Blog
About

  • Record: found
  • Abstract: found
  • Article: found
Is Open Access

Coordination of KSHV Latent and Lytic Gene Control by CTCF-Cohesin Mediated Chromosome Conformation

Read this article at

Bookmark
      There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

      Abstract

      Herpesvirus persistence requires a dynamic balance between latent and lytic cycle gene expression, but how this balance is maintained remains enigmatic. We have previously shown that the Kaposi's Sarcoma-Associated Herpesvirus (KSHV) major latency transcripts encoding LANA, vCyclin, vFLIP, v-miRNAs, and Kaposin are regulated, in part, by a chromatin organizing element that binds CTCF and cohesins. Using viral genome-wide chromatin conformation capture (3C) methods, we now show that KSHV latency control region is physically linked to the promoter regulatory region for ORF50, which encodes the KSHV immediate early protein RTA. Other linkages were also observed, including an interaction between the 5′ and 3′ end of the latency transcription cluster. Mutation of the CTCF-cohesin binding site reduced or eliminated the chromatin conformation linkages, and deregulated viral transcription and genome copy number control. siRNA depletion of CTCF or cohesin subunits also disrupted chromosomal linkages and deregulated viral latent and lytic gene transcription. Furthermore, the linkage between the latent and lytic control region was subject to cell cycle fluctuation and disrupted during lytic cycle reactivation, suggesting that these interactions are dynamic and regulatory. Our findings indicate that KSHV genomes are organized into chromatin loops mediated by CTCF and cohesin interactions, and that these inter-chromosomal linkages coordinate latent and lytic gene control.

      Author Summary

      Multiple mechanisms have been implicated in the control of herpesvirus latent and lytic gene regulation, but few mechanisms account for coordinate regulation of these two life cycles. Here, we show that the transcription control elements for KSHV latent and lytic genes are in close physical proximity. Mutations in the CTCF binding sites of the KSHV latency control region caused a loss of cohesin binding, and derepression of latent transcripts. Loss of CTCF binding also caused a loss of KSHV DNA copy number, and a failure to express lytic genes, including the immediate early gene Rta. Chromatin conformation capture (3C) methods indicated that the CTCF binding sites in the latency control region are linked to the promoter region of Rta. Additional chromatin linkages were detected between the 5′ and 3′ ends of the major latency transcripts, suggesting that chromatin loops organize both latent and lytic gene clusters. The interaction between latent and lytic control regions was subject to cell cycle regulation, consistent with earlier studies implicating cell cycle control of cohesin binding and viral transcription patterns. KSHV chromosome conformation was also disrupted by lytic cycle reactivation. We propose that CTCF-cohesin form dynamic linkages between viral regulatory domains to both insulate and coordinate latent and lytic gene expression.

      Related collections

      Most cited references 59

      • Record: found
      • Abstract: found
      • Article: not found

      High-resolution profiling of histone methylations in the human genome.

      Histone modifications are implicated in influencing gene expression. We have generated high-resolution maps for the genome-wide distribution of 20 histone lysine and arginine methylations as well as histone variant H2A.Z, RNA polymerase II, and the insulator binding protein CTCF across the human genome using the Solexa 1G sequencing technology. Typical patterns of histone methylations exhibited at promoters, insulators, enhancers, and transcribed regions are identified. The monomethylations of H3K27, H3K9, H4K20, H3K79, and H2BK5 are all linked to gene activation, whereas trimethylations of H3K27, H3K9, and H3K79 are linked to repression. H2A.Z associates with functional regulatory elements, and CTCF marks boundaries of histone methylation domains. Chromosome banding patterns are correlated with unique patterns of histone modifications. Chromosome breakpoints detected in T cell cancers frequently reside in chromatin regions associated with H3K4 methylations. Our data provide new insights into the function of histone methylation and chromatin organization in genome function.
        Bookmark
        • Record: found
        • Abstract: found
        • Article: not found

        A bivalent chromatin structure marks key developmental genes in embryonic stem cells.

        The most highly conserved noncoding elements (HCNEs) in mammalian genomes cluster within regions enriched for genes encoding developmentally important transcription factors (TFs). This suggests that HCNE-rich regions may contain key regulatory controls involved in development. We explored this by examining histone methylation in mouse embryonic stem (ES) cells across 56 large HCNE-rich loci. We identified a specific modification pattern, termed "bivalent domains," consisting of large regions of H3 lysine 27 methylation harboring smaller regions of H3 lysine 4 methylation. Bivalent domains tend to coincide with TF genes expressed at low levels. We propose that bivalent domains silence developmental genes in ES cells while keeping them poised for activation. We also found striking correspondences between genome sequence and histone methylation in ES cells, which become notably weaker in differentiated cells. These results highlight the importance of DNA sequence in defining the initial epigenetic landscape and suggest a novel chromatin-based mechanism for maintaining pluripotency.
          Bookmark
          • Record: found
          • Abstract: found
          • Article: not found

          Capturing chromosome conformation.

          We describe an approach to detect the frequency of interaction between any two genomic loci. Generation of a matrix of interaction frequencies between sites on the same or different chromosomes reveals their relative spatial disposition and provides information about the physical properties of the chromatin fiber. This methodology can be applied to the spatial organization of entire genomes in organisms from bacteria to human. Using the yeast Saccharomyces cerevisiae, we could confirm known qualitative features of chromosome organization within the nucleus and dynamic changes in that organization during meiosis. We also analyzed yeast chromosome III at the G1 stage of the cell cycle. We found that chromatin is highly flexible throughout. Furthermore, functionally distinct AT- and GC-rich domains were found to exhibit different conformations, and a population-average 3D model of chromosome III could be determined. Chromosome III emerges as a contorted ring.
            Bookmark

            Author and article information

            Affiliations
            [1 ]The Wistar Institute, Philadelphia, Pennsylvania, United States of America
            [2 ]The Kyungpook National University, College of Pharmacy, Daegu, Korea
            [3 ]The University of Pennsylvania, School of Dentistry, Philadelphia, Pennsylvania, United States of America
            [4 ]The University of Pennsylvania, School of Medicine, Philadelphia, Pennsylvania, United States of America
            Emory University, United States of America
            Author notes

            Conceived and designed the experiments: HK PML . Performed the experiments: HK AW. Analyzed the data: HK YY ER PML. Contributed reagents/materials/analysis tools: YY ER. Wrote the paper: HK PML.

            Contributors
            Role: Editor
            Journal
            PLoS Pathog
            plos
            plospath
            PLoS Pathogens
            Public Library of Science (San Francisco, USA )
            1553-7366
            1553-7374
            August 2011
            August 2011
            18 August 2011
            : 7
            : 8
            3158054
            21876668
            PPATHOGENS-D-11-00098
            10.1371/journal.ppat.1002140
            (Editor)
            Kang et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
            Counts
            Pages: 15
            Categories
            Research Article
            Biology
            Medicine

            Infectious disease & Microbiology

            Comments

            Comment on this article