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(Referência obtida automaticamente do Web of Science, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores.)

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

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Autor(es):
Oliveira, Jr., Antonio B. [1] ; Estrada, Cynthia Perez [2, 1] ; Aiden, Erez Lieberman [2, 1] ; Contessoto, Vinicius G. [1, 3] ; Onuchic, Jose N. [4, 5]
Número total de Autores: 5
Afiliação do(s) autor(es):
[1] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77251 - USA
[2] Baylor Coll Med, Ctr Genome Architecture, Dept Mol & Human Genet, Houston, TX 77030 - USA
[3] UNESP Univ Estadual Paulista, Inst Biociencias Letras & Crencias Exatas, Dept Fis, Sao Jose Do Rio Preto, SP - Brazil
[4] Rice Univ, Dept Phys & Astron, Ctr Theoret Biol Phys, Dept Chem, Houston, TX 77251 - USA
[5] Rice Univ, Dept Biosci, Houston, TX 77251 - USA
Número total de Afiliações: 5
Tipo de documento: Artigo Científico
Fonte: Journal of Physical Chemistry B; v. 125, n. 31, p. 8757-8767, AUG 12 2021.
Citações Web of Science: 0
Resumo

The 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. (AU)

Processo FAPESP: 16/13998-8 - Evolução racional por métodos computacionais aplicados na predição de mutações no desenvolvimento de enzimas para produção de biocombustíveis
Beneficiário:Vinícius de Godoi Contessoto
Modalidade de apoio: Bolsas no Brasil - Pós-Doutorado
Processo FAPESP: 17/09662-7 - Evolução racional por métodos computacionais aplicada em enzimas relacionadas com a produção de bioetanol
Beneficiário:Vinícius de Godoi Contessoto
Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado