Literature DB >> 33203573

A TAD Skeptic: Is 3D Genome Topology Conserved?

Ittai E Eres1, Yoav Gilad2.   

Abstract

The notion that topologically associating domains (TADs) are highly conserved across species is prevalent in the field of 3D genomics. However, what exactly is meant by 'highly conserved' and what are the actual comparative data that support this notion? To address these questions, we performed a historical review of the relevant literature and retraced numerous citation chains to reveal the primary data that were used as the basis for the widely accepted conclusion that TADs are highly conserved across evolution. A thorough review of the available evidence suggests the answer may be more complex than what is commonly presented.
Copyright © 2020 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  3D genome architecture; Hi-C; TADs; evolution; gene regulation; topologically associating domains

Mesh:

Substances:

Year:  2020        PMID: 33203573      PMCID: PMC8120795          DOI: 10.1016/j.tig.2020.10.009

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  60 in total

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Review 3.  Chromatin Domains: The Unit of Chromosome Organization.

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Journal:  Cell       Date:  2017-10-05       Impact factor: 41.582

5.  Biased gene retention during diploidization in Brassica linked to three-dimensional genome organization.

Authors:  Ting Xie; Fu-Gui Zhang; Hong-Yu Zhang; Xiao-Tao Wang; Ji-Hong Hu; Xiao-Ming Wu
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6.  A critical assessment of topologically associating domain prediction tools.

Authors:  Rola Dali; Mathieu Blanchette
Journal:  Nucleic Acids Res       Date:  2017-04-07       Impact factor: 16.971

7.  Comparison of computational methods for Hi-C data analysis.

Authors:  Francesco Ferrari; Silvio Bicciato; Mattia Forcato; Chiara Nicoletti; Koustav Pal; Carmen Maria Livi
Journal:  Nat Methods       Date:  2017-06-12       Impact factor: 28.547

8.  Comparison of computational methods for the identification of topologically associating domains.

Authors:  Marie Zufferey; Daniele Tavernari; Elisa Oricchio; Giovanni Ciriello
Journal:  Genome Biol       Date:  2018-12-10       Impact factor: 13.583

9.  Reorganization of 3D genome structure may contribute to gene regulatory evolution in primates.

Authors:  Ittai E Eres; Kaixuan Luo; Chiaowen Joyce Hsiao; Lauren E Blake; Yoav Gilad
Journal:  PLoS Genet       Date:  2019-07-19       Impact factor: 6.020

10.  Conservation and divergence of regulatory strategies at Hox Loci and the origin of tetrapod digits.

Authors:  Joost M Woltering; Daan Noordermeer; Marion Leleu; Denis Duboule
Journal:  PLoS Biol       Date:  2014-01-21       Impact factor: 8.029

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  10 in total

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Journal:  Am J Hum Genet       Date:  2021-02-04       Impact factor: 11.025

Review 2.  Charting the genomic landscape of seed-free plants.

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Journal:  Nat Plants       Date:  2021-04-05       Impact factor: 15.793

3.  TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors.

Authors:  Wenliang Wang; Aditi Chandra; Naomi Goldman; Sora Yoon; Emily K Ferrari; Son C Nguyen; Eric F Joyce; Golnaz Vahedi
Journal:  Nat Immunol       Date:  2022-06-20       Impact factor: 31.250

4.  Three-Dimensional Genome Map of the Filamentous Fungus Penicillium oxalicum.

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Journal:  Microbiol Spectr       Date:  2022-05-02

Review 5.  Epigenetics and Heart Development.

Authors:  Rajani M George; Anthony B Firulli
Journal:  Front Cell Dev Biol       Date:  2021-05-06

6.  Conservation of chromatin conformation in carnivores.

Authors:  Marco Corbo; Joana Damas; Madeline G Bursell; Harris A Lewin
Journal:  Proc Natl Acad Sci U S A       Date:  2022-03-01       Impact factor: 11.205

Review 7.  Mouse genomic and cellular annotations.

Authors:  Helen Long; Richard Reeves; Michelle M Simon
Journal:  Mamm Genome       Date:  2022-02-05       Impact factor: 2.957

8.  Topologically associating domains are disrupted by evolutionary genome rearrangements forming species-specific enhancer connections in mice and humans.

Authors:  Sarah E Gilbertson; Hannah C Walter; Katherine Gardner; Spencer N Wren; Golnaz Vahedi; Amy S Weinmann
Journal:  Cell Rep       Date:  2022-05-03       Impact factor: 9.995

Review 9.  The Clock Takes Shape-24 h Dynamics in Genome Topology.

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Journal:  Front Cell Dev Biol       Date:  2022-01-03

10.  Chromosomal neighbourhoods allow identification of organ specific changes in gene expression.

Authors:  Rishi Das Roy; Outi Hallikas; Mona M Christensen; Elodie Renvoisé; Jukka Jernvall
Journal:  PLoS Comput Biol       Date:  2021-09-10       Impact factor: 4.475

  10 in total

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