Literature DB >> 31092938

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

Ralph Stadhouders1,2, Guillaume J Filion3,4, Thomas Graf5,6.   

Abstract

How cells adopt different identities has long fascinated biologists. Signal transduction in response to environmental cues results in the activation of transcription factors that determine the gene-expression program characteristic of each cell type. Technological advances in the study of 3D chromatin folding are bringing the role of genome conformation in transcriptional regulation to the fore. Characterizing this role of genome architecture has profound implications, not only for differentiation and development but also for diseases including developmental malformations and cancer. Here we review recent studies indicating that the interplay between transcription and genome conformation is a driving force for cell-fate decisions.

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Year:  2019        PMID： 31092938     DOI： 10.1038/s41586-019-1182-7

Source DB:  PubMed          Journal:  Nature        ISSN： 0028-0836            Impact factor:   49.962


  150 in total

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Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

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Authors:  Boyan Bonev; Giacomo Cavalli
Journal:  Nat Rev Genet       Date:  2016-10-14       Impact factor: 53.242

Review 3.  Transcription factors: from enhancer binding to developmental control.

Authors:  François Spitz; Eileen E M Furlong
Journal:  Nat Rev Genet       Date:  2012-08-07       Impact factor: 53.242

Review 4.  The Human Transcription Factors.

Authors:  Samuel A Lambert; Arttu Jolma; Laura F Campitelli; Pratyush K Das; Yimeng Yin; Mihai Albu; Xiaoting Chen; Jussi Taipale; Timothy R Hughes; Matthew T Weirauch
Journal:  Cell       Date:  2018-02-08       Impact factor: 41.582

Review 5.  Emerging properties of animal gene regulatory networks.

Authors:  Eric H Davidson
Journal:  Nature       Date:  2010-12-16       Impact factor: 49.962

Review 6.  The 3D Genome as Moderator of Chromosomal Communication.

Authors:  Job Dekker; Leonid Mirny
Journal:  Cell       Date:  2016-03-10       Impact factor: 41.582

Review 7.  A census of human transcription factors: function, expression and evolution.

Authors:  Juan M Vaquerizas; Sarah K Kummerfeld; Sarah A Teichmann; Nicholas M Luscombe
Journal:  Nat Rev Genet       Date:  2009-04       Impact factor: 53.242

Review 8.  Dynamic regulation of transcriptional states by chromatin and transcription factors.

Authors:  Ty C Voss; Gordon L Hager
Journal:  Nat Rev Genet       Date:  2013-12-17       Impact factor: 53.242

Review 9.  Pioneer transcription factors, chromatin dynamics, and cell fate control.

Authors:  Kenneth S Zaret; Susan E Mango
Journal:  Curr Opin Genet Dev       Date:  2016-01-27       Impact factor: 5.578

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504
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  117 in total

1.  MATCHA: Probing multi-way chromatin interaction with hypergraph representation learning.

Authors:  Ruochi Zhang; Jian Ma
Journal:  Cell Syst       Date:  2020-05-20       Impact factor: 10.304

Review 2.  Chromatin accessibility dynamics during cell fate reprogramming.

Authors:  Dongwei Li; Xiaodong Shu; Ping Zhu; Duanqing Pei
Journal:  EMBO Rep       Date:  2021-01-22       Impact factor: 8.807

3.  DNA Rchitect: an R based visualizer for network analysis of chromatin interaction data.

Authors:  R N Ramirez; K Bedirian; S M Gray; A Diallo
Journal:  Bioinformatics       Date:  2020-01-15       Impact factor: 6.937

4.  A base-pair view of interactions between genes and their enhancers.

Authors:  Anne van Schoonhoven; Ralph Stadhouders
Journal:  Nature       Date:  2021-07       Impact factor: 49.962

Review 5.  Organelle size scaling over embryonic development.

Authors:  Chase C Wesley; Sampada Mishra; Daniel L Levy
Journal:  Wiley Interdiscip Rev Dev Biol       Date:  2020-01-31       Impact factor: 5.814

6.  CTCF chromatin residence time controls three-dimensional genome organization, gene expression and DNA methylation in pluripotent cells.

Authors:  Widia Soochit; Frank Sleutels; Gregoire Stik; Frank Grosveld; Ralph Stadhouders; Niels Galjart; Marek Bartkuhn; Sreya Basu; Silvia C Hernandez; Sarra Merzouk; Enrique Vidal; Ruben Boers; Joachim Boers; Michael van der Reijden; Bart Geverts; Wiggert A van Cappellen; Mirjam van den Hout; Zeliha Ozgur; Wilfred F J van IJcken; Joost Gribnau; Rainer Renkawitz; Thomas Graf; Adriaan Houtsmuller
Journal:  Nat Cell Biol       Date:  2021-07-29       Impact factor: 28.824

Review 7.  The relationship between genome structure and function.

Authors:  A Marieke Oudelaar; Douglas R Higgs
Journal:  Nat Rev Genet       Date:  2020-11-24       Impact factor: 53.242

8.  CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response.

Authors:  Grégoire Stik; Enrique Vidal; Mercedes Barrero; Sergi Cuartero; Maria Vila-Casadesús; Julen Mendieta-Esteban; Tian V Tian; Jinmi Choi; Clara Berenguer; Amaya Abad; Beatrice Borsari; François le Dily; Patrick Cramer; Marc A Marti-Renom; Ralph Stadhouders; Thomas Graf
Journal:  Nat Genet       Date:  2020-06-08       Impact factor: 38.330

9.  KLF4 is involved in the organization and regulation of pluripotency-associated three-dimensional enhancer networks.

Authors:  Dafne Campigli Di Giammartino; Andreas Kloetgen; Alexander Polyzos; Yiyuan Liu; Daleum Kim; Dylan Murphy; Abderhman Abuhashem; Paola Cavaliere; Boaz Aronson; Veevek Shah; Noah Dephoure; Matthias Stadtfeld; Aristotelis Tsirigos; Effie Apostolou
Journal:  Nat Cell Biol       Date:  2019-09-23       Impact factor: 28.824

10.  Smarca5-mediated epigenetic programming facilitates fetal HSPC development in vertebrates.

Authors:  Yanyan Ding; Wen Wang; Dongyuan Ma; Guixian Liang; Zhixin Kang; Yuanyuan Xue; Yifan Zhang; Lu Wang; Jian Heng; Yong Zhang; Feng Liu
Journal:  Blood       Date:  2021-01-14       Impact factor: 22.113
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