Abstract
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. Here, to investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Our results globally show that the release of promoter-proximal paused RNA polymerase into elongation functions as a critical switch at which a gene’s response to stress is determined. Highly transcribed and highly inducible genes display strong transcriptional directionality and selective assembly of general transcription factors on the core sense promoter. Heat-induced transcription at enhancers, instead, correlates with prior binding of cell-type, sequence-specific transcription factors. Activated Heat Shock Factor 1 (HSF1) binds to transcription-primed promoters and enhancers, and CTCF-occupied, non-transcribed chromatin. These results reveal chromatin architectural features that orient transcription at divergent regulatory elements and prime transcriptional responses genome-wide.
Highlights
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers
Precision nuclear Run-On sequencing (PRO-seq) does not discern which Pol is producing the RNA, but because our present study focuses on genes and enhancers, which are predominantly transcribed by Pol II3, 12, 19, 37–39, we refer to Pol II as the source of the PRO-seq signal analyzed hereon
The PRO-seq experiments were prepared and sequenced in two biologically-independent replicates, which strongly correlated, and accurate comparison of transcriptional programs in NHS versus HS was ensured by normalizing each data set against the 3′-regions (+100 kb from transcription start site (TSS) to −0.5 kb from polyA site) of long (>150 kb) genes, where the advancing or receding wave of transcription had not proceeded during the 30-min HS treatment (Supplementary Fig. 1b)
Summary
Programs of gene expression are executed by a battery of transcription factors that coordinate divergent transcription from a pair of tightly linked core initiation regions of promoters and enhancers. To investigate how divergent transcription is reprogrammed upon stress, we measured nascent RNA synthesis at nucleotide-resolution, and profiled histone H4 acetylation in human cells. Activated Heat Shock Factor 1 (HSF1) binds to transcription-primed promoters and enhancers, and CTCF-occupied, non-transcribed chromatin. These results reveal chromatin architectural features that orient transcription at divergent regulatory elements and prime transcriptional responses genome-wide. By rapidly provoking a transcriptional change by heat shock and directly measuring RNA synthesis from genes and distal regulatory elements, our results provide a global view on transcriptional reprogramming. Deciphering of gene networks and their distal regulatory elements uncovers functional mechanisms that induce hundreds and repress thousands of genes, simultaneously establishing a distinct enhancer repertoire and chromatin state in stressed human cells. Our results demonstrate how inhibition of the pause–release of promoter–proximal Pol II clears transcription complexes from the majority of transcribed genes upon stress, and how the increased free Pol II in the cell is directed to the coding strands of the activated genes, as well as to enhancers that are primed by lineage-specific transcription factors
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