Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298054 | ENA |
REPOSITORIES: ENA
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Project description:DNA methylation predominantly occurs at CG dinucleotides in vertebrate genomes, however, non-CG methylation (mCH) is also detectable in vertebrate tissues, most notably in the nervous system. In mammalian brains, it is well established that: i) mCH is targeted to CAC trinucleotides by DNMT3A, ii) enriched in gene bodies and repetitive elements, and iii) associated with transcriptional repression. However, the possible conservation of these mCH features in zebrafish is largely unexplored and has yet to be functionally demonstrated. In this study, we analyse the transcriptomes (RNA-seq) and methylome (RRBS) of developing zebrafish larvae (1-6 weeks) and adult brain (6 month). We additionally elucidate a role for dnmt3aa/dnmt3ab in mCH deposition via CRISP/CAS9 KO and WGBS of 4 week old brains
2020-12-18 | E-MTAB-9924 | biostudies-arrayexpress
Project description:Inflammation is associated with many cardiovascular pathologies, but the underlying mechanisms remain unclear. To explore this in more detail, we characterized the transcriptome of an immortalized adult human ventricular cardiomyocyte cell line (AC16) in response to tumor necrosis factor (TNFa). Using a combination of genomic approaches, including global nuclear run-on sequencing (GRO-seq) and chromatin immunoprecipitation coupled with sequencing (ChIP-seq), we identified ~30,000 transcribed regions in AC16 cells, which includes a set of RNA polymerases I and III (Pol I and Pol III) transcribed regions revealed in the presence of M-NM-1-amanitin. The set of transcribed regions produces both protein-coding and non-coding RNAs, many of which have not been annotated previously, including enhancer RNAs originating from NF-M-NM-:B binding sites. In addition, we observed that AC16 cells rapidly and dynamically reorganize their transcriptomes in response to TNFa stimulation in an NF-M-NM-:B-dependent manner, switching from a basal state to a proinflammatory state affecting a spectrum of cardiac-associated protein-coding and non-coding genes. Moreover, we observed distinct Pol II dynamics for up- and downregulated genes, with a rapid release of Pol II into productive elongation for TNFa-stimulated genes. Our studies shed new light on the regulation of the cardiomyocyte transcriptome in response to a proinflammatory signal and help to clarify the link between inflammation and cardiomyocyte function at the transcriptional level. Using GRO-seq and ChIP-seq (p65 and RNA Pol II) over a time course of TNFM-NM-1 signaling in AC16 human cardiomyocytes.
2014-02-27 | E-GEOD-51169 | biostudies-arrayexpress
Project description:Strongylocentrotus purpuratus cell-type specific transcriptomes II
| PRJNA273552 | ENA
Project description:Functional engagement of RNA polymerase II (Pol II) with eukaryotic chromosomes is a fundamental and highly regulated biological process. Here we present the first high-resolution map of Pol II occupancy across the entire yeast genome. We compared a wild-type strain with a strain bearing a substitution in the Sen1 helicase, which is a Pol II termination factor for non-coding RNA genes. The wildtype pattern of Pol II distribution provides unexpected insights into the mechanisms by which genes are repressed or silenced. Remarkably, a single amino acid substitution that compromises Sen1 function causes profound changes in Pol II distribution over both non-coding and protein-coding genes, establishing an important function of Sen1 in the regulation of transcription. Given the strong similarity of the yeast and human Sen1 proteins, our results suggest that progressive neurological disorders caused by substitutions in the human Sen1 homolog, Senataxin, may be due to misregulation of transcription. Keywords: transcription termination, attenuation, silencing, non-coding RNA, Pol II, ChIP-chip
2006-12-11 | GSE6293 | GEO