The chromatin remodelling complex NoRC safeguards genome stability by heterochromatin formation at telomeres and centromeres.
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ABSTRACT:
SUBMITTER: Postepska-Igielska A
PROVIDER: S-EPMC3736129 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Distinct chromatin organization features, such as centromeres and heterochromatin domains, are inherited epigenetically. However, the mechanisms that modulate the accuracy of epigenetic inheritance, especially at the individual nucleosome level, are not well-understood. Here, using ChIP and next-generation sequencing (ChIP-Seq), we characterized Ccp1, a homolog of the histone chaperone Vps75 in budding yeast that functions in centromere chromatin duplication and heterochromatin maintenance in fission yeast (Schizosaccharomyces pombe). We show that Ccp1 is enriched at the central core regions of the centromeres. Of note, among all histone chaperones characterized, deletion of the ccp1 gene uniquely reduced the rate of epigenetic switching, manifested as position effect variegation within the centromeric core region (CEN-PEV). In contrast, gene deletion of other histone chaperones either elevated the PEV switching rates or did not affect centromeric PEV. Ccp1 and the kinetochore components Mis6 and Sim4 were mutually dependent for centromere or kinetochore association at the proper levels. Moreover, Ccp1 influenced heterochromatin distribution at multiple loci in the genome, including the subtelomeric and the pericentromeric regions. We also found that Gar2, a protein predominantly enriched in the nucleolus, functions similarly to Ccp1 in modulating the epigenetic stability of centromeric regions, although its mechanism remained unclear. Together, our results identify Ccp1 as an important player in modulating epigenetic stability and maintaining proper organization of multiple chromatin domains throughout the fission yeast genome.
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Project description:BACKGROUND: Apicomplexan parasites are responsible for some of the most deadly parasitic diseases afflicting humans, including malaria and toxoplasmosis. These obligate intracellular parasites exhibit a complex life cycle and a coordinated cell cycle-dependant expression program. Their cell division is a coordinated multistep process. How this complex mechanism is organised remains poorly understood. METHODS AND FINDINGS: In this study, we provide evidence for a link between heterochromatin, cell division and the compartmentalisation of the nucleus in Toxoplasma gondii. We characterised a T. gondii chromodomain containing protein (named TgChromo1) that specifically binds to heterochromatin. Using ChIP-on-chip on a genome-wide scale, we report TgChromo1 enrichment at the peri-centromeric chromatin. In addition, we demonstrate that TgChromo1 is cell-cycle regulated and co-localised with markers of the centrocone. Through the loci-specific FISH technique for T. gondii, we confirmed that TgChromo1 occupies the same nuclear localisation as the peri-centromeric sequences. CONCLUSION: We propose that TgChromo1 may play a role in the sequestration of chromosomes at the nuclear periphery and in the process of T. gondii cell division.
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Project description:Active and repressed ribosomal RNA (rRNA) genes are characterised by specific epigenetic marks and differentially positioned nucleosomes at their promoters. Repression of the rRNA genes requires a non-coding RNA (pRNA) and the presence of the nucleolar remodeling complex (NoRC). ATP-dependent chromatin remodeling enzymes are essential regulators of DNA-dependent processes, and this regulation occurs via the modulation of DNA accessibility in chromatin. We have studied the targeting of NoRC to the rRNA gene promoter; its mechanism of nucleosome positioning, in which a nucleosome is placed over the transcription initiation site; and the functional role of the pRNA. We demonstrate that NoRC is capable of recognising and binding to the nucleosomal rRNA gene promoter on its own and binds with higher affinity the nucleosomes positioned at non-repressive positions. NoRC recognises the promoter nucleosome within a chromatin array and positions the nucleosomes, as observed in vivo. NoRC uses the release mechanism of positioning, which is characterised by a reduced affinity for the remodeled substrate. The pRNA specifically binds to NoRC and regulates the enzyme by switching off its ATPase activity. Given the known role of pRNA in tethering NoRC to the rDNA, we propose that pRNA is a key factor that links the chromatin modification activity and scaffolding function of NoRC.
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Project description:Centromeres and telomeres are essential structural components of eukaryotic genomes, and alterations in their structure and function contribute to various human diseases. Currently, our understanding of the chromatin architecture underlying centromeres and telomeres is limited owing to their highly repetitive DNA content. To overcome this, we applied long-read single-molecule chromatin fiber-sequencing (Fiber-seq) to a human cell line with a complete telomere-to-telomere (T2T) reference genome, resulting in single-nucleotide precise mapping of chromatin accessibility, nucleosome positioning, and transcription factor occupancy across 1.7 million intact ~16kb chromatin fibers - resolving the chromatin architecture for ~97% of human telomeric and centromeric DNA. We identify that the centromeric kinetochore binding region contains highly atypical chromatin that juxtaposes highly accessible and tightly compacted DNA - a feature unique to the kinetochore. This structure mirrors the alpha-satellite DNA repeat and appears driven via clustered CENP-B occupancy at hypo-CpG methylated repeats. In addition, telomeres often contain several kilobases of non-nucleosomal chromatin, and the transition between nucleosome-bound chromatin and the telomere cap is highly heterogeneous and often punctuated by CTCF-bound elements. Our findings uncover non-standard chromatin architectures as the predominant organizational structure of telomeres and the kinetochore binding region, and provide a framework for future studies of complete human epigenomes.
2022-05-10 | GSE186009 | GEO