Large-scale 3D chromatin reconstruction from chromosomal contacts

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

4 Scopus Citations
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Detail(s)

Original languageEnglish
Article number186
Journal / PublicationBMC Genomics
Volume20
Issue numberSuppl. 2
Online published4 Apr 2019
Publication statusPublished - 2019

Conference

Title17th Asia Pacific Bioinformatics Conference (APBC 2019)
PlaceChina
CityWuhan
Period14 - 16 January 2019

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Abstract

Background: Recent advances in genome analysis have established that chromatin has preferred 3D conformations, which bring distant loci into contact. Identifying these contacts is important for us to understand possible interactions between these loci. This has motivated the creation of the Hi-C technology, which detects long-range chromosomal interactions. Distance geometry-based algorithms, such as ChromSDE and ShRec3D, have been able to utilize Hi-C data to infer 3D chromosomal structures. However, these algorithms, being matrix-based, are space- and time-consuming on very large datasets. A human genome of 100 kilobase resolution would involve 30,000 loci, requiring gigabytes just in storing the matrices. Results: We propose a succinct representation of the distance matrices which tremendously reduces the space requirement. We give a complete solution, called SuperRec, for the inference of chromosomal structures from Hi-C data, through iterative solving the large-scale weighted multidimensional scaling problem. Conclusions: SuperRec runs faster than earlier systems without compromising on result accuracy. The SuperRec package can be obtained from http://www.cs.cityu.edu.hk/~shuaicli/SuperRec.

Research Area(s)

  • 3D chromosome structure, 3D genome, Chromosome conformation capture, Hi-C, Multidimensional scaling

Citation Format(s)

Large-scale 3D chromatin reconstruction from chromosomal contacts. / Zhang, Yanlin; Liu, Weiwei; Lin, Yu; Ng, Yen Kaow; Li, Shuaicheng.

In: BMC Genomics, Vol. 20, No. Suppl. 2, 186, 2019.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

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