GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data

Oluwatosin Oluwadare,Erez Lieberman Aiden,Max Highsmith,Jianlin Cheng,Douglass Turner

doi:10.1186/s12860-020-00304-y

Abstract

Advances in the study of chromosome conformation capture technologies, such as Hi-C technique - capable of capturing chromosomal interactions in a genome-wide scale - have led to the development of three-dimensional chromosome and genome structure reconstruction methods from Hi-C data. The three dimensional genome structure is important because it plays a role in a variety of important biological activities such as DNA replication, gene regulation, genome interaction, and gene expression. In recent years, numerous Hi-C datasets have been generated, and likewise, a number of genome structure construction algorithms have been developed.In this work, we outline the construction of a novel Genome Structure Database (GSDB) to create a comprehensive repository that contains 3D structures for Hi-C datasets constructed by a variety of 3D structure reconstruction tools. The GSDB contains over 50,000 structures from 12 state-of-the-art Hi-C data structure prediction algorithms for 32 Hi-C datasets.GSDB functions as a centralized collection of genome structures which will enable the exploration of the dynamic architectures of chromosomes and genomes for biomedical research. GSDB is accessible at http://sysbio.rnet.missouri.edu/3dgenome/GSDB

Highlights

The three-dimensional (3D) organization of the genome plays a significant role in many diverse biological functions and processes including gene expression [1], regulation [2, 3] and transcriptional regulation [4]
The Genome Structure Database (GSDB) contains Three Dimensional (3D) structures generated from different Hi-C structure reconstruction algorithms for Hi-C data collected from multiple sources
To the best of our knowledge, it is the first repository for 3D structures generated from multiple Hi-C reconstruction algorithms

Summary

Introduction

The three-dimensional (3D) organization of the genome plays a significant role in many diverse biological functions and processes including gene expression [1], regulation [2, 3] and transcriptional regulation [4]. Other microscopy methods developed to study the genome organization include stimulated emission depletion (STED) [11], stochastic optical reconstruction microscopy (STORM) [12], and photo-activated localization microscopy (PALM or FPALM) [13, 14]. While these techniques have proven very useful in providing insights into the organization of the genome for DNA fragments or chromatin regions, they are limited and unsuitable for an overall view of the genome-wide inter-and intra-chromosomal relationship study of the genome within the cell nucleus [15].

Results

Discussion

Conclusion