Literature DB >> 28528721

Perspectives on Gene Regulatory Network Evolution.

Marc S Halfon1.   

Abstract

Animal development proceeds through the activity of genes and their cis-regulatory modules (CRMs) working together in sets of gene regulatory networks (GRNs). The emergence of species-specific traits and novel structures results from evolutionary changes in GRNs. Recent work in a wide variety of animal models, and particularly in insects, has started to reveal the modes and mechanisms of GRN evolution. I discuss here various aspects of GRN evolution and argue that developmental system drift (DSD), in which conserved phenotype is nevertheless a result of changed genetic interactions, should regularly be viewed from the perspective of GRN evolution. Advances in methods to discover related CRMs in diverse insect species, a critical requirement for detailed GRN characterization, are also described.
Copyright © 2017 Elsevier Ltd. All rights reserved.

Entities:  

Keywords:  DSD; GRN; cis-regulatory module; developmental system drift; enhancer evolution; evodevo

Mesh：

Year:  2017        PMID： 28528721      PMCID： PMC5608025          DOI： 10.1016/j.tig.2017.04.005

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


  62 in total

Review 1.  Developmental gene regulatory network evolution: insights from comparative studies in echinoderms.

Authors:  Veronica F Hinman; Alys M Cheatle Jarvela
Journal:  Genesis       Date:  2014-03-06       Impact factor: 2.487

Review 2.  The evolution of hierarchical gene regulatory networks.

Authors:  Douglas H Erwin; Eric H Davidson
Journal:  Nat Rev Genet       Date:  2009-01-13       Impact factor: 53.242

3.  Modulation of AP and DV signaling pathways by the homeotic gene Ultrabithorax during haltere development in Drosophila.

Authors:  Prasad Mohit; Kalpana Makhijani; M B Madhavi; V Bharathi; Ashish Lal; Gururaj Sirdesai; V Ram Reddy; Palaparthi Ramesh; Ramakrishnan Kannan; Jyotsna Dhawan; L S Shashidhara
Journal:  Dev Biol       Date:  2006-01-18       Impact factor: 3.582

4.  FAIRE (Formaldehyde-Assisted Isolation of Regulatory Elements) isolates active regulatory elements from human chromatin.

Authors:  Paul G Giresi; Jonghwan Kim; Ryan M McDaniell; Vishwanath R Iyer; Jason D Lieb
Journal:  Genome Res       Date:  2006-12-19       Impact factor: 9.043

Review 5.  Emerging properties of animal gene regulatory networks.

Authors:  Eric H Davidson
Journal:  Nature       Date:  2010-12-16       Impact factor: 49.962

6.  Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila.

Authors:  Nicolas Gompel; Benjamin Prud'homme; Patricia J Wittkopp; Victoria A Kassner; Sean B Carroll
Journal:  Nature       Date:  2005-02-03       Impact factor: 49.962

7.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

Review 8.  The cancer genome.

Authors:  Michael R Stratton; Peter J Campbell; P Andrew Futreal
Journal:  Nature       Date:  2009-04-09       Impact factor: 49.962

9.  Co-option of an Ancestral Hox-Regulated Network Underlies a Recently Evolved Morphological Novelty.

Authors:  William J Glassford; Winslow C Johnson; Natalie R Dall; Sarah Jacquelyn Smith; Yang Liu; Werner Boll; Markus Noll; Mark Rebeiz
Journal:  Dev Cell       Date:  2015-09-03       Impact factor: 12.270

Review 10.  Deep conservation of cis-regulatory elements in metazoans.

Authors:  Ignacio Maeso; Manuel Irimia; Juan J Tena; Fernando Casares; José Luis Gómez-Skarmeta
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2013-11-11       Impact factor: 6.237
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  23 in total

Review 1.  From genome to anatomy: The architecture and evolution of the skeletogenic gene regulatory network of sea urchins and other echinoderms.

Authors:  Tanvi Shashikant; Jian Ming Khor; Charles A Ettensohn
Journal:  Genesis       Date:  2018-10       Impact factor: 2.487

2.  Tbx2a Modulates Switching of RH2 and LWS Opsin Gene Expression.

Authors:  Benjamin A Sandkam; Laura Campello; Conor O'Brien; Sri Pratima Nandamuri; William J Gammerdinger; Matthew A Conte; Anand Swaroop; Karen L Carleton
Journal:  Mol Biol Evol       Date:  2020-07-01       Impact factor: 16.240

3.  Quantitative Comparison of the Anterior-Posterior Patterning System in the Embryos of Five Drosophila Species.

Authors:  Zeba Wunderlich; Charless C Fowlkes; Kelly B Eckenrode; Meghan D J Bragdon; Arash Abiri; Angela H DePace
Journal:  G3 (Bethesda)       Date:  2019-07-09       Impact factor: 3.154

4.  Spatially and Temporally Distributed Complexity-A Refreshed Framework for the Study of GRN Evolution.

Authors:  Alessandro Minelli; Alberto Valero-Gracia
Journal:  Cells       Date:  2022-05-30       Impact factor: 7.666

5.  The Tiger Rattlesnake genome reveals a complex genotype underlying a simple venom phenotype.

Authors:  Mark J Margres; Rhett M Rautsaw; Jason L Strickland; Andrew J Mason; Tristan D Schramer; Erich P Hofmann; Erin Stiers; Schyler A Ellsworth; Gunnar S Nystrom; Michael P Hogan; Daniel A Bartlett; Timothy J Colston; David M Gilbert; Darin R Rokyta; Christopher L Parkinson
Journal:  Proc Natl Acad Sci U S A       Date:  2021-01-26       Impact factor: 12.779

Review 6.  Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory.

Authors:  Eric Bapteste; Philippe Huneman
Journal:  BMC Biol       Date:  2018-05-29       Impact factor: 7.431

7.  Gene expression profiling suggests differences in molecular mechanisms of fin elongation between cichlid species.

Authors:  Ehsan Pashay Ahi; Florian Richter; Laurène Alicia Lecaudey; Kristina M Sefc
Journal:  Sci Rep       Date:  2019-06-21       Impact factor: 4.379

Review 8.  Insights into the molecular evolution of fertilization mechanism in land plants.

Authors:  Vijyesh Sharma; Anthony J Clark; Tomokazu Kawashima
Journal:  Plant Reprod       Date:  2021-06-01       Impact factor: 3.767

9.  On the role of sparseness in the evolution of modularity in gene regulatory networks.

Authors:  Carlos Espinosa-Soto
Journal:  PLoS Comput Biol       Date:  2018-05-18       Impact factor: 4.475

10.  Gene regulatory network architecture in different developmental contexts influences the genetic basis of morphological evolution.

Authors:  Sebastian Kittelmann; Alexandra D Buffry; Franziska A Franke; Isabel Almudi; Marianne Yoth; Gonzalo Sabaris; Juan Pablo Couso; Maria D S Nunes; Nicolás Frankel; José Luis Gómez-Skarmeta; Jose Pueyo-Marques; Saad Arif; Alistair P McGregor
Journal:  PLoS Genet       Date:  2018-05-03       Impact factor: 5.917
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