Understanding Spatial Genome Organization: Methods and Insights

Genomics, Proteomics & Bioinformatics
Vijay RamaniZhijun Duan

Abstract

The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs) appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.

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Citations

Oct 22, 2016·BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology·Iain A SawyerMiroslav Dundr
Jan 31, 2017·Nature Methods·Vijay RamaniJay Shendure
May 30, 2017·Journal of Theoretical Biology·V R Chechetkin, V V Lobzin
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Oct 2, 2017·Genome Medicine·Arpit Mishra, R David Hawkins
Sep 1, 2017·Cancer Cell International·Markus Mandl, Reinhard Depping
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Mar 22, 2021·Nucleic Acids Research·Vikash Kumar YadavClaudia Köhler
Jul 15, 2021·Computational and Structural Biotechnology Journal·Jing LiMingzhou Li

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Methods Mentioned

BETA
acetylation
imaging techniques
transmission electron microscopy
fluorescence microscopy
immunoprecipitation
ChIP
DamID
Hi-C
histone acetylation
super-resolution microscopy

Software Mentioned

HIPmap
Firre
Micro
STORM
Hi
Xist
HOTTIP

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