Advances in technologies for 3D genomics research

Sci China Life Sci. 2020 Jun;63(6):811-824. doi: 10.1007/s11427-019-1704-2. Epub 2020 May 8.


The spatial structure of the orderly organized chromatin in the nucleus has important roles in maintaining normal cell function and in regulation of gene expression, and the high-throughput Hi-C and ChIA-PET methods have been widely used in various biological studies for determining potential spatial genome structures and their functions. However, there are still great difficulties and challenges in three-dimensional (3D) genomics research. More efficient, economical, and unbiased approaches to studying 3D genomics need to be developed for more widespread and easier applications. Here, we review the most recent studies on new 3D genomics research technologies, such as improvements of the traditional Hi-C and ChIA-PET methods, new approaches based on non-proximal-ligation strategies, and imaging-based methods improved in recent years. Especially, we review the CRISPR-based methods for functional validations in 3D genomics, which could be the forthcoming directions. We hope this review can show some insights into the potential improvements for future 3D genomics.

Keywords: 3D genomics; CRISPR; ChIA-PET; FISH; Hi-C.

Publication types

  • Review

MeSH terms

  • Animals
  • Cell Line, Tumor
  • Chromatin / genetics
  • Chromatin Immunoprecipitation Sequencing
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Computational Biology
  • Genomics / methods*
  • High-Throughput Screening Assays / methods*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Ligands
  • Nucleic Acid Conformation


  • Chromatin
  • Ligands