Two classes of endogenous small RNAs in Tetrahymena thermophila.

Endogenous small RNAs function in RNA interference (RNAi) pathways to guide RNA cleavage, translational repression, or methylation of DNA or chromatin. In Tetrahymena thermophila, developmentally regulated DNA elimination is governed by an RNAi mechanism involving approximately 27-30-nucleotide (nt) RNAs. Here we characterize the sequence features of the approximately 27-30-nt RNAs and a approximately 23-24-nt RNA class representing a second RNAi pathway. The approximately 23-24-nt RNAs accumulate strain-specifically manner and map to the genome in clusters that are antisense to predicted genes. These findings reveal the existence of distinct endogenous RNAi pathways in the unicellular T. thermophila, a complexity previously demonstrated only in multicellular organisms.

[1]  M. Yao,et al.  Communication Between Parental and Developing Genomes During Tetrahymena Nuclear Differentiation Is Likely Mediated by Homologous RNAs , 2005, Genetics.

[2]  B. Reinhart,et al.  Small RNAs Correspond to Centromere Heterochromatic Repeats , 2002, Science.

[3]  M. Gorovsky,et al.  A Dicer-like protein in Tetrahymena has distinct functions in genome rearrangement, chromosome segregation, and meiotic prophase. , 2005, Genes & development.

[4]  A. Djikeng,et al.  RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs. , 2001, RNA.

[5]  M. Gorovsky,et al.  Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement. , 2004, Genes & development.

[6]  D. Marks,et al.  The small RNA profile during Drosophila melanogaster development. , 2003, Developmental cell.

[7]  T. Tuschl,et al.  Cloning of Small RNA Molecules , 2003, Current protocols in molecular biology.

[8]  Sean D. Taverna,et al.  Methylation of Histone H3 at Lysine 9 Targets Programmed DNA Elimination in Tetrahymena , 2002, Cell.

[9]  E. Ullu,et al.  Small Sense and Antisense RNAs Derived from a Telomeric Retroposon Family in Giardia intestinalis , 2005, Eukaryotic Cell.

[10]  L. Lim,et al.  An Abundant Class of Tiny RNAs with Probable Regulatory Roles in Caenorhabditis elegans , 2001, Science.

[11]  B. Bartel MicroRNAs directing siRNA biogenesis , 2005, Nature Structural &Molecular Biology.

[12]  V. Ambros,et al.  MicroRNAs and Other Tiny Endogenous RNAs in C. elegans , 2003, Current Biology.

[13]  M. Yao,et al.  Programmed DNA Deletion As an RNA-Guided System of Genome Defense , 2003, Science.

[14]  Anastasia Khvorova,et al.  Functional siRNAs and miRNAs Exhibit Strand Bias , 2003, Cell.

[15]  Ronald H. A. Plasterk,et al.  Transposon silencing in the Caenorhabditis elegans germ line by natural RNAi , 2003, Nature.

[16]  C. Malone,et al.  Germ Line Transcripts Are Processed by a Dicer-Like Protein That Is Essential for Developmentally Programmed Genome Rearrangements of Tetrahymena thermophila , 2005, Molecular and Cellular Biology.

[17]  K. Collins,et al.  Starvation-induced Cleavage of the tRNA Anticodon Loop in Tetrahymena thermophila* , 2005, Journal of Biological Chemistry.

[18]  Richard W. Carthew,et al.  Silence from within: Endogenous siRNAs and miRNAs , 2005, Cell.

[19]  James A. Birchler,et al.  RNAi-mediated pathways in the nucleus , 2005, Nature Reviews Genetics.

[20]  C. Allis,et al.  Methylation of histone H3 at lysine 4 is highly conserved and correlates with transcriptionally active nuclei in Tetrahymena. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[21]  Xuemei Chen,et al.  Methylation Protects miRNAs and siRNAs from a 3′-End Uridylation Activity in Arabidopsis , 2005, Current Biology.

[22]  M. Yao,et al.  Nongenic, bidirectional transcription precedes and may promote developmental DNA deletion in Tetrahymena thermophila. , 2001, Genes & development.

[23]  Phillip D Zamore,et al.  Perspective: machines for RNAi. , 2005, Genes & development.

[24]  M. Gorovsky,et al.  Small RNAs in genome rearrangement in Tetrahymena. , 2004, Current opinion in genetics & development.

[25]  G. Macino,et al.  RNAi-dependent and RNAi-independent mechanisms contribute to the silencing of RIPed sequences in Neurospora crassa. , 2004, Nucleic acids research.

[26]  M. Yao,et al.  RNA-guided DNA deletion in Tetrahymena: an RNAi-based mechanism for programmed genome rearrangements. , 2005, Annual review of genetics.

[27]  T. Fujisawa,et al.  Analysis of a piwi-Related Gene Implicates Small RNAs in Genome Rearrangement in Tetrahymena , 2002, Cell.

[28]  Yifan Liu,et al.  Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  S. Hattman,et al.  Deoxyribonucleic acid methylation and chromatin organization in Tetrahymena thermophila , 1981, Molecular and cellular biology.

[30]  Franck Vazquez,et al.  Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. , 2004, Molecular cell.