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The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

ABSTRACT: The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

PROVIDER: PRJNA689216 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR13341827_1.fastq.gz	Fastqsanger.gz
	SRR13341827_2.fastq.gz	Fastqsanger.gz
	SRR13341828_1.fastq.gz	Fastqsanger.gz
	SRR13341828_2.fastq.gz	Fastqsanger.gz
	SRR13341829_1.fastq.gz	Fastqsanger.gz

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The 3' Pol II pausing at replication-dependent histone genes is regulated by Mediator through Cajal bodies’ association with histone locus bodies

Project description:The non-polyadenylated mRNAs of replication-dependent histones (RDHs) and small nuclear RNAs (snRNAs) are synthesized by RNA polymerase II at histone locus bodies (HLBs) and Cajal bodies (CBs), respectively. We previously showed that MED26-containing Mediator regulates the 3'-end processing of non-polyadenylated transcripts by recruiting Little Elongation Complex (LEC) to the genes. HLBs frequently associate with CBs, in which 3'-end processing factors for RDH genes are enriched; however, this association’s role has not been elucidated. Here, we show that disruption of the Mediator docking site for LEC by mutating the MED26-binding site of EAF1, a subunit of LEC, interferes with CBs’ association with HLBs, resulting in decreased inter-chromosome interaction between RDH gene clusters and increased aberrant unprocessed RDH gene transcripts. Our findings suggest a model in which LEC recruitment by Mediator plays a role in CBs’ association with HLBs to facilitate the 3'-end processing of RDH genes by supplying 3'-end processing factors.

2022-04-26 | GSE164144 | GEO

Cajal bodies are linked to genome conformation

Project description:Cajal bodies are linked to genome conformation

| PRJNA312097 | ENA

Cajal bodies are linked to genome conformation [smallRNA-Seq]

Project description:The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are unknown. We examined the non-random positioning of Cajal bodies (CBs), major NBs involved in spliceosomal snRNP assembly, and their role in genome organization. CBs are predominantly located at the periphery of chromosome territories at a multi-chromosome interface. Genome-wide chromatin conformation capture analysis (4C-seq) using CB-interacting loci revealed that CB-associated regions are enriched with highly expressed histone genes and U small nuclear and nucleoar RNA (sn/snoRNA) loci that form intra- and inter-chromosomal clusters. We observed a number of CB-dependent gene positioning events on chromosome 1. RNAi-mediated disassembly of CBs disrupts the CB-targeting gene clusters and suppresses the expression of U sn/snoRNA and histone genes. This loss of spliceosomal snRNP production resulted in increased splicing noise, even in CB-distal regions. We conclude that CBs contribute to genome organization with global effects on gene expression and RNA splicing fidelity.

2016-03-21 | GSE77915 | GEO

Cajal bodies are linked to genome conformation [4C-Seq]

2016-03-21 | GSE77914 | GEO

Cajal bodies are linked to genome conformation [RNA-Seq]

2016-03-21 | GSE77913 | GEO

Nopp140-chaperoned 2’-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity

Project description:Nopp140-chaperoned 2’-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity

| PRJNA724033 | ENA

Coilin and Pol II ChIP-seq in HeLa cells after RPL14 and RPL24 depletion

Project description:To investigate location of Cajal bodies (CB) inside the cell nucleus after RPL depletion, we performed ChIP-seq with an anti-Coilin antibody after siRNA knockdown of RPL14 and RPL24. ChIP-seq revealed a loss of association of CBs wih snRNA genes and histone genes in histone cluster 1 and 2 upon RPL KD. We also performed Pol 2 ChIP-seq to look at transcription of these gene loci upon RPL knockdown and found decreased Pol II binding along genes.

2024-03-27 | GSE199275 | GEO

Drosophila FACT Regulates Promoter Proximal Pol II Pausing and Chromatin Architecture [RNA-seq]

Project description:The highly conserved histone chaperone FACT (Facilitates Chromatin Transcription) is thought to contribute to the disassembly and reassembly of nucleosomes in the wake of RNA Polymerase II (Pol II) passage through chromatin. However, FACT’s roles in chromatin biology and transcriptional regulation in vivo in higher eukaryotes are not well understood. Here, we report that depletion of FACT leads to a reduction in the duration of promoter-proximal pausing by Pol II in Drosophila S2 cells. In addition, FACT depletion leads to a modest decrease in the occupancy of histone H3, and to decrease in occupancy of histone H2A.v in promoter-proximal nucleosomes. Finally, we observed a dramatic 5’ to 3’ repositioning of the co-transcriptionally deposited histone modifications H3K4me3 and H3K36me3 in the FACT depleted cells. Taken together, our findings are consistent with the model that FACT contributes to the interplay between chromatin architecture and control of Pol II promoter-proximal pausing.

2019-06-18 | GSE129235 | GEO

Drosophila FACT Regulates Promoter Proximal Pol II Pausing and Chromatin Architecture [ChIP-seq]

2019-06-18 | GSE113470 | GEO

CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing

Project description:This SuperSeries is composed of the following subset Series: GSE31485: CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [ChIP-Seq] GSE31486: CTCF promotes RNA pol II pausing and links DNA methylation to alternative splicing [RNA-Seq] Refer to individual Series

2011-10-05 | E-GEOD-31278 | biostudies-arrayexpress

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