Literature DB >> 34955367

Epigenome rewiring in human pluripotent stem cells.

Jielin Yan1, Danwei Huangfu2.   

Abstract

The epigenome plays a crucial role in modulating the activity of regulatory elements, thereby orchestrating diverse transcriptional programs during embryonic development. Human (h)PSC stepwise differentiation provides an excellent platform for capturing dynamic epigenomic events during lineage transition in human development. Here we discuss how recent technological advances, from epigenomic mapping to targeted perturbation, are providing a more comprehensive appreciation of remodeling of the chromatin landscape during human development with implications for aberrant rewiring in disease. We predict that the continuous innovation of hPSC differentiation methods, epigenome mapping, and CRISPR (clustered regularly interspaced short palindromic repeats) perturbation technologies will allow researchers to build toward not only a comprehensive understanding of the epigenomic mechanisms governing development, but also a highly flexible way to model diseases with opportunities for translation.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  3D genome; CRISPR; enhancers; epigenome; human pluripotent stem cells (hPSC)

Mesh:

Substances:

Year:  2021        PMID: 34955367      PMCID: PMC8840982          DOI: 10.1016/j.tcb.2021.12.001

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN: 0962-8924            Impact factor:   20.808


  104 in total

1.  Patch-Seq Links Single-Cell Transcriptomes to Human Islet Dysfunction in Diabetes.

Authors:  Joan Camunas-Soler; Xiao-Qing Dai; Yan Hang; Austin Bautista; James Lyon; Kunimasa Suzuki; Seung K Kim; Stephen R Quake; Patrick E MacDonald
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2.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex.

Authors:  Silvana Konermann; Mark D Brigham; Alexandro E Trevino; Julia Joung; Omar O Abudayyeh; Clea Barcena; Patrick D Hsu; Naomi Habib; Jonathan S Gootenberg; Hiroshi Nishimasu; Osamu Nureki; Feng Zhang
Journal:  Nature       Date:  2014-12-10       Impact factor: 49.962

3.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

4.  Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Authors:  Douglas H Phanstiel; Kevin Van Bortle; Damek Spacek; Gaelen T Hess; Muhammad Saad Shamim; Ido Machol; Michael I Love; Erez Lieberman Aiden; Michael C Bassik; Michael P Snyder
Journal:  Mol Cell       Date:  2017-09-07       Impact factor: 17.970

5.  Ultrastructural Details of Mammalian Chromosome Architecture.

Authors:  Nils Krietenstein; Sameer Abraham; Sergey V Venev; Nezar Abdennur; Johan Gibcus; Tsung-Han S Hsieh; Krishna Mohan Parsi; Liyan Yang; René Maehr; Leonid A Mirny; Job Dekker; Oliver J Rando
Journal:  Mol Cell       Date:  2020-03-25       Impact factor: 17.970

Review 6.  Organizational principles of 3D genome architecture.

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

7.  Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment.

Authors:  Jim R Hughes; Nigel Roberts; Simon McGowan; Deborah Hay; Eleni Giannoulatou; Magnus Lynch; Marco De Gobbi; Stephen Taylor; Richard Gibbons; Douglas R Higgs
Journal:  Nat Genet       Date:  2014-01-12       Impact factor: 38.330

8.  Manipulation of nuclear architecture through CRISPR-mediated chromosomal looping.

Authors:  Stefanie L Morgan; Natasha C Mariano; Abel Bermudez; Nicole L Arruda; Fangting Wu; Yunhai Luo; Gautam Shankar; Lin Jia; Huiling Chen; Ji-Fan Hu; Andrew R Hoffman; Chiao-Chain Huang; Sharon J Pitteri; Kevin C Wang
Journal:  Nat Commun       Date:  2017-07-13       Impact factor: 14.919

9.  YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment.

Authors:  Jonathan A Beagan; Michael T Duong; Katelyn R Titus; Linda Zhou; Zhendong Cao; Jingjing Ma; Caroline V Lachanski; Daniel R Gillis; Jennifer E Phillips-Cremins
Journal:  Genome Res       Date:  2017-05-23       Impact factor: 9.043

10.  Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Authors:  Morgan L Maeder; James F Angstman; Marcy E Richardson; Samantha J Linder; Vincent M Cascio; Shengdar Q Tsai; Quan H Ho; Jeffry D Sander; Deepak Reyon; Bradley E Bernstein; Joseph F Costello; Miles F Wilkinson; J Keith Joung
Journal:  Nat Biotechnol       Date:  2013-10-09       Impact factor: 54.908

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