scholarly journals RUNX1-mediated alphaherpesvirus-host trans-species chromatin interaction promotes viral transcription

2021 ◽  
Vol 7 (26) ◽  
pp. eabf8962
Author(s):  
Ke Xiao ◽  
Dan Xiong ◽  
Gong Chen ◽  
Jinsong Yu ◽  
Yue Li ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Host Cells ◽  
Chromatin Interaction ◽  
Open Chromatin ◽  
Chromosome Conformation ◽  
Dna Viruses ◽  
Genome Wide ◽  
A Genome ◽  
Genome Transcription ◽  
Active Transcription

Like most DNA viruses, herpesviruses precisely deliver their genomes into the sophisticatedly organized nuclei of the infected host cells to initiate subsequent transcription and replication. However, it remains elusive how the viral genome specifically interacts with the host genome and hijacks host transcription machinery. Using pseudorabies virus (PRV) as model virus, we performed chromosome conformation capture assays to demonstrate a genome-wide specific trans-species chromatin interaction between the virus and host. Our data show that the PRV genome is delivered by the host DNA binding protein RUNX1 into the open chromatin and active transcription zone. This facilitates virus hijacking host RNAPII to efficiently transcribe viral genes, which is significantly inhibited by either a RUNX1 inhibitor or RNA interference. Together, these findings provide insights into the chromatin interaction between viral and host genomes and identify new areas of research to advance the understanding of herpesvirus genome transcription.

scholarly journals A Genome-Wide CRISPR/Cas9 Screen Reveals the Requirement of Host Sphingomyelin Synthase 1 for Infection with Pseudorabies Virus Mutant gD–Pass

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1574
Author(s):  
Julia E. Hölper ◽  
Finn Grey ◽  
John Kenneth Baillie ◽  
Tim Regan ◽  
Nicholas J. Parkinson ◽  
...  
Keyword(s):  
Pseudorabies Virus ◽  
Resistant Cell ◽  
Dna Viruses ◽  
Sphingomyelin Synthase ◽  
Host Cell Proteins ◽  
Genome Wide ◽  
A Genome ◽  
Efficient Replication ◽  
Exogenous Expression ◽  
Virus Mutant

Herpesviruses are large DNA viruses, which encode up to 300 different proteins including enzymes enabling efficient replication. Nevertheless, they depend on a multitude of host cell proteins for successful propagation. To uncover cellular host factors important for replication of pseudorabies virus (PrV), an alphaherpesvirus of swine, we performed an unbiased genome-wide CRISPR/Cas9 forward screen. To this end, a porcine CRISPR-knockout sgRNA library (SsCRISPRko.v1) targeting 20,598 genes was generated and used to transduce porcine kidney cells. Cells were then infected with either wildtype PrV (PrV-Ka) or a PrV mutant (PrV-gD–Pass) lacking the receptor-binding protein gD, which regained infectivity after serial passaging in cell culture. While no cells survived infection with PrV-Ka, resistant cell colonies were observed after infection with PrV-gD–Pass. In these cells, sphingomyelin synthase 1 (SMS1) was identified as the top hit candidate. Infection efficiency was reduced by up to 90% for PrV-gD–Pass in rabbit RK13-sgms1KO cells compared to wildtype cells accompanied by lower viral progeny titers. Exogenous expression of SMS1 partly reverted the entry defect of PrV-gD–Pass. In contrast, infectivity of PrV-Ka was reduced by 50% on the knockout cells, which could not be restored by exogenous expression of SMS1. These data suggest that SMS1 plays a pivotal role for PrV infection, when the gD-mediated entry pathway is blocked.

scholarly journals MaxHiC: robust estimation of chromatin interaction frequency in Hi-C and capture Hi-C experiments

2020 ◽  
Author(s):  
Hamid Alinejad-Rokny ◽  
Rassa Ghavami ◽  
Hamid R. Rabiee ◽  
Narges Rezaei ◽  
Kin Tung Tam ◽  
...  
Keyword(s):  
Negative Binomial ◽  
Gc Content ◽  
Genomic Region ◽  
Background Correction ◽  
Ctcf Binding ◽  
Chromatin Interaction ◽  
Distribution Model ◽  
Chromosome Conformation ◽  
Genome Wide ◽  
A Genome

AbstractHi-C is a genome-wide chromosome conformation capture technology that detects interactions between pairs of genomic regions, and exploits higher order chromatin structures. Conceptually Hi-C data counts interaction frequencies between every position in the genome and every other position. Biologically functional interactions are expected to occur more frequently than random (background) interactions. To identify biologically relevant interactions, several background models that take biases such as distance, GC content and mappability into account have been proposed. Here we introduce MaxHiC, a background correction tool that deals with these complex biases and robustly identifies statistically significant interactions in both Hi-C and capture Hi-C experiments. MaxHiC uses a negative binomial distribution model and a maximum likelihood technique to correct biases in both Hi-C and capture Hi-C libraries. We systematically benchmark MaxHiC against major Hi-C background correction tools and demonstrate using published Hi-C and capture Hi-C datasets that 1) Interacting regions identified by MaxHiC have significantly greater levels of overlap with known regulatory features (e.g. active chromatin histone marks, CTCF binding sites, DNase sensitivity) and also disease-associated genome-wide association SNPs than those identified by currently existing models, and 2) the pairs of interacting regions are more likely to be linked by eQTL pairs and more likely to identify known enhancer-promoter pairs than any of the existing methods. We also demonstrate that interactions between different genomic region types have distinct distance distribution only revealed by MaxHiC. MaxHiC is publicly available as a python package for the analysis of Hi-C and capture Hi-C data.

Genome-wide profiling of histone 3 lysine 36 trimethylation in clear cell renal cell carcinoma.

2014 ◽  
Vol 32 (4_suppl) ◽  
pp. 464-464
Author(s):  
Thai Huu Ho ◽  
Jeong-Heon Lee ◽  
Rafael Nunez Nateras ◽  
Erik P. Castle ◽  
Melissa L. Stanton ◽  
...  
Keyword(s):  
Cell Lines ◽  
Dna Sequences ◽  
Open Chromatin ◽  
Sequencing Analysis ◽  
Gene Desert ◽  
Cell Renal Cell Carcinoma ◽  
Chip Sequencing ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

464 Background: Although the von Hippel-Lindau (VHL) tumor suppressor gene is mutated in 60% of ccRCC, deletion of VHL in mice is insufficient for tumorigenesis. Sequencing of ccRCC tumors identified mutations in SETD2, a histone H3 lysine 36 (H3K36) trimethyltransferase. We hypothesize that loss of SETD2 methyltransferase activity alters the genome wide pattern of H3K36 trimethylation (H3K36me3) in ccRCC, and contributes to the cancer phenotype. Methods: To generate a genome-wide profile of H3K36me3 in frozen nephrectomy samples and RCC cell lines, we optimized a chromatin immunoprecipitation (ChIP) protocol for the isolation of DNA associated with H3K36me3. H3K36me3 is associated with open chromatin and an H3K36me3-specific antibody was used for immunoprecipitation of endogenous H3K36me3-bound DNA. ChIP PCR primers were optimized for active genes, such as actin, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and a “gene desert” on chromosome 12 (negative control). ChIP libraries were then generated from 3 paired uninvolved kidney and RCC and 2 RCC cell lines. In order to identify H3K36Me3 upregulated regions in uninvolved kidney and RCC, reads from the ChIP sequencing were mapped to the human genome using Burrows-Wheeler Aligner and SICER algorithms. Results: Using ChIP PCR, we found that active genomic regions were enriched 15-30 fold over the negative controls indicating that the quality and yield of immunoprecipitated DNA/chromatin complexes from frozen tissue was sufficient for ChIP sequencing. A preliminary ChIP sequencing analysis of RCC cell lines and frozen ccRCC tissue indicates that H3K36me3 enriched DNA sequences were mapped to exons (31.3%) compared to introns (13.5%, p<0.001), consistent with the role of H3K36me3 in transcription. Conclusions: Genomic regions enriched for H3K36Me3 binding were identified from patient-derived tissue and RCC cell lines. Current efforts are focused on comparing the H3K36me3 profiles between matched tumor and uninvolved kidney ChIP libraries to generate a genome wide map of dysregulated H3K36me3 modifications.

scholarly journals Genome-Wide Transposon Mutagenesis Indicates that Mycobacterium marinum Customizes Its Virulence Mechanisms for Survival and Replication in Different Hosts

2015 ◽  
Vol 83 (5) ◽  
pp. 1778-1788 ◽  
Author(s):  
Eveline M. Weerdenburg ◽  
Abdallah M. Abdallah ◽  
Farania Rangkuti ◽  
Moataz Abd El Ghany ◽  
Thomas D. Otto ◽  
...  
Keyword(s):  
Insertion Site ◽  
Mycobacterium Marinum ◽  
Host Cells ◽  
Intracellular Pathogens ◽  
Virulence Determinants ◽  
Phagocytic Cells ◽  
General Hypothesis ◽  
Content Type ◽  
Genome Wide ◽  
A Genome

The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogenMycobacterium marinumwhether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show thatM. marinumcontains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore,M. marinumcontains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.

scholarly journals HIV Genome-Wide Protein Associations: a Review of 30 Years of Research

2016 ◽  
Vol 80 (3) ◽  
pp. 679-731 ◽  
Author(s):  
Guangdi Li ◽  
Erik De Clercq
Keyword(s):  
Life Cycle ◽  
Viral Entry ◽  
Large Body ◽  
Viral Proteins ◽  
Host Cells ◽  
Comprehensive Overview ◽  
Genome Wide ◽  
A Genome ◽  
Glycoprotein Gp120 ◽  
Physical Interactions

SUMMARYThe HIV genome encodes a small number of viral proteins (i.e., 16), invariably establishing cooperative associations among HIV proteins and between HIV and host proteins, to invade host cells and hijack their internal machineries. As a known example, the HIV envelope glycoprotein GP120 is closely associated with GP41 for viral entry. From a genome-wide perspective, a hypothesis can be worked out to determine whether 16 HIV proteins could develop 120 possible pairwise associations either by physical interactions or by functional associations mediated via HIV or host molecules. Here, we present the first systematic review of experimental evidence on HIV genome-wide protein associations using a large body of publications accumulated over the past 3 decades. Of 120 possible pairwise associations between 16 HIV proteins, at least 34 physical interactions and 17 functional associations have been identified. To achieve efficient viral replication and infection, HIV protein associations play essential roles (e.g., cleavage, inhibition, and activation) during the HIV life cycle. In either a dispensable or an indispensable manner, each HIV protein collaborates with another viral protein to accomplish specific activities that precisely take place at the proper stages of the HIV life cycle. In addition, HIV genome-wide protein associations have an impact on anti-HIV inhibitors due to the extensive cross talk between drug-inhibited proteins and other HIV proteins. Overall, this study presents for the first time a comprehensive overview of HIV genome-wide protein associations, highlighting meticulous collaborations between all viral proteins during the HIV life cycle.

scholarly journals A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function

Thorax ◽  
2011 ◽  
Vol 67 (5) ◽  
pp. 385-391 ◽  
Author(s):  
Jared M Bischof ◽  
Christopher J Ott ◽  
Shih-Hsing Leir ◽  
Nehal Gosalia ◽  
Lingyun Song ◽  
...  
Keyword(s):  
Lung Function ◽  
Epithelial Cells ◽  
Regulatory Elements ◽  
Open Chromatin ◽  
Genome Wide Analysis ◽  
Tracheal Epithelial Cells ◽  
Genome Wide ◽  
A Genome ◽  
Tracheal Epithelial

scholarly journals Comparative analysis reveals genomic features of stress-induced transcriptional readthrough

2017 ◽  
Vol 114 (40) ◽  
pp. E8362-E8371 ◽  
Author(s):  
Anna Vilborg ◽  
Niv Sabath ◽  
Yuval Wiesel ◽  
Jenny Nathans ◽  
Flonia Levy-Adam ◽  
...  
Keyword(s):  
Heat Shock ◽  
Osmotic Stress ◽  
Stress Responses ◽  
Failure Process ◽  
Mouse Fibroblast ◽  
Open Chromatin ◽  
Chromatin Signature ◽  
Genomic Features ◽  
Genome Wide ◽  
A Genome

Transcription is a highly regulated process, and stress-induced changes in gene transcription have been shown to play a major role in stress responses and adaptation. Genome-wide studies reveal prevalent transcription beyond known protein-coding gene loci, generating a variety of RNA classes, most of unknown function. One such class, termed downstream of gene-containing transcripts (DoGs), was reported to result from transcriptional readthrough upon osmotic stress in human cells. However, how widespread the readthrough phenomenon is, and what its causes and consequences are, remain elusive. Here we present a genome-wide mapping of transcriptional readthrough, using nuclear RNA-Seq, comparing heat shock, osmotic stress, and oxidative stress in NIH 3T3 mouse fibroblast cells. We observe massive induction of transcriptional readthrough, both in levels and length, under all stress conditions, with significant, yet not complete, overlap of readthrough-induced loci between different conditions. Importantly, our analyses suggest that stress-induced transcriptional readthrough is not a random failure process, but is rather differentially induced across different conditions. We explore potential regulators and find a role for HSF1 in the induction of a subset of heat shock-induced readthrough transcripts. Analysis of public datasets detected increases in polymerase II occupancy in DoG regions after heat shock, supporting our findings. Interestingly, DoGs tend to be produced in the vicinity of neighboring genes, leading to a marked increase in their antisense-generating potential. Finally, we examine genomic features of readthrough transcription and observe a unique chromatin signature typical of DoG-producing regions, suggesting that readthrough transcription is associated with the maintenance of an open chromatin state.

scholarly journals SLC19A1 is an importer of the immunotransmitter cGAMP

2019 ◽  
Author(s):  
Anthony F. Cordova ◽  
Christopher Ritchie ◽  
Gaelen T. Hess ◽  
Michael C. Bassik ◽  
Lingyin Li
Keyword(s):  
Immune Response ◽  
Clinical Trials ◽  
Cell Membrane ◽  
Cancer Therapeutics ◽  
Host Cells ◽  
Genome Wide ◽  
A Genome ◽  
Crispr Screen ◽  
Sting Pathway ◽  
Insight Into

Abstract2’3’-cyclic-GMP-AMP (cGAMP) is a second messenger that activates the antiviral Stimulator of Interferon Genes (STING) pathway. We recently identified a novel role for cGAMP as a soluble, extracellular immunotransmitter that is produced and secreted by cancer cells. Secreted cGAMP is then sensed by host cells, eliciting an antitumoral immune response. Due to the antitumoral effects of cGAMP, other CDN-based STING agonists are currently under investigation in clinical trials for metastatic solid tumors. However, it is unknown how cGAMP and other CDNs cross the cell membrane to activate intracellular STING. Using a genome-wide CRISPR screen we identified SLC19A1 as the first known importer of cGAMP and other CDNs, including the investigational new drug 2′3′-bisphosphosphothioate-cyclic-di-AMP (2′3′-CDAS). These discoveries will provide insight into cGAMP’s role as an immunotransmitter and aid in the development of more targeted CDN-based cancer therapeutics.

scholarly journals Germline variants at SOHLH2 influence multiple myeloma risk

2021 ◽  
Vol 11 (4) ◽  
Author(s):  
Laura Duran-Lozano ◽  
Gudmar Thorleifsson ◽  
Aitzkoa Lopez de Lapuente Portilla ◽  
Abhishek Niroula ◽  
Molly Went ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Genome Wide Association Study ◽  
Plasma Cells ◽  
Genomic Region ◽  
Open Chromatin ◽  
Risk Variant ◽  
Inherited Susceptibility ◽  
Genome Wide ◽  
A Genome ◽  
Insight Into

AbstractMultiple myeloma (MM) is caused by the uncontrolled, clonal expansion of plasma cells. While there is epidemiological evidence for inherited susceptibility, the molecular basis remains incompletely understood. We report a genome-wide association study totalling 5,320 cases and 422,289 controls from four Nordic populations, and find a novel MM risk variant at SOHLH2 at 13q13.3 (risk allele frequency = 3.5%; odds ratio = 1.38; P = 2.2 × 10−14). This gene encodes a transcription factor involved in gametogenesis that is normally only weakly expressed in plasma cells. The association is represented by 14 variants in linkage disequilibrium. Among these, rs75712673 maps to a genomic region with open chromatin in plasma cells, and upregulates SOHLH2 in this cell type. Moreover, rs75712673 influences transcriptional activity in luciferase assays, and shows a chromatin looping interaction with the SOHLH2 promoter. Our work provides novel insight into MM susceptibility.

scholarly journals Nuclease deficiencies alter plasma cell-free DNA methylation profiles

2021 ◽  
pp. gr.275426.121
Author(s):  
Diana Siao Cheng Han ◽  
Meng Ni ◽  
Rebecca Wing Yan Chan ◽  
Danny Ka Lok Wong ◽  
Linda T Hiraki ◽  
...  
Keyword(s):  
Fragment Size ◽  
Cpg Islands ◽  
Periodic Pattern ◽  
Open Chromatin ◽  
Cell Free Dna ◽  
Free Dna ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Deficient Mice

The effects of DNASE1L3 or DNASE1 deficiency on cell-free DNA (cfDNA) methylation was explored in plasma of mice deficient in these nucleases and in DNASE1L3-deficient humans. Compared to wild-type cfDNA, cfDNA in Dnase1l3-deficient mice was significantly hypomethylated, while cfDNA in Dnase1-deficient mice was hypermethylated. The cfDNA hypomethylation in Dnase1l3-deficient mice was due to increased fragmentation and representation from open chromatin regions (OCRs) and CpG islands (CGIs). These findings were absent in Dnase1-deficient mice, demonstrating the preference of DNASE1 to cleave in hypomethylated OCRs and CGIs. We also observed a substantial decrease of fragment ends and coverage at methylated CpGs in the absence of DNASE1L3, thereby demonstrating that DNASE1L3 prefers to cleave at methylated CpGs. Furthermore, we found that methylation levels of cfDNA varied by fragment size in a periodic pattern, with cfDNA of specific sizes being more hypomethylated and enriched for OCRs and CGIs. These findings were confirmed in DNASE1L3-deficient human cfDNA. Thus, we have found that nuclease-mediated cfDNA fragmentation markedly affected cfDNA methylation level on a genome-wide scale. This work provides a foundational understanding of the relationship between methylation, nuclease biology and cfDNA fragmentation.

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