A maximum likelihood algorithm for reconstructing 3D structures of human chromosomes from chromosomal contact data

BMC Genomics
Oluwatosin OluwadareJianlin Cheng

Abstract

The development of chromosomal conformation capture techniques, particularly, the Hi-C technique, has made the analysis and study of the spatial conformation of a genome an important topic in bioinformatics and computational biology. Aided by high-throughput next generation sequencing techniques, the Hi-C technique can generate genome-wide, large-scale intra- and inter-chromosomal interaction data capable of describing in details the spatial interactions within a genome. These data can be used to reconstruct 3D structures of chromosomes that can be used to study DNA replication, gene regulation, genome interaction, genome folding, and genome function. Here, we introduce a maximum likelihood algorithm called 3DMax to construct the 3D structure of a chromosome from Hi-C data. 3DMax employs a maximum likelihood approach to infer the 3D structures of a chromosome, while automatically re-estimating the conversion factor (α) for converting Interaction Frequency (IF) to distance. Our results show that the models generated by 3DMax from a simulated Hi-C dataset match the true models better than most of the existing methods. 3DMax is more robust to structural variability and noise. Compared on a real Hi-C dataset, 3DMax constructs chrom...Continue Reading

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Citations

May 3, 2019·Biological Procedures Online·Oluwatosin OluwadareJianlin Cheng
Aug 8, 2020·BMC Molecular and Cell Biology·Oluwatosin OluwadareJianlin Cheng
Mar 23, 2019·Scientific Reports·Tuan TrieuJianlin Cheng
Dec 17, 2020·PLoS Computational Biology·Samuel P IngramMichael J Merchant
Mar 22, 2021·Nucleic Acids Research·Vikash Kumar YadavClaudia Köhler
May 1, 2021·International Journal of Molecular Sciences·Van Hovenga, Oluwatosin Oluwadare
May 18, 2021·Computational and Structural Biotechnology Journal·Haiyan GongXiaotong Zhang
Jul 29, 2021·The Journal of Physical Chemistry. B·Antonio B Oliveira JuniorJosé N Onuchic
Aug 31, 2019·Methods : a Companion to Methods in Enzymology·Dario Meluzzi, Gaurav Arya

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Datasets Mentioned

BETA
GM06990
GSE18199
GM06690

Methods Mentioned

BETA
Hi-C
ICE

Software Mentioned

Java
Integrated Modeling Platform ( IMP )
Hi
dSCC
AdaGrad
3DMax
ChromSDE
3DMax1
ShRec3D
LorDG

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