Computational inference of physical spatial organization of eukaryotic genomes

doi:10.1007/s40484-016-0082-1

Quant. Biol.

2016, Vol. 4

Issue (4) : 302-309 https://doi.org/10.1007/s40484-016-0082-1

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Computational inference of physical spatial organization of eukaryotic genomes

Bingxiang Xu,Zhihua Zhang(

)

CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China

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Abstract

Background: Chromosomes are packed in the cell’s nucleus, and chromosomal conformation is critical to nearly all intranuclear biological reactions, including gene transcription and DNA replication. Nevertheless, chromosomal conformation is largely a mystery in terms of its formation and the regulatory machinery that accesses it.

Results: Thanks to recent technological developments, we can now probe chromatin interaction in substantial detail, boosting research interest in modeling genome spatial organization. Here, we review the current computational models that simulate chromosome dynamics, and explain the physical and topological properties of chromosomal conformation, as inferred from these newly generated data.

Conclusion: Novel models shall be developed to address questions beyond averaged structure in the near further.

Author Summary Genome is always working in the 3D space of the nucleus, and its 3D structure is critical for gene regulation. We review the computational methods that rebuild genome 3D structures from high throughput technologies, such as Hi-C. We also discuss the pros and cons in current methods and possible further directions in the field.

Keywords 3D genome models simulation

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Corresponding Author(s): Zhihua Zhang

Online First Date: 17 November 2016 Issue Date: 01 December 2016

Cite this article:

Bingxiang Xu,Zhihua Zhang. Computational inference of physical spatial organization of eukaryotic genomes[J]. Quant. Biol., 2016, 4(4): 302-309.

URL:

https://academic.hep.com.cn/qb/EN/10.1007/s40484-016-0082-1
https://academic.hep.com.cn/qb/EN/Y2016/V4/I4/302

Fig.1 Illustration of polymer models showing the dynamics of chromatin loops. (A) Dynamic loop model. (B) Random loop model. (C) SBS model. (D) Loop extrusion model.

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