Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
Review
. 2019 Apr 24:21:7.
doi: 10.1186/s12575-019-0094-0. eCollection 2019.

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

Oluwatosin Oluwadare  1 , Max Highsmith  1 , Jianlin Cheng  1   2
Affiliations
Review

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data

Oluwatosin Oluwadare et al. Biol Proced Online. .

Abstract

Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. In this review we describe, categorize, and compare the various methods developed to map chromosome and genome structures from 3C data-particularly Hi-C data. We summarize the improvements introduced by these methods, describe the approach used for method evaluation, and discuss how these advancements shape the future of genome structure construction.

Keywords: 3-D chromosome and genome structure; 3-D genome; Chromosome conformation capture; Contact-based modeling; Distance-based modeling; Hi-C; Optimization.

PubMed Disclaimer

Conflict of interest statement

Not applicable.Not applicable.The authors declare that they have no competing interests.Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Figures

Fig. 1
Fig. 1
Chromosome and genome 3-D structure representation for models from Hi-C data. The different models used for representing 3-D chromosome and genome structure by various methods using Hi-C data for modeling chromosomes and genome 3-D structure. a polymer model, b spheres, c points
Fig. 2
Fig. 2
Chromosome and genome 3-D structure reconstruction workflow. A summarization of the steps for genome and chromosome 3-D structure taken by the different methods. Starting from the user input in Step 1: The input preparation, usually, Hi-C contact matrix or sometimes with extra parameters requirement. Step 2: One of the three IF modeling approach is used to represent the IF depending on the method’s algorithm. Step 3: Modeling is done using defined sampling algorithms, and Step 4, a consensus average structure or a group of structure is generated depending on the method’s structure class
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Misteli T. Beyond the sequence: cellular organization of genome function. Cell. 2007;128(4):787–800. doi: 10.1016/j.cell.2007.01.028. - DOI - PubMed
    1. Cremer T, Cremer C. Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet. 2001;2(4):292. doi: 10.1038/35066075. - DOI - PubMed
    1. Branco MR, Pombo A. Chromosome organization: new facts, new models. Trends Cell Biol. 2007;17(3):127–134. doi: 10.1016/j.tcb.2006.12.006. - DOI - PubMed
    1. Hakim O, Misteli T. SnapShot: chromosome conformation capture. Cell. 2012;148(5):1068–10e1. doi: 10.1016/j.cell.2012.02.019. - DOI - PMC - PubMed
    1. Osório J. Chromosome biology: moving a TAD closer to unravelling chromosome architecture. Nat Rev Mol Cell Biol. 2015;16(12):701. doi: 10.1038/nrm4092. - DOI - PubMed