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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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Similar Datasets

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

| PRJNA477764 | ENA

Transcriptional cofactors display core promoter class-specificity in human

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

| PRJNA521352 | ENA

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

| PRJNA532544 | ENA

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

| PRJNA272312 | ENA

Cooperative binding of DNA sequence non-specific HMGbox Factor Ubf and TBP-TAF complex SL1 determines RNA Polymerase I promoter recognition in vivo and its dysfunction underlies the Ubf-E210K neuroregression syndrome

Project description:Transcription of the >200 rRNA genes (rDNA) by RNA Polymerase I (RPI) determines as much as 35% of total nuclear RNA synthesis and is a major determinant of cell growth implicated in a range of hypertrophic and developmental disorders. Activation of the rDNA involves the formation of an extended nucleosome free region (NFR) by the multi-HMGbox factor UBTF, which is also implicated with the RPI specific TBP-TAFI factor SL1 in preinitiation complex formation. However, neither factor alone displays significant DNA sequence binding specificity. Here we show that in cell cooperation between SL1 and the UBTF1 splice variant creates the sequence specificity required for promoter recognition. While both UBTF1 and UBTF2 splice variants bind throughout the rDNA NFR, only UBTF1 binds at the rDNA promoters. Conditional deletion of the Taf1b subunit of SL1 depleted UBTF1 from the rDNA promoters but not from elsewhere across the rDNA NFR. We show RPI promoters are particularly poor binding sites for UBTF and suggest an induced-fit model in which promoter-specific remodelling by UBTF1 creates high affinity sites for SL1 binding. A mouse model of the UBTF-E210K pediatric neurodegeneration syndrome suggests this mutation affects cooperativity of UBTF-SL1 promoter recruitment and further supports the induced-fit model.

2021-08-31 | E-MTAB-10433 | biostudies-arrayexpress

2022-02-03 | E-MTAB-11385 | biostudies-arrayexpress

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