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Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [PRO-seq]

ABSTRACT: Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [PRO-seq]

PROVIDER: PRJNA951642 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24046461_1.fastq.gz	Fastqsanger.gz
	SRR24046461_2.fastq.gz	Fastqsanger.gz
	SRR24046462_1.fastq.gz	Fastqsanger.gz
	SRR24046462_2.fastq.gz	Fastqsanger.gz
	SRR24046463_1.fastq.gz	Fastqsanger.gz

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Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate.

Project description:Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate.

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Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [ChIP-seq]

Project description:Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [ChIP-seq]

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Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [RNA-seq]

Project description:Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [RNA-seq]

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Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [PRO-seq]

Project description:Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA processing machineries, have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. Although H1s have a minor effect on global gene expression levels, they are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation rate of RNA polymerase II. Thus, H1 variants determine splicing fate by modulating the RNA polymerase II elongation rate.

2023-11-07 | GSE228793 | GEO

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [ChIP-seq]

2023-11-07 | GSE228239 | GEO

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [RNA-seq]

2023-11-07 | GSE228238 | GEO

Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate.

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

2023-11-07 | GSE228240 | GEO

Slow RNAPII transcription elongation rate, low levels of RNAPII pausing, and elevated histone H1 content at promoters associate with higher m6A deposition on nascent mRNAs

Project description:N6-methyladenosine modification (m6A) fine-tunes RNA fate in a variety of ways, thus regulating multiple fundamental biological processes. m6A writers bind to chromatin and interact with RNA polymerase II (RNAPII) during transcription. To evaluate how the dynamics of the transcription process impact m6A deposition, we studied RNAPII elongation rates in mouse embryonic stem cells with altered chromatin configurations, due to reductions in linker histone H1 content. We found that genes transcribed at slow speed are preferentially methylated and display unique signatures at their promoter region, namely high levels of histone H1, together with marks of bivalent chromatin and low RNAPII pausing. They are also highly susceptible to m6A loss upon histone H1 reduction. These results indicate that RNAPII velocity links chromatin structure and the deposition of m6A, highlighting the intricate relationship between different regulatory layers on nascent mRNA molecules.

2022-09-14 | GSE213270 | GEO

The transcriptional elongation rate regulates alternative polyadenylation in yeast

Project description:The transcriptional elongation rate regulates alternative polyadenylation in yeast

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Rate of elongation by RNA polymerase II is influenced by specific gene features and histone modifications

Project description:The rate of transcription elongation plays important roles in the timing of expression of full-length transcripts as well as for the regulation of alternative splicing. In this study we coupled Bru-Seq technology with 5,6-dichlorobenzimidazole 1-M-NM-2-D-ribofuranoside (DRB) to estimate the elongation rates of over 2,000 individual genes in human cells. This technique, BruDRB-Seq, revealed gene-specific differences in elongation rates with a median rate of around 1.5 kb/min. We found that genes with fast elongation rates showed higher densities of H3K79m2 and H4K20me1 marks compared to slower elongating genes. Furthermore, fast elongation rates had a positive correlation with gene length, low complexity DNA sequence and distance from nearest active transcription unit. Features that negatively correlated with elongation rate included exon density and the number of LINE sequences in the gene. The BruDRB-Seq technique offers new opportunities to interrogate mechanisms of regulation of transcription elongation. Measurement of RNA Pol II elogation rate. Normal fibroblasts (HF1 and TM), Cockayne syndrome group B fibroblasts, K562 and MCF-7 cells were exposed to DRB for 60 minutes, after which a washout was performed. Nascent RNA was labeled using bromouridine for 10 minutes immediately after the washout. The genomic region extending from actice Trancription Start Sites was used to determine the gene's elongation rate. Please note that the nf_0h_3* samples are duplicated sample records of GSM1062445 and GSM1062446, for the convenient retrieval of the complete raw data from SRA.

2014-04-01 | E-GEOD-55534 | biostudies-arrayexpress

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