Small RNA pathways in platypus

Small RNA pathways play evolutionarily conserved roles in gene regulation and in defense from pathogenic and parasitic nucleic acids. The character and expression patterns of small RNAs show conservation throughout animal lineages, but specific animal clades also show variations on these recurring themes, including speciesspecific small RNAs. The monotremes, with only platypus and four species of echidna as extant members, represent the basal branch of the mammalian lineage. Here, we examine the small RNA pathways of monotremes by deep sequencing of six platypus and echidna tissues. We find that highly conserved microRNA species display their signature tissue-specific expression patterns. In addition, we find small RNAs with unusual features that are unique to monotremes. Platypus and echidna testes contain a robust piRNA system which appears to be participating in ongoing transposon defense. [Supplementary Figures 1 and 2 and Supplementary Tables 1 – 7 can be found online at < >]

[1]  Miriam K. Konkel,et al.  Genome analysis of the platypus reveals unique signatures of evolution , 2008, Nature.

[2]  Anton J. Enright,et al.  A Slicer-independent role for Argonaute 2 in hematopoiesis and the microRNA pathway. , 2007, Genes & development.

[3]  C. Sander,et al.  A Mammalian microRNA Expression Atlas Based on Small RNA Library Sequencing , 2007, Cell.

[4]  Jeannie T. Lee,et al.  Sex chromosome silencing in the marsupial male germ line , 2007, Proceedings of the National Academy of Sciences.

[5]  Ravi Sachidanandam,et al.  Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control , 2007, Science.

[6]  Eugene Berezikov,et al.  A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish , 2007, Cell.

[7]  G. Hannon,et al.  MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. , 2007, Developmental cell.

[8]  Manolis Kellis,et al.  Discrete Small RNA-Generating Loci as Master Regulators of Transposon Activity in Drosophila , 2007, Cell.

[9]  T. Yatskievych,et al.  MicroRNA expression during chick embryo development , 2006, Developmental dynamics : an official publication of the American Association of Anatomists.

[10]  Ronald H. A. Plasterk,et al.  Mouse microRNA profiles determined with a new and sensitive cloning method , 2006, Nucleic acids research.

[11]  Beate Wittbrodt,et al.  Differences in vertebrate microRNA expression , 2006, Proceedings of the National Academy of Sciences.

[12]  N. Lau,et al.  Characterization of the piRNA Complex from Rat Testes , 2006, Science.

[13]  C. Sander,et al.  A novel class of small RNAs bind to MILI protein in mouse testes , 2006, Nature.

[14]  Ravi Sachidanandam,et al.  A germline-specific class of small RNAs binds mammalian Piwi proteins , 2006, Nature.

[15]  Toshiaki Watanabe,et al.  Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes. , 2006, Genes & development.

[16]  Haifan Lin,et al.  A novel class of small RNAs in mouse spermatogenic cells. , 2006, Genes & development.

[17]  Ning Li,et al.  Identification of microRNAs from different tissues of chicken embryo and adult chicken , 2006, FEBS letters.

[18]  R. Plasterk,et al.  Micro RNAs in Animal Development , 2006, Cell.

[19]  Eugene Berezikov,et al.  Cloning and expression of new microRNAs from zebrafish , 2006, Nucleic acids research.

[20]  Zuoren Yu,et al.  MicroRNA Mirn122a Reduces Expression of the Posttranscriptionally Regulated Germ Cell Transition Protein 2 (Tnp2) Messenger RNA (mRNA) by mRNA Cleavage1 , 2005, Biology of reproduction.

[21]  George Karypis,et al.  Data clustering in life sciences , 2005, Molecular biotechnology.

[22]  H. Horvitz,et al.  MicroRNA Expression in Zebrafish Embryonic Development , 2005, Science.

[23]  Chris Sander,et al.  The developmental miRNA profiles of zebrafish as determined by small RNA cloning. , 2005, Genes & development.

[24]  Florian Caiment,et al.  RNAi-Mediated Allelic trans-Interaction at the Imprinted Rtl1/Peg11 Locus , 2005, Current Biology.

[25]  Wigard P Kloosterman,et al.  In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes , 2005, Nature Methods.

[26]  J. M. Thomson,et al.  Argonaute2 Is the Catalytic Engine of Mammalian RNAi , 2004, Science.

[27]  T. Tuschl,et al.  Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs. , 2004, Molecular cell.

[28]  Mary Ann Handel,et al.  The XY body: a specialized meiotic chromatin domain. , 2004, Experimental cell research.

[29]  D. Bartel,et al.  MicroRNA-Directed Cleavage of HOXB8 mRNA , 2004, Science.

[30]  Yoichi Matsuda,et al.  Mili, a mammalian member of piwi family gene, is essential for spermatogenesis , 2004, Development.

[31]  D. Bartel.  MicroRNAs Genomics, Biogenesis, Mechanism, and Function , 2004, Cell.

[32]  Y. Matsuda,et al.  Two mouse piwi-related genes: miwi and mili , 2001, Mechanisms of Development.

[33]  L. Brown,et al.  Interval Estimation for a Binomial Proportion , 2001 .

[34]  P. Schuster,et al.  Complete suboptimal folding of RNA and the stability of secondary structures. , 1999, Biopolymers.

[35]  J. Felsenstein.  An alternating least squares approach to inferring phylogenies from pairwise distances. , 1997, Systematic biology.