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Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci.

ABSTRACT: Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci.

PROVIDER: PRJNA734617 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14713100.fastq.gz	Fastqsanger.gz
	SRR14713101.fastq.gz	Fastqsanger.gz
	SRR14713102.fastq.gz	Fastqsanger.gz
	SRR14713103.fastq.gz	Fastqsanger.gz
	SRR14713104.fastq.gz	Fastqsanger.gz

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Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci.

Project description:RB’s interaction with chromatin is key to understanding its molecular functions. Using a novel ChIP-sequencing protocol, we identify the precise chromatin loci bound by various forms of human RB. RB targets three fundamentally different types of loci (promoters, enhancers, CTCF-sites), that are largely distinguishable by the mutually exclusive presence of E2F1, c-JUN and CTCF. E2F/DP facilitates RB association with promoters, whereas AP-1 recruits RB to enhancers. RB’s association with promoters and enhancers fluctuates: G1-arrest enriched RB at promoters, while S-phase progression redistributed RB towards enhancers. RB binding to RB/CTCF sites was unaltered by cell cycle progression. RB-bound promoters include the classic E2F targets and are similar between cell types. However, RB-bound enhancers are associated with different gene categories, including, notably, MAPK signaling, and they vary between cell types. We propose that RB has a well-preserved role controlling E2F in G1, and cell type-specific effects at enhancers when cells enter S-phase.

2022-08-01 | GSE176035 | GEO

Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci and is redistributed by cell-cycle progression.

Project description:The interaction of RB with chromatin is key to understanding its molecular functions. Here, for first time, we identify the full spectrum of chromatin-bound RB. Rather than exclusively binding promoters, as is often described, RB targets three fundamentally different types of loci (promoters, enhancers, and insulators), which are largely distinguishable by the mutually exclusive presence of E2F1, c-Jun, and CTCF. While E2F/DP facilitates RB association with promoters, AP-1 recruits RB to enhancers. Although phosphorylation in CDK sites is often portrayed as releasing RB from chromatin, we show that the cell cycle redistributes RB so that it enriches at promoters in G1 and at non-promoter sites in cycling cells. RB-bound promoters include the classic E2F-targets and are similar between lineages, but RB-bound enhancers associate with different categories of genes and vary between cell types. Thus, RB has a well-preserved role controlling E2F in G1, and it targets cell-type-specific enhancers and CTCF sites when cells enter S-phase.

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Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci

Project description:Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci

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Chromatin-bound proteins co-localized with CTCF during mES cell neuronal differentiation

Project description:Using Chromatin immunoprecipitation combined with Selective Isolation of Chromatin Associated Proteins (ChIP-SICAP), we define the chromatin-bound proteins co-localized with CTCF in mouse embryonic stem cells (ES) and neuronal stem (NS) cells. We uncover the proteins that are differentially co-localized with CTCF in ES and NS cells. We show the link between the underlying role of RNA-binding proteins with consolidation of chromatin structure during mammalian development.

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Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [ATAC-Seq]

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Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [RNA-Seq]

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Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [capture-C]

Project description:Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [capture-C]

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Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [CUT&RUN]

Project description:Myeloid leukemia dependency MYNRL15 exemplifies class of CTCF-bound lncRNA loci [CUT&RUN]

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The CTCF paralog CTCFL disrupts cohesin at active promoters.

Project description:The CTCF paralog CTCFL disrupts cohesin at active promoters.

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ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function

Project description:CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF bound promoter enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF bound promoter enhancer loops are also disrupted after excision of ZNF143. ZNF143 CTCF bound promoter enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation that ZNF143 is a critical factor for CTCF bound promoter enhancer loops.

2020-10-22 | GSE144712 | GEO

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