Literature DB >> 22513408

Mechanisms of transcriptional precision in animal development.

Mounia Lagha1, Jacques P Bothma, Michael Levine.   

Abstract

We review recently identified mechanisms of transcriptional control that ensure reliable and reproducible patterns of gene expression in natural populations of developing embryos, despite inherent fluctuations in gene regulatory processes, variations in genetic backgrounds and exposure to diverse environmental conditions. These mechanisms are not responsible for switching genes on and off. Instead, they control the fine-tuning of gene expression and ensure regulatory precision. Several such mechanisms are discussed, including redundant binding sites within transcriptional enhancers, shadow enhancers, and 'poised' enhancers and promoters, as well as the role of 'redundant' gene interactions within regulatory networks. We propose that such regulatory mechanisms provide population fitness and 'fine-tune' the spatial and temporal control of gene expression. Published by Elsevier Ltd.

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Year:  2012        PMID: 22513408      PMCID: PMC4257495          DOI: 10.1016/j.tig.2012.03.006

Source DB:  PubMed          Journal:  Trends Genet        ISSN: 0168-9525            Impact factor:   11.639


  63 in total

1.  Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.

Authors:  Daniel A Gilchrist; Gilberto Dos Santos; David C Fargo; Bin Xie; Yuan Gao; Leping Li; Karen Adelman
Journal:  Cell       Date:  2010-11-12       Impact factor: 41.582

Review 2.  Binary fate decisions in differentiating neurons.

Authors:  David Jukam; Claude Desplan
Journal:  Curr Opin Neurobiol       Date:  2010-02       Impact factor: 6.627

3.  Transcriptional enhancers in animal development and evolution.

Authors:  Mike Levine
Journal:  Curr Biol       Date:  2010-09-14       Impact factor: 10.834

4.  A unique chromatin signature uncovers early developmental enhancers in humans.

Authors:  Alvaro Rada-Iglesias; Ruchi Bajpai; Tomek Swigut; Samantha A Brugmann; Ryan A Flynn; Joanna Wysocka
Journal:  Nature       Date:  2010-12-15       Impact factor: 49.962

Review 5.  Functional roles for noise in genetic circuits.

Authors:  Avigdor Eldar; Michael B Elowitz
Journal:  Nature       Date:  2010-09-09       Impact factor: 49.962

6.  Shadow enhancers foster robustness of Drosophila gastrulation.

Authors:  Michael W Perry; Alistair N Boettiger; Jacques P Bothma; Michael Levine
Journal:  Curr Biol       Date:  2010-09-14       Impact factor: 10.834

7.  Nanog variability and pluripotency regulation of embryonic stem cells--insights from a mathematical model analysis.

Authors:  Ingmar Glauche; Maria Herberg; Ingo Roeder
Journal:  PLoS One       Date:  2010-06-21       Impact factor: 3.240

8.  Dynamic chromatin organization during foregut development mediated by the organ selector gene PHA-4/FoxA.

Authors:  Tala H I Fakhouri; Jeff Stevenson; Andrew D Chisholm; Susan E Mango
Journal:  PLoS Genet       Date:  2010-08-12       Impact factor: 5.917

9.  Phenotypic robustness conferred by apparently redundant transcriptional enhancers.

Authors:  Nicolás Frankel; Gregory K Davis; Diego Vargas; Shu Wang; François Payre; David L Stern
Journal:  Nature       Date:  2010-05-30       Impact factor: 49.962

10.  Variability in gene expression underlies incomplete penetrance.

Authors:  Arjun Raj; Scott A Rifkin; Erik Andersen; Alexander van Oudenaarden
Journal:  Nature       Date:  2010-02-18       Impact factor: 49.962

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  73 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

Review 2.  Topology of mammalian developmental enhancers and their regulatory landscapes.

Authors:  Wouter de Laat; Denis Duboule
Journal:  Nature       Date:  2013-10-24       Impact factor: 49.962

Review 3.  Human genetic variation within neural crest enhancers: molecular and phenotypic implications.

Authors:  Alvaro Rada-Iglesias; Sara L Prescott; Joanna Wysocka
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2013-05-06       Impact factor: 6.237

Review 4.  Enhancer redundancy in development and disease.

Authors:  Evgeny Z Kvon; Zeba Wunderlich; Rachel Waymack; Mario Gad
Journal:  Nat Rev Genet       Date:  2021-01-12       Impact factor: 53.242

5.  Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila.

Authors:  Jemma L Webber; Jie Zhang; Alex Massey; Nicelio Sanchez-Luege; Ilaria Rebay
Journal:  Development       Date:  2018-07-02       Impact factor: 6.868

Review 6.  Genomic perspectives of transcriptional regulation in forebrain development.

Authors:  Alex S Nord; Kartik Pattabiraman; Axel Visel; John L R Rubenstein
Journal:  Neuron       Date:  2015-01-07       Impact factor: 17.173

Review 7.  Enhancer biology and enhanceropathies.

Authors:  Edwin Smith; Ali Shilatifard
Journal:  Nat Struct Mol Biol       Date:  2014-03       Impact factor: 15.369

8.  Core promoter functions in the regulation of gene expression of Drosophila dorsal target genes.

Authors:  Yonathan Zehavi; Olga Kuznetsov; Avital Ovadia-Shochat; Tamar Juven-Gershon
Journal:  J Biol Chem       Date:  2014-03-14       Impact factor: 5.157

9.  Transcriptional regulation of enhancers active in protodomains of the developing cerebral cortex.

Authors:  Kartik Pattabiraman; Olga Golonzhka; Susan Lindtner; Alex S Nord; Leila Taher; Renee Hoch; Shanni N Silberberg; Dongji Zhang; Bin Chen; HongKui Zeng; Len A Pennacchio; Luis Puelles; Axel Visel; John L R Rubenstein
Journal:  Neuron       Date:  2014-05-08       Impact factor: 17.173

Review 10.  Regeneration Genetics.

Authors:  Chen-Hui Chen; Kenneth D Poss
Journal:  Annu Rev Genet       Date:  2017-08-30       Impact factor: 16.830

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