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High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

ABSTRACT: High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

PROVIDER: PRJNA348315 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR4420460.fastq.gz	Fastqsanger.gz
	SRR4420470.fastq.gz	Fastqsanger.gz
	SRR4420461.fastq.gz	Fastqsanger.gz
	SRR4420471.fastq.gz	Fastqsanger.gz
	SRR4420452.fastq.gz	Fastqsanger.gz

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High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

Project description:The genomic repertoire of enhancers and promoters that control the transcriptional output of terminally differentiated cells includes cell type-specific and housekeeping elements. Whether the constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 bp from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised macrophage-specific enhancers and promoters. The role of ELFs in promoting constitutive transcription is suggested by multiple evidences: ELF sites enabled transcriptional activation by endogenous and minimal synthetic promoters; ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data indicate that a distinct subfamily of ETS proteins imparts high transcriptional activity to a broad range of housekeeping and tissue-specific cis-regulatory elements, which is consistent with the role of an ETS family ancestor in core promoter regulation in a lower eukaryote.

2017-03-13 | GSE88700 | GEO

High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

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High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

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High constitutive activity of a broad panel of housekeeping and tissue-specific <i>cis</i>-regulatory elements depends on a subset of ETS proteins.

Project description:Enhancers and promoters that control the transcriptional output of terminally differentiated cells include cell type-specific and broadly active housekeeping elements. Whether the high constitutive activity of these two groups of cis-regulatory elements relies on entirely distinct or instead also on shared regulators is unknown. By dissecting the cis-regulatory repertoire of macrophages, we found that the ELF subfamily of ETS proteins selectively bound within 60 base pairs (bp) from the transcription start sites of highly active housekeeping genes. ELFs also bound constitutively active, but not poised, macrophage-specific enhancers and promoters. The role of ELFs in promoting high-level constitutive transcription was suggested by multiple evidence: ELF sites enabled robust transcriptional activation by endogenous and minimal synthetic promoters, ELF recruitment was stabilized by the transcriptional machinery, and ELF proteins mediated recruitment of transcriptional and chromatin regulators to core promoters. These data suggest that the co-optation of a limited number of highly active transcription factors represents a broadly adopted strategy to equip both cell type-specific and housekeeping cis-regulatory elements with the ability to efficiently promote transcription.

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High activity of a broad panel of housekeeping and tissue-specific cis-regulatory elements depends on a subset of ETS proteins

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

2017-03-13 | GSE88702 | GEO

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset

Project description:This SuperSeries is composed of the following subset Series: GSE30989: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (ChIP-chip dataset) GSE30990: MOF-containing NSL complex specifically binds promoters of most, but stimulates only a specific subset of, housekeeping genes (expression dataset) Refer to individual Series

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The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (RNAi)

Project description:The MOF-containing NSL complex binds to many but not all promoters of active genes and potentially contributes to their proper gene expression. It is currently unknown what determines whether an active gene is bound or not. Here, we provide evidence that the NSL complex primarily targets active promoters of most housekeeping genes. There, it co-localizes with the chromatin remodeler NURF and the histone methyltransferase Trithorax. Moreover, despite binding to most housekeeping genes, the NSL complex regulates only a subset of them, which are depleted for certain insulator binding-proteins and enriched for the core promoter motif “Ohler 5”. We suggest that the combination of general chromatin factors and core promoter motifs is predictive for whether a housekeeping gene is transcriptionally regulated by the NSL complex. Transcriptome expression profiling comparing NSL1 RNAi-depleted cells with control RNAi cells using Affymetrix microarrays.

2011-10-28 | E-GEOD-30990 | biostudies-arrayexpress

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (ChIP)

Project description:The MOF-containing NSL complex binds to many but not all promoters of active genes and potentially contributes to their proper gene expression. It is currently unknown what determines whether an active gene is bound or not. Here, we provide evidence that the NSL complex primarily targets active promoters of most housekeeping genes. There, it co-localizes with the chromatin remodeler NURF and the histone methyltransferase Trithorax. Moreover, despite binding to most housekeeping genes, the NSL complex regulates only a subset of them, which are depleted for certain insulator binding-proteins and enriched for the core promoter motif “Ohler 5”. We suggest that the combination of general chromatin factors and core promoter motifs is predictive for whether a housekeeping gene is transcriptionally regulated by the NSL complex. ChIP-chip profiling of NSL1 in adult male and female whole fly extracts and the embryonically derived male S2 cell line.

2011-10-28 | E-GEOD-30989 | biostudies-arrayexpress

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (ChIP)

2011-10-29 | GSE30989 | GEO

The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset (RNAi)

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