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Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS]

ABSTRACT: Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS]

PROVIDER: PRJNA740018 | ENA |

REPOSITORIES: ENA

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Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates

Project description:Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates

| PRJNA740013 | ENA

Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [WGBS]

Project description:CpG methylation in genomic DNA is well known as a repressive epigenetic marker in eukaryotic transcription, and hypermethylation of the promoter region is correlated with silencing of gene expression. In contrast to the promoter region, the function of DNA methylation at transcription termination remains to be elucidated. A recent study has revealed that mouse DNA methyltransferase 3a (Dnmt3a) mainly functions in de novo methylation in the promoter and gene body regions (including transcription termination sites (TTSs)) during development. To investigate the relationship between DNA methylation overlapping the TTSs and transcription termination, we employed two strategies: informatic analysis using already deposited datasets of Dnmt3a-/- mouse cells and the zebrafish model system. Bioinformatic analysis using methylome and transcriptome data showed that hypomethylated differentially methylated regions overlapping the TTSs were associated with increased transcript counts and chimeric transcripts downstream of TTSs in Dnmt3a-/- Agouti-related protein neurons, but not in Dnmt3a-/- ES cells and MEFs. We experimentally detected increased read-through and chimeric transcripts downstream of hypomethylated TTSs in zebrafish maternal-zygotic Dnmt3aa-/- mutants. This study is the first to identify transcription termination defects in DNA hypomethylated TTSs in Dnmt3a-/- vertebrates.

2022-06-14 | GSE178690 | GEO

Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [RNA-Seq]

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Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [RNA-Seq]

Project description:Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates [RNA-Seq]

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Identification of transcription termination defects at DNA hypomethylated transcription termination sites in DNA methyltransferase 3a-deficient vertebrates

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

2022-06-14 | GSE178691 | GEO

DNA-directed termination of RNA Polymerase II transcription I

Project description:RNA polymerase II (RNAPII) transcription involves initiation from promoters, transcript elongation through the gene body, and cessation of transcription in the downstream terminator regions. In contrast to bacteria, where terminators often contain specific DNA elements to direct RNAP dissociation1, termination by RNAPII is thought to be driven entirely by protein co-factors1-3. Here we use biochemical reconstitution to shed new light on RNAPII termination. Unexpectedly, transcription through a terminator region by pure RNAPII results in a significant amount of intrinsic polymerase dissociation at specific sequences containing T-tracts. A combination of biochemistry and single molecule analysis indicates that such intrinsic termination involves pausing without backtracking prior to spontaneous RNAPII dissociation from the DNA template. Importantly, while the ‘torpedo’ Rat1-Rai1 RNA exonuclease (XRN2 in humans) works inefficiently on paused or stopped polymerases, it greatly stimulates intrinsic termination. By contrast, elongation factor Spt4-Spt5 (DSIF in humans) suppresses such termination. Genome-wide analysis in yeast using 3’-end sequencing further supports the idea that transcriptional termination occurs by transcript cleavage at the polyA site exposing a new RNA-end that allows loading of the Rat1-Rai1 torpedo, which then catches up with a destabilised RNAPII at intrinsic termination sites containing T-tracts to terminate transcription.

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DNA-directed termination of RNA Polymerase II transcription II

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The nucleosome DNA entry-exit site is important for transcription termination and prevention of pervasive transcription

Project description:Compared to the initiation and elongation stages of transcription, the role of chromatin in transcription termination is poorly understood. Through a yeast genetic screen, we identified histone H3 and H4 substitutions that cause transcription to read through the terminator of a small noncoding gene. The substitutions map to the nucleosome DNA entry-exit site, a region that controls nucleosome stability and certain histone modifications. Genome-wide studies on the strongest mutants revealed evidence of transcription read-through of noncoding and coding genes and reduced nucleosome occupancy. Replacement of the native sequence downstream of a gene with a “superbinder” sequence that increases nucleosome occupancy in vivo increased termination efficiency and suppressed the effect of a DNA entry-exit site substitution at this locus. Our results highlight the importance of the DNA entry-exit site in maintaining the integrity of the transcriptome and suggest that nucleosomes can facilitate termination by serving as a barrier to RNA polymerase.

2020-08-10 | GSE147389 | GEO

Rho dependent transcription termination is a dominant mechanism of transcription termination in Mycobacterium tuberculosis

Project description:Rho dependent transcription termination is a dominant mechanism of transcription termination in Mycobacterium tuberculosis

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AKT phosphorylates H3-threonine 45 to facilitate termination of gene transcription in response to DNA damage.

Project description:Purpose: In this study, we show that DNA damage-activated AKT phosphorylates threonine 45 of core histone H3 (H3-T45) Result: By genome-wide chromatin immunoprecipitation sequencing (ChIP-seq) analysis, H3-T45 phosphorylation was distributed throughout DNA damage-responsive gene loci, particularly immediately after the transcription termination site Conclusion: AKT-mediated phosphorylation of H3-T45 regulates the processing of the 3′ end of DNA damage-activated genes to facilitate transcriptional termination

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