full-Scan MS1 filtering with isotope peaks included (Count) and MS/MS filtering for DIA acquisition, centroid product mass analyzer, and Results only isolation scheme; use only scans within 5 min of MS/MS IDs).
PRM data analysis
A target list was built from the Cartesian product combination of known modifications and the Dictyostelium histone proteins (Uniprot, accessed 2020 Dec 31, 7 entries) using a custom Python script. Skyline-daily (version 20.1) was configured with these target peptides (all settings default except peptide settings: digestion enzyme ArgC [R|P], background proteome from Uniprot Dictyostelium histone FASTA (accessed 31 Dec 2020, 7 entries); transition settings: filter for precursor charges 1–3, ion charges 1–2, ion types y, b, p; from ion 1 to last ion; Full-Scan MS1 filtering with isotope peaks included (count) and MS/MS filtering for targeted acquisition, centroid product mass analyzer; include all matching scans). Data was imported and peaks were manually curated using isotope dot product, dot product when spectral library entries were available, and retention time information.
Statistical analysis of mass spectrometry data
Skyline Group Comparison feature was used to calculate differential abundances using the processed DIA data. Parameters included setting the Control group value to “vegetative”; value to compare against as either mound, fruiting, or streaming; Normalization method: Total Ion current; confidence level: 95%; scope: peptide; summary method: Tukey’s median polish; using zero for missing peaks.
mRNA was extracted from AX2 cells stored at − 80 °C using Dynabeads mRNA direct micro purification kit (Invitrogen). Samples were lysed using tissue homogenizer (Kontes) in the lysis buffer. Two biological replicates were assigned for each vegetative, streaming, mound, and fruiting stage respectively. In total 8 groups were prepared for RNA-seq libraries with 500 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). In short, mRNA was fragmented in a cationic buffer and underwent first and second strand synthesis, adenylation, molecular indexed adapter ligation and PCR amplification for 11 cycles. The amplified products were cleaned up by Agencourt AmPure XP Magnetic Beads (Beckman Coulter) and quality checked by Agilent 2200 Tapestation D1000. The optimal cluster density was determined by KAPA library quantification kit before pooling the samples into a pooled library (5 nM) and sequencing through Nextseq 500 platform.
The fastq files were filtered with Q score 30 or above and were trimmed for the sequencing adaptors using CutAdapt (version 2.5). The analysis pipeline started with pseudo-alignment of the reads using kallisto , followed by building an index and quantification process, which generated h5 files containing the raw binary files for preliminary differential analysis in sleuth . Differential analysis was conducted in EdgeR ; briefly, the DEGlist object was created, and genes were kept that achieved at least one count per million (cpm) in two biological replicate samples. The effective library size was computed using Trimmed Mean of M values (TMM) normalization. The significant genes were deducted by computing NB exact genewise tests with corrected p < 0.05. The gene ontology (GO term Gene Ontology Consortium 2015) for over-representation analysis and diagrams were generated by R package clusterProfiler (version 3.18.0) . Sequencing QC matrix is shown in Additional file 9: Table S8.
10 million D. discoideum cells were harvested and dissociated at different life cycle stages as described in  with the following modifications. After dissociation cells were cross-linked with 1x linking buffer (11 mM HEPES-NaOH, 110 mM NaCl, 1.1 mM EDTA, and 1.1 mM EGTA) with 1% formaldehyde for 10 min at RT and quenched by 2 M glycine. The samples were fragmented by applying a biorupter for 25 cycles in the cold room with 30 seconds on and 30 seconds off per cycle. The precleared chromatin was incubated with antibody-coupled bead slurries and rotated at 4 °C overnight. DNA was eluted from the beads by 200 μl TE with 1% SDS.
Histone ChIP-Seq libraries were generated using the Ovation Ultralow V2 kit (Nugen, 0344-32) according to the manufacturer’s instructions. Libraries were PCR amplified for 13-16 cycles depending on the antibody, and library quality was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies). Seventy-five bp reads were generated on the Illumina Nextseq 500 (Illumina). ChIP-seq were sequenced to a depth of at least 8 million total reads/sample.
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc (version 1.5) was use to summarize the fastQC (version 0.11.3) results , and the trimmed files were mapped to the Dictyostelium discoideum genome (version 2.5)  using bowtie2 (version 188.8.131.52) . The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2 (version 184.108.40.20660309) using H3 as controls [70, 71]. Both DNA input and H3 were used as controls. The peaks were visualized by Integrative Genomics Viewer (IGV 2.3.44). Differential binding analyses were performed by R package Diffbind (version 3.0.14) using log2 normalized ChIP read counts with FDR < 0.05 . The metagene analysis and genomic feature distribution were conducted by ChIPSeeker (version 1.26.2) using anotatePeak function with narrowpeak files as input . Transcription start site (TSS), exon, intron, and transcription termination site (TTS) were determined by using makeTxDbFromBiomart function from the Ensemble BioMart database (version 2.7). Promoters were defined by the regions 1500 bp upstream to the TSS, and downstream was defined as the 3000 bp downstream of gene end (TTS). Since some annotations may overlap, we adopt the default principle in ChIPSeeker to prioritize genomic annotation in the following order: promoter, exon, intron, downstream and intergenic. Sequencing QC matrix is shown in Additional file 9: Table S8.
To assess regions of open chromatin, frozen pellets of D discoideum cells from the various stages were washed twice with cold PBS and lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal-630. Nuclei were transposed using the Nextera DNA Library Prep Kit (Illumina, FC-121-1030). Transposed libraries were amplified for 11 cycles and size selected for fragments ranging 200-1000 bp. ATAC-seq experiments were sequenced to a minimum depth of 10 million reads/sample. For preparation of fresh samples, Dictyostelium were physically dissociated and washed twice with PBS with 0.04% BSA and lysed with 10 mM Tris-HCL (pH 7.4), 10 mM NaCl, 3 mM MgCl2, 0.5% Tween 20, 0.5% NP-50, 0.05% digitonin (Promega G944A), 1% BSA, and 0.5% cellulase on ice or room temperature for 30 min to fully lyse the cells. Validation of equivalent ATACseq lysine of different stages was performed by trypan blue staining and optimized by real-time PCR detection of ribosomal RNA release.
The raw fastq files were trimmed for the first and last 8 nucleotides, the multiqc was use to summarize the fastQC results , and the trimmed files were mapped to the Dictyostelium discoideum genome  using bowtie2 , and the mitochondria genome was removed in the alignment process. The duplicated reads were removed by picard and sorted bam files were subject to peak calling with MACS2 [70, 71]. The peaks were visualized in Integrative Genomics Viewer (IGV 2.3.44). Likewise, open chromatin regions and peak annotation were deducted with Diffbind  and ChIPSeeker, respectively . Sequencing QC matrix is shown in Additional file 9: Table S8.
The stage/unicellular/multicellular specific open chromatin regions, enriched histone binding sites, and the promoters of significant enriched genes were extracted as the input sequence for homer (version 4.11.1) . All the promoter sequences were obtained from dictyBase as the background sequence . The motif discovery was performed using “findMotif.pl” command from homer.
Orthologous gene analysis
The phylogenetic tree was constructed on interactive tree of life (iTOL version 6) . The orthologous genes among D. discoideum, C.elegans and S.pombe were obtained using metaphOrs (version 1.0) based on phylogeny orthology prediction at genomic scale . The comparison among the species and intersection regions were extracted using bedtools (version 2.27.1) . The graphs were generated on R (version 4.0.2), excel or prism (version 9).
The D. discoideum cells were harvested in mid-log phase for 5*108 cells. The cells were suspended in developmental buffer (5 mM Na2HPO4, 5 mM KH2PO4, 1 mM CaCl2, and 2 mM MgCl2) and washed 3 times. The multicellularity assays were performed on KK2 agar plates. 100 nM, 500 nM, and 1000 nM chemical inhibitors (Trichostatin A, T8552; BIX 01294 trihydrochloride hydrate, B9311; (R)-PFI-2, SML1408p; Sinefungin, ab144518) were added to the KK2 agar plates. The picture capture time points for the multicellularity assay with chemical treatment were set at 8 h, 16 h, 19 h, and 24 h. The picture capture time points for the multicellularity assay with mutant strains were set at 8 h, 16 h, 21 h, 25 h, and 41 h.
Cell number quantification and morphological measurement
To quantify the germ cell number in the fruiting bodies, the assay was performed as in . Germ cell number from individual fruiting bodies were collected by pipette and were placed in 20 μl PBS. The cells were counted with a hemocytometer (Hausser Scientific Cat.#3520). The diameter of the individual mound and fruiting bodies were measured using stereo Discovery V8 microscope.
Chemotaxis assays were performed as in . Briefly, the protocol was modified as follows. The D. discoideum cells were cultured in a density of 2× 106 cells/ml for the purpose of the experiment. The cells were pelleted in a 1X KK2 buffer (2.2 g KH2PO4, 0.7 g K2HPO4). The cells were starved for 5–8 h in a shaker and resuspended at a concentration of 1× 108 cells/ml. For making the chemotaxis plates, 4 wells were made in the 1X KK2 agar plates (1X KK2 buffer and 1.5 g Agar). 4 small dots at 6 mm from the edge of each well were marked on the agar plates for showing the location of cells deposition. 20 μl of 250 μM of folic acid (Millipore Sigma CAS 59-30-3) dissolved in 100 mM NaOH were injected into the wells by a P10 pipette for 20 min absorbing by the agar. 1 μl of D. discoideum were loaded on the dots and the plates were incubated at room temperature in a humidified chamber. The movement of cells were captured after 5 h using Zeiss steoREO Discovery V8 microscope. The number of cells were counted in each direction (north, south, east, and west) in a 30° angle range and plotted in Prism 8 (Version 8.1.1).
Annexin V, propidium iodide, and trypan blue staining
Cell viability was examined by trypan blue (VWR), propidium iodide (BD Biosciences), and Annexin V staining (BD Biosciences). For Annexin V staining, cells were washed twice with cold PBS and suspended in 1X Binding Buffer (10 mM Hepes pH 7.4, 140 mM NaCl, and 2.5 mM CaCl2) at a concentration of 1 million cells/ml. One hundred microliters of the solution was transferred to a new tube and 5 μl of FITC Annexin V was added to the cells and incubated for 15 min at room temperature in the dark. The samples were imaged using a fluorescent microscope (Nikon Eclipse E600) with 485/535 nm (FITC) filter and images were analyzed by ImageJ (1.0).
For trypan blue staining, 10 μl 0.4% solution of trypan blue was mixed with 10 μl of cells at 5E5 cells/ml. The mixture was counted on a hemacytometer immediately after mixture.
For PI staining, 1E6 D. discoideum cells were treated with 1 μM TSA, 5 μM sinefungin, or 10 μM BIX 01294 for 6 h. Cells were subsequently washed and resuspended with cold PBS supplemented with 5% FBS and stained with 2 mg/ml propidium iodide (BD Biosciences) at room temperature for 10 min. Stained cells were fixed with 1% PFA. Samples were analyzed by BD LSR Fortessa (BD Biosciences) and data analysis was performed using Flow Jo (Tree Star).
CRISPR-Cas9 knock-out experiment
The all-in-one sgRNA and Cas9 expression vector pTM1285 were obtained from Quantitative Biology Center (QBIC) Riken, Japan. The sgRNAs were designed on CRISPOR tool . sgRNA were ligated to predigested pTM1285 with BbsI (NEB), and stable competent cells were transformed with the resulting construct (NEB, C3040). Ligation was confirmed by PCR and Sanger sequencing. Primers used were sense oligo for the target 5′-AGCAN(1)NNNNNNNNNNNNNNNNNNN(20)-3′ and tracrRNA 5′-AAGCTTAAAAAAAGCACCGACTCGGTGCC-3′. The sequencing primer was 5′-AAGCTTAAAAAAAGCACCGACTCGGTGCC-3′. The validated plasmids were transformed into the cells using calcium phosphate precipitation method . Briefly, 10 μg plasmid DNA is co-precipitated with 60 μl of 1.25 M CaCl2 in HBS buffer (4.0 g NaCl, 0.18 g KCl, 0.05 g Na2HPO4, 2.5 g HEPES and 0.5 g D-glucose, pH adjusted to 7.1). The DNA solution was added to the plates for 30 min and then 12.5 ml Bis-Tris (2.1 g Bis-Tris, 10 g proteose peptone, 5 g yeast extract, and 10 g D-glucose in distilled water, pH adjusted to 7.1 with HCl) for 4–8 h. The condensed DNA on cell surface was transformed into the cells by 15–18% glycerol for exact 5 min and incubated with 12.5 ml Bis-Tris solution overnight to allow the expression of the selection marker. The medium was replaced by HL5 with 10-15 μg/ml of G418 after 16 h, and cultured for another 3 days. The cells were plated on SM agar plates with K. aerogenes and incubated for 3–4 days until plaque formed. The cells were transferred and expanded in the HL5 medium with 300 μg/ml streptomycin. Knock-out strains were validated by sanger sequencing.
Overexpression Dictyostelium strains
cDNA of hdaD and smcl1 was cloned into pJSK123 over-expression plasmid  between BamHI and AvrII sites. The recombinant plasmids were transformed into cells using calcium phosphate precipitation method . Briefly, 10 μg plasmid DNA is co-precipitated with 60 μl of 1.25 M CaCl2 in HBS buffer (4.0 g NaCl, 0.18 g KCl, 0.05 g Na2HPO4, 2.5 g HEPES and 0.5 g D-glucose, pH adjusted to 7.1). The DNA solution was added to the plates for 30 min and then 12.5 ml Bis-Tris (2.1 g Bis-Tris, 10 g proteose peptone, 5 g yeast extract, and 10 g D-glucose in distilled water, pH adjusted to 7.1 with HCl) was added for 4–8 h. The condensed DNA on the cell surface was transformed into the cells by 15–18% glycerol for 5 min and incubated with 12.5 ml Bis-Tris solution overnight to allow the expression of the selection marker. The medium was replaced with HL5 with 10–15 μg/ml of G418 after 16 h, and cultured for another 3 days. The cells were then plated on SM agar plates with K. aerogenes and incubated for 3–4 days until plaques formed. The cells were transferred and expanded in the HL5 medium with 300 μg/ml streptomycin. Over-expression strains were validated by real-time PCR.
Quantitative real-time PCR (qRT-PCR)
The differential expression of candidate genes were analyzed using qRT-PCR. Total RNA was extracted from D. discoideum cells using Invitrogen PureLink RNA (Invitrogen, 12183025). First strand cDNA synthesis was conducted using SuperScript III First-Strand Synthesis (Invitrogen, 18080051). qRT-PCR of cDNA was performed using iTaq Universal SYBR Green Supermix (Bio-Rad, 172-5122) on a CFX96 Real-Time System (Bio-Rad). The PCR assay contained 1:4 diluted reverse transcription products, 1X master mix, and 200 nM of each primer, and was performed with 5-min initial denaturation at 95 °C followed by 40 cyles of 95 °C for 5 s and 60 °C for 45 s. The mtRNA of D. discoideum was used for internal normalization for each gene. The comparative Ct method (ΔΔCt) was used to calculate gene expression. The primer sequences of the selected genes were designed using Macvector (15.5.0). The following gene-specific primers were used: mtRNA-forward, 5′-gggtagtttgactggggcgg-3′, mtRNA-reverse, 5′-cactttaatgggtgaacacc-3′; DDB_G0283437-forward, 5′-gagggtgtataggtacatttgcagag-3′, DDB_G0283437-reverse, 5′-tgggttccaatttcccaatcccaaac-3′; DDB_G02813787-forward, 5′-tccctaacaccaacatcaaccaacga-3′, DDB_G02813787-reverse, 5′-tatacatgaccagtttcggaggcaac-3′; DDB_G0288013-forward, 5′-acaagaaatcgattgggagatgt-3′, DDB_G0288013-reverse, 5′-tggcatttgttcttggatttttct-3′; DDB_G0279267-forward, 5′-tggctcaccaataccatcacctccat-3′, DDB_G0279267-reverse, 5′-cgagttcgaactattgctgttg-3′; DDB_G0274899-forward, 5′-ccagagggaaataatagtcctggt-3′, DDB_G0274899-reverse, 5′-ctccaattcgaaccacaaac-3′; DDB_G0267824-forward, 5′-gcagctggtagtagttcatcca-3′, DDB_G0267824-reverse, 5′-tgtgcatattcttctttaccctcaa-3′; DDB_G0277333-forward, 5′-tggcatttctcaggcagtttcgacca-3′, DDB_G0277333-reverse, 5′-ccaacatcagtgagggtattca-3′; DDB_G0293674-forward, 5′-accaacgtgctcttcgtcgtttgag-3′, DDB_G0293674-reverse, 5′-ggaacgatgtttgtcattacaccac-3′; DDB_G0294934-forward, 5′- gggtagtttgactggggcgg-3′, DDB_G0294934-reverse, 5′- cactttaatgggtgaacacc-3′; DDB_G0279267_OE-forward, 5′-tatggatccatgtcaacaattcatc-3′, DDB_G0279267_OE-reverse, 5′-tatcctaggttaatcgtcttcgctta-3′; DDB_ G0288013_OE-forward, 5′-tatggatccatggatattgcacaatcaattca-3′, DDB_ G0288013_OE-reverse, 5′-tatcctaggctataaagtttttaagaaattttg-3′, DDB_G0279267_Cat-forward, 5′- caacaatcatcacaattacc-3′, DDB_G0279267_Cat-reverse, 5′-tatcctaggttaatcgtcttcgctta-3′.
HEK 293 T cells (ATCC CRL-3216) were seeded on 6 well plates overnight, then treated with 0.25 μM, 0.5 μM, 1 μM, or 5 μM Trichostatin A (T8552, Millipore Sigma); or with 0.5 μM, 1 μM, 5 μM, or 10 μM Sinefungin (ab144518); or with 1 μM, 10 μM, 20 μM, or 30 μM BIX 01294 (B0311) for 16 h. Each concentration was seed with three replicates of 1 million cells before collection and analysis of effects on histone methylation and acetylation by western blotting.
Western blot analysis
Cells were lysed with RIPA buffer and quantified by Bradford assay (Biorad 5000006). Five to 10 μg of proteins were loaded for gel electrophoresis and transferred to nitrocellulose membrane (Bio rad 1620097) with 100 V for 1.5 h. The membranes were incubated in 5% milk for 1 h at room temperature and incubated with primary antibodies (1:1000 dilution). After washing with TBST 3 times, each for 10 min, the membranes were incubated with secondary antibody (Millipore 3136001, Rabbit IgG, 1:3000 dilution). The blots were reacted with chemiluminescent HRP substrate (Millipore WBKLS0500) and imaged in ChemiDoc Touch Imaging System (Bio rad).
The coding sequence of the catalytic domain of hdaD was cloned as an in-frame fusion to the His tagged vector pET28a. The recombinant protein was expressed in E. coli BL21. Overnight induction of protein expression was carried out with 1 mM IPTG at 18 °C. Bacteria were harvested at 4000 rpm, 4 °C, and resuspended in 10 mL protein purification lysis buffer (50 mM Tris-HCl pH 7.5, 0.25 M NaCl, 0.1% Triton-X, 1 mM PMSF, 1 mM DTT, 20 mM imidazole, and protease inhibitors). After freezing the pellet at − 80 °C for 1 h, the lysate was sonicated with a Bioruptor for 5 min on high level with 30 s on and 30 s off. Proteins were purified with Ni-NTA beads (Qiagen). Proteins and beads were washed 3 times with protein purification lysis buffer before incubating the beads with elution buffer (400 mM imidazole in protein purification lysis buffer, pH 8.0) for 30 min. Eluates were dialyzed overnight at 4 °C with dialysis buffer (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 1 mM DTT, and 20% glycerol). Bradford assays and SDS-page gel electrophoresis followed by coomassie staining were performed to determine the integrity and quantity of purified proteins. Histone proteins were purified from D. discoideum using the EZExtract core histone isolation kit (BioVision). In vitro deacetylation reactions were performed with 10 μg of histone proteins and 5 μg of hdaD protein or 5 μg GST-RPA-2 protein as a control. The deacetylation reaction was performed in a buffer solution (50 mM Tris-HCl, 4 mM KCl, 4 mM MgCl2, 0.2 mM DTT, 1 mM NAD+) and incubated at 30 °C for 30 min. Western blot analysis was performed as previously described.
Single-cell RNA sequencing data analysis
D. discoideum was dissociated into single cells from different stages by physical pipetting with PBS + 0.04% BSA. For each sample, the cells were counted and diluted to 1000 cell/μl in 1X PBS with 0.04% Bovine Serum Albumin (BSA) prior loading to 10X Genomics Chromium machine. 10X Chromium Single Cell 3′ v3 reagent kits were used according to the manufacturer’s instructions to generate scRNAseq libraries. Libraries were sequenced paired-end 150 bp on Illumina Hiseq4000/Novoseq (Novogene).
Single-cell RNA sequencing data analysis
Fastq files were processed with Cell Ranger (version 3.1.0) (https://support.10xgenomics.com) on the DolphinNext pipeline builder  to generate the merged gene-barcode matrix. Matrix was loaded into R (version 3.6.3) and analyzed mainly with Seurat package (, version 3.1.5). Low-quality cells or outliers were filtered out from the data by the following threshold: 200 < total Gene count < 7000, 500 < total UMI count < 30000. Filtered matrices were normalized with SCTransform  and reduced the dimension with principal component analysis. The batch effect was corrected by harmony . The significant principal components (PCs) are used to generate the UMAP plot for visualization. Clustering was performed by the Louvain algorithm based on K-nearest neighbor graph. Hurdle model tailored was used to perform differential expression analysis of the individual clusters . Gene Ontology (GO) analysis was performed with clusterProfiler (version 3.18.0) .
For trajectory inference analysis, the cells from vegetative, slug, and fruiting stages were down-sampled and merged. The uninformative genes were filtered out by keeping the genes expressing 3 UMIs per cell for at least 10 cells. The filtered matrices were normalized with full quantile normalization and reduced the dimension with PCA. The first 3 PCs were used for k-means clustering and subsequent analysis. Slingshot wase performed to predict the multicellularity lineage . The generalized additive model wse used to identify the temporally expressed gene through the pseudotime.
Dictyostelium cells were synchronized according to previously published methods [89, 90]. Briefly, the cells were grown to stationary phase with a density of 1.2 × 107/ml. These cells were diluted into fresh HL5 medium at a density of 106/ml. Then the cells were shifted to 11.5 °C incubation for 20 h in 6-well plates. At this time 1 μM TSA was added to the positive control cells. The synchronized cells were fixed in fixative (2.5% glutaraldehyde 1.25% paraformaldehyde and 0.03% picric acid in 0.1 M sodium cacodylate buffer (4.28 g sodium cacodylate, 25 g calcium chloride, 2.5 ml 0.2 N hydrochloric acid in 200 ml of distilled water, pH 7.4) with 1:1 dilution of cell medium for 16 h at 4 °C. Then, the cells were washed in 0.1 M cacodylate buffer and postfixed with 1% osmium tetroxide (OsO4)/1.5% potassium ferrocyanide (KFeCN6) for 1 h. The cells were washed twice in water, and once in maleate buffer (MB)(50 mM maleate acid, 0.2 N NaOH) and incubated in 1% uranyl acetate for 1 h followed by 2 washes in water and subsequent dehydration in grades of alcohol (10 min each; 50%, 70%, 90%, 2 × 10 min 100%). The samples were then put in propyleneoxide for 1 h and infiltrated overnight in a 1:1 mixture of propyleneoxide and TAAB Epon (TAAB Laboratories Equipment Ltd, https://taab.co.uk). The following day the samples were embedded in TAAB Epon and polymerized at 60 °C for 48 h. Ultrathin sections (about 60 nm) were cut on a Reichert Ultracut-S microtome, picked up on to copper grids, stained with lead citrate, and examined in a JEOL 1200EX transmission electron microscope or a TecnaiG2 Spirit BioTWIN, and 30 images of each condition were recorded with an AMT 2 k CCD camera.
The heterochromatin ratios were quantified with FIJI (Version 1.0). A 15% threshold was set for all the images which were then binarized to reveal heterochromatin regions for quantification. The heterochromatin regions were calculated for each of 30 nuclei (excluding the nucleolus) and calculated as a percentage.
Availability of data and materials
All ChIPseq, RNAseq, and ATACseq datasets are available in the GEO database accession # GSE137604 . The codes for all bioinformatic analyses are available at GitHub at https://github.com/BCHGreerlab/Dictyostelium . Unprocessed and uncompressed imaging data is available at https://data.mendeley.com/datasets/zfhh6xzck4/3. Mass spectrometry data is available in the PanoramaWeb project folder, https://panoramaweb.org/dictyostelium_histones.url. Mass spectrometry data is also available at ProteomeXchange repository ID: PXD024225 .
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General: We thank Peter Devreotes, Marc Edwards, Budri Sharif, and other members of the Devreotes lab for the Dictyostelium strain and experimental advice about Dictystelium culturing conditions. We thank J. Lieberman and A. Brunet for critical reading of the manuscript.
The review history is available as Additional file 10.
Peer review information
Barbara Cheifet was the primary editor of this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.
S.Y.W. was supported by Croucher Foundation and Charles King fellowships. E.A.P. was supported by an LSRF fellowship and by an NIH grant (K99AG064042). L.K.P. was supported by an NIH grant (T32CA009140). K.T. was supported by a JSPS fellowship. B.A.G. was supported by an NIH grant (R01GM110174). .P.L.G. was supported by grants from the Searle Scholars Program, Rita Allen Foundation, and by an NIH grant (DP2AG067490). This research was supported by NIH grants (R00AG043550 and DP2AG055947) to E.L.G.
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Differential ATAC peak regions.
ChIP-seq differential binding sites.
ChIP-seq annotated peak regions.
RNA-seq differentially expressed genes.
ATAC-seq and RNA-seq correlation.
Orthologous gene list.
Sequencing QC summary.
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Wang, S.Y., Pollina, E.A., Wang, IH. et al. Role of epigenetics in unicellular to multicellular transition in Dictyostelium. Genome Biol 22, 134 (2021). https://doi.org/10.1186/s13059-021-02360-9
- Dictyostelium discoideum