Literature DB >> 22510649

Chromatin as an expansive canvas for chemical biology.

Beat Fierz1, Tom W Muir.   

Abstract

Chromatin is extensively chemically modified and thereby acts as a dynamic signaling platform controlling gene function. Chromatin regulation is integral to cell differentiation, lineage commitment and organism development, whereas chromatin dysregulation can lead to age-related and neurodegenerative disorders as well as cancer. Investigating chromatin biology presents a unique challenge, as the issue spans many disciplines, including cell and systems biology, biochemistry and molecular biophysics. In recent years, the application of chemical biology methods for investigating chromatin processes has gained considerable traction. Indeed, chemical biologists now have at their disposal powerful chemical tools that allow chromatin biology to be scrutinized at the level of the cell all the way down to the single chromatin fiber. Here we present recent examples of how this rapidly expanding palette of chemical tools is being used to paint a detailed picture of chromatin function in organism development and disease.

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Year:  2012        PMID: 22510649      PMCID: PMC4005273          DOI: 10.1038/nchembio.938

Source DB:  PubMed          Journal:  Nat Chem Biol        ISSN: 1552-4450            Impact factor:   15.040


  99 in total

1.  Electron microscopic and biochemical evidence that chromatin structure is a repeating unit.

Authors:  P Oudet; M Gross-Bellard; P Chambon
Journal:  Cell       Date:  1975-04       Impact factor: 41.582

2.  Oncogenesis by sequestration of CBP/p300 in transcriptionally inactive hyperacetylated chromatin domains.

Authors:  Nicolas Reynoird; Brian E Schwartz; Manuela Delvecchio; Karin Sadoul; David Meyers; Chandrani Mukherjee; Cécile Caron; Hiroshi Kimura; Sophie Rousseaux; Philip A Cole; Daniel Panne; Christopher A French; Saadi Khochbin
Journal:  EMBO J       Date:  2010-07-30       Impact factor: 11.598

Review 3.  Chromatin higher-order structure and dynamics.

Authors:  Christopher L Woodcock; Rajarshi P Ghosh
Journal:  Cold Spring Harb Perspect Biol       Date:  2010-04-07       Impact factor: 10.005

4.  Selective anchoring of TFIID to nucleosomes by trimethylation of histone H3 lysine 4.

Authors:  Michiel Vermeulen; Klaas W Mulder; Sergei Denissov; W W M Pim Pijnappel; Frederik M A van Schaik; Radhika A Varier; Marijke P A Baltissen; Henk G Stunnenberg; Matthias Mann; H Th Marc Timmers
Journal:  Cell       Date:  2007-09-20       Impact factor: 41.582

5.  Crystal structure of the nucleosome core particle at 2.8 A resolution.

Authors:  K Luger; A W Mäder; R K Richmond; D F Sargent; T J Richmond
Journal:  Nature       Date:  1997-09-18       Impact factor: 49.962

6.  Mechanism of protein access to specific DNA sequences in chromatin: a dynamic equilibrium model for gene regulation.

Authors:  K J Polach; J Widom
Journal:  J Mol Biol       Date:  1995-11-24       Impact factor: 5.469

7.  Control of inducible gene expression by signal-dependent transcriptional elongation.

Authors:  Diana C Hargreaves; Tiffany Horng; Ruslan Medzhitov
Journal:  Cell       Date:  2009-07-10       Impact factor: 41.582

8.  Methylation of H3-lysine 79 is mediated by a new family of HMTases without a SET domain.

Authors:  Qin Feng; Hengbin Wang; Huck Hui Ng; Hediye Erdjument-Bromage; Paul Tempst; Kevin Struhl; Yi Zhang
Journal:  Curr Biol       Date:  2002-06-25       Impact factor: 10.834

9.  Expressed protein ligation: a general method for protein engineering.

Authors:  T W Muir; D Sondhi; P A Cole
Journal:  Proc Natl Acad Sci U S A       Date:  1998-06-09       Impact factor: 11.205

10.  The site-specific installation of methyl-lysine analogs into recombinant histones.

Authors:  Matthew D Simon; Feixia Chu; Lisa R Racki; Cecile C de la Cruz; Alma L Burlingame; Barbara Panning; Geeta J Narlikar; Kevan M Shokat
Journal:  Cell       Date:  2007-03-09       Impact factor: 41.582

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  56 in total

1.  Site-selective protein-modification chemistry for basic biology and drug development.

Authors:  Nikolaus Krall; Filipa P da Cruz; Omar Boutureira; Gonçalo J L Bernardes
Journal:  Nat Chem       Date:  2015-11-30       Impact factor: 24.427

Review 2.  Small molecule epigenetic inhibitors targeted to histone lysine methyltransferases and demethylases.

Authors:  Zhanxin Wang; Dinshaw J Patel
Journal:  Q Rev Biophys       Date:  2013-09-02       Impact factor: 5.318

3.  Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks.

Authors:  Zhonglei Chen; Adrian T Grzybowski; Alexander J Ruthenburg
Journal:  Chembiochem       Date:  2014-08-22       Impact factor: 3.164

Review 4.  Chromatin regulation at the frontier of synthetic biology.

Authors:  Albert J Keung; J Keith Joung; Ahmad S Khalil; James J Collins
Journal:  Nat Rev Genet       Date:  2015-02-10       Impact factor: 53.242

5.  Micro- and nanofluidic technologies for epigenetic profiling.

Authors:  Toshiki Matsuoka; Byoung Choul Kim; Christopher Moraes; Minsub Han; Shuichi Takayama
Journal:  Biomicrofluidics       Date:  2013-07-24       Impact factor: 2.800

Review 6.  Quantitative proteomic analysis of histone modifications.

Authors:  He Huang; Shu Lin; Benjamin A Garcia; Yingming Zhao
Journal:  Chem Rev       Date:  2015-02-17       Impact factor: 60.622

7.  Electrophoretic stretching and imaging of single native chromatin fibers in nanoslits.

Authors:  Jia-Wei Yeh; Kylan Szeto
Journal:  Biomicrofluidics       Date:  2017-07-25       Impact factor: 2.800

8.  Genomic targeting of epigenetic probes using a chemically tailored Cas9 system.

Authors:  Glen P Liszczak; Zachary Z Brown; Samuel H Kim; Rob C Oslund; Yael David; Tom W Muir
Journal:  Proc Natl Acad Sci U S A       Date:  2017-01-09       Impact factor: 11.205

Review 9.  Choline's role in maintaining liver function: new evidence for epigenetic mechanisms.

Authors:  Mihai G Mehedint; Steven H Zeisel
Journal:  Curr Opin Clin Nutr Metab Care       Date:  2013-05       Impact factor: 4.294

10.  Lysine Acetylation Facilitates Spontaneous DNA Dynamics in the Nucleosome.

Authors:  Jongseong Kim; Jaehyoun Lee; Tae-Hee Lee
Journal:  J Phys Chem B       Date:  2015-11-23       Impact factor: 2.991

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