Functional organization of the human 4D Nucleome

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review

76 Scopus Citations
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Author(s)

  • Haiming Chen
  • Jie Chen
  • Lindsey A. Muir
  • Scott Ronquist
  • Walter Meixner
  • Mats Ljungman
  • Thomas Ried
  • Indika Rajapakse

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)8002-8007
Journal / PublicationProceedings of the National Academy of Sciences of the United States of America
Volume112
Issue number26
Online published15 Jun 2015
Publication statusPublished - 30 Jun 2015

Abstract

The 4D organization of the interphase nucleus, or the 4D Nucleome (4DN), reflects a dynamical interaction between 3D genome structure and function and its relationship to phenotype. We present initial analyses of the human 4DN, capturing genome-wide structure using chromosome conformation capture and 3D imaging, and function using RNA-sequencing. We introduce a quantitative index that measures underlying topological stability of a genomic region. Our results show that structural features of genomic regions correlate with function with surprising persistence over time. Furthermore, constructing genome-wide gene-level contact maps aided in identifying gene pairs with high potential for coregulation and colocalization in a manner consistent with expression via transcription factories. We additionally use 2D phase planes to visualize patterns in 4DN data. Finally, we evaluated gene pairs within a circadian gene module using 3D imaging, and found periodicity in the movement of clock circadian regulator and period circadian clock 2 relative to each other that followed a circadian rhythm and entrained with their expression.

Research Area(s)

  • 4D Nucleome, Interphase nucleus, Laplacian, Networks, Phase plane

Citation Format(s)

Functional organization of the human 4D Nucleome. / Chen, Haiming; Chen, Jie; Muir, Lindsey A. et al.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 112, No. 26, 30.06.2015, p. 8002-8007.

Research output: Journal Publications and ReviewsRGC 21 - Publication in refereed journalpeer-review