Literature DB >> 18711447

The evolution and functional diversification of animal microRNA genes.

Na Liu1, Katsutomo Okamura, David M Tyler, Michael D Phillips, Wei-Jen Chung, Eric C Lai.   

Abstract

microRNAs (miRNAs) are an abundant class of approximately 22 nucleotide (nt) regulatory RNAs that are pervasive in higher eukaryotic genomes. In order to fully understand their prominence in genomes, it is necessary to elucidate the molecular mechanisms that can diversify miRNA activities. In this review, we describe some of the many strategies that allow novel miRNA functions to emerge, with particular emphasis on how miRNA genes evolve in animals. These mechanisms include changes in their sequence, processing, or expression pattern; acquisition of miRNA* functionality or antisense processing; and de novo gene birth. The facility and versatility of miRNAs to evolve and change likely underlies how they have become dominant constituents of higher genomes.

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Year:  2008        PMID: 18711447      PMCID: PMC2712117          DOI: 10.1038/cr.2008.278

Source DB:  PubMed          Journal:  Cell Res        ISSN: 1001-0602            Impact factor:   25.617


  105 in total

Review 1.  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

2.  The small RNA profile during Drosophila melanogaster development.

Authors:  Alexei A Aravin; Mariana Lagos-Quintana; Abdullah Yalcin; Mihaela Zavolan; Debora Marks; Ben Snyder; Terry Gaasterland; Jutta Meyer; Thomas Tuschl
Journal:  Dev Cell       Date:  2003-08       Impact factor: 12.270

3.  MicroRNA genes are transcribed by RNA polymerase II.

Authors:  Yoontae Lee; Minju Kim; Jinju Han; Kyu-Hyun Yeom; Sanghyuk Lee; Sung Hee Baek; V Narry Kim
Journal:  EMBO J       Date:  2004-09-16       Impact factor: 11.598

Review 4.  The evolution of gene regulation by transcription factors and microRNAs.

Authors:  Kevin Chen; Nikolaus Rajewsky
Journal:  Nat Rev Genet       Date:  2007-02       Impact factor: 53.242

5.  A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands.

Authors:  Alexander Stark; Natascha Bushati; Calvin H Jan; Pouya Kheradpour; Emily Hodges; Julius Brennecke; David P Bartel; Stephen M Cohen; Manolis Kellis
Journal:  Genes Dev       Date:  2008-01-01       Impact factor: 11.361

6.  Regulation of Drosophila neurogenesis by RNA:RNA duplexes?

Authors:  E C Lai; J W Posakony
Journal:  Cell       Date:  1998-06-26       Impact factor: 41.582

7.  A mammalian microRNA expression atlas based on small RNA library sequencing.

Authors:  Pablo Landgraf; Mirabela Rusu; Robert Sheridan; Alain Sewer; Nicola Iovino; Alexei Aravin; Sébastien Pfeffer; Amanda Rice; Alice O Kamphorst; Markus Landthaler; Carolina Lin; Nicholas D Socci; Leandro Hermida; Valerio Fulci; Sabina Chiaretti; Robin Foà; Julia Schliwka; Uta Fuchs; Astrid Novosel; Roman-Ulrich Müller; Bernhard Schermer; Ute Bissels; Jason Inman; Quang Phan; Minchen Chien; David B Weir; Ruchi Choksi; Gabriella De Vita; Daniela Frezzetti; Hans-Ingo Trompeter; Veit Hornung; Grace Teng; Gunther Hartmann; Miklos Palkovits; Roberto Di Lauro; Peter Wernet; Giuseppe Macino; Charles E Rogler; James W Nagle; Jingyue Ju; F Nina Papavasiliou; Thomas Benzing; Peter Lichter; Wayne Tam; Michael J Brownstein; Andreas Bosio; Arndt Borkhardt; James J Russo; Chris Sander; Mihaela Zavolan; Thomas Tuschl
Journal:  Cell       Date:  2007-06-29       Impact factor: 41.582

8.  The K box, a conserved 3' UTR sequence motif, negatively regulates accumulation of enhancer of split complex transcripts.

Authors:  E C Lai; C Burks; J W Posakony
Journal:  Development       Date:  1998-10       Impact factor: 6.868

9.  microRNA target predictions across seven Drosophila species and comparison to mammalian targets.

Authors:  Dominic Grün; Yi-Lu Wang; David Langenberger; Kristin C Gunsalus; Nikolaus Rajewsky
Journal:  PLoS Comput Biol       Date:  2005-06-24       Impact factor: 4.475

10.  The limits of subfunctionalization.

Authors:  Thomas MacCarthy; Aviv Bergman
Journal:  BMC Evol Biol       Date:  2007-11-07       Impact factor: 3.260

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  61 in total

Review 1.  Evolution of microRNA diversity and regulation in animals.

Authors:  Eugene Berezikov
Journal:  Nat Rev Genet       Date:  2011-11-18       Impact factor: 53.242

2.  "Hypothesis for the modern RNA world": a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity.

Authors:  Irma Lozada-Chávez; Peter F Stadler; Sonja J Prohaska
Journal:  Orig Life Evol Biosph       Date:  2012-02-10       Impact factor: 1.950

3.  MicroRNA repertoire for functional genome research in tilapia identified by deep sequencing.

Authors:  Biao Yan; Zhen-Hua Wang; Chang-Dong Zhu; Jin-Tao Guo; Jin-Liang Zhao
Journal:  Mol Biol Rep       Date:  2014-04-22       Impact factor: 2.316

4.  The fate of miRNA* strand through evolutionary analysis: implication for degradation as merely carrier strand or potential regulatory molecule?

Authors:  Li Guo; Zuhong Lu
Journal:  PLoS One       Date:  2010-06-30       Impact factor: 3.240

5.  Evidence for Alteration of Gene Regulatory Networks through MicroRNAs of the HIV-infected brain: novel analysis of retrospective cases.

Authors:  Erick T Tatro; Erick R Scott; Timothy B Nguyen; Shahid Salaria; Sugato Banerjee; David J Moore; Eliezer Masliah; Cristian L Achim; Ian P Everall
Journal:  PLoS One       Date:  2010-04-26       Impact factor: 3.240

6.  Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.

Authors:  Fabrice Legeai; Guillaume Rizk; Thomas Walsh; Owain Edwards; Karl Gordon; Dominique Lavenier; Nathalie Leterme; Agnès Méreau; Jacques Nicolas; Denis Tagu; Stéphanie Jaubert-Possamai
Journal:  BMC Genomics       Date:  2010-05-05       Impact factor: 3.969

7.  Expansion of the miRNA pathway in the hemipteran insect Acyrthosiphon pisum.

Authors:  Stéphanie Jaubert-Possamai; Claude Rispe; Sylvie Tanguy; Karl Gordon; Thomas Walsh; Owain Edwards; Denis Tagu
Journal:  Mol Biol Evol       Date:  2010-02-23       Impact factor: 16.240

8.  Direct sequencing and expression analysis of a large number of miRNAs in Aedes aegypti and a multi-species survey of novel mosquito miRNAs.

Authors:  Song Li; Edward A Mead; Shaohui Liang; Zhijian Tu
Journal:  BMC Genomics       Date:  2009-12-04       Impact factor: 3.969

Review 9.  MicroRNA-biogenesis and Pre-mRNA splicing crosstalk.

Authors:  Noam Shomron; Carmit Levy
Journal:  J Biomed Biotechnol       Date:  2009-07-06

10.  Haplotype distribution and evolutionary pattern of miR-17 and miR-124 families based on population analysis.

Authors:  Li Guo; Beili Sun; Fei Sang; Wei Wang; Zuhong Lu
Journal:  PLoS One       Date:  2009-11-23       Impact factor: 3.240

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