Voss TC, Hager GL. Dynamic regulation of transcriptional states by chromatin and transcription factors. Nat Rev Genet. 2014;15:69–81.
Article
CAS
PubMed
Google Scholar
Spitz F, Furlong EEM. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13:613–26.
Article
CAS
PubMed
Google Scholar
Brkljacic J, Grotewold E. Combinatorial control of plant gene expression. Biochim Biophys Acta Gene Regul Mech. 1860;2017:31–40.
Google Scholar
Sexton BS, Druliner BR, Vera DL, Avey D, Zhu F, Dennis JH. Hierarchical regulation of the genome: global changes in nucleosome organization potentiate genome response. Oncotarget. 2016;7:6460–75.
Article
PubMed
PubMed Central
Google Scholar
Birney E, Stamatoyannopoulos JA, Dutta A, Guigó R, Gingeras TR, Margulies EH, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007;447:799–816.
Article
CAS
PubMed
Google Scholar
Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 2014;515:355–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maher KA, Bajic M, Kajala K, Reynoso M, Pauluzzi G, West DA, et al. Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules. Plant Cell. 2018;30:15–36.
Article
CAS
PubMed
Google Scholar
Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, et al. High-resolution mapping of open chromatin in the rice genome. Genome Res. 2012;22:151–62.
Article
CAS
PubMed
PubMed Central
Google Scholar
O’Malley RC, Huang S-SC, Song L, Lewsey MG, Bartlett A, Nery JR, et al. Cistrome and Epicistrome features shape the regulatory DNA landscape. Cell. 2016;166:1598.
Article
PubMed
CAS
Google Scholar
Lu Z, Marand AP, Ricci WA, Ethridge CL, Zhang X, Schmitz RJ. The prevalence, evolution and chromatin signatures of plant regulatory elements. Nat Plants. 2019; Available from: https://doi.org/10.1038/s41477-019-0548-z.
Lane AK, Niederhuth CE, Ji L, Schmitz RJ. pENCODE: a plant encyclopedia of DNA elements. Annu Rev Genet. 2014;48:49–70.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buenrostro JD, Giresi PG, Zaba LC, Chang HY, Greenleaf WJ. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat Methods. 2013;10:1213–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Boyle AP, Song L, Lee B-K, London D, Keefe D, Birney E, et al. High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res. 2011;21:456–64.
Article
CAS
PubMed
PubMed Central
Google Scholar
Henikoff JG, Belsky JA, Krassovsky K, MacAlpine DM, Henikoff S. Epigenome characterization at single base-pair resolution. Proc Natl Acad Sci U S A. 2011;108:18318–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Iwafuchi-Doi M, Donahue G, Kakumanu A, Watts JA, Mahony S, Pugh BF, et al. The Pioneer transcription factor FoxA maintains an accessible nucleosome configuration at enhancers for tissue-specific gene activation. Mol Cell. 2016;62:79–91.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, et al. Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize. Genome Biol. 2017;18:137.
Article
PubMed
PubMed Central
CAS
Google Scholar
Rodgers-Melnick E, Vera DL, Bass HW, Buckler ES. Open chromatin reveals the functional maize genome. Proc Natl Acad Sci U S A. 2016;113:E3177–84.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sullivan AM, Arsovski AA, Lempe J, Bubb KL, Weirauch MT, Sabo PJ, et al. Mapping and dynamics of regulatory DNA and transcription factor networks in a. thaliana. Cell Rep. 2014;8:2015–30.
Article
CAS
PubMed
Google Scholar
Vera DL, Madzima TF, Labonne JD, Alam MP, Hoffman GG, Girimurugan SB, et al. Differential nuclease sensitivity profiling of chromatin reveals biochemical footprints coupled to gene expression and functional DNA elements in maize. Plant Cell. 2014;26:3883–93.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao H, Zhang W, Zhang T, Lin Y, Hu Y, Fang C, et al. Genome-wide MNase hypersensitivity assay unveils distinct classes of open chromatin associated with H3K27me3 and DNA methylation in Arabidopsis thaliana. Genome Biol. 2020;21:24.
Article
PubMed
PubMed Central
CAS
Google Scholar
Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012;22:1748–59.
Article
CAS
PubMed
PubMed Central
Google Scholar
Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337:1190–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sandmann T, Girardot C, Brehme M, Tongprasit W, Stolc V, Furlong EEM. A core transcriptional network for early mesoderm development in Drosophila melanogaster. Genes Dev. 2007;21:436–49.
Article
CAS
PubMed
PubMed Central
Google Scholar
Borok MJ, Tran DA, Ho MCW, Drewell RA. Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila. Development. 2010;137:5–13.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hirsch N, Eshel R, Bar Yaacov R, Shahar T, Shmulevich F, Dahan I, et al. Unraveling the transcriptional regulation of TWIST1 in limb development. PLoS Genet. 2018;14:e1007738.
Article
PubMed
PubMed Central
CAS
Google Scholar
Weber B, Zicola J, Oka R, Stam M. Plant enhancers: a call for discovery. Trends Plant Sci. 2016;21:974–87.
Article
CAS
PubMed
Google Scholar
Clark RM, Wagler TN, Quijada P, Doebley J. A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet. 2006;38:594.
Article
CAS
PubMed
Google Scholar
Studer A, Zhao Q, Ross-Ibarra J, Doebley J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat Genet. 2011;43:1160–3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wills DM, Whipple CJ, Takuno S, Kursel LE, Shannon LM, Ross-Ibarra J, et al. From many, one: genetic control of prolificacy during maize domestication. PLoS Genet. 2013;9:e1003604.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lu Z, Hofmeister BT, Vollmers C, DuBois RM, Schmitz RJ. Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes. Nucleic Acids Res. 2017;45:e41.
Article
PubMed
CAS
Google Scholar
Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, et al. Widespread long-range cis-regulatory elements in the maize genome. Nat Plants. 2019; Available from: https://doi.org/10.1038/s41477-019-0547-0.
Eveland AL, Goldshmidt A, Pautler M, Morohashi K, Liseron-Monfils C, Lewis MW, et al. Regulatory modules controlling maize inflorescence architecture. Genome Res. 2014;24:431–43.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bommert P, Nagasawa NS, Jackson D. Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus. Nat Genet. 2013;45:334–7.
Article
CAS
PubMed
Google Scholar
Turpin ZM, Vera DL, Savadel SD, Lung P-Y, Wear EE, Mickelson-Young L, et al. Chromatin structure profile data from DNS-seq: differential nuclease sensitivity mapping of four reference tissues of B73 maize (Zea mays L). Data Brief. 2018;20:358–63.
Article
PubMed
PubMed Central
Google Scholar
Pautler M, Eveland AL, LaRue T, Yang F, Weeks R, Lunde C, et al. FASCIATED EAR4 encodes a bZIP transcription factor that regulates shoot meristem size in maize. Plant Cell. 2015;27:104–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolduc N, Yilmaz A, Mejia-Guerra MK, Morohashi K, O’Connor D, Grotewold E, et al. Unraveling the KNOTTED1 regulatory network in maize meristems. Genes Dev. 2012;26:1685–90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pass DA, Sornay E, Marchbank A, Crawford MR, Paszkiewicz K, Kent NA, et al. Genome-wide chromatin mapping with size resolution reveals a dynamic sub-nucleosomal landscape in Arabidopsis. PLoS Genet. 2017;13:e1006988.
Article
PubMed
PubMed Central
CAS
Google Scholar
Girimurugan SB, Liu Y, Lung PY, Vera D, Dennis J. iSeg: an efficient algorithm for segmentation of genomic and epigenomic data. bioRxiv. biorxiv.org; 2017; Available from: http://www.biorxiv.org/content/early/2017/09/05/184515.abstract.
Baucom RS, Estill JC, Chaparro C, Upshaw N, Jogi A, Deragon J-M, et al. Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet. 2009;5:e1000732.
Article
PubMed
PubMed Central
CAS
Google Scholar
Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O’Connor CH, et al. Transposable elements contribute to dynamic genome content in maize. Plant J. 2019; Available from: https://doi.org/10.1111/tpj.14489.
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, et al. Improved maize reference genome with single-molecule technologies. Nature. Nature Research; 2017 [cited 2017 Jun 12]; Available from: https://doi.org/10.1038/nature22971.
Zhao H, Zhang W, Chen L, Wang L, Marand AP, Wu Y, et al. Proliferation of Regulatory DNA Elements Derived from Transposable Elements in the Maize Genome. Plant Physiology. 2018. p. 2789–803. Available from: https://doi.org/10.1104/pp.17.01467.
Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, et al. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. PLoS Genet. 2020;16:e1008462.
Article
CAS
PubMed
PubMed Central
Google Scholar
Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize. Nature. 1997;386:485–8.
Article
CAS
PubMed
Google Scholar
Danisman S. TCP transcription factors at the Interface between environmental challenges and the Plant’s growth responses. Front Plant Sci. 2016;7:1930.
Article
PubMed
PubMed Central
Google Scholar
Wimalanathan K, Friedberg I, Andorf CM, Lawrence-Dill CJ. Maize GO annotation—methods, evaluation, and review (maize-GAMER). Plant Direct. 2018;2:e00052.
Article
PubMed
PubMed Central
CAS
Google Scholar
Satoh-Nagasawa N, Nagasawa N, Malcomber S, Sakai H, Jackson D. A trehalose metabolic enzyme controls inflorescence architecture in maize. Nature. 2006;441:227–30.
Article
CAS
PubMed
Google Scholar
Bommert P. thick tassel dwarf1 encodes a putative maize ortholog of the Arabidopsis CLAVATA1 leucine-rich repeat receptor-like kinase. Development. 2005. p. 1235–45. Available from: https://doi.org/10.1242/dev.01671.
Bailey TL. DREME: motif discovery in transcription factor ChIP-seq data. Bioinformatics. 2011;27:1653–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Natoli G, Andrau J-C. Noncoding transcription at enhancers: general principles and functional models. Annu Rev Genet. 2012;46:1–19.
Article
CAS
PubMed
Google Scholar
Gil N, Ulitsky I. Production of spliced Long noncoding RNAs specifies regions with increased enhancer activity. Cell Syst. 2018;7:537–47 e3.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chekanova JA. Long non-coding RNAs and their functions in plants. Curr Opin Plant Biol. 2015;27:207–16.
Article
CAS
PubMed
Google Scholar
Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, et al. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell. 2014;55:383–96.
Article
CAS
PubMed
Google Scholar
Kim D-H, Sung S. Vernalization-triggered intragenic chromatin loop formation by Long noncoding RNAs. Dev Cell. 2017;40:302–12 e4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Böhmdorfer G, Wierzbicki AT. Control of chromatin structure by Long noncoding RNA. Trends Cell Biol. 2015;25:623–32.
Article
PubMed
PubMed Central
CAS
Google Scholar
De Quattro C, Enrico Pè M, Bertolini E. Long noncoding RNAs in the model species Brachypodium distachyon. Sci Rep. 2017;7:11252.
Article
PubMed
PubMed Central
CAS
Google Scholar
Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 2011;25:1915–27.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ulitsky I. Evolution to the rescue: using comparative genomics to understand long non-coding RNAs. Nat Rev Genet. 2016;17:601–14.
Article
CAS
PubMed
Google Scholar
ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012;489:57–74.
Article
CAS
Google Scholar
Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, et al. RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. Proc Natl Acad Sci U S A. 2015;112:14728–33.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hsu F-M, Yen M-R, Wang C-T, Lin C-Y, Wang C-JR, Chen P-Y. Optimized reduced representation bisulfite sequencing reveals tissue-specific mCHH islands in maize. Epigenetics Chromatin. 2017;10:42.
Article
PubMed
PubMed Central
CAS
Google Scholar
Bukowski R, Guo X, Lu Y, Zou C, He B, Rong Z, et al. Construction of the third-generation Zea mays haplotype map. Gigascience. 2018;7:1–12.
Article
PubMed
Google Scholar
Yu J, Holland JB, McMullen MD, Buckler ES. Genetic design and statistical power of nested association mapping in maize. Genetics. 2008;178:539–51.
Article
PubMed
PubMed Central
Google Scholar
Carles CC, Lertpiriyapong K, Reville K, Fletcher JC. The ULTRAPETALA1 gene functions early in Arabidopsis development to restrict shoot apical meristem activity and acts through WUSCHEL to regulate floral meristem determinacy. Genetics. 2004;167:1893–903.
Article
CAS
PubMed
PubMed Central
Google Scholar
Barazesh S, McSteen P. Barren inflorescence1 functions in organogenesis during vegetative and inflorescence development in maize. Genetics. 2008;179:389–401.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gallavotti A, Long JA, Stanfield S, Yang X, Jackson D, Vollbrecht E, et al. The control of axillary meristem fate in the maize ramosa pathway. Development. 2010;137:2849–56.
Article
CAS
PubMed
PubMed Central
Google Scholar
Flint-Garcia SA, Thuillet A-C, Yu J, Pressoir G, Romero SM, Mitchell SE, et al. Maize association population: a high-resolution platform for quantitative trait locus dissection. Plant J Wiley Online Library. 2005;44:1054–64.
CAS
Google Scholar
Rice BR, Fernandes SB, Lipka AE. Multi-Trait Genome-wide Association Studies Reveal Loci Associated with Maize Inflorescence and Leaf Architecture. Plant Cell Physiol. 2020; Available from: https://doi.org/10.1093/pcp/pcaa039.
Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Series B Stat Methodol. 1995;57:289–300.
Google Scholar
Upadyayula N, da Silva HS, Bohn MO, Rocheford TR. Genetic and QTL analysis of maize tassel and ear inflorescence architecture. Theor Appl Genet. 2006;112:592–606.
Article
CAS
PubMed
Google Scholar
Vollbrecht E, Springer PS, Goh L, Buckler ES 4th, Martienssen R. Architecture of floral branch systems in maize and related grasses. Nature. 2005;436:1119–26.
Article
CAS
PubMed
Google Scholar
Springer N, de León N, Grotewold E. Challenges of translating gene regulatory information into agronomic improvements. Trends Plant Sci. 2019;24:1075–82.
Article
CAS
PubMed
Google Scholar
Gage JL, White MR, Edwards JW, Kaeppler S, de Leon N. Selection signatures underlying dramatic male inflorescence transformation during modern hybrid maize breeding. Genetics. 2018;210:1125–38.
Article
PubMed
PubMed Central
Google Scholar
Dong Z, Xiao Y, Govindarajulu R, Feil R, Siddoway ML, Nielsen T, et al. The regulatory landscape of a core maize domestication module controlling bud dormancy and growth repression. Nat Commun. 2019;10:3810.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lewis MW, Bolduc N, Hake K, Htike Y, Hay A, Candela H, et al. Gene regulatory interactions at lateral organ boundaries in maize. Development. 2014;141:4590–7.
Article
CAS
PubMed
Google Scholar
Bai F, Reinheimer R, Durantini D, Kellogg EA, Schmidt RJ. TCP transcription factor, BRANCH ANGLE DEFECTIVE 1 (BAD1), is required for normal tassel branch angle formation in maize. Proc Natl Acad Sci U S A. 2012;109:12225–30.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chapman MA, Tang S, Draeger D, Nambeesan S, Shaffer H, Barb JG, et al. Genetic analysis of floral symmetry in van Gogh’s sunflowers reveals independent recruitment of CYCLOIDEA genes in the Asteraceae. PLoS Genet. 2012;8:e1002628.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiao Y, Lee YK, Gladman N, Chopra R, Christensen SA, Regulski M, et al. MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway. Nat Commun. 2018;9:822.
Article
PubMed
PubMed Central
CAS
Google Scholar
Almeida DM, Gregorio GB, Oliveira MM, Saibo NJM. Five novel transcription factors as potential regulators of OsNHX1 gene expression in a salt tolerant rice genotype. Plant Mol Biol. 2017;93:61–77.
Article
CAS
PubMed
Google Scholar
Wang S-T, Sun X-L, Hoshino Y, Yu Y, Jia B, Sun Z-W, et al. MicroRNA319 positively regulates cold tolerance by targeting OsPCF6 and OsTCP21 in Rice (Oryza sativa L.). PLoS One. 2014;9:e91357.
Article
PubMed
PubMed Central
CAS
Google Scholar
Steiner E, Efroni I, Gopalraj M, Saathoff K, Tseng T-S, Kieffer M, et al. The Arabidopsis O-linked N-acetylglucosamine transferase SPINDLY interacts with class I TCPs to facilitate cytokinin responses in leaves and flowers. Plant Cell. 2012;24:96–108.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danisman S, van der Wal F, Dhondt S, Waites R, de Folter S, Bimbo A, et al. Arabidopsis class I and class II TCP transcription factors regulate jasmonic acid metabolism and leaf development antagonistically. Plant Physiol. 2012;159:1511–23.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kosugi S, Ohashi Y. DNA binding and dimerization specificity and potential targets for the TCP protein family. Plant J. 2002;30:337–48.
Article
CAS
PubMed
Google Scholar
Viola IL, Uberti Manassero NG, Ripoll R, Gonzalez DH. The Arabidopsis class I TCP transcription factor AtTCP11 is a developmental regulator with distinct DNA-binding properties due to the presence of a threonine residue at position 15 of the TCP domain. Biochem J. 2011;435:143–55.
Article
CAS
PubMed
Google Scholar
Li C, Potuschak T, Colón-Carmona A, Gutiérrez RA, Doerner P. Arabidopsis TCP20 links regulation of growth and cell division control pathways. Proc Natl Acad Sci U S A. 2005;102:12978–83.
Article
CAS
PubMed
PubMed Central
Google Scholar
Burdo B, Gray J, Goetting-Minesky MP, Wittler B, Hunt M, Li T, et al. The maize TFome--development of a transcription factor open reading frame collection for functional genomics. Plant J. 2014;80:356–66.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gaudinier A, Brady SM. Mapping transcriptional networks in plants: data-driven discovery of novel biological mechanisms. Annu Rev Plant Biol. 2016;67:575–94.
Article
CAS
PubMed
Google Scholar
Park PJ. ChIP–seq: advantages and challenges of a maturing technology. Nat Rev Genet Nature Publishing Group. 2009;10:669–80.
Article
CAS
Google Scholar
Galli M, Khakhar A, Lu Z, Chen Z, Sen S, Joshi T, et al. The DNA binding landscape of the maize AUXIN RESPONSE FACTOR family. Nat Commun. 2018;9:4526.
Article
PubMed
PubMed Central
CAS
Google Scholar
Pisignano G, Pavlaki I, Murrell A. Being in a loop: how long non-coding RNAs organise genome architecture. Essays Biochem. 2019;63:177–86.
Article
PubMed
CAS
Google Scholar
Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, et al. Long Noncoding RNAs with Enhancer-like Function in Human Cells. Cell. 2010. p. 46–58. Available from: https://doi.org/10.1016/j.cell.2010.09.001.
Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, et al. Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature. 2016. p. 452–5. Available from: https://doi.org/10.1038/nature20149.
Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, et al. Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. Nature. 2017. p. 343–6. Available from: https://doi.org/10.1038/nature23451.
Marchese FP, Raimondi I, Huarte M. The multidimensional mechanisms of long noncoding RNA function. Genome Biol. 2017;18:206.
Article
PubMed
PubMed Central
CAS
Google Scholar
Mattioli K, Volders P-J, Gerhardinger C, Lee JC, Maass PG, Melé M, et al. High-throughput functional analysis of lncRNA core promoters elucidates rules governing tissue specificity. Genome Res. 2019;29:344–55.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sigova AA, Mullen AC, Molinie B, Gupta S, Orlando DA, Guenther MG, et al. Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A. 2013;110:2876–81.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li L, Eichten SR, Shimizu R, Petsch K, Yeh C-T, Wu W, et al. Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol. 2014;15:R40.
Article
PubMed
PubMed Central
Google Scholar
Wang B, Tseng E, Regulski M, Clark TA, Hon T, Jiao Y, et al. Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing. Nat Commun. 2016;7:11708.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, et al. A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature. 2011;472:120–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tan JY, Smith AAT, Ferreira da Silva M, Matthey-Doret C, Rueedi R, Sönmez R, et al. cis-Acting Complex-Trait-Associated lincRNA Expression Correlates with Modulation of Chromosomal Architecture. Cell Rep. 2017;18:2280–8.
Liu X, Galli M, Camehl I, Gallavotti A. RAMOSA1 ENHANCER LOCUS2-mediated transcriptional repression regulates vegetative and reproductive architecture. Plant Physiol. 2019;179:348–63.
Article
CAS
PubMed
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19:1639–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
Article
PubMed
PubMed Central
CAS
Google Scholar
Lawrence M, Huber W, Pages H, Aboyoun P, Carlson M, Gentleman R, et al. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013;9:e1003118.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhao H, Sun Z, Wang J, Huang H, Kocher J-P, Wang L. CrossMap: a versatile tool for coordinate conversion between genome assemblies. Bioinformatics. 2014;30:1006–7.
Article
PubMed
CAS
Google Scholar
Gel B, Díez-Villanueva A, Serra E, Buschbeck M, Peinado MA, Malinverni R. regioneR: an R/Bioconductor package for the association analysis of genomic regions based on permutation tests. Bioinformatics. 2016;32:289–91.
CAS
PubMed
Google Scholar
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33:290–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kersey PJ, Allen JE, Armean I, Boddu S, Bolt BJ, Carvalho-Silva D, et al. Ensembl genomes 2016: more genomes, more complexity. Nucleic Acids Res. 2016;44:D574–80.
Article
CAS
PubMed
Google Scholar
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and cufflinks. Nat Protoc Nature Publishing Group. 2012;7:562–78.
Article
CAS
Google Scholar
Schurch NJ, Schofield P, Gierliński M, Cole C, Sherstnev A, Singh V, et al. How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? RNA. 2016;22:839–51.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
De Quattro C, Mica E, Pè ME, Bertolini E. Brachypodium distachyon Long noncoding RNAs: genome-wide identification and expression analysis. In: Sablok G, Budak H, Ralph PJ, editors. Brachypodium genomics: methods and protocols. New York: Springer New York; 2018. p. 31–42.
Chapter
Google Scholar
Quinn JJ, Chang HY. Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet. 2016;17:47–62.
Article
CAS
PubMed
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42:D222–30.
Article
CAS
PubMed
Google Scholar
Kong L, Zhang Y, Ye Z-Q, Liu X-Q, Zhao S-Q, Wei L, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35:W345–9.
Article
PubMed
PubMed Central
Google Scholar
Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 2015;43:D130–7.
Article
CAS
PubMed
Google Scholar
Zhang L, Chia J-M, Kumari S, Stein JC, Liu Z, Narechania A, et al. A genome-wide characterization of microRNA genes in maize. PLoS Genet. 2009;5:e1000716.
Article
PubMed
PubMed Central
CAS
Google Scholar
Thompson BE, Basham C, Hammond R, Ding Q, Kakrana A, Lee T-F, et al. The dicer-like1 homolog fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize. Plant Cell. 2014;26:4702–17.
Article
CAS
PubMed
PubMed Central
Google Scholar
Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J. PatMaN: rapid alignment of short sequences to large databases. Bioinformatics. 2008;24:1530–1.
Article
PubMed
PubMed Central
CAS
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Soneson C, Love MI, Robinson MD. Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences. F1000Res. 2015;4:1521.
Article
PubMed
CAS
Google Scholar
Zhang JD, Hatje K, Sturm G, Broger C, Ebeling M, Burtin M, et al. Detect tissue heterogeneity in gene expression data with BioQC. BMC Genomics. 2017;18:277.
Article
CAS
PubMed
PubMed Central
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Article
PubMed
PubMed Central
CAS
Google Scholar
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008;9:559.
Article
PubMed
PubMed Central
CAS
Google Scholar
Xi Y, Li W. BSMAP: whole genome bisulfite sequence MAPping program. BMC Bioinformatics. 2009;10:232.
Article
PubMed
PubMed Central
CAS
Google Scholar
Yu G, Wang L-G, Han Y, He Q-Y. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS. 2012;16:284–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jin J, Tian F, Yang D-C, Meng Y-Q, Kong L, Luo J, et al. PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Res. 2017;45:D1040–5.
Article
CAS
PubMed
Google Scholar
Wallace JG, Bradbury PJ, Zhang N, Gibon Y, Stitt M, Buckler ES. Association mapping across numerous traits reveals patterns of functional variation in maize. PLoS Genet. 2014;10:e1004845.
Article
PubMed
PubMed Central
Google Scholar
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, et al. The genetic architecture of maize flowering time. Science. 2009;325:714–8.
Article
CAS
PubMed
Google Scholar
Brown PJ, Upadyayula N, Mahone GS, Tian F, Bradbury PJ, Myles S, et al. Distinct genetic architectures for male and female inflorescence traits of maize. PLoS Genet. 2011;7:e1002383.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics. 2007;23:2633–5.
Article
CAS
PubMed
Google Scholar
Churchill GA, Doerge RW. Empirical threshold values for quantitative trait mapping. Genetics Genetics Soc America. 1994;138:963–71.
CAS
Google Scholar
Ziegler GR, Hartsock RH, Baxter I. Zbrowse: an interactive GWAS results browser. PeerJ Comput Sci. 2015;1:e3.
Article
CAS
Google Scholar
Parvathaneni RK, Bertolini E, et al. The regulatory landscape of early maize inflorescence development. MNase-seq and GWAS datasets. Gene Expression Omnibus. GSE136685. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE136685 (2019).