Literature DB >> 26395902

Evolutionary impact of transposable elements on genomic diversity and lineage-specific innovation in vertebrates.

Ian A Warren1, Magali Naville1, Domitille Chalopin1,2, Perrine Levin1, Chloé Suzanne Berger1, Delphine Galiana1, Jean-Nicolas Volff3.   

Abstract

Since their discovery, a growing body of evidence has emerged demonstrating that transposable elements are important drivers of species diversity. These mobile elements exhibit a great variety in structure, size and mechanisms of transposition, making them important putative actors in organism evolution. The vertebrates represent a highly diverse and successful lineage that has adapted to a wide range of different environments. These animals also possess a rich repertoire of transposable elements, with highly diverse content between lineages and even between species. Here, we review how transposable elements are driving genomic diversity and lineage-specific innovation within vertebrates. We discuss the large differences in TE content between different vertebrate groups and then go on to look at how they affect organisms at a variety of levels: from the structure of chromosomes to their involvement in the regulation of gene expression, as well as in the formation and evolution of non-coding RNAs and protein-coding genes. In the process of doing this, we highlight how transposable elements have been involved in the evolution of some of the key innovations observed within the vertebrate lineage, driving the group's diversity and success.

Keywords:  Diversity; Lineage-specific evolution; New genes; Transposable elements; Vertebrates

Mesh:

Substances:

Year:  2015        PMID: 26395902     DOI: 10.1007/s10577-015-9493-5

Source DB:  PubMed          Journal:  Chromosome Res        ISSN: 0967-3849            Impact factor:   5.239


  230 in total

1.  From "junk" to gene: curriculum vitae of a primate receptor isoform gene.

Authors:  Silke S Singer; Daniela N Männel; Thomas Hehlgans; Jürgen Brosius; Jürgen Schmitz
Journal:  J Mol Biol       Date:  2004-08-20       Impact factor: 5.469

2.  Segmental copy number variation shapes tissue transcriptomes.

Authors:  Charlotte N Henrichsen; Nicolas Vinckenbosch; Sebastian Zöllner; Evelyne Chaignat; Sylvain Pradervand; Frédéric Schütz; Manuel Ruedi; Henrik Kaessmann; Alexandre Reymond
Journal:  Nat Genet       Date:  2009-03-08       Impact factor: 38.330

3.  Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements.

Authors:  Deena Emera; Claudio Casola; Vincent J Lynch; Derek E Wildman; Dalen Agnew; Günter P Wagner
Journal:  Mol Biol Evol       Date:  2011-08-02       Impact factor: 16.240

Review 4.  V(D)J recombination: mechanisms of initiation.

Authors:  David G Schatz; Patrick C Swanson
Journal:  Annu Rev Genet       Date:  2011-08-19       Impact factor: 16.830

5.  Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells.

Authors:  Jichang Wang; Gangcai Xie; Manvendra Singh; Avazeh T Ghanbarian; Tamás Raskó; Attila Szvetnik; Huiqiang Cai; Daniel Besser; Alessandro Prigione; Nina V Fuchs; Gerald G Schumann; Wei Chen; Matthew C Lorincz; Zoltán Ivics; Laurence D Hurst; Zsuzsanna Izsvák
Journal:  Nature       Date:  2014-10-15       Impact factor: 49.962

6.  Melanoma loss-of-function mutants in Xiphophorus caused by Xmrk-oncogene deletion and gene disruption by a transposable element.

Authors:  M Schartl; U Hornung; H Gutbrod; J N Volff; J Wittbrodt
Journal:  Genetics       Date:  1999-11       Impact factor: 4.562

7.  Human polymorphism at microRNAs and microRNA target sites.

Authors:  Matthew A Saunders; Han Liang; Wen-Hsiung Li
Journal:  Proc Natl Acad Sci U S A       Date:  2007-02-20       Impact factor: 11.205

8.  Arc/Arg3.1 is essential for the consolidation of synaptic plasticity and memories.

Authors:  Niels Plath; Ora Ohana; Björn Dammermann; Mick L Errington; Dietmar Schmitz; Christina Gross; Xiaosong Mao; Arne Engelsberg; Claudia Mahlke; Hans Welzl; Ursula Kobalz; Anastasia Stawrakakis; Esperanza Fernandez; Robert Waltereit; Anika Bick-Sander; Eric Therstappen; Sam F Cooke; Veronique Blanquet; Wolfgang Wurst; Benedikt Salmen; Michael R Bösl; Hans-Peter Lipp; Seth G N Grant; Tim V P Bliss; David P Wolfer; Dietmar Kuhl
Journal:  Neuron       Date:  2006-11-09       Impact factor: 17.173

9.  Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy.

Authors:  Vincent J Lynch; Mauris C Nnamani; Aurélie Kapusta; Kathryn Brayer; Silvia L Plaza; Erik C Mazur; Deena Emera; Shehzad Z Sheikh; Frank Grützner; Stefan Bauersachs; Alexander Graf; Steven L Young; Jason D Lieb; Francesco J DeMayo; Cédric Feschotte; Günter P Wagner
Journal:  Cell Rep       Date:  2015-01-29       Impact factor: 9.423

Review 10.  Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?

Authors:  Flávio S J de Souza; Lucía F Franchini; Marcelo Rubinstein
Journal:  Mol Biol Evol       Date:  2013-03-13       Impact factor: 16.240

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  44 in total

1.  Repetitive DNA in eukaryotic genomes.

Authors:  Maria Assunta Biscotti; Ettore Olmo; J S Pat Heslop-Harrison
Journal:  Chromosome Res       Date:  2015-09       Impact factor: 5.239

2.  A survey of endogenous retrovirus (ERV) sequences in the vicinity of multiple sclerosis (MS)-associated single nucleotide polymorphisms (SNPs).

Authors:  Christine Brütting; Alexander Emmer; Malte Kornhuber; Martin S Staege
Journal:  Mol Biol Rep       Date:  2016-05-12       Impact factor: 2.316

3.  Adaptive Evolution Leads to Cross-Species Incompatibility in the piRNA Transposon Silencing Machinery.

Authors:  Swapnil S Parhad; Shikui Tu; Zhiping Weng; William E Theurkauf
Journal:  Dev Cell       Date:  2017-09-14       Impact factor: 12.270

4.  Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals.

Authors:  Christopher B Mulholland; Atsuya Nishiyama; Joel Ryan; Ryohei Nakamura; Merve Yiğit; Ivo M Glück; Carina Trummer; Weihua Qin; Michael D Bartoschek; Franziska R Traube; Edris Parsa; Enes Ugur; Miha Modic; Aishwarya Acharya; Paul Stolz; Christoph Ziegenhain; Michael Wierer; Wolfgang Enard; Thomas Carell; Don C Lamb; Hiroyuki Takeda; Makoto Nakanishi; Sebastian Bultmann; Heinrich Leonhardt
Journal:  Nat Commun       Date:  2020-11-24       Impact factor: 14.919

5.  Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo.

Authors:  L M Legault; K Doiron; A Lemieux; M Caron; D Chan; F L Lopes; G Bourque; D Sinnett; S McGraw
Journal:  Epigenetics       Date:  2020-02-14       Impact factor: 4.528

6.  An intriguing relationship between teleost Rex3 retroelement and environmental temperature.

Authors:  Federica Carducci; Maria Assunta Biscotti; Mariko Forconi; Marco Barucca; Adriana Canapa
Journal:  Biol Lett       Date:  2019-09-04       Impact factor: 3.703

7.  Production of Small Noncoding RNAs from the flamenco Locus Is Regulated by the gypsy Retrotransposon of Drosophila melanogaster.

Authors:  Vincenzo Guida; Filippo M Cernilogar; Angela Filograna; Roberto De Gregorio; Hirotsugu Ishizu; Mikiko C Siomi; Gunnar Schotta; Gian Carlo Bellenchi; Davide Andrenacci
Journal:  Genetics       Date:  2016-08-24       Impact factor: 4.562

8.  Meiotic Cells Counteract Programmed Retrotransposon Activation via RNA-Binding Translational Repressor Assemblies.

Authors:  Raphaelle Laureau; Annie Dyatel; Gizem Dursuk; Samantha Brown; Hannah Adeoye; Jia-Xing Yue; Matteo De Chiara; Anthony Harris; Elçin Ünal; Gianni Liti; Ian R Adams; Luke E Berchowitz
Journal:  Dev Cell       Date:  2020-12-04       Impact factor: 12.270

9.  Co-option of the lineage-specific LAVA retrotransposon in the gibbon genome.

Authors:  Mariam Okhovat; Kimberly A Nevonen; Brett A Davis; Pryce Michener; Samantha Ward; Mark Milhaven; Lana Harshman; Ajuni Sohota; Jason D Fernandes; Sofie R Salama; Rachel J O'Neill; Nadav Ahituv; Krishna R Veeramah; Lucia Carbone
Journal:  Proc Natl Acad Sci U S A       Date:  2020-07-20       Impact factor: 11.205

Review 10.  KRAB zinc finger proteins.

Authors:  Gabriela Ecco; Michael Imbeault; Didier Trono
Journal:  Development       Date:  2017-08-01       Impact factor: 6.868

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