Human betaherpesvirus 5
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA212434 | ENA |
REPOSITORIES: ENA
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Project description:Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. Here, we present hCMV genome-wide nucleosome occupancy and nascent transcript maps during infection of permissive human primary cells. We show that nucleosomes occupy nuclear viral DNA in a nonrandom and highly predictable fashion. At early times of infection, nucleosomes associate with the hCMV genome largely according to their intrinsic DNA sequence preferences, indicating that initial nucleosome formation is genetically encoded in the virus. However, as infection proceeds to the late phase, nucleosomes redistribute extensively to establish patterns mostly determined by nongenetic factors. We propose that these factors include key regulators of viral gene expression encoded at the hCMV major immediate-early (IE) locus. Indeed, mutant virus genomes defcient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-defcient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function. [i] H3 ChIP-chip measurements of WT human cytomegalovirus (strain TB40E) following infection of MRC-5 cells. WT 8 hours postinfection, with corresponding mock IgG input control: 3 replicates; WT virus, 48 hours postinfection with corresponding mock IgG input contro: 3 replicates. [ii] MNase-chip measurements of WT and dlIE1 human cytomegalovirus nucleosomes following infection of MRC-5 cells. WT 8 hours postinfection, with corresponding sonicated DNA input control: 6 replicates; WT virus 48 hours postinfection, with corresponding sonicated DNA input control: 6 replicates; WT 96 hours postinfection, with corresponding sonicated DNA input control: 2 replicates; dlIE1 virus 8 hours postinfection, with corresponding sonicated DNA input control: 2 replicates; dlIE1 virus 96 hours postinfection, with corresponding sonicated DNA input control: 2 replicates. [iii] Total and nascent RNA measurements of WT and dlIE1 human cytomegalovirus transcripts following infection of MRC-5 cells. WT 8 hours postinfection: 2 replicates; WT virus 96 hours postinfection: 2 replicates; dlIE1 8 hours postinfection: 2 replicates; dlIE1 virus 96 hours postinfection: 2 replicates; sonicated DNA input control: 10 replicates.
2013-07-17 | E-GEOD-48875 | biostudies-arrayexpress
Project description:Human CMV (hCMV) establishes lifelong infections in most of us, causing developmental defects in human embryos and life-threatening disease in immunocompromised individuals. During productive infection, the viral >230,000-bp dsDNA genome is expressed widely and in a temporal cascade. The hCMV genome does not carry histones when encapsidated but has been proposed to form nucleosomes after release into the host cell nucleus. Here, we present hCMV genome-wide nucleosome occupancy and nascent transcript maps during infection of permissive human primary cells. We show that nucleosomes occupy nuclear viral DNA in a nonrandom and highly predictable fashion. At early times of infection, nucleosomes associate with the hCMV genome largely according to their intrinsic DNA sequence preferences, indicating that initial nucleosome formation is genetically encoded in the virus. However, as infection proceeds to the late phase, nucleosomes redistribute extensively to establish patterns mostly determined by nongenetic factors. We propose that these factors include key regulators of viral gene expression encoded at the hCMV major immediate-early (IE) locus. Indeed, mutant virus genomes defcient for IE1 expression exhibit globally increased nucleosome loads and reduced nucleosome dynamics compared with WT genomes. The temporal nucleosome occupancy differences between IE1-defcient and WT viruses correlate inversely with changes in the pattern of viral nascent and total transcript accumulation. These results provide a framework of spatial and temporal nucleosome organization across the genome of a major human pathogen and suggest that an hCMV major IE protein governs overall viral chromatin structure and function.
2013-07-17 | GSE48875 | GEO
Project description:Human cytomegalovirus chemokine, vCXCL-1, modulates normal dissemination kinetics of murine cytomegalovirus in vivo.
| PRJNA544685 | ENA
Project description:Decoding human cytomegalovirus using ribosome profiling
| PRJNA177721 | ENA
Project description:Genome-wide maps of nucleosome organization in human CD4+ T-cells, CD8+ T-cells, granulocytes, and from in vitro reconstitution.
2011-04-19 | GSE25133 | GEO
Project description:This study uncovers a temporal hierarchy of chromatin re-organization during G1 that is linked to the developmental and temporal control of replication timing, revealing a novel link between development and genome organization. Analysis of time-course 4C-seq for several baits to study dynamic changes in chromatin organization during early G1
2015-04-22 | E-GEOD-66579 | biostudies-arrayexpress
Project description:Transcriptome-wide characterization of human cytomegalovirus in natural infection and experimental latency
| PRJNA389726 | ENA
Project description:Nucleosome organization determines chromatin state, which subsequently controls genes expression or silencing. Nucleosome remodeling occurs during somatic cell reprogramming, but it remains undetermined to what degree the re-established nucleosome organization resembles between induced pluripotent stem cells (iPSCs) and embryonic stem cells (ESCs). Here, we generated genome-wide maps of nucleosomes in mouse ESCs and iPSCs reprogrammed from somatic cells belonging to three different germ layers using a secondary reprogramming system. Pairwise comparisons show that nucleosome organization is nearly identical between ESCs and iPSCs regardless of the iPSCs’ tissue of origin. A distinct nucleosome occupancy pattern was observed at silent transcriptional units. Transcription factor binding sites possess characteristic nucleosomal architecture such that their access is governed under rotational setting and translational setting accordingly. Gene expression profiles further reveal that the transcriptional programs are highly correlated between iPSCs and ESCs. These findings indicate that nucleosome organizations can be accurately remodeled during nuclear reprogramming. Gene expression profiles of 5 cell lines with or without biological replicates
2014-12-09 | E-GEOD-46716 | biostudies-arrayexpress
Project description:Genome-wide maps of nucleosome organization in human CD4+ T-cells, CD8+ T-cells, granulocytes, and from in vitro reconstitution. 8 samples include: nucleosome-bound DNA isolated from primary human CD4+ T-cells, nucleosome bound-DNA isolated from primary human CD8+ T-cells, nucleosome-bound DNA isolated from primary human granulocytes, nucleosome-bound DNA isoalted from in vitro reconstitution of nucleosomes with human genomic DNA, control DNA generated by micrococcal nuclease treatment of human genomic DNA, RNA-seq from human CD4+ T-cells, RNA-seq from human CD8+ T-cells, RNA-seq from human Granulocytes.
2011-04-19 | E-GEOD-25133 | biostudies-arrayexpress
Project description:Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Downregulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting that the chromatin assembly pathway might be linked to fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements, through identifying YY1-binding sites in 8-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the 8-cell and morula stages and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.
2023-07-16 | GSE220074 | GEO