Literature DB >> 25957680

Making sense of transcription networks.

Trevor R Sorrells1, Alexander D Johnson2.   

Abstract

When transcription regulatory networks are compared among distantly related eukaryotes, a number of striking similarities are observed: a larger-than-expected number of genes, extensive overlapping connections, and an apparently high degree of functional redundancy. It is often assumed that the complexity of these networks represents optimized solutions, precisely sculpted by natural selection; their common features are often asserted to be adaptive. Here, we discuss support for an alternative hypothesis: the common structural features of transcription networks arise from evolutionary trajectories of "least resistance"--that is, the relative ease with which certain types of network structures are formed during their evolution.
Copyright © 2015 Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 25957680      PMCID: PMC4531093          DOI: 10.1016/j.cell.2015.04.014

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  89 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

Review 2.  Preservation of duplicate genes by complementary, degenerative mutations.

Authors:  A Force; M Lynch; F B Pickett; A Amores; Y L Yan; J Postlethwait
Journal:  Genetics       Date:  1999-04       Impact factor: 4.562

3.  Network motifs: simple building blocks of complex networks.

Authors:  R Milo; S Shen-Orr; S Itzkovitz; N Kashtan; D Chklovskii; U Alon
Journal:  Science       Date:  2002-10-25       Impact factor: 47.728

4.  Cell biology. Irremediable complexity?

Authors:  Michael W Gray; Julius Lukes; John M Archibald; Patrick J Keeling; W Ford Doolittle
Journal:  Science       Date:  2010-11-12       Impact factor: 47.728

5.  Core transcriptional regulatory circuitry in human embryonic stem cells.

Authors:  Laurie A Boyer; Tong Ihn Lee; Megan F Cole; Sarah E Johnstone; Stuart S Levine; Jacob P Zucker; Matthew G Guenther; Roshan M Kumar; Heather L Murray; Richard G Jenner; David K Gifford; Douglas A Melton; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2005-09-23       Impact factor: 41.582

6.  The frailty of adaptive hypotheses for the origins of organismal complexity.

Authors:  Michael Lynch
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-09       Impact factor: 11.205

7.  optix drives the repeated convergent evolution of butterfly wing pattern mimicry.

Authors:  Robert D Reed; Riccardo Papa; Arnaud Martin; Heather M Hines; Brian A Counterman; Carolina Pardo-Diaz; Chris D Jiggins; Nicola L Chamberlain; Marcus R Kronforst; Rui Chen; Georg Halder; H Frederik Nijhout; W Owen McMillan
Journal:  Science       Date:  2011-07-21       Impact factor: 47.728

Review 8.  Autoregulation of eukaryotic transcription factors.

Authors:  E Bateman
Journal:  Prog Nucleic Acid Res Mol Biol       Date:  1998

9.  Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network.

Authors:  John S Reece-Hoyes; Carles Pons; Alos Diallo; Akihiro Mori; Shaleen Shrestha; Sreenath Kadreppa; Justin Nelson; Stephanie Diprima; Amelie Dricot; Bryan R Lajoie; Philippe Souza Moraes Ribeiro; Matthew T Weirauch; David E Hill; Timothy R Hughes; Chad L Myers; Albertha J M Walhout
Journal:  Mol Cell       Date:  2013-06-20       Impact factor: 17.970

10.  Induction of ectopic eyes by targeted expression of the eyeless gene in Drosophila.

Authors:  G Halder; P Callaerts; W J Gehring
Journal:  Science       Date:  1995-03-24       Impact factor: 47.728

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  50 in total

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Authors:  Adam R Hamilton; Ian M Traniello; Allyson M Ray; Arminius S Caldwell; Samuel A Wickline; Gene E Robinson
Journal:  J Exp Biol       Date:  2019-07-16       Impact factor: 3.312

2.  Transcription factor network efficiency in the regulation of Candida albicans biofilms: it is a small world.

Authors:  Virginia E Glazier; Damian J Krysan
Journal:  Curr Genet       Date:  2018-01-09       Impact factor: 3.886

Review 3.  Personalized Therapy of Hypertension: the Past and the Future.

Authors:  Paolo Manunta; Mara Ferrandi; Daniele Cusi; Patrizia Ferrari; Jan Staessen; Giuseppe Bianchi
Journal:  Curr Hypertens Rep       Date:  2016-03       Impact factor: 5.369

Review 4.  Nuclear Receptor Function through Genomics: Lessons from the Glucocorticoid Receptor.

Authors:  Daniel M Cohen; David J Steger
Journal:  Trends Endocrinol Metab       Date:  2017-05-08       Impact factor: 12.015

5.  Assessing regulatory information in developmental gene regulatory networks.

Authors:  Isabelle S Peter; Eric H Davidson
Journal:  Proc Natl Acad Sci U S A       Date:  2017-06-06       Impact factor: 11.205

6.  Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors.

Authors:  Erin E Sparks; Colleen Drapek; Allison Gaudinier; Song Li; Mitra Ansariola; Ning Shen; Jessica H Hennacy; Jingyuan Zhang; Gina Turco; Jalean J Petricka; Jessica Foret; Alexander J Hartemink; Raluca Gordân; Molly Megraw; Siobhan M Brady; Philip N Benfey
Journal:  Dev Cell       Date:  2016-10-27       Impact factor: 12.270

7.  IndeCut evaluates performance of network motif discovery algorithms.

Authors:  Mitra Ansariola; Molly Megraw; David Koslicki
Journal:  Bioinformatics       Date:  2018-05-01       Impact factor: 6.937

8.  Protein-coding changes preceded cis-regulatory gains in a newly evolved transcription circuit.

Authors:  Candace S Britton; Trevor R Sorrells; Alexander D Johnson
Journal:  Science       Date:  2020-01-03       Impact factor: 47.728

9.  Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9.

Authors:  S Ali Shariati; Antonia Dominguez; Shicong Xie; Marius Wernig; Lei S Qi; Jan M Skotheim
Journal:  Mol Cell       Date:  2019-05-02       Impact factor: 17.970

Review 10.  Transcriptional control of sexual development in Cryptococcus neoformans.

Authors:  Matthew E Mead; Christina M Hull
Journal:  J Microbiol       Date:  2016-04-20       Impact factor: 3.422

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