Telomerase function and binding at endogenous G-rich regions (Hi-C Seq)
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ABSTRACT:
PROVIDER: PRJNA599165 | ENA |
REPOSITORIES: ENA
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Project description:Telomerase majorly functions at telomeres but under adverse conditions acts at endogenous regions, which is often observed in cancer calls. By mapping the global occupancy of the catalytic subunit of telomerase (Est2), we reveal that telomerase binds to multiple genomic loci, which we termed ‘non-telomere-binding sites’ (NTBS). We characterized under when and why Est2 binds to such sites and could show that telomerase is inactive but becomes activated upon global DNA damage. Indicating that those regions are of particular risk for genome stability. Using biochemical and molecular experiments we further characterized Est2 binding to NTBS. In contrast to Est2 binding to telomere neither Cdc13 nor Ku70/80 is crucial for the binding to NTBS. Strikingly, using Hi-C, we demonstrate that chromatin organization is essential and drives the interaction of Est2-NTBS binding. The here presented results provide a novel model of telomerase regulation using endogenous regions as “parking spots” awaiting its canonical function at telomeres.
2020-01-07 | GSE143186 | GEO
Project description:Telomerase function and binding at endogenous G-rich regions
| PRJNA599158 | ENA
Project description:Telomerase majorly functions at telomeres but under adverse conditions acts at endogenous regions, which is often observed in cancer calls. By mapping the global occupancy of the catalytic subunit of telomerase (Est2), we reveal that telomerase binds to multiple genomic loci, which we termed ‘non-telomere-binding sites’ (NTBS). We characterized under when and why Est2 binds to such sites and could show that telomerase is inactive but becomes activated upon global DNA damage. Indicating that those regions are of particular risk for genome stability. Using biochemical and molecular experiments we further characterized Est2 binding to NTBS. In contrast to Est2 binding to telomere neither Cdc13 nor Ku70/80 is crucial for the binding to NTBS. Strikingly, using Hi-C, we demonstrate that chromatin organization is essential and drives the interaction of Est2-NTBS binding. The here presented results provide a novel model of telomerase regulation using endogenous regions as “parking spots” awaiting its canonical function at telomeres.
2020-01-07 | GSE143184 | GEO
Project description:Telomerase function and binding at endogenous G-rich regions (ChIP)
| PRJNA599159 | ENA
Project description:This SuperSeries is composed of the SubSeries listed below.
2020-01-07 | GSE143187 | GEO
Project description:First we developed a new, simple, and robust assay called CoP (Column Purified chromatin) for profiling of accessible regions by directly purifying fragmentized crosslinked chromatin with DNA purification column. The CoP chromatin regions by CoP-seq are consistent with the accessible regions detected by ATAC-seq and FARIE-seq. Then we integrated CoP-seq and Hi-C technique (Hi-CoP) for interactions of accessible chromatin regions which represent active cis-regulatory elements in cells. Our data showed that Hi-CoP assay can robustly detect interactions of regulatory regions.
2020-01-29 | GSE144412 | GEO
Project description:Symmetrical dimethylation on arginine-3 of histone H4 (H4R3me2s) has been reported to occur at several repressed genes, but its specific regulation and genomic distribution remained unclear. Here, we show that the type-II protein arginine methyltransferase PRMT5 controls H4R3me2s in mouse embryonic fibroblasts (MEFs). In these differentiated cells, we find that the genome-wide pattern of H4R3me2s is highly similar to that in embryonic stem cells. In both the cell types, H4R3me2s peaks are detected predominantly at G + C-rich regions. Promoters are consistently marked by H4R3me2s, independently of transcriptional activity. Remarkably, H4R3me2s is mono-allelic at imprinting control regions (ICRs), at which it marks the same parental allele as H3K9me3, H4K20me3 and DNA methylation. These repressive chromatin modifications are regulated independently, however, since PRMT5-depletion in MEFs resulted in loss of H4R3me2s, without affecting H3K9me3, H4K20me3 or DNA methylation. Conversely, depletion of ESET (KMT1E) or SUV420H1/H2 (KMT5B/C) affected H3K9me3 and H4K20me3, respectively, without altering H4R3me2s at ICRs. Combined, our data indicate that PRMT5-mediated H4R3me2s uniquely marks the mammalian genome, mostly at G + C-rich regions, and independently from transcriptional activity or chromatin repression. Furthermore, comparative bioinformatics analyses suggest a putative role of PRMT5-mediated H4R3me2s in chromatin configuration in the nucleus. High throughput sequencing data from H4R3me2s native ChIP samples from mouse embryonic stem cells and fibroblasts were generated using Illumina Hi-seq 2000.
2013-10-04 | E-GEOD-37604 | biostudies-arrayexpress
Project description:Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. Hi-C experiments where ligation is performed on beads (tethered) on male Drosophila salivary glands from three independent biological replicates. Also one Hi-C experiment where the ligation is performed in solution (conventional).
2015-11-05 | E-GEOD-72510 | biostudies-arrayexpress
Project description:Telomerase deficiency and progressive telomere erosion in human somatic cells results in senescence. Small RNAs that target telomeres have been observed in diverse organisms but their functions are not well characterized. We define an endogenous small RNA pathway in Caenorhabditis elegans that promotes heterochromatin formation at telomeres via Dicer, the perinuclear Argonaute protein WAGO-1 and the nuclear Argonaute protein HRDE-1. Loss of telomerase induces biogenesis of siRNAs that target the telomeric lncRNA TERRA, whereas loss of both telomerase and small RNA-mediated telomeric silencing induces TERRA expression, DNA damage, and an accelerated sterility phenotype. The latter phenotypes can be rescued by exogenous telomeric siRNAs or by loss of the DNA damage response protein EXO-1. Thus, endogenous siRNAs interact with TERRA to promote heterochromatin formation in a manner that is critical for the stability of naturally eroding telomeres. We propose that small RNA-mediated heterochromatin defects could contribute to proliferative aging by promoting genome stability.
2019-03-13 | GSE111800 | GEO
Project description:Gene repression and silencers are poorly understood. We reasoned that H3K27me3-rich regions (MRRs) of the genome defined from clusters of H3K27me3 peaks may be used to identify silencers that can regulate gene expression via proximity or looping. MRRs were associated with chromatin interactions and interact preferentially with each other. MRR component removal at interaction anchors by CRISPR led to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. The MRR knockout cells also showed changes in phenotype associated with cell identity, and altered xenograft tumor growth. MRR-associated genes and long-range chromatin interactions were susceptible to H3K27me3 depletion. Our results characterized H3K27me3-rich regions and their mechanisms of functioning via looping.
2020-12-01 | GSE133183 | GEO