Literature DB >> 18087752

Evolution of the vertebrate Y RNA cluster.

Axel Mosig1, Meng Guofeng, Bärbel M R Stadler, Peter F Stadler.   

Abstract

Relatively little is known about the evolutionary histories of most classes of non-protein coding RNAs. Here we consider Y RNAs, a relatively rarely studied group of related pol-III transcripts. A single cluster of functional genes is preserved throughout tetrapod evolution, which however exhibits clade-specific tandem duplications, gene-losses, and rearrangements.

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Year:  2007        PMID： 18087752     DOI： 10.1007/s12064-007-0003-y

Source DB:  PubMed          Journal:  Theory Biosci        ISSN： 1431-7613            Impact factor:   1.315


  30 in total

1.  DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment.

Authors:  B Morgenstern
Journal:  Bioinformatics       Date:  1999-03       Impact factor: 6.937

2.  Application of phylogenetic networks in evolutionary studies.

Authors:  Daniel H Huson; David Bryant
Journal:  Mol Biol Evol       Date:  2005-10-12       Impact factor: 16.240

3.  The phylogenetic distribution of metazoan microRNAs: insights into evolutionary complexity and constraint.

Authors:  Lorenzo F Sempere; Charles N Cole; Mark A McPeek; Kevin J Peterson
Journal:  J Exp Zool B Mol Dev Evol       Date:  2006-11-15       Impact factor: 2.656

4.  Functional requirement of noncoding Y RNAs for human chromosomal DNA replication.

Authors:  Christo P Christov; Timothy J Gardiner; Dávid Szüts; Torsten Krude
Journal:  Mol Cell Biol       Date:  2006-09       Impact factor: 4.272

5.  Evolutionary patterns of non-coding RNAs.

Authors:  Athanasius F Bompfünewerer; Christoph Flamm; Claudia Fried; Guido Fritzsch; Ivo L Hofacker; Jörg Lehmann; Kristin Missal; Axel Mosig; Bettina Müller; Sonja J Prohaska; Bärbel M R Stadler; Peter F Stadler; Andrea Tanzer; Stefan Washietl; Christina Witwer
Journal:  Theory Biosci       Date:  2005-04       Impact factor: 1.919

6.  Y3 is the most conserved small RNA component of Ro ribonucleoprotein complexes in vertebrate species.

Authors:  A D Farris; C A O'Brien; J B Harley
Journal:  Gene       Date:  1995-03-10       Impact factor: 3.688

7.  Conserved features of Y RNAs revealed by automated phylogenetic secondary structure analysis.

Authors:  A D Farris; G Koelsch; G J Pruijn; W J van Venrooij; J B Harley
Journal:  Nucleic Acids Res       Date:  1999-02-15       Impact factor: 16.971

8.  Ro ribonucleoproteins contribute to the resistance of Deinococcus radiodurans to ultraviolet irradiation.

Authors:  X Chen; A M Quinn; S L Wolin
Journal:  Genes Dev       Date:  2000-04-01       Impact factor: 11.361

9.  Gene encoding human Ro-associated autoantigen Y5 RNA.

Authors:  R Maraia; A L Sakulich; E Brinkmann; E D Green
Journal:  Nucleic Acids Res       Date:  1996-09-15       Impact factor: 16.971

10.  Ro RNP associated Y RNAs are highly conserved among mammals.

Authors:  G J Pruijn; P A Wingens; S L Peters; J P Thijssen; W J van Venrooij
Journal:  Biochim Biophys Acta       Date:  1993-12-14
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  31 in total

1.  The zipcode-binding protein ZBP1 influences the subcellular location of the Ro 60-kDa autoantigen and the noncoding Y3 RNA.

Authors:  Soyeong Sim; Jie Yao; David E Weinberg; Sherry Niessen; John R Yates; Sandra L Wolin
Journal:  RNA       Date:  2011-11-23       Impact factor: 4.942

2.  Nematode sbRNAs: homologs of vertebrate Y RNAs.

Authors:  Ilenia Boria; Andreas R Gruber; Andrea Tanzer; Stephan H Bernhart; Ronny Lorenz; Michael M Mueller; Ivo L Hofacker; Peter F Stadler
Journal:  J Mol Evol       Date:  2010-03-27       Impact factor: 2.395

3.  The subcellular distribution of an RNA quality control protein, the Ro autoantigen, is regulated by noncoding Y RNA binding.

Authors:  Soyeong Sim; David E Weinberg; Gabriele Fuchs; Keum Choi; Jina Chung; Sandra L Wolin
Journal:  Mol Biol Cell       Date:  2008-12-30       Impact factor: 4.138

4.  The tedious task of finding homologous noncoding RNA genes.

Authors:  Peter Menzel; Jan Gorodkin; Peter F Stadler
Journal:  RNA       Date:  2009-10-27       Impact factor: 4.942

Review 5.  Emerging roles for the Ro 60-kDa autoantigen in noncoding RNA metabolism.

Authors:  Soyeong Sim; Sandra L Wolin
Journal:  Wiley Interdiscip Rev RNA       Date:  2011-04-21       Impact factor: 9.957

6.  Dynamic interaction of Y RNAs with chromatin and initiation proteins during human DNA replication.

Authors:  Alice Tianbu Zhang; Alexander R Langley; Christo P Christov; Eyemen Kheir; Thomas Shafee; Timothy J Gardiner; Torsten Krude
Journal:  J Cell Sci       Date:  2011-05-24       Impact factor: 5.285

7.  The midblastula transition defines the onset of Y RNA-dependent DNA replication in Xenopus laevis.

Authors:  Clara Collart; Christo P Christov; James C Smith; Torsten Krude
Journal:  Mol Cell Biol       Date:  2011-07-26       Impact factor: 4.272

8.  Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

Authors:  Rami A Dalloul; Julie A Long; Aleksey V Zimin; Luqman Aslam; Kathryn Beal; Le Ann Blomberg; Pascal Bouffard; David W Burt; Oswald Crasta; Richard P M A Crooijmans; Kristal Cooper; Roger A Coulombe; Supriyo De; Mary E Delany; Jerry B Dodgson; Jennifer J Dong; Clive Evans; Karin M Frederickson; Paul Flicek; Liliana Florea; Otto Folkerts; Martien A M Groenen; Tim T Harkins; Javier Herrero; Steve Hoffmann; Hendrik-Jan Megens; Andrew Jiang; Pieter de Jong; Pete Kaiser; Heebal Kim; Kyu-Won Kim; Sungwon Kim; David Langenberger; Mi-Kyung Lee; Taeheon Lee; Shrinivasrao Mane; Guillaume Marcais; Manja Marz; Audrey P McElroy; Thero Modise; Mikhail Nefedov; Cédric Notredame; Ian R Paton; William S Payne; Geo Pertea; Dennis Prickett; Daniela Puiu; Dan Qioa; Emanuele Raineri; Magali Ruffier; Steven L Salzberg; Michael C Schatz; Chantel Scheuring; Carl J Schmidt; Steven Schroeder; Stephen M J Searle; Edward J Smith; Jacqueline Smith; Tad S Sonstegard; Peter F Stadler; Hakim Tafer; Zhijian Jake Tu; Curtis P Van Tassell; Albert J Vilella; Kelly P Williams; James A Yorke; Liqing Zhang; Hong-Bin Zhang; Xiaojun Zhang; Yang Zhang; Kent M Reed
Journal:  PLoS Biol       Date:  2010-09-07       Impact factor: 8.029

9.  Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.

Authors:  Claudia S Copeland; Manja Marz; Dominic Rose; Jana Hertel; Paul J Brindley; Clara Bermudez Santana; Stephanie Kehr; Camille Stephan-Otto Attolini; Peter F Stadler
Journal:  BMC Genomics       Date:  2009-10-08       Impact factor: 3.969

10.  Non-coding RNA annotation of the genome of Trichoplax adhaerens.

Authors:  Jana Hertel; Danielle de Jong; Manja Marz; Dominic Rose; Hakim Tafer; Andrea Tanzer; Bernd Schierwater; Peter F Stadler
Journal:  Nucleic Acids Res       Date:  2009-01-16       Impact factor: 16.971
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