Precise Maps of RNA Polymerase Reveal How Promoters Direct Initiation and Pausing
By Hojoong Kwak, Nicholas J Fuda, Leighton J. Core, J. Lis. Science, 2013
806 citations recorded by the source corpus.
Pressing Pause The pausing of RNA polymerase II (Pol II) near promoters is an important and distinct regulatory step in the process of transcribing DNA into RNA. Although protein factors and DNA elements involved in pausing have been identified, the post-initiation events that lead to pausing are poorly understood. Kwak et al. (p. 950) present an approach, termed PRO-seq, for monitoring the position of actively transcribing RNA polymerase with single-nucleotide precision. The approach was used to explore the mechanism of promoter proximal pausing and showed that precise positioning between core promoter elements and the pause site is critical. The findings show how the promoter dictates transcriptional pausing and detects the preferential localization of active transcription complexes within the genome. The promoter region of a gene regulates the enzyme complex that synthesizes RNA transcripts via initiation and pausing. Transcription regulation occurs frequently through promoter-associated pausing of RNA polymerase II (Pol II). We developed a precision nuclear run-on and sequencing (PRO-seq) assay to map the genome-wide distribution of transcriptionally engaged Pol II at base pair resolution. Pol II accumulates immediately downstream of promoters, at intron-exon junctions that are efficiently used for splicing, and over 3′ polyadenylation sites. Focused analyses of promoters reveal that pausing is not fixed relative to initiation sites, nor is it specified directly by the position of a particular core promoter element or the first nucleosome. Core promoter elements function beyond initiation, and when optimally positioned they act collectively to dictate the position and strength of pausing. This "complex interaction" model was tested with insertional mutagenesis of the Drosophila Hsp70 core promoter.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/83720f5ac5570f13c9fe71facd50dcb0cdeba24e
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Heng Li
- Steven L. Salzberg
- Sergey Koren
- Adam M. Phillippy
- Michael C. Schatz
- Fritz J. Sedlazeck
- Brian Walenz
- Richard Durbin
Citations in the corpus
- The complete sequence of a human genome (2021, methodology): “ILMN PRO-Seq alignments were filtered by unique 51-mers to avoid cross mapping in these repetitive regions, and so may appear sparser than reality.”
- Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers (2014, positive): “PRO-seq reads (100 bases) were processed essentially as in Kwak et al. 22 .”
- From telomere to telomere: the transcriptional and epigenetic state of human repeat elements (2021, background): “Sites of accumulating RNA polymerase activity (20, 47), such as promoter-proximal pause sites, 3’ cleavage/polyA regions, splice junctions and enhancers, indicate points of transcription regulation (20, 48).”