Developing bioimaging and quantitative methods to study 3D genome

Abstract

The recent advances in chromosome configuration capture (3C)-based series molecular methods and optical super-resolution (SR) techniques offer powerful tools to investigate three dimensional (3D) genomic structure in prokaryotic and eukaryotic cell nucleus. In this review, we focus on the progress during the last decade in this exciting field. Here we at first introduce briefly genome organization at chromosome, domain and sub-domain level, respectively; then we provide a short introduction to various super-resolution microscopy techniques which can be employed to detect genome 3D structure. We also reviewed the progress of quantitative and visualization tools to evaluate and visualize chromatin interactions in 3D genome derived from Hi-C data. We end up with the discussion that imaging methods and 3C-based molecular methods are not mutually exclusive - - - - actually they are complemental to each other and can be combined together to study 3D genome organization.

Graphical abstract

Keywords

3D Genome / quantitative methods / bioimaging / super resolution

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ACKNOWLEDGEMENTS

Due to the space constraints, we regret that we are unable to address the importance of all work in the field. This work is supported by National Basic Research Project (973 Program, No. 2012CB316503) and the National Natural Science Foundation of China (Nos. 31361163004 and 91019016). The authors also thank many colleagues in Prof. Michael Q. Zhang’s laboratory and Prof. Peng Xi’s laboratory who shared their enthusiasm, ideas, experimental and computational results to make this review possible.

COMPLIANCE WITH ETHICS GUIDELINES

The authors Juntao Gao, Xusan Yang, Mohamed Nadhir Djekidel, Yang Wang, Peng Xi and Michael Q. Zhang declare that they have no conflict of interest.

This article does not contain any studies with human or animal subjects performed by any of the authors.

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2016 Higher Education Press and Springer-Verlag Berlin Heidelberg