Literature DB >> 24342920

Dynamic regulation of transcriptional states by chromatin and transcription factors.

Ty C Voss1, Gordon L Hager1.   

Abstract

The interaction of regulatory proteins with the complex nucleoprotein structures that are found in mammalian cells involves chromatin reorganization at multiple levels. Mechanisms that support these transitions are complex on many timescales, which range from milliseconds to minutes or hours. In this Review, we discuss emerging concepts regarding the function of regulatory elements in living cells. We also explore the involvement of these dynamic and stochastic processes in the evolution of fluctuating transcriptional activity states that are now commonly reported in eukaryotic systems.

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Year:  2013        PMID： 24342920      PMCID： PMC6322398          DOI： 10.1038/nrg3623

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


  124 in total

1.  The glucocorticoid receptor: rapid exchange with regulatory sites in living cells.

Authors:  J G McNally; W G Müller; D Walker; R Wolford; G L Hager
Journal:  Science       Date:  2000-02-18       Impact factor: 47.728

2.  PRL gene expression in individual living mammotropes displays distinct functional pulses that oscillate in a noncircadian temporal pattern.

Authors:  Spencer L Shorte; Gilles M Leclerc; Rafael Vazquez-Martinez; David C Leaumont; William J Faught; L Stephen Frawley; Fredric R Boockfor
Journal:  Endocrinology       Date:  2002-03       Impact factor: 4.736

3.  Removal of promoter nucleosomes by disassembly rather than sliding in vivo.

Authors:  Hinrich Boeger; Joachim Griesenbeck; J Seth Strattan; Roger D Kornberg
Journal:  Mol Cell       Date:  2004-06-04       Impact factor: 17.970

4.  Delay-induced stochastic oscillations in gene regulation.

Authors:  Dmitri Bratsun; Dmitri Volfson; Lev S Tsimring; Jeff Hasty
Journal:  Proc Natl Acad Sci U S A       Date:  2005-09-30       Impact factor: 11.205

5.  FoxA1 translates epigenetic signatures into enhancer-driven lineage-specific transcription.

Authors:  Mathieu Lupien; Jérôme Eeckhoute; Clifford A Meyer; Qianben Wang; Yong Zhang; Wei Li; Jason S Carroll; X Shirley Liu; Myles Brown
Journal:  Cell       Date:  2008-03-21       Impact factor: 41.582

Review 6.  Transcriptional regulatory circuits: predicting numbers from alphabets.

Authors:  Harold D Kim; Tal Shay; Erin K O'Shea; Aviv Regev
Journal:  Science       Date:  2009-07-24       Impact factor: 47.728

Review 7.  Impulse control: temporal dynamics in gene transcription.

Authors:  Nir Yosef; Aviv Regev
Journal:  Cell       Date:  2011-03-18       Impact factor: 41.582

8.  Overlapping chromatin-remodeling systems collaborate genome wide at dynamic chromatin transitions.

Authors:  Stephanie A Morris; Songjoon Baek; Myong-Hee Sung; Sam John; Malgorzata Wiench; Thomas A Johnson; R Louis Schiltz; Gordon L Hager
Journal:  Nat Struct Mol Biol       Date:  2013-12-08       Impact factor: 15.369

9.  Frequency-modulated nuclear localization bursts coordinate gene regulation.

Authors:  Long Cai; Chiraj K Dalal; Michael B Elowitz
Journal:  Nature       Date:  2008-09-25       Impact factor: 49.962

10.  An expansive human regulatory lexicon encoded in transcription factor footprints.

Authors:  Shane Neph; Jeff Vierstra; Andrew B Stergachis; Alex P Reynolds; Eric Haugen; Benjamin Vernot; Robert E Thurman; Sam John; Richard Sandstrom; Audra K Johnson; Matthew T Maurano; Richard Humbert; Eric Rynes; Hao Wang; Shinny Vong; Kristen Lee; Daniel Bates; Morgan Diegel; Vaughn Roach; Douglas Dunn; Jun Neri; Anthony Schafer; R Scott Hansen; Tanya Kutyavin; Erika Giste; Molly Weaver; Theresa Canfield; Peter Sabo; Miaohua Zhang; Gayathri Balasundaram; Rachel Byron; Michael J MacCoss; Joshua M Akey; M A Bender; Mark Groudine; Rajinder Kaul; John A Stamatoyannopoulos
Journal:  Nature       Date:  2012-09-06       Impact factor: 49.962
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  217 in total

Review 1.  Vision from next generation sequencing: multi-dimensional genome-wide analysis for producing gene regulatory networks underlying retinal development, aging and disease.

Authors:  Hyun-Jin Yang; Rinki Ratnapriya; Tiziana Cogliati; Jung-Woong Kim; Anand Swaroop
Journal:  Prog Retin Eye Res       Date:  2015-02-07       Impact factor: 21.198

2.  Genome-wide footprinting: ready for prime time?

Authors:  Myong-Hee Sung; Songjoon Baek; Gordon L Hager
Journal:  Nat Methods       Date:  2016-03       Impact factor: 28.547

Review 3.  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

Review 4.  Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective: Multiple transcription factors can effect chromatin pioneer functions through dynamic interactions with ATP-dependent chromatin remodeling factors.

Authors:  Erin E Swinstead; Ville Paakinaho; Diego M Presman; Gordon L Hager
Journal:  Bioessays       Date:  2016-09-16       Impact factor: 4.345

5.  The Pioneer Transcription Factor FoxA Maintains an Accessible Nucleosome Configuration at Enhancers for Tissue-Specific Gene Activation.

Authors:  Makiko Iwafuchi-Doi; Greg Donahue; Akshay Kakumanu; Jason A Watts; Shaun Mahony; B Franklin Pugh; Dolim Lee; Klaus H Kaestner; Kenneth S Zaret
Journal:  Mol Cell       Date:  2016-04-07       Impact factor: 17.970

6.  It is time to take timing seriously in clinical genetics.

Authors:  György Kosztolányi
Journal:  Eur J Hum Genet       Date:  2014-12-24       Impact factor: 4.246

Review 7.  Elucidating the mechanisms of transcription regulation during heart development by next-generation sequencing.

Authors:  Keisuke Nimura; Yasufumi Kaneda
Journal:  J Hum Genet       Date:  2015-07-23       Impact factor: 3.172

Review 8.  Epigenetic contributions to the developmental origins of adult lung disease.

Authors:  Lisa A Joss-Moore; Robert H Lane; Kurt H Albertine
Journal:  Biochem Cell Biol       Date:  2014-10-13       Impact factor: 3.626

9.  The transcriptome dynamics of single cells during the cell cycle.

Authors:  Daniel Schwabe; Sara Formichetti; Jan Philipp Junker; Martin Falcke; Nikolaus Rajewsky
Journal:  Mol Syst Biol       Date:  2020-11       Impact factor: 11.429

10.  Single molecule tracking of Ace1p in Saccharomyces cerevisiae defines a characteristic residence time for non-specific interactions of transcription factors with chromatin.

Authors:  David A Ball; Gunjan D Mehta; Ronit Salomon-Kent; Davide Mazza; Tatsuya Morisaki; Florian Mueller; James G McNally; Tatiana S Karpova
Journal:  Nucleic Acids Res       Date:  2016-08-26       Impact factor: 16.971
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