Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila

Couvillion, M. T., Lee, S. R., Hogstad, B., Malone, C. D., Tonkin, L. A., Sachidanandam, R., Hannon, G. J., Collins, K. (2009) Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes and Development, 23 (17). pp. 2016-2032. ISSN 08909369 (ISSN)

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Abstract

PAZ/PIWI domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23- to 24-nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether, Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length, while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs. © 2009 by Cold Spring Harbor Laboratory Press.

Item Type:	Paper
Uncontrolled Keywords:	Argonaute Dicer Endogenous small RNA RNA silencing RNA-dependent RNA polymerase Piwi protein protozoal DNA protozoal RNA article biogenesis gene function nonhuman priority journal protein binding protein expression protein function protein localization protozoal genetics RNA sequence Tetrahymena thermophila Animals Expressed Sequence Tags Gene Expression Regulation, Developmental MicroRNAs Microsatellite Repeats Molecular Sequence Data Protozoan Proteins RNA, Protozoan Sequence Analysis, RNA Twist Transcription Factor Ciliophora Tetrahymena
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 > protein structure, function, modification > protein types > Piwi protein bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification organism description > bacteria bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > piRNA bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types
CSHL Authors:	Hannon, Gregory J. Malone, Colin D. Sachidanandam, Ravi
Communities:	CSHL labs > Hannon lab CSHL labs > Sachidanandam lab School of Biological Sciences > Publications
Depositing User:	Matt Covey
Date:	2009
Date Deposited:	09 Jan 2013 16:42
Last Modified:	22 Sep 2014 18:27
PMCID:	PMC2751968
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/26441

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