Evolution of promoter-proximal pausing enabled a new layer of transcription control

Abstract

Promoter-proximal pausing of RNA polymerase II (Pol II) is a key regulatory step during transcription. To understand the evolution and function of pausing, we analyzed transcription in 20 organisms across the tree of life. Unicellular eukaryotes have a slow acceleration of Pol II near transcription start sites that matured into a longer and more focused pause in metazoans. Increased pause residence time coincides with the evolution of new subunits in the NELF and 7SK complexes. In mammals, depletion of NELF reverts a focal pause to a proto-paused-like state driven in part by DNA sequence. Loss of this focal pause compromises transcriptional activation for a set of heat shock genes. Overall, we discovered how pausing evolved and increased regulatory complexity in metazoans.

DNA-sequence and epigenomic determinants of local rates of transcription elongation

“…The negative correlation we observe with a cytosine at the 3 ′ end of a nascent transcript echoes a similar finding for promoter-proximal pausing, where paused Pol II shows a strong preference for cytosines at the active site [9, 37, 39]. These studies have also shown some enrichment for G at the preceding position, as in our findings, although the motifs they identified were generally more dominated by Cs and Gs than ours.…”

“…In general, the k-mers associated with increased elongation rate were A+T-rich, with some presence of Gs, and they were particularly enriched for A/T dinucleotides (TT, TA, AA). The negative correlation with cytosines echoes similar findings in E. coli [35] and findings for promoter-proximal pausing in mammals [9,37,39], and the positive correlation with A+T-rich sequences is consistent with reports of negative correlations with G+C content [6,7,15] with some differences (see Discussion). Altogether, between 159 and 232 k-mers were assigned non-zero coefficients across replicates (Supplementary Fig.…”

“…In addition to epigenomic factors, it is well known that DNA sequences can also influence local elongation rates, based on studies ranging from bacteria [35] to yeast [36] and mammals [37] (reviewed in [14]). Promoter-proximal pausing in Drosophila and mammals is also associated with particular sequence motifs [9,[37][38][39]. Recently it was shown using NET-seq and PRO-seq data for S. cereviseae that nucleotide 5-mers were strongly predictive of local elongation rates, beyond what could be explained by G+C content, DNA folding energy, or sequencing bias [11].…”

The landscape of the histone-organized chromatin of Bdellovibrionota bacteria

“…Surprisingly, we also observe evidence for very strong polymerase pausing over Bacteriovorax genes, in contrast to what has been reported for bacteria such as E. coli 53 , and similar to what is seen in many (though not all) eukaryotes. Regulation of productive transcriptional elongation might therefore be a key mechanism of modulating gene expression in bacteria with histone-based chromatin.…”

“…Polymerase pausing and its later controlled release are decisive steps in gene regulation in many eukaryotes 46 , having been first described in the fruit fly Drosophila melanogaster [47][48][49][50] , and also shown to be widespread in mammals 51,52 , most metazoans, and some plants, but curiously absent in yeast and Arabidopsis thaliana 53 . Bacteria do exhibit sequence-dependent polymerase pausing but this has been primarily reported in the context of transcription elongation and termination [54][55][56][57][58][59] and E. coli promoters are not characterized by the typical peaks associated with pausing in global run-on GRO-seq datasets 53 . The strong KAS-seq peaks we observe are not due to transcription termination-associated pausing because they are found in all possible orientations of gene pairs, including between two divergent promoters (Figure 3B-C).…”