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ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ATAC-seq]

ABSTRACT: ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ATAC-seq]

PROVIDER: PRJNA934293 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23440121_1.fastq.gz	Fastqsanger.gz
	SRR23440121_2.fastq.gz	Fastqsanger.gz
	SRR23440122_1.fastq.gz	Fastqsanger.gz
	SRR23440122_2.fastq.gz	Fastqsanger.gz

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ELL3 promotes stem cell native to primed transition through LINE-based enhancers

Project description:ELL3 promotes stem cell native to primed transition through LINE-based enhancers

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ELL3 promotes stem cell native to primed transition through LINE-based enhancers [4C-seq]

Project description:Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos. Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure. ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells. We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

2023-06-20 | GSE229447 | GEO

ELL3 promotes stem cell native to primed transition through LINE-based enhancers [RNA-Seq]

Project description:ELL3 promotes stem cell native to primed transition through LINE-based enhancers [RNA-Seq]

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ELL3 promotes stem cell native to primed transition through LINE-based enhancers [4C-seq]

Project description:ELL3 promotes stem cell native to primed transition through LINE-based enhancers [4C-seq]

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ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]

Project description:ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]

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ELL3 promotes stem cell native to primed transition through LINE-based enhancers [RNA-Seq]

Project description:Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

2023-06-20 | GSE208226 | GEO

ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ChIP-Seq]

Project description:Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naïve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naïve-primed transition through regulating the young LINE-1 based enhancers.

2023-06-20 | GSE207397 | GEO

ELL3 promotes stem cell native to primed transition through LINE-based enhancers [ATAC-seq]

Project description:Long interspersed nuclear elements-1 (LINE-1) are the clade of retrotransposons still possessing autonomous mobility in mammals. LINE-1 transcription contributed to global chromatin opening in mouse early embryos.Whether LINE-1 element plays a direct role in the local regulation of its nearby genes remains largely obscure.ELL3 occupies and represses the youngest LINE-1 family members L1Md_T and L1Md_Gf in naÃ¯ve mouse ES cells.We found that the enhancer function of the evolutionally young LINE-1s, and suggests that ELL3 act as a key drivers of the naÃ¯ve-primed transition through regulating the young LINE-1 based enhancers.

2023-06-20 | GSE225176 | GEO

The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation

Project description:Enhancers play a central role in precisely regulating the spatiotemporal expression of developmentally regulated genes. The molecular mechanisms and factors required for controlling the inactive or poised enhancers and their function in future gene activation remain elusive. Here, we have identified that Ell3, a member of the Ell (Eleven-nineteen Lysine-rich Leukemia gene) family of RNA Pol II elongation factors, predominately occupies active and inactive enhancers of many developmentally regulated genes in mouse embryonic stem cells. Ell3 localizes to active enhancers of key stem cell renewal genes, but is not required for maintaining the undifferentiated state. Instead, Ell3 binding to inactive or poised enhancers is essential for marking them for stem cell specification through regulating the activation of key lineage-specific genes throughout differentiation. Ell3M-bM-^@M-^Ys association with enhancers is required for setting up proper Pol II occupancy at the proximal promoter regions of neighboring genes. This functional interaction between Ell3 and proximal promoter Pol II is dependent on cohesin. The depletion of cohesin subunits removes Ell3 from the enhancers and results in reduction in the levels of promoter proximally paused Pol II. Our study demonstrates that Ell3 is required for stem cell fate specification through regulating Pol II pausing on key developmental genes in the undifferentiated state and for their proper expression during differentiation. ChIP-seq of Ell3 in mES cells. ChIP-seq of Pol II in mES cells after Ell3 shRNA and non-targeting shRNA. RNA-seq of mES cells after Ell3 shRNA and non-targeting shRNA. RNA-seq of mouse embryoid bodies at day five after non-targeting shRNA.

2012-12-30 | E-GEOD-38148 | biostudies-arrayexpress

The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation

Project description:Enhancers play a central role in precisely regulating the spatiotemporal expression of developmentally regulated genes. The molecular mechanisms and factors required for controlling the inactive or poised enhancers and their function in future gene activation remain elusive. Here, we have identified that Ell3, a member of the Ell (Eleven-nineteen Lysine-rich Leukemia gene) family of RNA Pol II elongation factors, predominately occupies active and inactive enhancers of many developmentally regulated genes in mouse embryonic stem cells. Ell3 localizes to active enhancers of key stem cell renewal genes, but is not required for maintaining the undifferentiated state. Instead, Ell3 binding to inactive or poised enhancers is essential for marking them for stem cell specification through regulating the activation of key lineage-specific genes throughout differentiation. Ell3’s association with enhancers is required for setting up proper Pol II occupancy at the proximal promoter regions of neighboring genes. This functional interaction between Ell3 and proximal promoter Pol II is dependent on cohesin. The depletion of cohesin subunits removes Ell3 from the enhancers and results in reduction in the levels of promoter proximally paused Pol II. Our study demonstrates that Ell3 is required for stem cell fate specification through regulating Pol II pausing on key developmental genes in the undifferentiated state and for their proper expression during differentiation.

2012-12-30 | GSE38148 | GEO

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