Literature DB >> 25668787

Chromatin regulation at the frontier of synthetic biology.

Albert J Keung1, J Keith Joung2, Ahmad S Khalil3, James J Collins4.   

Abstract

As synthetic biology approaches are extended to diverse applications throughout medicine, biotechnology and basic biological research, there is an increasing need to engineer yeast, plant and mammalian cells. Eukaryotic genomes are regulated by the diverse biochemical and biophysical states of chromatin, which brings distinct challenges, as well as opportunities, over applications in bacteria. Recent synthetic approaches, including 'epigenome editing', have allowed the direct and functional dissection of many aspects of physiological chromatin regulation. These studies lay the foundation for biomedical and biotechnological engineering applications that could take advantage of the unique combinatorial and spatiotemporal layers of chromatin regulation to create synthetic systems of unprecedented sophistication.

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Year:  2015        PMID: 25668787      PMCID: PMC4846386          DOI: 10.1038/nrg3900

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


  129 in total

Review 1.  Fundamentally different logic of gene regulation in eukaryotes and prokaryotes.

Authors:  K Struhl
Journal:  Cell       Date:  1999-07-09       Impact factor: 41.582

Review 2.  The adjustable nucleosome: an epigenetic signaling module.

Authors:  Bryan M Turner
Journal:  Trends Genet       Date:  2012-05-24       Impact factor: 11.639

3.  Heritable gene repression through the action of a directed DNA methyltransferase at a chromosomal locus.

Authors:  Alexander E Smith; Paul J Hurd; Andrew J Bannister; Tony Kouzarides; Kevin G Ford
Journal:  J Biol Chem       Date:  2008-02-13       Impact factor: 5.157

4.  Programmable bacteria detect and record an environmental signal in the mammalian gut.

Authors:  Jonathan W Kotula; S Jordan Kerns; Lev A Shaket; Layla Siraj; James J Collins; Jeffrey C Way; Pamela A Silver
Journal:  Proc Natl Acad Sci U S A       Date:  2014-03-17       Impact factor: 11.205

5.  Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.

Authors:  Minjia Tan; Hao Luo; Sangkyu Lee; Fulai Jin; Jeong Soo Yang; Emilie Montellier; Thierry Buchou; Zhongyi Cheng; Sophie Rousseaux; Nisha Rajagopal; Zhike Lu; Zhen Ye; Qin Zhu; Joanna Wysocka; Yang Ye; Saadi Khochbin; Bing Ren; Yingming Zhao
Journal:  Cell       Date:  2011-09-16       Impact factor: 41.582

6.  Dynamics and memory of heterochromatin in living cells.

Authors:  Nathaniel A Hathaway; Oliver Bell; Courtney Hodges; Erik L Miller; Dana S Neel; Gerald R Crabtree
Journal:  Cell       Date:  2012-06-14       Impact factor: 41.582

7.  Synthetic chromosome arms function in yeast and generate phenotypic diversity by design.

Authors:  Jessica S Dymond; Sarah M Richardson; Candice E Coombes; Timothy Babatz; Héloïse Muller; Narayana Annaluru; William J Blake; Joy W Schwerzmann; Junbiao Dai; Derek L Lindstrom; Annabel C Boeke; Daniel E Gottschling; Srinivasan Chandrasegaran; Joel S Bader; Jef D Boeke
Journal:  Nature       Date:  2011-09-14       Impact factor: 49.962

Review 8.  Chromatin as an expansive canvas for chemical biology.

Authors:  Beat Fierz; Tom W Muir
Journal:  Nat Chem Biol       Date:  2012-04-17       Impact factor: 15.040

9.  Nucleosome-driven transcription factor binding and gene regulation.

Authors:  Cecilia Ballaré; Giancarlo Castellano; Laura Gaveglia; Sonja Althammer; Juan González-Vallinas; Eduardo Eyras; Francois Le Dily; Roser Zaurin; Daniel Soronellas; Guillermo P Vicent; Miguel Beato
Journal:  Mol Cell       Date:  2012-11-21       Impact factor: 17.970

10.  Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.

Authors:  Baohui Chen; Luke A Gilbert; Beth A Cimini; Joerg Schnitzbauer; Wei Zhang; Gene-Wei Li; Jason Park; Elizabeth H Blackburn; Jonathan S Weissman; Lei S Qi; Bo Huang
Journal:  Cell       Date:  2013-12-19       Impact factor: 41.582

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  34 in total

1.  CRISPR-mediated Activation of Latent HIV-1 Expression.

Authors:  Prajit Limsirichai; Thomas Gaj; David V Schaffer
Journal:  Mol Ther       Date:  2015-11-26       Impact factor: 11.454

Review 2.  CRISPR technologies for precise epigenome editing.

Authors:  Muneaki Nakamura; Yuchen Gao; Antonia A Dominguez; Lei S Qi
Journal:  Nat Cell Biol       Date:  2021-01-08       Impact factor: 28.824

Review 3.  From profiles to function in epigenomics.

Authors:  Stefan H Stricker; Anna Köferle; Stephan Beck
Journal:  Nat Rev Genet       Date:  2016-11-21       Impact factor: 53.242

Review 4.  DNA-based memory devices for recording cellular events.

Authors:  Ravi U Sheth; Harris H Wang
Journal:  Nat Rev Genet       Date:  2018-11       Impact factor: 53.242

Review 5.  Atypical teratoid/rhabdoid tumors-current concepts, advances in biology, and potential future therapies.

Authors:  Michael C Frühwald; Jaclyn A Biegel; Franck Bourdeaut; Charles W M Roberts; Susan N Chi
Journal:  Neuro Oncol       Date:  2016-01-10       Impact factor: 12.300

Review 6.  Genome and Epigenome Editing in Mechanistic Studies of Human Aging and Aging-Related Disease.

Authors:  Cia-Hin Lau; Yousin Suh
Journal:  Gerontology       Date:  2016-12-15       Impact factor: 5.140

Review 7.  Rational engineering of synthetic microbial systems: from single cells to consortia.

Authors:  Philip Bittihn; M Omar Din; Lev S Tsimring; Jeff Hasty
Journal:  Curr Opin Microbiol       Date:  2018-03-22       Impact factor: 7.934

8.  Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities.

Authors:  Dilara Sen; Albert J Keung
Journal:  Methods Mol Biol       Date:  2018

9.  Nucleosomes Are Essential for Proper Regulation of a Multigated Promoter in Saccharomyces cerevisiae.

Authors:  Robert M Yarrington; Jenna M Goodrum; David J Stillman
Journal:  Genetics       Date:  2015-12-01       Impact factor: 4.562

10.  Information Integration and Energy Expenditure in Gene Regulation.

Authors:  Javier Estrada; Felix Wong; Angela DePace; Jeremy Gunawardena
Journal:  Cell       Date:  2016-06-30       Impact factor: 41.582

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