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Regulatory architecture of housekeeping genes is driven by promoter assemblies [Pol2]

ABSTRACT: Regulatory architecture of housekeeping genes is driven by promoter assemblies [Pol2]

PROVIDER: PRJNA561371 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10010804_1.fastq.gz	Fastqsanger.gz
	SRR10010804_2.fastq.gz	Fastqsanger.gz
	SRR10010805_1.fastq.gz	Fastqsanger.gz
	SRR10010805_2.fastq.gz	Fastqsanger.gz
	SRR10010806_1.fastq.gz	Fastqsanger.gz

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Regulatory architecture of housekeeping genes is driven by promoter assemblies

Project description:Regulatory architecture of housekeeping genes is driven by promoter assemblies

| PRJNA561369 | ENA

Regulatory architecture of housekeeping genes is driven by promoter assemblies [Pol2]

Project description:Pol2 ChIA-PET in control and Ronin KO ES cells.

2023-04-15 | GSE136143 | GEO

Regulatory architecture of housekeeping genes is driven by promoter assemblies [Ronin]

Project description:Regulatory architecture of housekeeping genes is driven by promoter assemblies [Ronin]

| PRJNA561372 | ENA

Regulatory architecture of housekeeping genes is driven by promoter assemblies.

Project description:Genes that are key to cell identity are generally regulated by cell-type-specific enhancer elements bound by transcription factors, some of which facilitate looping to distant gene promoters. In contrast, genes that encode housekeeping functions, whose regulation is essential for normal cell metabolism and growth, generally lack interactions with distal enhancers. We find that Ronin (Thap11) assembles multiple promoters of housekeeping and metabolic genes to regulate gene expression. This behavior is analogous to how enhancers are brought together with promoters to regulate cell identity genes. Thus, Ronin-dependent promoter assemblies provide a mechanism to explain why housekeeping genes can forgo distal enhancer elements and why Ronin is important for cellular metabolism and growth control. We propose that clustering of regulatory elements is a mechanism common to cell identity and housekeeping genes but is accomplished by different factors binding distinct control elements to establish enhancer-promoter or promoter-promoter interactions, respectively.

| S-EPMC10329844 | biostudies-literature

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

Regulatory architecture of housekeeping genes is driven by promoter assemblies

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-04-15 | GSE136145 | GEO

Regulatory architecture of housekeeping genes is driven by promoter assemblies [Ronin]

Project description:Ronin ChIA-PET in R1 mouse ES cells.

2023-04-15 | GSE136144 | 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 – 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

CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer

Project description:CHD6 eviction of promoter nucleosomes maintains housekeeping transcriptional program in prostate cancer

| PRJNA1102338 | ENA

HSF1-expression: Molecular mechanisms that distinguish TFIID housekeeping from regulatable SAGA promoters

Project description:An important distinction is frequently made between constitutively expressed housekeeping genes versus regulated genes. Although generally characterized by different DNA elements, chromatin architecture and cofactors, it is not known to what degree promoter classes strictly follow regulatability rules and which molecular mechanisms dictate such differences. We show that SAGA-dominated/TATA-box promoters are more responsive to changes in the amount of activator, even compared to TFIID/TATA-like promoters that depend on the same activator Hsf1. Regulatability is therefore an inherent property of promoter class. Further analyses show that SAGA/TATA-box promoters are more dynamic because TBP recruitment through SAGA is susceptible to removal by Mot1. In addition, the nucleosome configuration upon activator depletion shifts on SAGA/TATA-box promoters and seems less amenable to preinitiation complex formation. The results explain the fundamental difference between housekeeping and regulatable genes, revealing an additional facet of combinatorial control: an activator can elicit a different response dependent on core promoter class.

2016-11-11 | GSE81479 | GEO

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