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Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [ChIP-seq]

ABSTRACT: Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [ChIP-seq]

PROVIDER: PRJNA1078735 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR28027821_1.fastq.gz	Fastqsanger.gz
	SRR28027821_2.fastq.gz	Fastqsanger.gz
	SRR28027822_1.fastq.gz	Fastqsanger.gz
	SRR28027822_2.fastq.gz	Fastqsanger.gz
	SRR28027823_1.fastq.gz	Fastqsanger.gz

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Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.

Project description:Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function.

| PRJNA1078774 | ENA

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [Micro-C]

Project description:Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [Micro-C]

| PRJNA1078734 | ENA

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [PRO-seq]

Project description:Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [PRO-seq]

| PRJNA1078740 | ENA

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [PRO-seq]

Project description:Interactions between distal loci in mammalian genomes, including those involving enhancers and promoters, are thought to be a central mechanism of gene regulation in mammals, yet the protein regulators of these interactions remain largely undetermined. The zinc finger transcription factor ZNF143/ZFP143 has been strongly implicated as a factor that regulates chromatin interactions, functioning either with or without CTCF. However, ZNF143/ZFP143’s role in this process and its function with or without CTCF are not well understood. Here, we tagged both CTCF and ZNF143/ZFP143 with dual-purpose degron/imaging tags to combinatorically assess their loop function and effect on each other. We find that ZNF143/ZFP143 possesses no general looping function, and that it largely functions independently to CTCF. Instead, ZNF143/ZFP143 is an essential and highly conserved transcription factor possessing an extremely stable chromatin residence time (>20 min) that regulates an important subset of mitochondrial and ribosomal genes.

2024-03-07 | GSE256227 | GEO

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [ChIP-seq]

2024-03-07 | GSE256226 | GEO

Putative looping factor ZNF143/ZFP143 is an essential transcriptional regulator with no looping function [Micro-C]

2024-03-07 | GSE256225 | GEO

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

Project description:Gene expression is orchestrated by transcription factors (TFs), which bind to DNA in a sequence-specific manner, and by spatial genome structure, which constrains and shapes TF activity. Zinc finger protein 143 (ZNF143/ZFP143) is a TF that has been implicated in both gene activation and 3D genome organisation. We have generated an acute ZNF143/ZFP143 depletion system to study its direct consequences on chromatin looping and gene transcription. The effects of ZNF143/ZFP143 depletion are inconsistent with it being a looping factor, which we further confirmed by systematic analysis of previous studies. However, degradation of ZNF143/ZFP143 led to the down-regulation of hundreds of its targets, which were found to be enriched in nuclear-encoded mitochondrial genes. By studying the consequences of ZNF143/ZFP143 loss in monoculture and in an in vitro embryonic development model, we establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by modulating mitochondrial functions.

2024-03-08 | PXD049480 | Pride

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

Project description:Gene expression is orchestrated by transcription factors, which function within the context of a three-dimensional genome. Zinc finger protein 143 (ZNF143/ZFP143) is a transcription factor that has been implicated in both gene activation and chromatin looping. To study the direct consequences of ZNF143/ZFP143 loss, we generated a ZNF143/ZFP143 degron line. Our results show that ZNF143/ZFP143 depletion has no effect on chromatin looping. Systematic analysis of ZNF143/ZFP143 occupancy data revealed that a commonly used antibody cross-reacts with CTCF, leading to its incorrect association with chromatin loops. Nevertheless, ZNF143/ZFP143 specifically activates nuclear-encoded mitochondrial genes and its loss leads to severe mitochondrial dysfunction. Using an in vitro embryo model, we find that ZNF143/ZFP143 is an essential regulator of organismal development. Our results establish ZNF143/ZFP143 as a conserved transcriptional regulator of cell proliferation and differentiation by safeguarding mitochondrial activity.

2024-08-23 | GSE271837 | GEO

ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF

2024-03-08 | GSE260914 | GEO

The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer (ChIP-seq)

Project description:Estrogen signaling in breast cancer cells relies on long-range chromatin interactions connecting distal regulatory elements bound by the estrogen receptor 1 (ESR1) to target gene promoters. This ensures stimulus and subtype-specific transcriptional responses. Expanding on the function of CTCF and the cohesin complex in breast cancer, we demonstrate that the chromatin-looping factor ZNF143 binds the promoter of most early-response estrogen target genes connected to distal regulatory elements in ESR1-positive breast cancer cells. Its chromatin occupancy is unaffected by estrogen stimulation, supporting a stable three-dimensional genomic architecture within the early response to estrogen. Its loss abrogates the estrogen-induced transcriptional response and growth of breast cancer cells. When taking into account CTCF, ZNF143 and cohesin complex subunits, we show that chromatin-looping factors are genetically altered in over 20% of ESR1-positive primary breast tumors. Furthermore, the overexpression of ZNF143, CTCF and RAD21, a cohesin complex subunit, in ESR1-positive breast tumors associates with a worse clinical outcome. Overall, our results suggest that ZNF143 is a new critical effector of the estrogen response and highlights the contribution of the chromatin looping machinery to ESR1-positive breast cancer development. Examination of genome-wide ZNF143 binding in MCF-7 cells

2016-08-09 | E-GEOD-76454 | biostudies-arrayexpress

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