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The chromatin remodeler Ino80 mediates RNAPII pausing site determination
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The chromatin remodeler Ino80 mediates RNAPII pausing site determination
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Journal Article
The chromatin remodeler Ino80 mediates RNAPII pausing site determination
2021
Overview
Background
Promoter-proximal pausing of RNA polymerase II (RNAPII) is a critical step for the precise regulation of gene expression. Despite the apparent close relationship between promoter-proximal pausing and nucleosome, the role of chromatin remodeler governing this step has mainly remained elusive.
Results
Here, we report highly confined RNAPII enrichments downstream of the transcriptional start site in
Saccharomyces cerevisiae
using PRO-seq experiments. This non-uniform distribution of RNAPII exhibits both similar and different characteristics with promoter-proximal pausing in
Schizosaccharomyces pombe
and metazoans. Interestingly, we find that Ino80p knockdown causes a significant upstream transition of promoter-proximal RNAPII for a subset of genes, relocating RNAPII from the main pausing site to the alternative pausing site. The proper positioning of RNAPII is largely dependent on nucleosome context. We reveal that the alternative pausing site is closely associated with the + 1 nucleosome, and nucleosome architecture around the main pausing site of these genes is highly phased. In addition, Ino80p knockdown results in an increase in fuzziness and a decrease in stability of the + 1 nucleosome. Furthermore, the loss of INO80 also leads to the shift of promoter-proximal RNAPII toward the alternative pausing site in mouse embryonic stem cells.
Conclusions
Based on our collective results, we hypothesize that the highly conserved chromatin remodeler Ino80p is essential in establishing intact RNAPII pausing during early transcription elongation in various organisms, from budding yeast to mouse.
Publisher
BioMed Central,Springer Nature B.V,BMC
Subject
/ Animal Genetics and Genomics
/ Animalia
/ Animals
/ Biomedical and Life Sciences
/ genome
/ Genomes
/ Mammals
/ Mice
/ Microbial Genetics and Genomics
/ PRO-seq
/ Promoter-proximal RNAPII pausing
/ RNA Polymerase II - metabolism
/ Saccharomyces cerevisiae - enzymology
/ Saccharomyces cerevisiae - genetics
/ Saccharomyces cerevisiae Proteins - physiology
/ Schizosaccharomyces - genetics
/ The chromatin remodeler Ino80p
/ Yeast
/ yeasts
