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Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE185763 | GEO | 2022/02/17

REPOSITORIES: GEO

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Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes.

Project description:Interactions of the RNA polymerase II (Pol II) preinitiation complex (PIC) and paused early elongation complexes with the first downstream (+1) nucleosome are thought to be functionally important. However, current methods are limited for investigating these relationships, both for cellular chromatin and the human cytomegalovirus (HCMV) genome. Digestion with human DNA fragmentation factor (DFF) before immunoprecipitation (DFF-ChIP) precisely revealed both similarities and major differences in PICs driven by TBP on the host genome in comparison with PICs driven by TBP or the viral-specific, late initiation factor UL87 on the viral genome. Host PICs and paused Pol II complexes are frequently found in contact with the +1 nucleosome and paused Pol II can also be found in a complex involved in the initial invasion of the +1 nucleosome. In contrast, viral transcription complexes have very limited nucleosomal interactions, reflecting a relative lack of chromatinization of transcriptionally active regions of HCMV genomes.

| S-EPMC9010409 | biostudies-literature

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

Project description:To characterize transcription throughout the HCMV infection, paired-end PRO-Seq was performed on human foreskin fibroblasts (HFF) infected with human cytomegalovirus (HCMV) for 4 h, 12 h, 24 h, 48 h, and 72 h using the TB40/e strain. Cells were treated with 1µM flavopiridol 1 hour prior to isolation. Additionally, PRO-Cap was performed on untreated HFFs after 72 h of infection. Each experiment was performed with adapters containing 8 nt of random sequence flanking both ends (16 total bases of randomness) to enable deduplication.

2022-02-17 | GSE185762 | GEO

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

Project description:To investigate the chromatin structure surrounding human RNA polymerase II (Pol II) transcription on host and viral genomes, chromatin immunoprecipitation (ChIP) was performed following digestion of HCMV infected primary human foreskin fibroblasts (HFFs) with DNA Fragmentation Factor (DFF). DFF is a human endonuclease responsible for cleaving between nucleosomes during apoptosis. We found that utilizing DFF as the front end for ChIP-Seq in place of sonication or Micrococcal nuclease (MNase) offered new insights into the connections between active transcription and the local chromatin on the host and that these connections were completely absent on the HCMV genome.

2022-02-17 | GSE185618 | GEO

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

Project description:Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes

| PRJNA770683 | ENA

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

Project description:Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [Pro-seq]

| PRJNA770685 | ENA

Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

Project description:Differences in RNA polymerase II complexes and their interactions with surrounding chromatin on human and cytomegalovirus genomes [ChIP-seq]

| PRJNA770185 | ENA

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer.

Project description:Transcriptional dysregulation is a hallmark of prostate cancer (PCa). We mapped the RNA polymerase II-associated (RNA Pol II-associated) chromatin interactions in normal prostate cells and PCa cells. We discovered thousands of enhancer-promoter, enhancer-enhancer, as well as promoter-promoter chromatin interactions. These transcriptional hubs operate within the framework set by structural proteins - CTCF and cohesins - and are regulated by the cooperative action of master transcription factors, such as the androgen receptor (AR) and FOXA1. By combining analyses from metastatic castration-resistant PCa (mCRPC) specimens, we show that AR locus amplification contributes to the transcriptional upregulation of the AR gene by increasing the total number of chromatin interaction modules comprising the AR gene and its distal enhancer. We deconvoluted the transcription control modules of several PCa genes, notably the biomarker KLK3, lineage-restricted genes (KRT8, KRT18, HOXB13, FOXA1, ZBTB16), the drug target EZH2, and the oncogene MYC. By integrating clinical PCa data, we defined a germline-somatic interplay between the PCa risk allele rs684232 and the somatically acquired TMPRSS2-ERG gene fusion in the transcriptional regulation of multiple target genes - VPS53, FAM57A, and GEMIN4. Our studies implicate changes in genome organization as a critical determinant of aberrant transcriptional regulation in PCa.

| S-EPMC7410051 | biostudies-literature

Stability, flexibility, and dynamic interactions of colliding RNA polymerase II elongation complexes.

Project description:Multiple RNA polymerase II (RNAPII) molecules can transcribe a gene simultaneously, but what happens when such polymerases collide--for example due to polymerase pausing or DNA damage? Here, RNAPII collision was characterized using a reconstituted system for simultaneous transcription by two polymerases. When progression of leading polymerase is obstructed, rear-end collision entails a transient state in which the elongation complexes interact, followed by substantial backtracking of trailing polymerase. Elongation complexes remain stable on DNA, with their activity and the integrity of transcription bubbles remaining intact. Subsequent TFIIS-stimulated transcript cleavage allows resumed forward translocation, resulting in trailing polymerase oscillating at the obstruction. Conversely, if leading polymerase is merely stalled at a pause site, collision and TFIIS cooperate to drive it through. We propose that dynamic interactions between RNAPII elongation complexes help regulate polymerase traffic and that their conformational flexibility buffers the effect of collisions with objects on DNA, thereby maintaining stability in the face of obstacles to transcription.

| S-EPMC2791892 | biostudies-literature

Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue.

Project description:Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Here we show that Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II, and report crystal structures of the Bye1 TLD bound to Pol II and three different Pol II-nucleic acid complexes. Like TFIIS, Bye1 binds with its TLD to the Pol II jaw and funnel. In contrast to TFIIS, however, it neither alters the conformation nor the in vitro functions of Pol II. In vivo, Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.

| S-EPMC3780847 | biostudies-literature

Structures of RNA polymerase II complexes with Bye1, a chromatin-binding PHF3/DIDO homologue

Project description:Bypass of Ess1 (Bye1) is a nuclear protein with a domain resembling the central domain in the transcription elongation factor TFIIS. Bye1 binds with its TFIIS-like domain (TLD) to RNA polymerase (Pol) II. Using a Bye1-TAP strain ChIP-chip was performed to examine the genome-wide association of Bye1 with chromatin in vivo. Bye1 is recruited to chromatin via its TLD and occupies the 5'-region of active genes. A plant homeo domain (PHD) in Bye1 binds histone H3 tails with trimethylated lysine 4, and this interaction is enhanced by the presence of neighboring posttranslational modifications (PTMs) that mark active transcription and conversely is impaired by repressive PTMs. We identify putative human homologs of Bye1, the proteins PHD finger protein 3 and death-inducer obliterator, which are both implicated in cancer. These results establish Bye1 as the founding member of a unique family of chromatin transcription factors that link histones with active PTMs to transcribing Pol II.

2013-09-23 | E-MTAB-1894 | biostudies-arrayexpress

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