RNA polymerase II elongation through chromatin

Abstract

The machinery that transcribes protein-coding genes in eukaryotic cells must contend with repressive chromatin structures in order to find its target DNA sequences. Diverse arrays of proteins modify the structure of chromatin at gene promoters to help transcriptional regulatory proteins access their DNA recognition sites. The way in which disruption of chromatin structure at a promoter is transmitted through a whole gene has not been defined. Recent breakthroughs suggest that the passage of an RNA polymerase through a gene is coupled to mechanisms that propagate the breakdown of chromatin.

Histone Hyperacetylation in the Coding Region of Chromatin Undergoing Transcription in SV40 Minichromosomes Is a Dynamic Process Regulated Directly by the Presence of RNA Polymerase II

“…As shown in Figure 6A we observed that the ratio of PCR products from the early and late regions following ISFIP analysis with antibody to hyperacetylated H4 were essentially identical to the ratio to antibody to hyperacetylated H3 in chromosomes obtained 30 Since the results from the duplex PCR analysis supported the hypothesis that the less acetylated histones in chromatin fragments lacking RNAPII were the result of the action of HATs and HDACs, we then determined whether unacetylated H4 and H3 were still present in the chromatin fragments lacking RNAPII in sodium butyrate treated cells. If as we hypothesized, the unacetylated H4 and H3 seen in the ISFIP analysis were the result of the combination of HAT and HDAC activity, we expected that in the sodium butyrate treated cells there would be little if any unacetylated H4 or H3 following an ISFIP analysis.…”

“…The presence of hyperacetylated histones within the coding regions of actively transcribed SV40 chromosomes was not unexpected since hyperacetylated histones have been reported to be associated with transcription by many laboratories (28)(29)(30)2) . Since we have previously shown that RNAPII can be found throughout the SV40 genome during infection (7), it was not surprising to see that the hyperacetylated H4 and H3 could also be found throughout the genome.…”

New insights into the biogenesis of nuclear RNA polymerases?This paper is one of a selection of papers published in this special issue entitled “Canadian Society of Biochemistry, Molecular & Cellular Biology 52nd Annual Meeting — Protein Folding: Principles and Diseases” and has undergone the Journal's usual peer review process.

“…They include the DNA-binding transcriptional regulators (Tjian and Maniatis 1994;Triezenberg 1995;Ptashne and Gann 1997;Carey 1998), the general transcription factors (Orphanides et al 1996;Conaway and Conaway 1997;Hampsey 1998;Coulombe and Burton 1999), and the co-activators or co-repressors (Conaway et al 2005;Kornberg 2005;Roeder 2005;Marr et al 2006). Studying the role of the RNAP co-regulators has revealed the existence of a multitude of proteins that participate in transcriptional regulation by acting on the organization or chemical modification of chromatin, the template of RNAPs in eukaryotic cells (Kornberg and Lorch 1999;Orphanides and Reinberg 2000;Li et al 2007).…”

The Epigenetic Landscape of Lineage Choice: Lessons From the Heritability of Cd4 and Cd8 Expression

“…Nucleosomal packaging can physically impede transcription by RNA polymerase and thus different degrees of packing can modulate transcriptional outcomes (reviewed in (Orphanides and Reinberg, 2000)). Looser packed, transcriptionally permissive chromatin is termed "euchromatin", while more tightly packed, repressive chromatin is called "heterochromatin".…”