Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles

Wang, J., Czech, B., Crunk, A., Wallace, A., Mitreva, M., Hannon, G. J., Davis, R. E. (2011) Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles. Genome Research, 21 (9). pp. 1462-1477. ISSN 10889051 (ISSN)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/21685128
DOI: 10.1101/gr.121426.111

Abstract

Eukaryotic cells express several classes of small RNAs that regulate gene expression and ensure genome maintenance. Endogenous siRNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs) mainly control gene and transposon expression in the germline, while microRNAs (miRNAs) generally function in post-transcriptional gene silencing in both somatic and germline cells. To provide an evolutionary and developmental perspective on small RNA pathways in nematodes, we identified and characterized known and novel small RNA classes through gametogenesis and embryo development in the parasitic nematode Ascaris suum and compared them with known small RNAs of Caenorhabditis elegans. piRNAs, Piwi-clade Argonautes, and other proteins associated with the piRNA pathway have been lost in Ascaris. miRNAs are synthesized immediately after fertilization in utero, before pronuclear fusion, and before the first cleavage of the zygote. This is the earliest expression of small RNAs ever described at a developmental stage long thought to be transcriptionally quiescent. A comparison of the two classes of Ascaris endo-siRNAs, 22G-RNAs and 26G-RNAs, to those in C. elegans, suggests great diversification and plasticity in the use of small RNA pathways during spermatogenesis in different nematodes. Our data reveal conserved characteristics of nematode small RNAs as well as features unique to Ascaris that illustrate significant flexibility in the use of small RNAs pathways, some of which are likely an adaptation to Ascaris' life cycle and parasitism. © 2011 by Cold Spring Harbor Laboratory Press.

Item Type: Paper
Uncontrolled Keywords: argonaute protein microRNA Piwi protein small interfering RNA article Ascaris suum Caenorhabditis elegans controlled study developmental stage embryo development fertilization gametogenesis genetic conservation genetic transcription human nematode nematode life cycle stage nonhuman nucleotide sequence parasitism priority journal RNA sequence spermatogenesis zygote Animals Ascaris Base Sequence Cluster Analysis Conserved Sequence Embryonic Development Gene Expression Gene Expression Profiling Gene Expression Regulation, Developmental Genetic Variation High-Throughput Nucleotide Sequencing Inverted Repeat Sequences Molecular Sequence Data RNA, Small Interfering Sequence Analysis, RNA Eukaryota Nematoda
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > sRNA
CSHL Authors:
Communities: CSHL labs > Hannon lab
CSHL Cancer Center Shared Resources > Bioinformatics Service
CSHL Cancer Center Shared Resources > DNA Sequencing Service
Depositing User: Matt Covey
Date: 2011
Date Deposited: 09 Jan 2013 16:17
Last Modified: 26 Dec 2014 19:31
PMCID: PMC3166831
Related URLs:
URI: http://repository.cshl.edu/id/eprint/26424

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