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RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [NET-seq]

ABSTRACT: RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [NET-seq]

PROVIDER: PRJNA885861 | ENA |

REPOSITORIES: ENA

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RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation

Project description:RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation

| PRJNA885855 | ENA

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [NET-seq]

Project description:The controlled release of promoter-proximal RNA polymerase II (Pol II) pausing into productive elongation is a major step in gene regulation. Yet, functionally analyzing Pol II pausing is difficult because the factors that regulate pause release are generally essential. Here, we identified heterozygous loss-of-function mutations in SUPT5H, encoding SPT5, in individuals with β-thalassemia trait unlinked to the β-globin locus. Recapitulating the pathogenic mutations in human erythroid cells or acute treatment with transcription inhibitors replicates the patient phenotype of altered globin gene expression. Furthermore, in SUPT5H-edited cells, Pol II pause release was globally disrupted. We observed dynamic patterns of pausing at cell cycle and erythroid differentiation genes at the transition from progenitors to precursors during erythropoiesis. At this same transition, in SUPT5H-edited cells, we observed delayed differentiation and altered cell cycle kinetics, as well as a delay in the onset of gene expression programs. Therefore, hindering pause release perturbs cell cycle and delays differentiation at key stages of erythropoiesis, revealing a role for Pol II pausing in the temporal coordination between the cell cycle and differentiation.

2023-07-21 | GSE214557 | GEO

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [CRISPR]

Project description:RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [CRISPR]

| PRJNA885860 | ENA

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [RNA-seq]

Project description:RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [RNA-seq]

| PRJNA885863 | ENA

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [CRISPR]

2023-07-21 | GSE214556 | GEO

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation [RNA-seq]

2023-07-21 | GSE214558 | GEO

RNA Polymerase II pausing temporally coordinates cell cycle progression and erythroid differentiation

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

2023-07-21 | GSE214559 | GEO

Aging is associated with increased chromatin accessibility and reduced polymerase pausing in liver [NET-seq]

Project description:Regulation of gene expression is linked to the organization of the genome. With age, chromatin alterations occur on all levels of genome organization, accompanied by changes in the gene expression profile. However, little is known about the changes on the level of transcriptional regulation. Here, we used a multi-omics approach and integrated ATAC-, RNA- and NET-seq to identify age-related changes in the chromatin landscape of murine liver and to investigate how these are linked to transcriptional regulation. We provide the first systematic inventory of the connection between aging, chromatin accessibility and transcriptional regulation in a whole tissue. Aging in murine liver is characterized by an increase in chromatin accessibility at promoter regions, but not in an increase of transcriptional output. Instead, aging is accompanied by a decrease of promoter-proximal pausing of RNA polymerase II (Pol II), while initiation of transcription is not decreased as assessed by RNA polymerase mapping using CUT&RUN. Based on the data reported we propose that these age-related changes in transcriptional regulation are due to a reduced stability of the pausing complex.

2022-09-01 | GSE198188 | GEO

Native elongating transcript sequencing (NET-seq) of wild type Saccharomyces cerevisiae and of DST1, RCO1, SET1, SET2, EAF3 deletion strains

Project description:We present an approach (native elongating transcript sequencing, NET-seq), based on deep sequencing of 3M-bM-^@M-^Y ends of nascent transcripts associated with RNA polymerase, to monitor transcription at nucleotide resolution. Application of NET-seq in Saccharomyces cerevisiae reveals that while promoters are generally capable of divergent transcription, the Rpd3S deacetylation complex enforces strong directionality to most promoters by suppressing antisense transcript initiation. Our studies also reveal pervasive polymerase pausing and backtracking throughout the body of transcripts. Average pause density shows prominent peaks at each of the first four nucleosomes, with the peak location occurring in good agreement with in vitro biophysical measurements. Thus nucleosome-induced pausing represents a major barrier to transcriptional elongation in vivo. Examination of nascent transcripts in yeast and mutant strains

2011-01-19 | E-GEOD-25107 | biostudies-arrayexpress

Nascent elongating transcript sequencing (NET-seq) show different pause registers with apyrase treatment during library preparation

Project description:Transcriptional pausing aids gene regulation by cellular RNA polymerases (RNAPs). In many bacteria, a surface-exposed domain inserted into the catalytic trigger loop (TL) of RNAP, called SI3 in Escherichia coli, modulates pausing and is essential for growth. Here we describe a viable E. coli strain lacking SI3 enabled by a suppressor TL substitution (β'Ala941→Thr; ∆SI3*). ∆SI3* increased transcription rate in vitro relative to ∆SI3, possibly explaining its viability, but retained both positive and negative effects of ∆SI3 on pausing. ∆SI3* inhibited pauses stabilized by nascent RNA structures (pause hairpins; PHs) but enhanced other pauses. Using NET-seq, we found that ∆SI3*-enhanced pauses resemble the consensus elemental pause sequence whereas sequences at ∆SI3*-suppressed pauses, which exhibited greater association with PHs, were more divergent. ∆SI3*-suppressed pauses also were associated with apparent pausing one nt upstream from the consensus sequence, often generating tandem pause sites. These '–2 pauses' were stimulated by pyrophosphate in vitro and by addition of apyrase to degrade residual NTPs during NET-seq sample processing. We propose that some pauses are readily reversible by pyrophosphorolysis or single-nucleotide cleavage. Our results document multiple ways that SI3 modulates pausing in vivo and may explain discrepancies in consensus pause sequences in some NET-seq studies.

2023-11-01 | GSE240163 | GEO

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