Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.

Published Online November 23, 2006
Science DOI: 10.1126/science.1132839

Reports

Submitted on July 21, 2006
Accepted on November 15, 2006

Distinct Populations of Primary and Secondary Effectors During RNAi in C. elegans

Julia Pak 1 and Andrew Fire 1*

1 Departments of Pathology and Genetics, Stanford University School of Medicine, Stanford, CA 94305-5324, USA.

* To whom correspondence should be addressed.
Andrew Fire , E-mail: afire{at}stanford.edu

RNA interference (RNAi) is a phylogenetically widespread gene silencing process triggered by double-stranded RNA (dsRNA). In plants and C. elegans, two distinct populations of small RNAs have been proposed to participate in RNAi: "Primary siRNAs" (derived from Dicer nuclease-mediated cleavage of the original trigger) and "Secondary siRNAs" (additional small RNAs whose synthesis requires an RNA-directed RNA polymerase [RdRP]). Analyzing small RNAs associated with ongoing RNAi in C. elegans, we found secondary siRNAs to comprise the vast majority. The bulk of secondary siRNAs exhibited structure and sequence indicative of a biosynthetic mode where each molecule derives from an independent de novo initiation by RdRP. Analysis of endogenous small RNAs indicated that a fraction derive from a biosynthetic mechanism that is similar to that of secondary siRNAs formed during RNAi, suggesting that small antisense transcripts derived from cellular mRNAs by RdRP activity may have key roles in cellular regulation.


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans.
T. Han, A. P. Manoharan, T. T. Harkins, P. Bouffard, C. Fitzpatrick, D. S. Chu, D. Thierry-Mieg, J. Thierry-Mieg, and J. K. Kim (2009)
PNAS 106, 18674-18679
   Abstract »    Full Text »    PDF »
Distinct and overlapping roles for two Dicer-like proteins in the RNA interference pathways of the ancient eukaryote Trypanosoma brucei.
K. L. Patrick, H. Shi, N. G. Kolev, K. Ersfeld, C. Tschudi, and E. Ullu (2009)
PNAS 106, 17933-17938
   Abstract »    Full Text »    PDF »
Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila.
M. T. Couvillion, S. R. Lee, B. Hogstad, C. D. Malone, L. A. Tonkin, R. Sachidanandam, G. J. Hannon, and K. Collins (2009)
Genes & Dev. 23, 2016-2032
   Abstract »    Full Text »    PDF »
A single RNA-dependent RNA polymerase assembles with mutually exclusive nucleotidyl transferase subunits to direct different pathways of small RNA biogenesis.
S. R. Lee, K. B. Talsky, and K. Collins (2009)
RNA 15, 1363-1374
   Abstract »    Full Text »    PDF »
Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs.
S. Granneman, G. Kudla, E. Petfalski, and D. Tollervey (2009)
PNAS 106, 9613-9618
   Abstract »    Full Text »    PDF »
Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA.
P. Tedder, E. Zubko, D. R. Westhead, and P. Meyer (2009)
RNA 15, 1012-1020
   Abstract »    Full Text »    PDF »
Computational and analytical framework for small RNA profiling by high-throughput sequencing.
N. Fahlgren, C. M. Sullivan, K. D. Kasschau, E. J. Chapman, J. S. Cumbie, T. A. Montgomery, S. D. Gilbert, M. Dasenko, T. W.H. Backman, S. A. Givan, et al. (2009)
RNA 15, 992-1002
   Abstract »    Full Text »    PDF »
Experimental discovery of sRNAs in Vibrio cholerae by direct cloning, 5S/tRNA depletion and parallel sequencing.
J. M. Liu, J. Livny, M. S. Lawrence, M. D. Kimball, M. K. Waldor, and A. Camilli (2009)
Nucleic Acids Res. 37, e46
   Abstract »    Full Text »    PDF »
Small RNA Silencing Pathways in Germ and Stem Cells.
A.A. Aravin and G.J. Hannon (2009)
Cold Spring Harb Symp Quant Biol
   Abstract »    PDF »
Compromised Virus-Induced Gene Silencing in RDR6-Deficient Plants.
F. E. Vaistij and L. Jones (2009)
Plant Physiology 149, 1399-1407
   Abstract »    Full Text »    PDF »
Silencing-associated and meiosis-specific small RNA pathways in Paramecium tetraurelia.
G. Lepere, M. Nowacki, V. Serrano, J.-F. Gout, G. Guglielmi, S. Duharcourt, and E. Meyer (2009)
Nucleic Acids Res. 37, 903-915
   Abstract »    Full Text »    PDF »
The evolution of RNAi as a defence against viruses and transposable elements.
D. J Obbard, K. H.J Gordon, A. H Buck, and F. M Jiggins (2009)
Phil Trans R Soc B 364, 99-115
   Abstract »    Full Text »    PDF »
RNA interference and retinoblastoma-related genes are required for repression of endogenous siRNA targets in Caenorhabditis elegans.
A. Grishok, S. Hoersch, and P. A. Sharp (2008)
PNAS 105, 20386-20391
   Abstract »    Full Text »    PDF »
Transmission Dynamics of Heritable Silencing Induced by Double-Stranded RNA in Caenorhabditis elegans.
R. M. Alcazar, R. Lin, and A. Z. Fire (2008)
Genetics 180, 1275-1288
   Abstract »    Full Text »    PDF »
Specific Gene Silencing by Artificial MicroRNAs in Physcomitrella patens: An Alternative to Targeted Gene Knockouts.
B. Khraiwesh, S. Ossowski, D. Weigel, R. Reski, and W. Frank (2008)
Plant Physiology 148, 684-693
   Abstract »    Full Text »    PDF »
An Argonaute Transports siRNAs from the Cytoplasm to the Nucleus.
S. Guang, A. F. Bochner, D. M. Pavelec, K. B. Burkhart, S. Harding, J. Lachowiec, and S. Kennedy (2008)
Science 321, 537-541
   Abstract »    Full Text »    PDF »
Inhibition of 3' modification of small RNAs in virus-infected plants require spatial and temporal co-expression of small RNAs and viral silencing-suppressor proteins.
R. Lozsa, T. Csorba, L. Lakatos, and J. Burgyan (2008)
Nucleic Acids Res. 36, 4099-4107
   Abstract »    Full Text »    PDF »
Structural and Genetic Requirements for the Biogenesis of Tobacco Rattle Virus-Derived Small Interfering RNAs.
L. Donaire, D. Barajas, B. Martinez-Garcia, L. Martinez-Priego, I. Pagan, and C. Llave (2008)
J. Virol. 82, 5167-5177
   Abstract »    Full Text »    PDF »
Two molecular features contribute to the Argonaute specificity for the microRNA and RNAi pathways in C. elegans.
G. Jannot, M.-E. L. Boisvert, I. H. Banville, and M. J. Simard (2008)
RNA 14, 829-835
   Abstract »    Full Text »    PDF »
Diversification of the Core RNA Interference Machinery in Chlamydomonas reinhardtii and the Role of DCL1 in Transposon Silencing.
J. A. Casas-Mollano, J. Rohr, E.-J. Kim, E. Balassa, K. van Dijk, and H. Cerutti (2008)
Genetics 179, 69-81
   Abstract »    Full Text »    PDF »
The Caenorhabditis elegans rsd-2 and rsd-6 Genes Are Required for Chromosome Functions During Exposure to Unfavorable Environments.
W. Han, P. Sundaram, H. Kenjale, J. Grantham, and L. Timmons (2008)
Genetics 178, 1875-1893
   Abstract »    Full Text »    PDF »
The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members.
T. A. Farazi, S. A. Juranek, and T. Tuschl (2008)
Development 135, 1201-1214
   Abstract »    Full Text »    PDF »
The Caenorhabditis elegans ekl (Enhancer of ksr-1 Lethality) Genes Include Putative Components of a Germline Small RNA Pathway.
C. E. Rocheleau, K. Cullison, K. Huang, Y. Bernstein, A. C. Spilker, and M. V. Sundaram (2008)
Genetics 178, 1431-1443
   Abstract »    Full Text »    PDF »
Biochemical Activities of Arabidopsis RNA-dependent RNA Polymerase 6.
J. Curaba and X. Chen (2008)
J. Biol. Chem. 283, 3059-3066
   Abstract »    Full Text »    PDF »
Successive accumulation of two size classes of viroid-specific small RNA in potato spindle tuber viroid-infected tomato plants.
S. Machida, N. Yamahata, H. Watanuki, R. A. Owens, and T. Sano (2007)
J. Gen. Virol. 88, 3452-3457
   Abstract »    Full Text »    PDF »
A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing.
P. Parameswaran, R. Jalili, L. Tao, S. Shokralla, B. Gharizadeh, M. Ronaghi, and A. Z. Fire (2007)
Nucleic Acids Res.
   Abstract »    Full Text »    PDF »
Distinct ribonucleoprotein reservoirs for microRNA and siRNA populations in C. elegans.
S. G. Gu, J. Pak, S. Barberan-Soler, M. Ali, A. Fire, and A. M. Zahler (2007)
RNA 13, 1492-1504
   Abstract »    Full Text »    PDF »
Transitivity in Arabidopsis can be primed, requires the redundant action of the antiviral Dicer-like 4 and Dicer-like 2, and is compromised by viral-encoded suppressor proteins.
G. Moissiard, E. A. Parizotto, C. Himber, and O. Voinnet (2007)
RNA 13, 1268-1278
   Abstract »    Full Text »    PDF »
piRNAs--the ancient hunters of genome invaders.
J. V. Hartig, Y. Tomari, and K. Forstemann (2007)
Genes & Dev. 21, 1707-1713
   Abstract »    Full Text »    PDF »
Genes misregulated in C. elegans deficient in Dicer, RDE-4, or RDE-1 are enriched for innate immunity genes.
N. C. Welker, J. W. Habig, and B. L. Bass (2007)
RNA 13, 1090-1102
   Abstract »    Full Text »    PDF »
Patterns of Known and Novel Small RNAs in Human Cervical Cancer.
W.-O. Lui, N. Pourmand, B. K. Patterson, and A. Fire (2007)
Cancer Res. 67, 6031-6043
   Abstract »    Full Text »    PDF »
Common Functions for Diverse Small RNAs of Land Plants.
M. J. Axtell, J. A. Snyder, and D. P. Bartel (2007)
PLANT CELL 19, 1750-1769
   Abstract »    Full Text »    PDF »
The regulation of genes and genomes by small RNAs.
V. Ambros and X. Chen (2007)
Development 134, 1635-1641
   Abstract »    Full Text »    PDF »
An SNF2 Protein Associated with Nuclear RNA Silencing and the Spread of a Silencing Signal between Cells in Arabidopsis.
L. M. Smith, O. Pontes, I. Searle, N. Yelina, F. K. Yousafzai, A. J. Herr, C. S. Pikaard, and D. C. Baulcombe (2007)
PLANT CELL 19, 1507-1521
   Abstract »    Full Text »    PDF »


To Advertise     Find Products

Science. ISSN 0036-8075 (print), 1095-9203 (online)