Dataset Information

Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.

ABSTRACT: In this study, we focus on the following question: do genomic regions enriched in cancer variant mutations have significantly different chromatin folding patterns? We utilize publicly available Hi-C data to characterize chromatin folding patterns in healthy (GM12878) and cancer (K562) cells based on status of A/B compartmentalization and random vs non-random chromatin physical interactions. We then perform statistical testing to assess if chromatin folding patterns in cancer variant-enriched loci are significantly different from non-enriched loci. Our results indicate that loci with cancer variant status have significantly altered (FDR < 0.05) chromatin folding patterns.

SUBMITTER: Perez-Rathke A

PROVIDER: S-EPMC8172279 | biostudies-literature | 2019 May

REPOSITORIES: biostudies-literature

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Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.

Perez-Rathke Alan A Mali Samira S Du Lin L Liang Jie J

... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics 20190501

In this study, we focus on the following question: do genomic regions enriched in cancer variant mutations have significantly different chromatin folding patterns? We utilize publicly available Hi-C data to characterize chromatin folding patterns in healthy (GM12878) and cancer (K562) cells based on status of A/B compartmentalization and random vs non-random chromatin physical interactions. We then perform statistical testing to assess if chromatin folding patterns in cancer variant-enriched loc ...[more]

PMID: 34085045

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Project description:Herpes simplex virus 1 (HSV-1) transcription is restricted in latently infected neurons and the genomes are in mostly silenced chromatin, whereas all viral genes are transcribed in lytically infected cells, in which the genomes are dynamically chromatinized. Epigenetic regulation modulates HSV-1 transcription during lytic, latent, and reactivating infections but the precise mechanisms are not fully defined. Nucleosomes are dynamic: they slide, breathe, assemble, and disassemble. We and others have proposed that the most dynamic HSV-1 chromatin is transcriptionally competent, whereas the least dynamic is silenced. However, the mechanisms yielding the unusually dynamic viral chromatin remain unknown. Histone variants affect nucleosome dynamics. The dynamics of H2A, H2A.X, and macroH2A were enhanced in infected cells, whereas those of H2A.B were uniquely decreased. We constructed stably transduced cells expressing tagged histone H2A, H2A.B, macroH2A, or H2B, which assembles the H2A/H2B nucleosome dimers with all H2A variants. All H2A variants, as well as ectopic and endogenous H2B were assembled into HSV-1 chromatin evenly throughout the genome but canonical H2A was relatively depleted whereas H2A.B was enriched, particularly in the most dynamic viral chromatin. When viral transcription and DNA replication were restricted, H2A.B became as depleted from the viral chromatin through the entire genome as H2A. We propose that lytic HSV-1 nucleosomes are enriched in the dynamic variant H2A.B/H2B dimers to promote HSV-1 chromatin dynamics and transcriptional competency and conclude that the dynamics of HSV-1 chromatin are determined in part by the H2A variants.ImportanceHerpes simplex virus 1 (HSV-1) transcription is epigenetically regulated during latent and lytic infections, and epigenetic inhibitors have been proposed as potential antiviral drugs to modulate latency and reactivation. However, the detailed epigenetic mechanisms of regulation of HSV-1 transcription have not been fully characterized and may differ from those regulating cellular transcription. Whereas lytic HSV-1 chromatin is unusually dynamic, latent silenced HSV-1 chromatin is not. The mechanisms resulting in the unique dynamics of the lytic chromatin remain unknown. Here we identify the enrichment of the highly dynamic histone 2A variant H2A in the most dynamic viral chromatin, which provides a mechanistic understanding of its unique dynamics. Future work to identify the mechanisms of enrichment in H2A.B on the viral chromatin may identify novel druggable epigenetic regulators that modulate HSV-1 latency and reactivation.

Dataset Information

Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.

Publications

Alterations in Chromatin Folding Patterns in Cancer Variant-Enriched Loci.

Similar Datasets

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