Literature DB >> 33235358

The relationship between genome structure and function.

A Marieke Oudelaar1, Douglas R Higgs2.   

Abstract

Precise patterns of gene expression in metazoans are controlled by three classes of regulatory elements: promoters, enhancers and boundary elements. During differentiation and development, these elements form specific interactions in dynamic higher-order chromatin structures. However, the relationship between genome structure and its function in gene regulation is not completely understood. Here we review recent progress in this field and discuss whether genome structure plays an instructive role in regulating gene expression or is a reflection of the activity of the regulatory elements of the genome.

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Year:  2020        PMID： 33235358     DOI： 10.1038/s41576-020-00303-x

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  198 in total

Review 1.  Developmental enhancers and chromosome topology.

Authors:  Eileen E M Furlong; Michael Levine
Journal:  Science       Date:  2018-09-28       Impact factor: 47.728

Review 2.  Chromosome Conformation Capture and Beyond: Toward an Integrative View of Chromosome Structure and Function.

Authors:  Rachel Patton McCord; Noam Kaplan; Luca Giorgetti
Journal:  Mol Cell       Date:  2020-01-27       Impact factor: 17.970

Review 3.  Methods for mapping 3D chromosome architecture.

Authors:  Rieke Kempfer; Ana Pombo
Journal:  Nat Rev Genet       Date:  2019-12-17       Impact factor: 53.242

Review 4.  Organizational principles of 3D genome architecture.

Authors:  M Jordan Rowley; Victor G Corces
Journal:  Nat Rev Genet       Date:  2018-12       Impact factor: 53.242

Review 5.  Long-range enhancer-promoter contacts in gene expression control.

Authors:  Stefan Schoenfelder; Peter Fraser
Journal:  Nat Rev Genet       Date:  2019-08       Impact factor: 53.242

Review 6.  Transcription factors and 3D genome conformation in cell-fate decisions.

Authors:  Ralph Stadhouders; Guillaume J Filion; Thomas Graf
Journal:  Nature       Date:  2019-05-15       Impact factor: 49.962

Review 7.  Advances in epigenetics link genetics to the environment and disease.

Authors:  Giacomo Cavalli; Edith Heard
Journal:  Nature       Date:  2019-07-24       Impact factor: 49.962

Review 8.  Defining functional DNA elements in the human genome.

Authors:  Manolis Kellis; Barbara Wold; Michael P Snyder; Bradley E Bernstein; Anshul Kundaje; Georgi K Marinov; Lucas D Ward; Ewan Birney; Gregory E Crawford; Job Dekker; Ian Dunham; Laura L Elnitski; Peggy J Farnham; Elise A Feingold; Mark Gerstein; Morgan C Giddings; David M Gilbert; Thomas R Gingeras; Eric D Green; Roderic Guigo; Tim Hubbard; Jim Kent; Jason D Lieb; Richard M Myers; Michael J Pazin; Bing Ren; John A Stamatoyannopoulos; Zhiping Weng; Kevin P White; Ross C Hardison
Journal:  Proc Natl Acad Sci U S A       Date:  2014-04-21       Impact factor: 12.779

9.  Systematic identification of silencers in human cells.

Authors:  Baoxu Pang; Michael P Snyder
Journal:  Nat Genet       Date:  2020-02-24       Impact factor: 38.330

10.  Chromatin interaction analyses elucidate the roles of PRC2-bound silencers in mouse development.

Authors:  Chew Yee Ngan; Chee Hong Wong; Harianto Tjong; Wenbo Wang; Rachel L Goldfeder; Cindy Choi; Hao He; Liang Gong; Junyan Lin; Barbara Urban; Julianna Chow; Meihong Li; Joanne Lim; Vivek Philip; Stephen A Murray; Haoyi Wang; Chia-Lin Wei
Journal:  Nat Genet       Date:  2020-02-24       Impact factor: 38.330
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  19 in total

Review 1.  Characterizing cis-regulatory elements using single-cell epigenomics.

Authors:  Sebastian Preissl; Kyle J Gaulton; Bing Ren
Journal:  Nat Rev Genet       Date:  2022-07-15       Impact factor: 59.581

2.  Chromatin structure undergoes global and local reorganization during murine dendritic cell development and activation.

Authors:  Daisuke Kurotaki; Kenta Kikuchi; Kairong Cui; Wataru Kawase; Keita Saeki; Junpei Fukumoto; Akira Nishiyama; Kisaburo Nagamune; Keji Zhao; Keiko Ozato; Pedro P Rocha; Tomohiko Tamura
Journal:  Proc Natl Acad Sci U S A       Date:  2022-08-15       Impact factor: 12.779

Review 3.  Three-dimensional genome organization in immune cell fate and function.

Authors:  Sergi Cuartero; Grégoire Stik; Ralph Stadhouders
Journal:  Nat Rev Immunol       Date:  2022-09-20       Impact factor: 108.555

Review 4.  3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells.

Authors:  George Papadogkonas; Dionysios-Alexandros Papamatheakis; Charalampos Spilianakis
Journal:  Front Immunol       Date:  2022-06-22       Impact factor: 8.786

5.  Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus.

Authors:  Sumbal Wahid; Meili Xie; Sehrish Sarfraz; Jie Liu; Chuanji Zhao; Zetao Bai; Chaobo Tong; Xiaohui Cheng; Feng Gao; Shengyi Liu
Journal:  Int J Mol Sci       Date:  2022-06-03       Impact factor: 6.208

Review 6.  Erythroid Cell Research: 3D Chromatin, Transcription Factors and Beyond.

Authors:  Charlotte Andrieu-Soler; Eric Soler
Journal:  Int J Mol Sci       Date:  2022-05-30       Impact factor: 6.208

Review 7.  Roles of transposable elements in the regulation of mammalian transcription.

Authors:  Raquel Fueyo; Julius Judd; Cedric Feschotte; Joanna Wysocka
Journal:  Nat Rev Mol Cell Biol       Date:  2022-02-28       Impact factor: 113.915

Review 8.  Fine mapping with epigenetic information and 3D structure.

Authors:  Gisela Orozco
Journal:  Semin Immunopathol       Date:  2022-01-12       Impact factor: 9.623

9.  CTCF-mediated chromatin looping provides a topological framework for the formation of phase-separated transcriptional condensates.

Authors:  Ryanggeun Lee; Moo-Koo Kang; Yong-Jin Kim; Bobae Yang; Hwanyong Shim; Sugyung Kim; Kyungwoo Kim; Chul Min Yang; Byeong-Gyu Min; Woong-Jae Jung; Eun-Chong Lee; Jung-Sik Joo; Gunhee Park; Won-Ki Cho; Hyoung-Pyo Kim
Journal:  Nucleic Acids Res       Date:  2022-01-11       Impact factor: 16.971

10.  Dynamic Runx1 chromatin boundaries affect gene expression in hematopoietic development.

Authors:  Dominic D G Owens; Giorgio Anselmi; A Marieke Oudelaar; Damien J Downes; Alessandro Cavallo; Joe R Harman; Ron Schwessinger; Akin Bucakci; Lucas Greder; Sara de Ornellas; Danuta Jeziorska; Jelena Telenius; Jim R Hughes; Marella F T R de Bruijn
Journal:  Nat Commun       Date:  2022-02-09       Impact factor: 17.694
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