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A Super Enhancer derived enhancer RNA acts together with CTCF/Cohesin in trans to regulate erythropoiesis

ABSTRACT: A Super Enhancer derived enhancer RNA acts together with CTCF/Cohesin in trans to regulate erythropoiesis

PROVIDER: PRJNA1219658 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR32243552.fastq.gz	Fastqsanger.gz
	SRR32243553.fastq.gz	Fastqsanger.gz
	SRR32243554.fastq.gz	Fastqsanger.gz
	SRR32243555.fastq.gz	Fastqsanger.gz
	SRR32243556.fastq.gz	Fastqsanger.gz

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A Super Enhancer derived enhancer RNA acts together with CTCF/Cohesin in trans to regulate erythropoiesis

Project description:Enhancer RNAs (eRNAs) function in diverse modes and increasing studies have shown that they play important roles in normal development and disease. However, their role in erythropoiesis is not fully understood. We analyzed published RNA-seq and Promoter Capture Hi-C data from mouse fetal liver cells and embryonic stem cells to identify enhancer RNAs in erythroid cells with long-range interactions. We discovered an erythroid-specific enhancer RNA (CpoxeRNA) transcribed from an enhancer region upstream of Cpox, an enzyme important for heme synthesis. CpoxeRNA is crucial for erythropoiesis, as knockdown of CpoxeRNA results in impaired enucleation and cell proliferation during terminal erythropoiesis. CpoxeRNA interacts with cohesin and acts both in cis and in trans to regulate erythroid genes. Thus, we have identified a trans-acting eRNA, CpoxeRNA, as an important regulator of terminal erythropoiesis.

2025-04-30 | GSE288876 | GEO

The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (RNA-seq)

Project description:Enhancer-derived RNAs are thought to contribute locally to their parent enhancers’ functions. Whether large domains of clustered enhancers (super-enhancers, SEs) also produce cis-acting RNAs, however, remains unclear. Unlike typical enhancers, SEs form large spans of robustly transcribed chromatin, amassing capped and polyadenylated RNAs that are sufficiently abundant to sustain trans functions. Here, we show that one such RNA, alncRNA-EC7/Bloodlinc, is transcribed from a SE of the erythroid membrane transporter SLC4A1/BAND3 but diffuses beyond this site. Bloodlinc localizes to trans-chromosomal loci encoding critical regulators/effectors of terminal erythropoiesis and directly binds chromatin-organizing and transcription factors, including the chromatin attachment factor HNRNPU. Inhibiting Bloodlinc or Hnrnpu compromises the terminal erythropoiesis gene program, blocking red cell production, whereas expressing Bloodlinc ectopically stimulates this program and can promote erythroblast proliferation and enucleation in the absence of differentiation stimuli. Thus, Bloodlinc represents a novel type of trans-acting SE RNA that potentiates red blood cell development.

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The super-enhancer derived alncRNA-EC7/Bloodlinc potentiates red blood cell development in trans (ChIRP-seq)

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Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis

Project description:Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis

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Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex

Project description:This SuperSeries is composed of the SubSeries listed below. Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERÎ± at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Refer to individual Series

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Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (ChIP-seq)

Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERÎ± at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Chromatin Immunoprecipitation (ChIP) assay followed by high throughput sequencing (ChIP-seq)

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Project description:The enhancer regions of the myogenic master regulator MyoD give rise to at least two enhancer RNAs. CEeRNA regulates transcription of the adjacent MyoD gene while DRReRNA affects expression of Myogenin in trans. We found that DRReRNA is recruited at the Myogenin locus where it colocalizes with Myogenin nascent transcripts. DRReRNA associates with the Cohesin complex and such association correlates with its transactivating properties. Despite being expressed in undifferentiated cells, Cohesin is not loaded on Myogenin until the cells start expressing DRReRNA, which is then required for Cohesin chromatin recruitment and maintenance. Functionally, depletion of either Cohesin or DRReRNA reduces chromatin accessibility, prevents Myogenin activation, and hinders muscle cell differentiation. Thus, DRReRNA ensures spatially appropriate Cohesin loading in trans to regulate gene expression.

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Enhancer Activation Requires Trans-Recruitment of a Mega Transcription Factor Complex (Gro-seq)

Project description:Enhancers provide critical information directing cell-type specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1-2MDa complex of diverse DNA-binding transcription factors by ERÎ± at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome. Global Run On (GRO) assay followed by high throughput sequencing (GRO-seq)

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Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [ATAC-seq]

Project description:Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [ATAC-seq]

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Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [RNA-seq]

Project description:Hemogen /BRG1 cooperativity modulates promoter and enhancer activation during erythropoiesis [RNA-seq]

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