Chromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal

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Autor(es): dc.contributorRice University-
Autor(es): dc.contributorUniversidade Estadual Paulista (UNESP)-
Autor(es): dc.contributorBaylor College of Medicine-
Autor(es): dc.creatorOliveira Junior, Antonio B.-
Autor(es): dc.creatorEstrada, Cynthia Perez-
Autor(es): dc.creatorAiden, Erez Lieberman-
Autor(es): dc.creatorContessoto, Vinícius G.-
Autor(es): dc.creatorOnuchic, José N.-
Data de aceite: dc.date.accessioned2025-08-21T18:28:16Z-
Data de disponibilização: dc.date.available2025-08-21T18:28:16Z-
Data de envio: dc.date.issued2022-04-29-
Data de envio: dc.date.issued2022-04-29-
Data de envio: dc.date.issued2021-08-12-
Fonte completa do material: dc.identifierhttp://dx.doi.org/10.1021/acs.jpcb.1c04174-
Fonte completa do material: dc.identifierhttp://hdl.handle.net/11449/229329-
Fonte: dc.identifier.urihttp://educapes.capes.gov.br/handle/11449/229329-
Descrição: dc.descriptionThe human genome is organized within a nucleus where chromosomes fold into an ensemble of different conformations. Chromosome conformation capture techniques such as Hi-C provide information about the genome architecture by creating a 2D heat map. Initially, Hi-C map experiments were performed in human interphase cell lines. Recently, efforts were expanded to several different organisms, cell lines, tissues, and cell cycle phases where obtaining high-quality maps is challenging. Poor sampled Hi-C maps present high sparse matrices where compartments located far from the main diagonal are difficult to observe. Aided by recently developed models for chromatin folding and dynamics investigation, we introduce a framework to enhance the compartments' information far from the diagonal observed in experimental sparse matrices. The simulations were performed using the Open-MiChroM platform aided by new trained parameters in the minimal chromatin model (MiChroM) energy function. The simulations optimized on a downsampled experimental map (10% of the original data) allow the prediction of a contact frequency similar to that of the complete (100%) experimental Hi-C. The modeling results open a discussion on how simulations and modeling can increase the statistics and help fill in some Hi-C regions not captured by poor sampling experiments. Open-MiChroM simulations allow us to explore the 3D genome organization of different organisms, cell lines, and cell phases that often do not produce high-quality Hi-C maps.-
Descrição: dc.descriptionCenter for Theoretical Biological Physics Department of Physics & Astronomy Rice University-
Descrição: dc.descriptionInstituto de Biociências Letras e Ciências Exatas UNESP Univ. Estadual Paulista Departamento de Física-
Descrição: dc.descriptionThe Center for Genome Architecture Department of Molecular and Human Genetics Baylor College of Medicine-
Descrição: dc.descriptionInstituto de Biociências Letras e Ciências Exatas UNESP Univ. Estadual Paulista Departamento de Física-
Formato: dc.format8757-8767-
Idioma: dc.languageen-
Relação: dc.relationJournal of Physical Chemistry B-
???dc.source???: dc.sourceScopus-
Título: dc.titleChromosome Modeling on Downsampled Hi-C Maps Enhances the Compartmentalization Signal-
Tipo de arquivo: dc.typelivro digital-
Aparece nas coleções:Repositório Institucional - Unesp

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