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Reading the Covalent Topoisomerase1-DNA Intermediate: A Transcriptional Code Broadly Required for Signal-dependent Enhancer Activation [Human CUT&RUN]

ABSTRACT: Acutely activated enhancers require the actions of Topo1cc, including those induced by 17β-oestradiol (E2), dihydrotestosterone (DHT) and tumor necrosis factor alpha (TNFa). Topo1cc at these acutely activated enhancers is “read” by Ku70, which in this context serves as a required transcriptional coactivator, based on nucleating a Ku70/heterochromatin protein1 gamma (HP1γ) complex to facilitate the recruitment of mediator subunit Med26 for eRNA transcription.

ORGANISM(S): Homo sapiens

PROVIDER: GSE190284 | GEO | 2022/08/04

REPOSITORIES: GEO

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Cbx3 Maintains Lineage Specificity During Neural Differentiation [RNA-seq]

Project description:Cbx3 (HP1γ) that is a member of the heterochromatin protein 1 family play important roles in development and differentiation. To determine the regulatroy mechanisms of Cbx3 during neural differentiation from ESCs to NPCs, we performed RNA-seq analysis of ESCs or ESC-derived NPCs depleted for Cbx3 or Cbx3-assocatied Mediator subunit Med26.

2017-03-27 | GSE89574 | GEO

Ku70/HP1g are presented at the KCl induced acutely activated enhancers [ChIP-seq]

Project description:Ku70/HP1g are serving as the marker for the KCl induced acutely enhancer activation in cortical neurons.

2022-08-04 | GSE185648 | GEO

Cbx3 Maintains Lineage Specificity During Neural Differentiation [ChIP-seq]

Project description:Cbx3 (HP1γ) that is a member of the heterochromatin protein 1 familiy enriched in gene bodies of pluripotent ESCs but promoters of differentiated pre-iPSCs. To determine whether Cbx3 becomes enriched at promoters to influence gene regulation during differentiation, we converted ESCs to NPCs in monolayer culuture and performed genomewide ChIP-seq of Cbx3. Our results shows that Cbx3 enriches at the promoters of genes upon differentiation of ESCs to NPCs and stablizes the binding of Mediator subunit Med26 to pre-initiation complex (PIC) in NPCs.

2017-03-27 | GSE89573 | GEO

EP400 Deposits H3.3 into Promoters and Enhancers During Gene Activation

Project description:Purpose: We wanted to know how histone variants H3.3 and H2AZ are deposited into genes and enhancers during gene activation Methods: U2OS cells were harvested at 70% confluency with formaldehyde crosslinking for ChIP-seq without crosslinking for RNA-seq. ChIP DNA were purified through standard chromatin immunoprecipitation using an Pol II, MED26, EP400, H3.3, H2AZ, H3k4me1 and K3K18ac antibodies. Libraries were prepared with a KAPA LTP kit and sequenced using the Illumina HiSeq 2000 platform. Total RNA was extracted with Trizol, digested with DNaseI and further purified by acid phenol. Libraries were prepared with Illumina TruSeq RNA Sample Prep Kits v2 and were sequenced on Illumina HiSeq 2000. Conclusion: Our biochemical and genomics (ChIP-Seq and mRNA-Seq) data show that EP400 contributes to H3.3 deposition in significantly with less of an effect on H2AZ in both genes and enhancers Enrichment of EP400, Pol II, MED26, Histone varinat H3.3 and H2AZ, and enhancers marks H3K4me1 and H3K18ac in either Mock and/or EP400 knockdown conditions on chromatin were generated by ChIP-Seq. mRNA profiles under Mock siRNA or EP400siRNA were generated by deep sequencing, using Illumina HiSeq 2000.

2015-12-18 | E-GEOD-73742 | biostudies-arrayexpress

Identification of Med26 target genes in Human HEK 293T cells

Project description:Med26 is a subunit of the Human Mediator complex. The Mediator complex is an evolutionarily conserved coregulatory complex that interacts with RNA polymerase II to regulate gene expression. In metazoa, Mediator is composed of some 30 distinct subunits. Mediator exists in multiple, functionally distinct forms that share a common core of subunits and can be distinguished by the presence or absence of a kinase module composed of Med12, Med13, Cdk8, and Cyclin C. In higher eukaryotes, a subset of Mediator complexes is associated with an additional subunit, Med26. This Med26-containing Mediator copurifies from cells with little or no kinase module, but near-stoichiometric Pol II. Evidence suggests that Med26-containing Mediator plays a key role in transcriptional activation however, the mechanism(s) by which Med26 contributes to this process are not known. To identify Med26 target genes, we used Affymetrix U133A plus 2.0 expression arrays to analyze mRNA expression in 293T cells from which Med26 had been depleted by transient transfection by each of three different siRNAs. Three different independent Med26 siRNA knockdowns were compared to a non-targeting control in triplicate, for a total of 12 samples.

2011-08-31 | E-GEOD-28715 | biostudies-arrayexpress

Identification of Med26 target genes in Human HEK 293T cells

2011-09-01 | GSE28715 | GEO

Genome-wide interference of chromatin architecture and Mediator in transcriptional bursting and gene network regulation

Project description:Gene expression is a stochastic process that occurs in bursts of RNA synthesis. We applied a mathematical model to scRNA-Seq data to infer bursting dynamics transcriptome-wide under multiple perturbations in a wide range of cell types and identified possible molecular mechanisms. We find that mediator complex subunit MED26 primarily regulates frequency, MYC regulates burst size, while cohesin and super-enhancers can modulate both. Despite comparable effect sizes on RNA levels amongst these perturbations, we find that acute depletion of MED26 plays a larger role in perturbing gene regulatory networks. Furthermore, this perturbation acts downstream of both chromatin spatial architecture and preinitiation complex formation, indicating that later steps in the initiation of transcriptional bursts are primary nodes for integrating gene networks in single cells.

2024-06-30 | GSE241338 | GEO

Knockdown of HP1γ in H1792 cells

Project description:For analysis of genes regulated by HP1γ in LUAD, we used microarray analysis to determine the global changes in gene expression upon HP1γ knockdown in H1792 cells and identified distinct sets of up-regulated and down-regulated genes upon depletion of HP1γ.

2018-11-13 | GSE111321 | GEO

HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells (RNA-seq)

Project description:The heterochromatin protein 1 (HP1) family members are canonical effectors and propagators of gene repression mediated by histone H3 lysine 9 (H3K9) methylation. HP1γ exhibits an increased interaction with active transcription elongation-associated factors in embryonic stem cells (ESCs) compared to somatic cells. However, whether this association has a functional consequence remains elusive. Here we find that genic HP1γ colocalizes and enhances enrichment of transcription elongation-associated H3K36me3 rather than H3K9me3. Unexpectedly, sustained H3K36me3 deposition is dependent on HP1γ. HP1γ-deleted ESCs display reduced H3K36me3 enrichment, concomitant with decreased expression at shared genes which function to maintain cellular homeostasis. Both the H3K9me3-binding chromodomain and histone binding ability of HP1γ are dispensable for maintaining H3K36me3 levels. Instead, the chromoshadow together with the hinge domain of HP1γ that confer protein and nucleic acid-binding ability are sufficient because they retain the ability to interact with NSD1, an H3K36 methyltransferase. HP1γ-deleted ESCs have a slower self-renewal rate and an impaired ability to differentiate towards cardiac mesoderm. Our findings reveal a requirement for HP1γ in faithful establishment of transcription elongation in ESCs, which regulates pluripotency.

2020-11-01 | GSE144862 | GEO

HP1γ regulates H3K36 methylation and pluripotency in embryonic stem cells (ChIP-Seq)

2020-11-01 | GSE144861 | GEO

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