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3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations

Author

Listed:
  • Pengze Wu

    (Peking University)

  • Tingting Li

    (Peking University)

  • Ruifeng Li

    (Peking University)

  • Lumeng Jia

    (Peking University)

  • Ping Zhu

    (Peking University)

  • Yifang Liu

    (Tsinghua University)

  • Qing Chen

    (Peking University)

  • Daiwei Tang

    (Tsinghua University)

  • Yuezhou Yu

    (Peking University)

  • Cheng Li

    (Peking University
    Peking University)

Abstract

The Hi-C method is widely used to study the functional roles of the three-dimensional (3D) architecture of genomes. Here, we integrate Hi-C, whole-genome sequencing (WGS) and RNA-seq to study the 3D genome architecture of multiple myeloma (MM) and how it associates with genomic variation and gene expression. Our results show that Hi-C interaction matrices are biased by copy number variations (CNVs) and can be used to detect CNVs. Also, combining Hi-C and WGS data can improve the detection of translocations. We find that CNV breakpoints significantly overlap with topologically associating domain (TAD) boundaries. Compared to normal B cells, the numbers of TADs increases by 25% in MM, the average size of TADs is smaller, and about 20% of genomic regions switch their chromatin A/B compartment types. In summary, we report a 3D genome interaction map of aneuploid MM cells and reveal the relationship among CNVs, translocations, 3D genome reorganization, and gene expression regulation.

Suggested Citation

  • Pengze Wu & Tingting Li & Ruifeng Li & Lumeng Jia & Ping Zhu & Yifang Liu & Qing Chen & Daiwei Tang & Yuezhou Yu & Cheng Li, 2017. "3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations," Nature Communications, Nature, vol. 8(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:8:y:2017:i:1:d:10.1038_s41467-017-01793-w
    DOI: 10.1038/s41467-017-01793-w
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