Bidirectional promoters generate pervasive transcription in yeast

Abstract

Genome-wide pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs. These recently identified transcripts either exist stably in cells (stable unannotated transcripts, SUTs) or are rapidly degraded by the RNA surveillance pathway (cryptic unstable transcripts, CUTs). One characteristic of pervasive transcription is the extensive overlap of SUTs and CUTs with previously annotated features, which prompts questions regarding how these transcripts are generated, and whether they exert function. Single-gene studies have shown that transcription of SUTs and CUTs can be functional, through mechanisms involving the generated RNAs or their generation itself. So far, a complete transcriptome architecture including SUTs and CUTs has not been described in any organism. Knowledge about the position and genome-wide arrangement of these transcripts will be instrumental in understanding their function. Here we provide a comprehensive analysis of these transcripts in the context of multiple conditions, a mutant of the exosome machinery and different strain backgrounds of Saccharomyces cerevisiae. We show that both SUTs and CUTs display distinct patterns of distribution at specific locations. Most of the newly identified transcripts initiate from nucleosome-free regions (NFRs) associated with the promoters of other transcripts (mostly protein-coding genes), or from NFRs at the 3' ends of protein-coding genes. Likewise, about half of all coding transcripts initiate from NFRs associated with promoters of other transcripts. These data change our view of how a genome is transcribed, indicating that bidirectionality is an inherent feature of promoters. Such an arrangement of divergent and overlapping transcripts may provide a mechanism for local spreading of regulatory signals-that is, coupling the transcriptional regulation of neighbouring genes by means of transcriptional interference or histone modification.

Figure 1. Transcript maps

a, Expression data along 50 kb of chromosome XIII (x-axis) for the Watson (W, upper half) and the Crick (C, lower half) strands. Normalized signal intensities are shown for the profiled samples (y-axis): 3 replicates each for rrp6Δ S96 haploid strain, S96 haploid strain in SDC, S1003 diploid strain in YPGal and S1003 diploid strain in YPE; and 3 rows (summarizing 9 replicates) for S1003 diploid strain in YPD. Vertical lines represent inferred transcript boundaries. Nucleosome positions (green tracks, darker for more significant scores22) and genome annotations are shown in the centre: annotated ORFs (blue boxes) and their mapped UTRs (dashed grey lines), SUTs (orange boxes), CUTs (purple boxes) and transcript start sites (arrows). b ~ g, Examples of transcriptional arrangements; layout as in a. b, tandem gene pair with antisense, GAL80 shares a NFR with SUT719, antisense of SUR7; c, antisense SUT253 originating from both a 5’ NFR (of YLR049C) and a 3’ NFR (of YLR050C); d, antisense SUT238 originating from a 5’ NFR (of YPT52); e, SUT665 originating from a 3’ NFR (of BUD2); f, divergent promoter of two ORF-Ts with a long UTRs; g, CUT596 originating from a 5’ NFR (of NUP145).

Figure 2. Properties of divergent transcript pairs

a, Nucleosome density relative to TSSs, averaged over ORF-Ts (black line), SUTs (green line) and CUTs (red line). b, Scatterplot and histograms of shared NFR length (d₁) and distance between TSSs (d₂) of divergent pairs sharing a 5’ NFR. The line corresponds to the regression d₁ = d₂ − 2c, where the value c = 22 bases was determined from the mode of the distribution of differences between d₁ and d₂, and corresponds to a typical distance between NFR and TSS. c, Scatterplot of the sum of 5’ UTR lengths (d₃ + d₄) vs. the distance (d₅) between coding sequences of divergent ORF-T pairs. The solid line corresponds to the regression d₅ = d₃ + d₄ + b, where the value b = 180 bases for the typical TSS distance between divergent pairs is taken from panel b above. The vertical dotted line at d₅ = 452 bases is an estimate of the minimal distance for two ORFs to have separate NFRs.

Figure 3. 5’ and 3’ NFR sharing

a, Nucleosome density relative to TSSs, averaged over all transcripts (left panel) and relative to translation stop sites, averaged over all ORF-Ts (right panel). b, Transcripts initiating from 5’ or 3’ NFRs of other transcripts. The first block of bars corresponds to unannotated transcripts (1,063), the second to ORF-Ts (4,039), and the third to all transcripts (5,339) with mapped 5’ NFRs. Within each block, the bars correspond to different orientations of the transcript relative to the 5’ or 3’ NFR it originates from: divergently from a 5’ NFR (light blue), in tandem from a 5’ NFR (dark blue), in antisense to an ORF from a 3’ NFR (light orange), in tandem to an ORF from a 3’ NFR (dark orange), in any orientation from a 5’ or 3’ NFR (pink). See Supplementary Table 11 for a list of these pairs.