Pol II docking and pausing at growth and stress genes in C. elegans

Abstract

Fluctuations in nutrient availability profoundly impact gene expression. Previous work revealed postrecruitment regulation of RNA polymerase II (Pol II) during starvation and recovery in Caenorhabditis elegans, suggesting that promoter-proximal pausing promotes rapid response to feeding. To test this hypothesis, we measured Pol II elongation genome wide by two complementary approaches and analyzed elongation in conjunction with Pol II binding and expression. We confirmed bona fide pausing during starvation and also discovered Pol II docking. Pausing occurs at active stress-response genes that become downregulated in response to feeding. In contrast, "docked" Pol II accumulates without initiating upstream of inactive growth genes that become rapidly upregulated upon feeding. Beyond differences in function and expression, these two sets of genes have different core promoter motifs, suggesting alternative transcriptional machinery. Our work suggests that growth and stress genes are both regulated postrecruitment during starvation but at initiation and elongation, respectively, coordinating gene expression with nutrient availability.

Figure 1

scRNAs coincide with accumulation of elongating RNA Pol II. Coverage of A) the 5′ end of scRNAs, B) the 3′ end of scRNAs, C) GRO-seq reads and D) Pol II ChIP-seq reads is plotted relative to the beginning of 789 contiguous regions (contigs) of scRNA coverage. E) Coverage of 5′ end of scRNA reads (black) and GRO-seq reads (red) in the immediate proximity of the contig start is plotted. Only scRNA contigs within 100 bp of annotated TSSs for protein coding genes are included (WS220). Coverages are the median boot-strap estimates of the mean. See also Fig S1, S2, and S3.

Figure 2

TFIIS mutation alters the size distribution of scRNAs. A) The difference in relative coverage between wild type and the TFIIS mutant is plotted relative to the beginning of 789 scRNA contigs within 100 bp of annotated protein coding gene TSSs. Each bin shows the mean change in coverage over a 5 bp window. Coverage is the median boot-strap estimate of the mean. B) A boxplot comparing the coefficient of variation (CV) for the distance between the 3′ ends of scRNAs and the beginning of the contig is plotted. The CV was calculated for each contig separately. In order to address possible effects resulting from the smaller TFIIS mutant library sizes, the wild-type data was resampled to calculate a boot-strap estimate of the CV. C) Three examples of the distribution of the 3′ end of scRNAs are plotted for wild-type and the TFIIS mutant. All genes are plotted with their 5′ end to the left regardless of strand.

Figure 3

Pol II accumulates upstream of true TSSs at genes with relatively little elongation. A) Coverage of the 5′ end of scRNAs, 3′ end of scRNAs, GRO-seq reads and Pol II ChIP-seq reads is plotted relative to 5,192 true TSSs. B) Coverage of GRO- seq and Pol II ChIP-seq reads is plotted relative to 590 empirically identified SL1 trans-splice sites. Coverages for A and B are the median boot-strap estimates of the mean. C) Mean Pol II ChIP-seq coverage around 5,192 true TSSs is plotted for deciles of scRNA abundance mapping within 100 bp downstream of the TSS. The bottom five deciles of scRNA are each made up of loci with no scRNAs mapping to them and are merged. Dotted, dashed, and solid black lines show the 90%, 80%, and 60% bootstrap confidence intervals of the mean, respectively, based on computing the mean of a sample of 10% of the data 1000 times. F44E5.4 and F44E5.5 were omitted (see Supplemental Experimental Procedures). D) A heatmap of Pol II ChIP-seq coverage is plotted for the same genes as in C. Genes are sorted by the number of scRNA reads mapping within 100 bp downstream of the TSS. See also Fig S4 and S5.

Figure 4

Clustering genes based on patterns of Pol II ChIP-seq coverage around true TSSs identifies genes with “docked” and “active” Pol II. A) Average coverage of Pol II ChIP-seq, GRO-seq and 3′ scRNA-seq is plotted for each of the three clusters around true TSSs. Coverages are the median boot-strap estimates of the mean. Browser shots of representative genes from the B) docked and C) active clusters are shown. All genes are plotted with their 5′ end to the left regardless of strand.

Figure 5

Divergent transcription does not account for accumulation of Pol II upstream of TSSs. A) Pol II ChIP-seq coverage around 5,192 true TSSs is plotted. Genes are first divided by whether they have antisense GRO-seq reads 200 bp upstream of the TSS, and those that do are grouped by quartiles of antisense read count. B, C) Coverage of Pol II ChIP-seq (black), B) 3′ scRNA-seq and C) GRO-seq is plotted around true TSSs of genes in the docked (left) and active (right) cluster. Antisense (red) and sense (blue) coverage are plotted separately. Coverages for A, B and C are the median boot-strap estimates of the mean.

Figure 6

Docked and active genes have different functions and nutrient-dependent regulation. A) Functional enrichments are plotted for the active and docked cluster using the online service ‘Revigo’, which arranges Gene Ontology (GO) terms using multi-dimensional scaling based on their position in the GO graph. Points are colored by whether they are enriched in the ‘docked’ or the ‘active’ cluster (corrected Hypergeometric p-value < 0.01). The size of the point is scaled according to how many genes are annotated with that functional term in the cluster. B) Gene expression during early L1 development (left) and L1 arrest and 3 hr recovery (right) is plotted for the docked (orange) and active (blue) clusters, as well as for all genes (black). Vertical bars on the ‘all genes’ line show the 95% confidence interval of the mean constructed by subsampling 10% of the data 1000 times. C) Venn diagrams showing the numbers of genes in the docked and active clusters whose expression increases, and increases significantly during the first 6 hours of recovery expressed’ at a FDR of 1%. We tested for differential expression in 3,093 genes that had detectable mRNA reads (FDR 1%) and also had true TSS calls. D) Coverage of Pol II ChIP-seq data around docked genes is plotted during L1 arrest and after 1 hr recovery. In contrast to other figures, Pol II ChIP-seq data is from Baugh and coworkers (Baugh et al., 2009). All coverages are the median boot-strap estimates of the mean. See also Fig S6 and Table S3.

Figure 7

Docked and active genes have distinct sets of core promoter motifs. A) The positional frequency of the Inr and TATA motifs is plotted relative to true TSSs for each of the three clusters. B) The coverage of Pol II ChIP-seq, the 3′ ends of scRNAs, and GRO-seq around true TSSs for genes in each cluster is plotted. Genes are split by whether or not they have a canonical TATA motif. C) Pol II initiation and elongation are differentially regulated for growth and starvation genes. Upstream accumulation of uninitiated Pol II (docked) is associated with growth and development genes not expressed during starvation but up-regulated by feeding. In contrast, promoter-proximal pausing of early elongation is associated with genes expressed during starvation and down-regulated during growth, which includes stress-response genes. Starvation genes are much more likely than growth genes to have a TATA box, suggesting alternative core transcriptional machinery in the pre-initiation complex of these two sets of genes. We propose that upstream accumulation of docked Pol II involves at least one unknown factor that docks Pol II, represented by a pentagon. See also Tables S4 and S5.