Loss of structural specificity in 3D genome organization upon viral infection is predicted by polymer physics

The Journal of Chemical Physics, Journal Year: 2025, Volume and Issue: 162(1)

Published: Jan. 2, 2025

In the last years, it has been proved that some viruses are able to re-structure chromatin organization and alter epigenomic landscape of host genome. addition, they affect physical mechanisms shaping 3D structure, with a consequent impact on gene activity. Here, we investigate polymer physics genome re-organization upon SARS-CoV-2 viral infection how can structural variability within population single-cell configurations. Using published Hi-C data molecular dynamics simulations, build ensembles configurations representing conformations in control infected conditions. We focus genomic length scales TADs consider, as case study, models real loci containing DDX58 IL6 genes, belonging, respectively, antiviral interferon response pro-inflammatory genes. Clustering analysis applied ensemble reveals generally increased more heterogeneous structures This points toward scenario which leads loss specificity with, likely, correct regulation cell

Language: Английский

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Lipoplexes’ Structure, Preparation, and Role in Managing Different Diseases

AAPS PharmSciTech, Journal Year: 2024, Volume and Issue: 25(5)

Published: June 7, 2024

Language: Английский

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Overview and Prospects of DNA Sequence Visualization

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(2), P. 477 - 477

Published: Jan. 8, 2025

Due to advances in big data technology, deep learning, and knowledge engineering, biological sequence visualization has been extensively explored. In the post-genome era, enables visual representation of both structured unstructured data. However, a universal method for all types sequences not reported. Biological are rapidly expanding exponentially acquisition, extraction, fusion, inference from critical supporting technologies research. These areas important require in-depth exploration. This paper elaborates on comprehensive overview methods DNA four different perspectives-two-dimensional, three-dimensional, four-dimensional, dynamic approaches-and discusses strengths limitations each detail. Furthermore, this proposes two potential future research directions response challenges inefficient graphical feature extraction association network generation existing methods. The first direction is construction graphs data, second cross-modal using machine learning review anticipated provide valuable insights contributions computational biology, bioinformatics, genomic computing, genetic breeding, evolutionary analysis, other related disciplines fields medicine, chemistry, statistics, computing. It an reference value recommendation systems question answering systems.

Language: Английский

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Polymer models of chromatin organization in virally infected cells

Biochemical Society Transactions, Journal Year: 2025, Volume and Issue: 53(01)

Published: Feb. 7, 2025

Genome architecture is closely tied to essential biological functions, yet a complete understanding of the mechanisms governing DNA folding remains significant challenge. Theoretical models based on polymer physics have been applied decipher complexity chromatin and uncover physical processes shaping its structure. Importantly, recent findings suggest that certain viruses can alter 3D organization host genome. In this review, we highlight advances in development used study how structure within cell re-organizes following viral infection, with particular emphasis SARS-CoV-2 virus, capable altering genome at different scales, including A/B compartments, TADs gene-enhancer regulatory contacts.

Language: Английский

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BmNPV interacts with super-enhancer regions of the host chromatin to hijack cellular transcription machinery

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(6)

Published: March 20, 2025

Abstract Effective transcriptional activation relies on the spatial interaction between specific DNA elements. interactions have also been observed viruses and their hosts, with limited understanding of involved details. Baculovirus is a representative species virus has reported to interact host genome in our previous study. However, biological significance baculovirus-host trans-species its underlying mechanisms remain elusive. Here, using Bombyx mori nucleopolyhedrovirus (BmNPV) as model virus, we combine epigenome, transcriptome, biochemical assays investigate interaction. Our data show that BmNPV hijacks regulatory capacity super-enhancers (SEs) by physically interacting these regions genome. This results usurpation activating an SE-binding transcription factor GATA thereby impairing SE-induced target antiviral genes. Moreover, hijacked spread through cis-interaction viral DNA, leading enhanced gene expression. Overall, provide novel insights into intricate interplay expression networks broaden vision exploitation cellular machinery.

Language: Английский

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Chromatin structure and gene transcription of recombinant p53 adenovirus vector within host

Frontiers in Molecular Biosciences, Journal Year: 2025, Volume and Issue: 12

Published: Feb. 28, 2025

Introduction The recombinant human p53 adenovirus (Ad-p53) offers a promising approach for cancer therapy, yet its chromatin structure and effects on host organization gene expression are not fully understood. Methods In this study, we employed in situ ChIA-PET to investigate the colorectal cell line HCT116 with knockout, comparing them cells infected adenovirus-vector expressing p53. We examined alterations interactions following treatment anti-cancer drug 5-fluorouracil (5-FU). Results Our results indicate that Ad-p53 forms specific architecture within vector mainly interacts repressive or inactive regions of chromatin, without significantly affecting associated genes. Additionally, does affect topologically associating domains (TADs) A/B compartments genome. Discussion These findings suggest while boosts expression, enhancing sensitivity substantially altering architecture.

Language: Английский

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Loopy virus or controlled contortionist? 3D regulation of HCMV gene expression by CTCF-driven chromatin interactions

Journal of Virology, Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 30, 2024

ABSTRACT Three-dimensional chromatin control of eukaryotic transcription is pivotal for regulating gene expression. This additional layer epigenetic regulation also utilized by DNA viruses, including herpesviruses. Dynamic, spatial genomic organization often involves looping anchored host-encoded CCCTC-binding factor (CTCF) and other factors, which crosstalk between promoters enhancers. Herein, we review the contribution CTCF-mediated in during herpesvirus infection, with a specific focus on betaherpesvirus, human cytomegalovirus (HCMV).

Language: Английский

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HeteroKGRep: Heterogeneous Knowledge Graph based Drug Repositioning

Knowledge-Based Systems, Journal Year: 2024, Volume and Issue: 305, P. 112638 - 112638

Published: Oct. 19, 2024

Language: Английский

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4D nucleome: dynamic three-dimensional genome organization over time

Experimental & Molecular Medicine, Journal Year: 2024, Volume and Issue: 56(4), P. 761 - 762

Published: April 25, 2024

Language: Английский

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