The chromatin remodeler Ino80 mediates RNAPII pausing site determination

Abstract

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.

The pleiotropic roles of SPT5 in transcription

“…Although a relative enrichment of engaged Pol II at promoters is observed for some genes in lower organisms such as Schizosaccharomyces pombe (S. pombe) and S. cerevisiae [ 42 , 43 ], promoter-proximal pausing is substantially more apparent and pervasive in more advanced species and has been considered as a gained regulatory transcriptional step through evolution to meet the demand for more precise and prompt control of gene expression in complex processes such as development [ 44–48 ]. The paused Pol II typically dwells within a 20–120 bp window downstream of the transcription start site (TSS).…”

The INO80 ATP-dependent chromatin remodelling complex alleviates stalled Polymerase II to promote non-coding RNA transcription termination

“…As pausing at ATG sites has been associated with Polymerase backtracking and stalling 50 , our results strongly suggest that INO80 alleviates stalled or terminally arrested Polymerases, which if not timely removed can affect Pol II processivity and gene expression. According to a recent study using ex-vivo PRO-seq analysis, it was proposed that the depletion of INO80 causes Pol II to pause at alternative sites in a small number of genes 73 . Whether these alternative sites are associated to the ATG pausing is unclear.…”

INO80 Is Required for the Cell Cycle Control, Survival, and Differentiation of Mouse ESCs by Transcriptional Regulation

“…Ino80 is an ATP-dependent chromatin remodeler that plays indispensable roles in development, cancer progression, and gene transcription [ 9 , 10 , 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 ]. Germline deletion of Ino80 leads to embryonic lethality due to failure in gastrulation, growth retardation, and massive cell death [ 14 , 15 , 23 ].…”

“…Germline deletion of Ino80 leads to embryonic lethality due to failure in gastrulation, growth retardation, and massive cell death [ 14 , 15 , 23 ]. The Ino80 complex is highly enriched at the transcription start site (TSS) and can either promote or repress gene expression in a context-dependent manner [ 17 , 24 , 25 , 27 , 28 , 29 ]. In the promotion of gene expression, Ino80 permits Mediator and RNA polymerase II (RNAPII) to be recruited for gene activation while maintaining an open chromatin architecture [ 24 ].…”

“…A component of the Ino80 complex, Yin-Yang-1, functions as a transcription factor and promotes gene transcription in mouse E13.5 cerebral cortex and HEK293 cells [ 27 , 29 ]. A recent study showed that Ino80 participates in the stability of the +1 nucleosome, helps RNAPII pausing site determination, and ensures correct early transcription elongation [ 25 ]. However, Ino80 also participates in transcriptional repression in mESCs and spermatocytes; it binds to the TSS and recruits the H3K27me3 repressive mark to contribute to transcriptional repression [ 17 , 28 ].…”