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Fig. 4 | Genome Biology

Fig. 4

From: High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts

Fig. 4

Widespread dynamic regulation of alternative TSSs within ORFs during cell-fate transitions. a Integrative Genomics Viewer (IGV) tracks showing examples of internal TSSs whose levels changed during cell-fate transitions (T1, T3, and T3). The scale for TSS-seq, TES-seq, and mRNA-seq values are displayed for ECM10, TRZ1, and VPS41. b Number of TSS switching events of genes that showed expression of main TSSs within the ORF sequences and which showed TSS switching during T1, T2, or T3 to canonical TSSs in the promoter sequence. Switching events were defined as in Fig. 3c. c Examples of switching events between TSSs expressed in ORFs (internal TSSs) and TSSs in promoters. Negative controls representing mock-treated samples for T1 and T2 (no induction of transition (T) for main TSS and upstream alternative TSS (UA)) were included. The y-axis represents TPM values of the internal and promoter TSS. d Numbers of TSSs expressed within ORFs (internal TSSs). Different cutoffs were used to define internal TSSs. Relaxed cutoff: internal TSSs increasing by 2-fold or more during transition. Stringent cutoff: internal TSSs belonging to putative transcripts encoding for an ORF that is at least 300 nucleotides in length and whose expression levels are at least one third that of the full-length mRNA at the same time point. Domain cutoff: internal transcripts with a predicted PFAM domain. The “stringent” and “domain” categories are subsets of the “relaxed” category. e Numbers of internal TSSs (stringent cutoff) identified by TSS seq, supported by transcripts with 5′ ends identified by TIF-seq. f The distribution of 5′ UTR length for the associated transcripts originating from internal TSSs approximated by computing the distance to the first in-frame AUG. n = 96/101/84 TSSs for T1/T2/T3 respectively. g Meta-profiles of ribosome footprints for internal TSSs (stringent cutoff). The ribosome footprint dataset was from Brar et al. [21]. h Examples of genes (SAS4 and TEL1) that display expression from an internal TSS and whose internal transcripts are bound by ribosomes. The data for, and scales for TSS-seq, TES-seq, mRNA-seq, and the matching time-point for the ribosome footprint dataset are shown

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