The chromatin remodeler Ino80 mediates alternative RNAPII pausing site determination
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ABSTRACT:
PROVIDER: PRJNA665997 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12720975_1.fastq.gz | Fastqsanger.gz | |||
| SRR12720975_2.fastq.gz | Fastqsanger.gz | |||
| SRR12720976_1.fastq.gz | Fastqsanger.gz | |||
| SRR12720976_2.fastq.gz | Fastqsanger.gz | |||
| SRR12720977_1.fastq.gz | Fastqsanger.gz |
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Project description:Promoter-proximal pausing of RNAPII is a critical step in early transcription elongation to precisely regulate gene expression. Here, we observed evidence of promoter-proximal pausing like distributions of RNAPII in S. cerevisiae. We find that Ino80p loss caused the transition of RNAPII pausing to the alternative pausing site at which is tightly associated with the +1 nucleosome. These Ino80p dependent genes showed better nucleosome positioning around the main pausing site which suggested the regulation of RNAPII pausing by Ino80p in a nucleosome context-dependent manner. Furthermore, we examined the similar INO80 dependent RNAPII pausing site determination in mESCs. Altogether, we hypothesize a highly conserved role of the chromatin remodeling Ino80 complex in controlling the early RNAPII elongation to establish intact pausing in various organisms, from budding yeast to mouse.
2021-08-20 | GSE158622 | GEO
Project description:The mechanistics by which ATP-dependent chromatin remodelers process (epi)genetic information to generate hallmark features of chromatin are fundamental for genome regulation. Here, we advance whole-genome reconstitutions into a fully definable, recombinant approach for probing how remodelers determine nucleosome positioning. Using wild type and structure-guided mutant versions of the Saccharomyces cerevisiae 15-subunit INO80 remodeler, we show that INO80-intrinsic nucleosome positioning relies on direct DNA shape read-out. This requires especially the interplay between the INO80 nuclear actin and core modules, to a lesser extent the HMG-box Nhp10 module and not histone modifications/variants or the Rvb1/2 AAA+-ATPase activity. Extrinsically, nucleosome positioning is guided by the barrier Reb1 via Ino80 ATPase activity modulation or by mere DNA double strand breaks. Taken together, we present a defined and unbiased approach to understand remodeler-mediated nucleosome positioning and delineate how INO80 processes genomic information into nucleosome positioning.
2020-04-30 | GSE145093 | GEO
Project description:In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.
2021-05-25 | GSE162374 | GEO
Project description:In the multi-subunit INO80 chromatin-remodeling complex, all the auxiliary subunits assemble on three distinct domains of the catalytic chromatin remodeler INO80, which are N-terminal domain, HSA domain, and ATPase domain. While the ATPase and HSA domains and the auxiliary subunits assembling on the domains are known to be responsible for ATP hydrolysis and chromatin remodeling, it is largely unknown how the auxiliary subunits assembling on the INO80 N-terminal domain regulate the chromatin status. We identify both conserved and non-conserved auxiliary subunits of the INO80 complex in Arabidopsis thaliana. All the auxiliary subunits assemble on the conserved N-terminal domain, HSA domain, and ATPase domain of INO80 in Arabidopsis. While the auxiliary subunits assembling on the INO80 ATPase domain are required for the ATPase-dependent function, the INO80 N-terminal domain and the auxiliary subunits assembling on the domain can regulate gene expression and development even when the ATPase domain is absent, suggesting that INO80 has an ATPase-independent role. Furthermore, we find that a subclass of the COMPASS histone H3K4 methyltransferase complexes assemble on the INO80 N-terminal domain in the INO80 complex and function together with the other auxiliary subunits assembling on the INO80 N-terminal domain, thereby facilitating the ATPase-independent function. This study suggests that the conserved chromatin remodeler INO80 has an ATPase-independent role and demonstrates that the auxiliary subunits assembling on the INO80 N-terminal domain are required for the ATPase-independent role.
2021-05-25 | GSE162373 | GEO
Project description:RNA polymerase II (RNAPII) pausing release is a recently recognized checkpoint for transcriptional regulation. The biological roles of RNAPII pausing release and the mechanisms that by which extracellular signals control it are incompletely understood. Here we identify a novel mechanism by which VEGF stimulates RNAPII pausing-release through acetylation of ETS1, a master endothelial cell transcriptional regulator. In endothelial cells (ECs), ETS1 uniquely bound transcribed gene promoters and stimulated their expression by broadly increasing RNA polymerase II (RNAPII) pause release. VEGF enhanced ETS1 chromatin occupancy. Furthermore, VEGF increased ETS1 acetylation, enhancing its binding by BRD4 and thereby stimulating RNAPII pause release. This ETS1-mediated transduction of VEGF signaling to increase RNAPII pausing release was essential for EC angiogenic responses in vitro and in vivo. Together, our results define a new angiogenic pathway in which VEGF enhances ETS1-Brd4 interaction to broadly promote RNAPII pause release and drive angiogenesis.
2016-12-31 | GSE93030 | GEO
Project description:Neuroadaptations in the nucleus accumbens (NAc) underlie cue-induced cocaine craving that intensifies (“incubates”) during withdrawal and contributes to persistent relapse vulnerability. Long-lasting gene changes govern perpetual behavioral abnormalities but the role of epigenetic plasticity in cocaine craving during prolonged withdrawal is poorly understood. Here we show that chromatin remodeler INO80 in the NAc mediates cocaine-induced, withdrawal-dependent plasticity and incubated cocaine craving.
2019-10-29 | GSE119627 | GEO
Project description:The INO80 complex is a chromatin remodeler that regulates DNA replication, repair, and transcription. Although the INO80 complex plays a crucial role in various chromatin-associated processes, the mechanism of its recruitment to specific genomic loci is not well understood. Here we used a native ChIP-MS approach to quantitatively profile modifications present on nucleosomes co-purified with INO80 from MNAse-digested HeLa chromatin.
2023-12-10 | PXD042210 | Pride
Project description:Genome information processing by the INO80 chromatin remodeler positions nucleosomes
| PRJNA606027 | ENA
Project description:The SNF2 ATPase-independent function of the INO80 chromatin remodeler
| PRJNA681620 | ENA
Project description:Purpose: The ultimate goal of this study is the identification of transcription elongation-related chromatin remodeler and its in vivo mechanism in fission yeast through Next-generation sequencing (NGS) based ChIP-seq technique. Methods: Every ChIP-seq cells were grown up to mid-log phase and harvested after final 1% formaldehyde fixation and 125mM glycine quencing. Cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. ChIP cells were disrupted by glass bead vortexing in ChIP lysis buffer and sonicated by Sonic Dismembrator Model 500, Fisher Scientific. Debris of the sonicate was excluded by centrifugation by 14,800rpm at 4 Celcius degree. IP samples were aliqouted from the sonicate and immunoprecipiated by proper amount of antibody and protein A/G beads, washed by ChIP lysis buffer for over-night at 4 Celcius degrees. IP samples were washed and eluted by proper buffers in Sigmaprep spin column. Proteins in both IP and input samples were degraded by 2hr 30ug proteinase K rxn and de-crosslinked at 65 Celcius degrees for at least 8hrs. The IP and input DNA were eluted by Quiagen PCR purification kit. Results: RNAPII and factor ChIP-seq in various mutants of chromatin remodelers showed that FUN30 family promotes transcription at gene coding regions. RNAPII ChIP-seq in fft3Δ, spt16-1 and fft3Δspt16-1 demonstrated that RNAPII regulation function of Fft3 is largely overlapped with that of Spt16. Histone H3 ChIP-seq results in fft3Δ and spt16-18 demonstrated that Fft3 is major chromatin remodeler to promote nucleosome turnover through nucleosome disassembly. Finally, histone H3 and RNAPII ChIP-seq in fft3Δ, H3/H4DD and fft3Δ H3/H4DD were showed that Fft3 facilitates RNAPII elongation at ORF regions through nucleosome barrier regulation. Conclusions: Fun30-Fft3 is major chromatin remodeler to facilitate RNAPII elongation by nucleosome disassembly-driven nucleosome barrier alleviation in fission yeast.
2016-12-18 | GSE83600 | GEO