RNA polymerase is poised for activation across the genome

Abstract

Regulation of gene expression is integral to the development and survival of all organisms. Transcription begins with the assembly of a pre-initiation complex at the gene promoter 1 , followed by initiation of RNA synthesis and the transition to productive elongation 2-4 . In many cases, recruitment of RNA polymerase II (Pol II) to a promoter is necessary and sufficient for activation of genes. However, there are a few notable exceptions to this paradigm, including heat shock genes and several proto-oncogenes, whose expression is attenuated by regulated stalling of polymerase elongation within the promoter-proximal region 5-13 . To determine the importance of polymerase stalling for transcription regulation, we carried out a genome-wide search for Drosophila melanogaster genes with Pol II stalled within the promoter-proximal region. Our data show that stalling is widespread, occurring at hundreds of genes that respond to stimuli and developmental signals. This finding indicates a role for regulation of polymerase elongation in the transcriptional responses to dynamic environmental and developmental cues.

dDsk2 regulates H2Bub1 and RNA polymerase II pausing at dHP1c complex target genes

“…Standardized peak density plots were determined using the StdPeakLocation function in the htSeqTools package. The PI was computed for all genes longer than 500 bp as the ratio between RPKM detected within ± 250 bp around the TSS and in the last 500 bp of the gene 24 . Statistical significance for PI difference was assessed using the Kruskal-Wallis test.…”

“…In comparison with non-target genes, the distribution of total RNA pol II (RPB1) is strongly biased towards the TSS. Consequently, the pausing index (PI), determined as the ratio of total RNA pol II abundance at TSS ± 250 bp with respect to the last 500 bp of the gene 24 , is significantly higher (Po0.0001, Kruskal-Wallis; Fig. 3b) .…”

“…Originally considered a rare event, pausing of the promoter-proximal Pol IIo ser5 form phosphorylated at Ser5 in the C-Terminal Domain (CTD) is becoming increasingly recognized as a crucial step in transcription regulation (reviewed in refs 20,21), in particular of developmentally regulated and stimulus-responsive genes [22][23][24][25] . Specific factors such as NELF and DSIF are known to mediate pausing, and pause release requires their phosphorylation by P-TEFb.…”

“…3a). RNA pol II pausing is generally high at developmentally regulated genes [22][23][24][25] . Accordingly, dHP1c complex target genes show features of strong RNA pol II pausing (Fig.…”

Transcriptional Regulation of the Endogenous Danger Signal Tenascin-C: A Novel Autocrine Loop in Inflammation

“…MDDCs were stimulated for 0, 0.5, 2, and 4 h with LPS before chromatin immunoprecipitation analysis as described previously (28). Cross-linked samples were immunoprecipitated using the RNA Pol II Ab sc-8993 (Santa Cruz Biotechnology, Santa Cruz, CA) and underwent quantitative PCR using a primer pair specific to the transcription start site of tenascin-C (forward, 59-gcaaatgggttccttccctggccga-39, and reverse, 59-aaggatgtctggaggcgaggcgt-39).…”