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Mar Biotechnol (NY)
2012 Aug 01;144:459-67. doi: 10.1007/s10126-011-9426-z.
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Identification and characterization of piRNA-like small RNAs in the gonad of sea urchin (Strongylocentrotus nudus).
Wei Z
,
Liu X
,
Zhang H
.
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Piwi-interacting RNAs (piRNAs) and their partner PIWI proteins play an essential role in fertility, germline stem cell development, as well as the basic control and evolution of animal genomes. However, research was rare with regard to piRNA population in sea urchin, a model animal intensively used for development and genetics studies. Utilizing Solexa sequencing, we present an identification of 13,051 piRNA-like RNAs expressed in male gonad of Strongylocentrotus nudus. Out of 202 tested RNAs, 94 sequences were confirmed to express in female gonad using microarray assay, suggesting that both male and female gonads are piRNA-like RNA-enriched organs. These RNAs with "U" at the 5'' end or "A" at position of 10, in size from 26 to 30 nucleotides, were predominantly 28 nt in length and tend to be clustered in small regions in genome, achieving the longest piRNA-like RNA-enriched region about 5.5 kb in scaffold78427. Alignment results showed 11 RNAs were homologous to the known piRNAs. Furthermore, BLASTn searching against sea urchin repeat element database showed these piRNA-like RNAs matched to 101 types of DNA transposons and retrotransposons, of which SPRP1, Harbinger-N2, piggyBac-N10, SINE2-1, and piggyBac-N11 were the most frequent hit elements, suggesting a transposon silencing function of these piRNA-like RNAs.
Aravin,
A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice.
2008, Pubmed
Aravin,
A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice.
2008,
Pubmed
Aravin,
Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline.
2001,
Pubmed
Aravin,
The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race.
2007,
Pubmed
Armisen,
Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis.
2009,
Pubmed
Betel,
Computational analysis of mouse piRNA sequence and biogenesis.
2007,
Pubmed
Brennecke,
Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila.
2007,
Pubmed
Das,
Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline.
2008,
Pubmed
Deng,
miwi, a murine homolog of piwi, encodes a cytoplasmic protein essential for spermatogenesis.
2002,
Pubmed
Devor,
PiRNA-like RNAs in the marsupial Monodelphis domestica identify transcription clusters and likely marsupial transposon targets.
2008,
Pubmed
Friedländer,
High-resolution profiling and discovery of planarian small RNAs.
2009,
Pubmed
Gao,
In situ synthesis of oligonucleotide microarrays.
2004,
Pubmed
Girard,
A germline-specific class of small RNAs binds mammalian Piwi proteins.
2006,
Pubmed
Grimson,
Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals.
2008,
Pubmed
Gunawardane,
A slicer-mediated mechanism for repeat-associated siRNA 5' end formation in Drosophila.
2007,
Pubmed
Houwing,
Zili is required for germ cell differentiation and meiosis in zebrafish.
2008,
Pubmed
Houwing,
A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish.
2007,
Pubmed
Kapitonov,
Self-synthesizing DNA transposons in eukaryotes.
2006,
Pubmed
,
Echinobase
Kawaoka,
The Bombyx ovary-derived cell line endogenously expresses PIWI/PIWI-interacting RNA complexes.
2009,
Pubmed
Kim,
Biogenesis of small RNAs in animals.
2009,
Pubmed
Kin,
fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences.
2007,
Pubmed
Klattenhoff,
Biogenesis and germline functions of piRNAs.
2008,
Pubmed
Lu,
Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila.
2010,
Pubmed
Malone,
Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary.
2009,
Pubmed
Murchison,
Conservation of small RNA pathways in platypus.
2008,
Pubmed
Ohnishi,
Small RNA class transition from siRNA/piRNA to miRNA during pre-implantation mouse development.
2010,
Pubmed
Palakodeti,
The PIWI proteins SMEDWI-2 and SMEDWI-3 are required for stem cell function and piRNA expression in planarians.
2008,
Pubmed
Rouget,
Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo.
2010,
Pubmed
Sai Lakshmi,
piRNABank: a web resource on classified and clustered Piwi-interacting RNAs.
2008,
Pubmed
Saito,
Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome.
2006,
Pubmed
Thomson,
The biogenesis and function of PIWI proteins and piRNAs: progress and prospect.
2009,
Pubmed
Vagin,
A distinct small RNA pathway silences selfish genetic elements in the germline.
2006,
Pubmed
Watanabe,
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,
Pubmed
Yeung,
Pyrosequencing of small non-coding RNAs in HIV-1 infected cells: evidence for the processing of a viral-cellular double-stranded RNA hybrid.
2009,
Pubmed
