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

Vinícius G Contessoto; Ryan R Cheng; Arya Hajitaheri; Esteban Dodero-Rojas; Matheus F Mello; Erez Lieberman-Aiden; Peter G Wolynes; Michele Di Pierro; José N Onuchic

doi:10.1093/nar/gkaa818

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

Nucleic Acids Res. 2021 Jan 8;49(D1):D172-D182. doi: 10.1093/nar/gkaa818.

Authors

Vinícius G Contessoto^{1

2

3}, Ryan R Cheng¹, Arya Hajitaheri^{1

4}, Esteban Dodero-Rojas^{1

5}, Matheus F Mello^{1

6}, Erez Lieberman-Aiden^{1

7}, Peter G Wolynes^{1

8

9

10}, Michele Di Pierro^{1

11}, José N Onuchic^{1

8

9

10}

Affiliations

¹ Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
² Brazilian Biorenewables National Laboratory-LNBR, Brazilian Center for Research in Energy and Materials-CNPEM, Campinas, SP 13083-100, Brazil.
³ Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP 15054-000, Brazil.
⁴ Department of Computer Science, University of Houston, Houston, TX 77204, USA.
⁵ Theoretical and Computational Physics Laboratory, University of Costa Rica, San José 5 11501, Costa Rica.
⁶ Chemical Engineering Department, Military Institute of Engineering, Rio de Janeiro, RJ 22290-270, Brazil.
⁷ The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
⁸ Department of Physics & Astronomy, Rice University, Houston, TX 77005, USA.
⁹ Department of Chemistry, Rice University, Houston, TX 77005, USA.
¹⁰ Department of Biosciences, Rice University, Houston, TX 77005, USA.
¹¹ Department of Physics, Northeastern University, Boston, MA 02115, USA.

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 insitu 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. The NDB is available at https://ndb.rice.edu.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

A549 Cells
Chromatin / metabolism
Chromatin / ultrastructure*
Computational Biology / methods*
Databases, Genetic*
Epigenesis, Genetic*
Genome, Human*
Humans
In Situ Hybridization, Fluorescence
Internet
Molecular Conformation
Molecular Sequence Annotation
Software

Substances

Chromatin

Grants and funding

UM1 HG009375/HG/NHGRI NIH HHS/United States