Similar Datasets
Project description:lncRNAs regulate protein functions via formation of protein-RNA complexes. Previous studies have shown that expression of viral lncRNA, polyadenylated nuclear RNA (PAN RNA) is essential for inducible viral genomic looping and distal gene activation during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation. Here we show an underlying molecular mechanism and regulation of KSHV latency by a viral lncRNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. Knock-out of the viral RNA binding protein, ORF57 protein, leads to decreased inducible and static viral genomic loops in latent chromatin and a failure to form RNA polymerase II aggregates in the nucleus during reactivation. We identified that CHD4's enzymatic activity silences viral gene expression by preventing nuclear aggregate formation. Furthermore, integrated genomic and proteomic studies together show that KSHV episomes frequently tether near the host cell centromeres and colocalize with a CHD4 protein complex, ChAHP. KSHV episomes detached from these sites when reactivation is triggered, and PAN RNA binds and inhibits CHD4 DNA binding in vitro. Our studies suggest that CHD4 exhibits strong repressor function by preventing inducible enhancer-promoter looping, and is therefore important for the ability of KSHV to establish and maintain latency in a “poised” state at specific host genomic loci.
2022-03-17 | GSE163098 | GEO
Project description:lncRNAs regulate protein functions via formation of protein-RNA complexes. Previous studies have shown that expression of viral lncRNA, polyadenylated nuclear RNA (PAN RNA) is essential for inducible viral genomic looping and distal gene activation during Kaposi's sarcoma-associated herpesvirus (KSHV) reactivation. Here we show an underlying molecular mechanism and regulation of KSHV latency by a viral lncRNA-CHD4 (chromodomain helicase DNA binding protein 4) interaction. Knock-out of the viral RNA binding protein, ORF57 protein, leads to decreased inducible and static viral genomic loops in latent chromatin and a failure to form RNA polymerase II aggregates in the nucleus during reactivation. We identified that CHD4's enzymatic activity silences viral gene expression by preventing nuclear aggregate formation. Furthermore, integrated genomic and proteomic studies together show that KSHV episomes frequently tether near the host cell centromeres and colocalize with a CHD4 protein complex, ChAHP. KSHV episomes detached from these sites when reactivation is triggered, and PAN RNA binds and inhibits CHD4 DNA binding in vitro. Our studies suggest that CHD4 exhibits strong repressor function by preventing inducible enhancer-promoter looping, and is therefore important for the ability of KSHV to establish and maintain latency in a “poised” state at specific host genomic loci.
2022-03-17 | GSE163694 | GEO
Project description:Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin
| PRJNA687212 | ENA
Project description:Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin [CUT&RUN]
| PRJNA684898 | ENA
Project description:Integrated analyses reveal CHD4 mediating establishment and maintenance of latent KSHV chromatin [Capture Hi-C]
| PRJNA687215 | ENA
Project description:Eukaryotic genomes are structurally organized via the formation of multiple loops that create gene expression regulatory units called topologically associating domains (TADs). Here we revealed the KSHV TAD structure at 500 bp resolution and constructed a 3D KSHV genomic structural model with 2 kb binning. The latent KSHV genome formed very similar genomic architectures in three different naturally infected PEL cell lines and in an experimentally infected epithelial cell line. The majority of the TAD boundaries were occupied by structural maintenance of chromosomes (SMC1) cohesin complex and CCCTC-binding factor (CTCF), and the KSHV transactivator was recruited to those sites during reactivation. Triggering KSHV gene expression decreased prewired genomic loops within the regulatory unit, while contacts extending outside of regulatory borders increased, leading to formation of a larger regulatory unit with a shift from repressive to active compartments (B to A). The 3D genomic structural model proposes that the immediate early promoter region is localized on the periphery of the 3D viral genome during latency, while highly inducible noncoding RNA regions moved toward the inner space of the structure, resembling the configuration of a "bird cage" during reactivation. The compartment-like properties of viral episomal chromatin structure and its reorganization during the transition from latency may help facilitate viral gene transcription. IMPORTANCE The 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain structures. However, the architectural framework of the genomes of large double-stranded DNA viruses such as the herpesvirus family has not been reported. Prior studies with Kaposi's sarcoma-associated herpesvirus (KSHV) have indicated that the viral chromatin shares many biological properties exhibited by the host cell genome, essentially behaving as a mini human chromosome. Thus, we hypothesized that the KSHV genome may be organized in a similar manner. In this report, we describe the domain structure of the latent and lytic KSHV genome at 500 bp resolution and present a 3D genomic structural model for KSHV under each condition. These results add new insights into the complex regulation of the viral life cycle.
| S-EPMC9327698 | biostudies-literature
Project description:The ovarian reserve defines female reproductive lifespan, which in humans spans decades due to the maintenance of meiotic arrest in non-growing oocytes (NGO) residing in primordial follicles. Unknown is how the chromatin state of NGOs is established to enable long-term maintenance of the ovarian reserve. Here, we show that a chromatin remodeler, CHD4, a member of the Nucleosome Remodeling and Deacetylase (NuRD) complex, establishes chromatin states required for formation and maintenance of the ovarian reserve. Conditional loss of CHD4 in perinatal mouse oocytes results in acute death of NGOs and depletion of the ovarian reserve. CHD4 establishes closed chromatin at regulatory elements of pro-apoptotic genes to prevent cell death and at specific genes required for meiotic prophase I to facilitate the transition from meiotic prophase I oocytes to meiotic arrested NGOs. In addition, CHD4 establishes closed chromatin at the regulatory elements of pro-apoptotic genes in male germ cells, allowing male germ cell survival. These results demonstrate a role for CHD4 in defining a chromatin state that ensures germ cell survival, thereby enabling the long-term maintenance of both female and male germ cells.
| S-EPMC11343143 | biostudies-literature
Project description:Epigenetic alterations contribute to leukemogenesis in childhood acute myeloid leukemia and therefore are of interest for potential therapeutic strategies. Herein, we performed large-scale ribonucleic acid interference screens using small hairpin ribonucleic acids in acute myeloid leukemia cells and non-transformed bone marrow cells to identify leukemia-specific dependencies. One of the target genes displaying the strongest effects on acute myeloid leukemia cell growth and less pronounced effects on nontransformed bone marrow cells, was the chromatin remodeling factor CHD4 Using ribonucleic acid interference and CRISPR-Cas9 approaches, we showed that CHD4 was essential for cell growth of leukemic cells in vitro and in vivo Loss of function of CHD4 in acute myeloid leukemia cells caused an arrest in the G0 phase of the cell cycle as well as downregulation of MYC and its target genes involved in cell cycle progression. Importantly, we found that inhibition of CHD4 conferred anti-leukemic effects on primary childhood acute myeloid leukemia cells and prevented disease progression in a patient-derived xenograft model. Conversely, CHD4 was not required for growth of normal hematopoietic cells. Taken together, our results identified CHD4 as a potential therapeutic target in childhood acute myeloid leukemia.
| S-EPMC6029541 | biostudies-literature
Project description:The three-dimensional structure of chromatin organized by genomic loops facilitates RNA polymerase II access to distal promoters. The Kaposi's sarcoma-associated herpesvirus (KSHV) lytic transcriptional program is initiated by a single viral transactivator, K-Rta. Here we report the KSHV genomic structure and its relationship with K-Rta recruitment sites using Capture Hi-C analyses. High-resolution 3D viral genomic maps identify a number of direct physical, long-range, and dynamic genomic interactions. Mutant KSHV chromosomes harboring point mutations in the K-Rta responsive elements (RE) significantly attenuate not only the directly proximate downstream gene, but also distal gene expression in a domain-specific manner. Genomic loops increase in the presence of K-Rta, while abrogation of K-Rta binding impairs the formation of inducible genomic loops, decreases the expression of genes networked through the looping, and diminishes KSHV replication. Our study demonstrates that genomic architectural dynamics plays an essential role in herpesvirus gene expression.
| S-EPMC5754359 | biostudies-literature
Project description:During embryogenesis, the initial chromatin state is established during a period of rapid proliferative activity. We have measured with 3-min time resolution how heritable patterns of chromatin structure are initially established and maintained during the midblastula transition (MBT). We find that regions of accessibility are established sequentially, where enhancers are opened in advance of promoters and insulators. These open states are stably maintained in highly condensed mitotic chromatin to ensure faithful inheritance of prior accessibility status across cell divisions. The temporal progression of establishment is controlled by the biological timers that control the onset of the MBT. In general, acquisition of promoter accessibility is controlled by the biological timer that measures the nucleo-cytoplasmic (N:C) ratio, whereas timing of enhancer accessibility is regulated independently of the N:C ratio. These different timing classes each associate with binding sites for two transcription factors, GAGA-factor and Zelda, previously implicated in controlling chromatin accessibility at ZGA.
| S-EPMC5156528 | biostudies-literature