Click
here to close Hello! We notice that
you are using Internet Explorer, which is not supported by Echinobase
and may cause the site to display incorrectly. We suggest using a
current version of Chrome,
FireFox,
or Safari.
???displayArticle.abstract???
MicroRNAs are regulators in regulation of broad range of phenotypes. The purple urchin, Strongylocentrotus nudus, is one of the most important marine economic animals that widely distributed in the cold seas along the coasts of eastern pacific area. To date, only 45 microRNAs have been identified in a related species, Strongylocentrotus purpurtus, and there is no report on S. nudus microRNAs. Herein, solexa sequencing technology was used to high throughput sequencing analysis of microRNAs in small RNA library isolated from five tissues of S. nudus. Totally, 8,966,865 reads were yielded, 131,015 of which were related to 415 unique microRNAs including 345 deuterostoma conserved and 70 urchin specific microRNAs, as well as 5 microRNA* sequences. The miRNA features including length distribution, end variations and genomic locations were characterized. Annotation of targets revealed a broad range of biological processes and signal transduction pathways that regulated by urchin miRNAs, of which signal transduction mechanisms was the subgroup containing the maximum targets. In addition, the expression of 100 miRNAs in female gonad was confirmed using microRNA microarray analysis. This study provides a first large scale cloning and characterization of S.nudus miRNAs and their potential targets, providing the foundation for further characterization for their role in the regulation of diversity of physiological processes.
Figure 1. Length distribution of raw reads and mapped reads. A: distribution of mature sequences of unique miRNAs identified in this research; B: distribution of sequenced reads related to miRNAs.
Figure 2. Targets and characters of identified S.nudus miRNAs. A: KOG classes of predicted targets; B: conservation profile of identified miRNAs, values on Y axis indicate the number of conserved miRNA between S.nudus and queried specie; C: Top 25 miRNAs with maximum signal detected in female gonad, spu-mir-71, -22 and -31 refer to known S.purpuratus miRNAs which added in to probes.
Figure 3. Clustered profile of S. nudus microRNAs in 3 selected scaffolds. A: miRNA gene clusters in urchin. The location of microRNAs in 3 scaffolds were showed. Rightward arrow indicate the locatzation o f mature sequences at the positive strand, while leftward arrow indicate at minus strand. Double arrow represented miRNA and their miRNA* were located in the same pre-miRNA sequences at 5' and 3' termini respectively. B: Sequences alignment of 21 miRNAs clustered in scaffold78427, no significant sequences similiarity was found in these miRNAs. C: Three microRNAs and their microRNA*s, upper-case letters refer to mature sequences, while underlined leters refer to miRNA* sequences.
Figure 4. Sequences alignment of Snu-mir-375 and its homologous miRNAs
Figure 5. Distribution of predicted targets of miRNAs clustered scaffold78427. ACTM: Amino acid transport and metabolism; CTM: Carbohydrate transport and metabolism; CWMEB: Cell wall/ membrane/ envelope biogenesis; PMPTC: Post-translational modification, protein turnover, chaperones; CSD: Chromatin structure and dynamics; IITM: Inorganic ion transport and metabolism; ITSVT: Intracellular trafficking, secretion and vesicular transport; LTM: Lipid transport and metabolism; NTM: Nucleotide transport and metabolism; RRR: Replication, recombination and repair; RSB: ribosomal structure and biogenesis; RPM: RNA processing and modification; SMBTC: Secondary metabolites biosynthesis, transport and catabolism; STM: Signal transduction mechanisms.
Alves,
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana.
2009, Pubmed
Alves,
Comprehensive prediction of novel microRNA targets in Arabidopsis thaliana.
2009,
Pubmed
Ambros,
MicroRNA pathways in flies and worms: growth, death, fat, stress, and timing.
2003,
Pubmed
Bartel,
MicroRNAs: genomics, biogenesis, mechanism, and function.
2004,
Pubmed
Beilharz,
microRNA-mediated messenger RNA deadenylation contributes to translational repression in mammalian cells.
2009,
Pubmed
Brennecke,
bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila.
2003,
Pubmed
Cai,
Novel microRNAs in silkworm (Bombyx mori).
2010,
Pubmed
Carmell,
RNase III enzymes and the initiation of gene silencing.
2004,
Pubmed
Chang,
MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode.
2004,
Pubmed
Chen,
MicroRNAs modulate hematopoietic lineage differentiation.
2004,
Pubmed
Chen,
Identification and characterization of novel amphioxus microRNAs by Solexa sequencing.
2009,
Pubmed
Christodoulou,
Ancient animal microRNAs and the evolution of tissue identity.
2010,
Pubmed
,
Echinobase
Cullen,
Transcription and processing of human microRNA precursors.
2004,
Pubmed
Dai,
Characterization of microRNAs in cephalochordates reveals a correlation between microRNA repertoire homology and morphological similarity in chordate evolution.
2009,
Pubmed
Davidson,
The sea urchin genome: where will it lead us?
2006,
Pubmed
,
Echinobase
Fahlgren,
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes.
2007,
Pubmed
Fernandez-Valverde,
Dynamic isomiR regulation in Drosophila development.
2010,
Pubmed
Friedman,
Most mammalian mRNAs are conserved targets of microRNAs.
2009,
Pubmed
Fu,
Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.
2008,
Pubmed
Gao,
In situ synthesis of oligonucleotide microarrays.
2004,
Pubmed
Glazov,
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach.
2008,
Pubmed
Guerra-Assunção,
MapMi: automated mapping of microRNA loci.
2010,
Pubmed
Hao,
Identification and characterization of microRNAs and endogenous siRNAs in Schistosoma japonicum.
2010,
Pubmed
Hendrix,
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data.
2010,
Pubmed
Kato,
Dynamic expression of small non-coding RNAs, including novel microRNAs and piRNAs/21U-RNAs, during Caenorhabditis elegans development.
2009,
Pubmed
Kim,
Functional links between clustered microRNAs: suppression of cell-cycle inhibitors by microRNA clusters in gastric cancer.
2009,
Pubmed
Kim,
MicroRNA biogenesis: coordinated cropping and dicing.
2005,
Pubmed
Legeai,
Bioinformatic prediction, deep sequencing of microRNAs and expression analysis during phenotypic plasticity in the pea aphid, Acyrthosiphon pisum.
2010,
Pubmed
Li,
MicroRNAome of porcine pre- and postnatal development.
2010,
Pubmed
Liang,
Identification of miRNA from Porphyra yezoensis by high-throughput sequencing and bioinformatics analysis.
2010,
Pubmed
Lu,
Adenylation of plant miRNAs.
2009,
Pubmed
Meister,
Mechanisms of gene silencing by double-stranded RNA.
2004,
Pubmed
Okamura,
The regulatory activity of microRNA* species has substantial influence on microRNA and 3' UTR evolution.
2008,
Pubmed
Poy,
A pancreatic islet-specific microRNA regulates insulin secretion.
2004,
Pubmed
Schwarz,
Asymmetry in the assembly of the RNAi enzyme complex.
2003,
Pubmed
Sodergren,
The genome of the sea urchin Strongylocentrotus purpuratus.
2006,
Pubmed
,
Echinobase
Starega-Roslan,
Structural basis of microRNA length variety.
2011,
Pubmed
Stark,
Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes.
2007,
Pubmed
Wagner,
Signal integration by JNK and p38 MAPK pathways in cancer development.
2009,
Pubmed
Wei,
Characterization and comparative profiling of the small RNA transcriptomes in two phases of locust.
2009,
Pubmed
Wheeler,
The deep evolution of metazoan microRNAs.
2009,
Pubmed
Wu,
Alternative processing of primary microRNA transcripts by Drosha generates 5' end variation of mature microRNA.
2009,
Pubmed
Xu,
The Drosophila microRNA Mir-14 suppresses cell death and is required for normal fat metabolism.
2003,
Pubmed
Zhao,
Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.).
2010,
Pubmed
