The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome

Author(s)

Contessoto, Vinicius G. ^{[1, 2, 3]} ; Cheng, Ryan R. ^[1] ; Hajitaheri, Arya ^{[1, 4]} ; Dodero-Rojas, Esteban ^{[1, 5]} ; Mello, Matheus F. ^{[1, 6]} ; Lieberman-Aiden, Erez ^{[1, 7]} ; Wolynes, Peter G. ^{[8, 1, 9, 10]} ; Di Pierro, Michele ^{[1, 11]} ; Onuchic, Jose N. ^{[8, 1, 9, 10]}

Affiliation:Show less -

^[1] Rice Univ, Ctr Theoret Biol Phys, Houston, TX 77005 - USA

^[2] Sao Paulo State Univ UNESP, Inst Biosci Humanities & Exact Sci, Dept Phys, BR-15054000 Sao Jose Do Rio Preto, SP - Brazil

^[3] Brazilian Ctr Res Energy & Mat CNPEM, Brazilian Biorenewables Natl Lab LNBR, BR-13083100 Campinas, SP - Brazil

^[4] Univ Houston, Dept Comp Sci, Houston, TX 77204 - USA

^[5] Univ Costa Rica, Theoret & Computat Phys Lab, San Jose 11501 5 - Costa Rica

^[6] Mil Inst Engn, Chem Engn Dept, BR-22290270 Rio De Janeiro, RJ - Brazil

^[7] Baylor Coll Med, Ctr Genome Architecture, Dept Mol & Human Genet, Houston, TX 77030 - USA

^[8] Rice Univ, Dept Chem, Houston, TX 77005 - USA

^[9] Rice Univ, Dept Biosci, Houston, TX 77005 - USA

^[10] Rice Univ, Dept Phys & Astron, Houston, TX 77005 - USA

^[11] Northeastern Univ, Dept Phys, Boston, MA 02115 - USA

• Document type: Journal article
• Source: Nucleic Acids Research; v. 49, n. D1, p. D172-D182, JAN 8 2021.
• Web of Science Citations: 2

Abstract

We introduce the Nucleome Data Bank (NDB), a web-based platform to simulate and analyze the three-dimensional (3D) organization of genomes. The NDB enables physics-based simulation of chromosomal structural dynamics through the MEGABASE + MiChroM computational pipeline. The input of the pipeline consists of epigenetic information sourced from the Encode database; the output consists of the trajectories of chromosomal motions that accurately predict Hi-C and fluorescence in situ hybridization data, as well as multiple observations of chromosomal dynamics in vivo. As an intermediate step, users can also generate chromosomal sub-compartment annotations directly from the same epigenetic input, without the use of any DNA-DNA proximity ligation data. Additionally, the NDB freely hosts both experimental and computational structural genomics data. Besides being able to perform their own genome simulations and download the hosted data, users can also analyze and visualize the same data through custom-designed web-based tools. In particular, the one-dimensional genetic and epigenetic data can be overlaid onto accurate 3D structures of chromosomes, to study the spatial distribution of genetic and epigenetic features. The NDB aims to be a shared resource to biologists, biophysicists and all genome scientists. (AU)

• FAPESP's process: 17/09662-7 - Rational Evolution by Computational Methods Applied in Enzymes Related to Bioethanol Production
• Grantee: Vinícius de Godoi Contessoto
• Support Opportunities: Scholarships abroad - Research Internship - Post-doctor