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Enhancer-promoter association determines cell specificity in mouse pluripotent cells

ABSTRACT: Enhancer-promoter association determines cell specificity in mouse pluripotent cells

PROVIDER: PRJNA475949 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7308620_1.fastq.gz	Fastqsanger.gz
	SRR7308620_2.fastq.gz	Fastqsanger.gz
	SRR7308621_1.fastq.gz	Fastqsanger.gz
	SRR7308621_2.fastq.gz	Fastqsanger.gz
	SRR7308622_1.fastq.gz	Fastqsanger.gz

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Enhancer-promoter association determines cell specificity in mouse pluripotent cells

Project description:Enhancer-promoter association is emerging as a common pattern to determine gene function in eukaryotes. However, it remains as an uncultivated land on how its diversity influences gene expression. In this study, we select three defined Sox2 associated enhancers, representing different distal interaction categories, to further explore its biological effects. We construct three enhancer-knock-out cells via CRISPR/Cas9 system in mouse embryonic stem cells. With multiple-level evidences, we realize these associations carried out various biological features. Embryonic cell specific association determines cell proliferation and cell cycle and also involves in cardiac function, which has been validated in vivo. On the other hand, the common or indirect association prefers to regulate cell metabolic process and nerve development in cell function. Our study will enable an alternative way for gene spatiotemporal regulation study and advance our understanding of its diversity since first described decades ago.

2020-07-01 | GSE115750 | GEO

Enhancer-core promoter specificity separates developmental and housekeeping regulation

Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters M-bM-^@M-^S one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genesM-bM-^@M-^Y core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome. STARR-seq was performed in S2 and OSC cells using two core promoters each representing housekeeping and developmental transcription programs. Data for housekeeping promoters (hkCP) are presented in this series; Data for developmental core promoters (dCP) samples are presented in GSE40739.

2014-12-10 | E-GEOD-57876 | biostudies-arrayexpress

Enhancer-core promoter specificity separates developmental and housekeeping regulation

Project description:Gene transcription in animals involves the assembly of the RNA polymerase II complex at core promoters and its cell type-specific activation by genomic enhancers that can be located more distally. However, how ubiquitous expression of housekeeping genes is achieved has remained less clear. In particular, it is unknown whether ubiquitously active enhancers exist and how developmental and housekeeping gene regulation is separated. An attractive hypothesis is that different types of core promoters might exhibit an intrinsic specificity towards certain types of enhancers. Here, we show that thousands of enhancers in D. melanogaster S2 cells and ovarian somatic cells (OSCs) exhibit a marked specificity towards one of two core promoters – one derived from a ubiquitously expressed ribosomal protein gene and another from a developmentally regulated transcription factor. Enhancers that activate the housekeeping core promoter are functional across the two different cell types, while developmental enhancers exhibit strong cell type specificity. Both enhancer classes differ in their overall genomic distribution, the functions of neighbouring genes,these genes’ core promoter elements, as well as the associated factors. Our results provide evidence for a sequence-encoded enhancer-core promoter specificity that separates developmental and housekeeping gene regulatory programs for thousands of enhancers and their target genes across the entire genome.

2014-12-10 | GSE57876 | GEO

Transcriptional cofactors display core promoter class-specificity

Project description:Transcriptional cofactors display core promoter class-specificity

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GFI1B determines specificity of lung tissue-resident multipotent ILC

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Transcriptional cofactors display core promoter class-specificity in human

Project description:Transcriptional cofactors display core promoter class-specificity in human

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DNA Promoter Hypermethylation of Melanocyte Lineage Genes Determines Melanoma Phenotype

Project description:DNA Promoter Hypermethylation of Melanocyte Lineage Genes Determines Melanoma Phenotype

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Promoter architecture determines cotranslational regulation of mRNA

Project description:Information that regulates gene expression is encoded throughout each gene but if different regulatory regions can be understood in isolation, or if they interact, is unknown. Here we measure mRNA levels for 10,000 open reading frames (ORFs) transcribed from either an inducible or constitutive promoter. We find that the strength of cotranslational regulation on mRNA levels is determined by promoter architecture. By using a novel computational genetic screen of 6402 RNA-seq experiments, we identify the RNA helicase Dbp2 as the mechanism by which cotranslational regulation is reduced specifically for inducible promoters. Finally, we find that for constitutive genes, but not inducible genes, most of the information encoding regulation of mRNA levels in response to changes in growth rate is encoded in the ORF and not in the promoter. Thus, the ORF sequence is a major regulator of gene expression, and a nonlinear interaction between promoters and ORFs determines mRNA levels.

2017-06-28 | GSE100452 | GEO

Dinucleotide regulation by REXO2 maintains promoter specificity in mammalian mitochondria

Project description:Dinucleotide regulation by REXO2 maintains promoter specificity in mammalian mitochondria

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Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage

Project description:Conversion of MyoD to a neurogenic factor: binding site specificity determines lineage

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