Control of Transcriptional Elongation

Abstract

Elongation is becoming increasingly recognized as a critically controlled step in transcriptional regulation. While traditional genetic and biochemical studies have identified major players of transcriptional elongation, our understanding of the importance and roles of these factors is evolving rapidly through the recent advances in genome-wide and single-molecule technologies. Here we focus on how elongation can modulate the transcriptional outcome through the rate-liming step of RNA polymerase II pausing near promoters, and how the participating factors were identified. Among the factors we describe are NELF and DSIF, the pausing factors, and P-TEFb, the key player in pause release. We also describe non-exclusive models for how pausing is achieved by making use of high resolution genome-wide mapping of paused Pol II relative to promoter elements and the first nucleosome. We also discuss Pol II elongation through the bodies of genes and the roles of FACT and Spt6, the factors that allow Pol II to move through nucleosomes.

Cis-regulatory elements used to control gene expression in plants

“…RNA polymerase II is bound in the next step and TFIIF attaches to it. Thereupon TFIIE and TFIIH join the complex and the full transcription apparatus is formed (Kwak and Lis 2013).…”

Chromatin proteomic profiling reveals novel proteins associated with histone-marked genomic regions

“…Proteins associated with the elongation apparatus included pause-control factors, elongation factors, and several RNA-binding proteins (Fig. 3C) (32,33). Recent studies indicate that RNA-binding proteins can be associated with specific portions of chromatin, in part because of their interaction with RNA species associated with the transcriptional machinery (34,35).…”

DNA topology and transcription

“…[15][16][17][18] Proper gene expression occurs largely through the regulation of RNA polymerase transcription which arises at multiple stages: nucleosome remodeling and promoter selection, early transcription from the melting of DNA by the transcriptional machinery through the release of RNA polymerase from promoterproximal pause sites, transcript elongation, promoter-enhancer interaction, 3-D genomic architecture, and antisense activity. [19][20][21][22][23][24][25] Although there are no steps purely managed by DNA topology, a growing body of evidence indicates that DNA topology is an important player in the biochemical team. In this review our goal is to dissect the key regulatory steps of transcription, highlighting the importance and the consequences of topological changes within different types of genomic domains.…”