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Genome-wide measurement of H3K4me3 and H3K36me3 levels following depletion of RNAPII from the nucleus via an anchor-away system.

ABSTRACT: Genome-wide measurement of H3K4me3 and H3K36me3 levels following depletion of RNAPII from the nucleus via an anchor-away system.

PROVIDER: PRJNA552549 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9641330_1.fastq.gz	Fastqsanger.gz
	SRR9641330_2.fastq.gz	Fastqsanger.gz
	SRR9641340_1.fastq.gz	Fastqsanger.gz
	SRR9641340_2.fastq.gz	Fastqsanger.gz
	SRR9641350_1.fastq.gz	Fastqsanger.gz

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Genome-wide measurement of H3K4me3 and H3K36me3 levels following depletion of RNAPII from the nucleus via an anchor-away system.

Project description:Despite the well-reported association between H3K4me3 and transcription, depletion of RNAPII from the nucleus has little effect on H3K4me3, while having a much larger effect on H3K36me3

2019-07-04 | GSE133791 | GEO

CRAC of yeast RNA polymerase II in various thermosensitive strains at permissive and non-permissive temperature and anchor-away strains with the addition of rapamycin.

Project description:We obtained RNA polymerase II occupancy profile across the genome of S.cerevisiae in several strains, Wild type at 25 and 37 degrees C, RNA15-1 at 25 and 37 degrees C, anchor-away parental strain plus rapamycin, Reb1 anchor-away plus rapamycin, Rap1 anchor-away plus rapamycin, Nrd1-AID plus auxin, and nrd1-AID without auxin. This allowed us to compare polymerase profiles when these proteins are depleted from the nucleus.

2018-01-10 | GSE97913 | GEO

CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

Project description:We obtained RNA polymerase II occupancy profiles across the genome of S.cerevisiae strains: Abf1 anchor-away cells after addition of rapamycin for different time points (including no addition of rapamycin) and Rap1-AID auxin-degron cells after addition of auxin for different time points (including no addition of auxin) . This allowed us to compare polymerase occupancy profiles when these proteins are depleted from the nucleus or degraded.

2018-12-20 | GSE114589 | GEO

CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

Project description:CRAC of yeast RNA polymerase II in anchor-away and auxin-degron strains.

| PRJNA471852 | ENA

Spt4 helps RNAPII pass the +2 nucleosome barrier in vivo

Project description:Aim and Methods: To understand the precise role of Spt4 in budding yeast, various high throughput sequencing techniques were used. Nucleosome positions were studied using MNase-seq in WT and spt4∆ cells. The position of RNAPII was examined using NET-seq in spt4∆ cells or cells in which Spt4 has been anchored away to the cytoplasm (Spt4 AA). RNAPII was also mapped in cells in which Spt5 has been anchored away to the cytoplasm (Spt5 AA). Steady-state transcript levels were assessed using RNA-seq in samples coupled with NET-seq. The position of the Spt4 on RNAPII was mapped at single nucleotide resolution using TEF-seq. With the same technique, the position of Spt5 on RNAPII was investigated in wild type (WT) and spt4 knock-out (spt4∆) cells. The position and levels of the pre-initiation complex were assessed using ChIP-seq on Sua7(TFIIB) in WT and spt4∆ cells. Results: The interaction between the Spt4/5 complex and RNAPII periodically changes as RNAPII transitions through nucleosomes. The dynamic interaction of Spt5 with RNAPII is dependent on Spt4. In spt4∆ and Spt4 AA cells, RNAPII distribution is altered in a similar way compared to their respective controls. After transcribing into nucleosomes, RNAPII accumulates upstream of nucleosome dyads, especially around the +2 nucleosome. In Spt5 AA cells, the distribution and amount of RNAPII on genes are severely affected. Nucleosome positions are altered in spt4∆ cells. Although the position of the +1 nucleosome remains unchanged, nucleosome spacing from this point is increased, and the level of increase in nucleosome spacing correlates with the level of RNAPII accumulation. Conclusion: This work suggests that Spt4 regulates nucleosome positioning by a mechanism related to transcription and promotes RNAPII movement through nucleosome barriers, especially the barrier set by the +2 nucleosome.

2021-09-27 | GSE159291 | GEO

Targeted Profiling of Epitranscriptomic Reader, Writer and Eraser Proteins Regulated by H3K36me3

Project description:Trimethylation of lysine 36 on histone H3 (H3K36me3), an epigenetic mark associated with actively transcribed genes, plays an important role in multiple cellular processes, including transcription elongation, DNA methylation, DNA repair, and RNA m6A methylation, etc. Aberrant expression and mutations of the main methyltransferase for H3K36me3, i.e., SET domain-containing 2 (SETD2), were shown to be associated with various cancers. Here, we performed targeted profiling of 154 epitranscriptomic RWE proteins using a scheduled liquid chromatography-parallel-reaction monitoring (LC-PRM) method coupled with the use of stable isotope-labeled (SIL) peptides as internal standards to investigate how H3K36me3 modulates the chromatin occupancies of epitranscriptomic reader, writer, and eraser (RWE) proteins. Our results showed consistent changes in chromatin occupancies of RWE proteins upon losses of H3K36me3 and H4K16ac, and a role of H3K36me3 in recruiting METTL3 to chromatin upon DNA double strand break induction. In addition, protein-protein interaction network and Kaplan-Meier survival analyses revealed the importance of METTL14 and TRMT11 in kidney cancer. Taken together, our work revealed cross-talks between H3K36me3 and epitranscriptomic RWE proteins and uncovered potential roles of these RWE proteins in H3K36me3-mediated biological processes.

2023-05-25 | PXD041343 | Pride

Phase separation of CTD of RNAPII

Project description:The carboxy-terminal domain (CTD) of the largest subunit of RNA Polymerase II (RNAPII) consists of multiple tandem repeats of the heptapeptide consensus Y1-S2-P3-T4-S5-P6-S7. RNAPII CTD is intrinsically disordered and has been shown to promote liquid-liquid phase-separation (LLPS) of RNAPII in vivo. However, understanding the precise role of the conserved heptad residues in LLPS has been hampered by the lack of direct characterization of the biochemical properties of the CTD. Here, we generated a systematic array of RNAPII CTD variants to unravel the sequence-encoded molecular grammar underlying LLPS of the human CTD.

2024-09-19 | PXD049700 | Pride

The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis

Project description:This SuperSeries is composed of the following subset Series: GSE30971: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [Expression Profile] GSE30972: The Histone Methyltransferase Wbp7 Controls Macrophage Function through GPI Glycolipid Anchor Synthesis. [ChIP_seq] Refer to individual Series

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Disruption of RNAPII transcription elongation links Oncogenic splicing factor mutations to replciation stress and targetable alterations in chromatin landscape [H3K36me3 ChIP-Seq]

Project description:To investigate changes in the H3K36me3 distribution across different conditions, we peformed ChIP-seq using antibody against the H3K36me3 in K562 cells at 4 days after modified allele expression We then performed coverage plot analyses using data obtained from ChIP-seq from IP fractions to investigate H3K36me3 distribution changes

2024-03-12 | GSE254788 | GEO

pSer2-RNAPII interaction partners in MEF cells (label free)

Project description:Deregulation of RNA Polymerase II (RNAPII) by oncogenic signaling leads to collisions of RNAPII with DNA synthesis machinery (transcription-replication conflicts, TRCs). TRCs can result in DNA damage and underlie genomic instability in tumor cells. Here we provide evidence that elongating RNAPII promotes activation of the ATM kinase at TRCs to drive DNA repair. We show the ATPase Wrnip1 that binds and protects stalled replication forks, associates with RNAPII and limits ATM activation. Wrnip1 binding to elongating RNAPII requires catalytic activity of the ubiquitin ligase Huwe1. Mutation of Huwe1 promotes the transfer of Wrnip1 onto replisome and induces TRCs stimulating ATM activation on RNAPII. This mechanism is evoked early upon replicative stress to induce Wrnip1 translocation and ATM signaling at TRCs. Thus, although primarily considered as genotoxic events, TRCs can provide a mechanism to maintain genome stability under replicative stress.

2023-07-31 | PXD037680 | Pride

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