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Sequence, Biogenesis, and Function of Diverse sRNA Classes Bound to the Piwi-family Proteins of Tetrahymena thermophila

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 23-24 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.

ORGANISM(S): Tetrahymena thermophila

PROVIDER: GSE17006 | GEO | 2009/11/23

SECONDARY ACCESSION(S): PRJNA117745

REPOSITORIES: GEO

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Sequence, Biogenesis, and Function of Diverse sRNA Classes Bound to the Piwi-family Proteins of Tetrahymena thermophila

Project description: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 23-24 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. 11 libraries were analyzed. 5 are total sRNA (from knockout strains or WT background strains), and 6 are Argonaute-bound sRNA

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