Publications

Fahlgren N, Carrington JC. (2010) miRNA Target Prediction in Plants. Methods Mol Biol 592, 51-7.

Gu W, Shirayama M, Conte D Jr, Vasale J, Batista PJ, Claycomb JM, Moresco JJ, Youngman EM, Keys J, Stoltz MJ, Chen CC, Chaves DA, Duan S, Kasschau KD, Fahlgren N, Yates JR 3rd, Mitani S, Carrington JC, Mello CC. (2009) Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell 36, 231-44.

Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, Wang XJ, Chen ZJ. (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci U S A 106, 17835-40.

Rubio-Somoza I, Cuperus JT, Weigel D, Carrington JC. (2009) Regulation and functional specialization of small RNA-target nodes during plant development. Curr Opin Plant Biol 12, 622-627.

Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TW, Givan SA, Carrington JC. (2009) Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA 15, 992-1002.

Chitwood DH, Nogueira FT, Howell MD, Montgomery TA, Carrington JC, Timmermans MC. (2009) Pattern formation via small RNA mobility Genes Dev 23, 549-54.

Haas BJ et. al. (2009) Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature 461, 393-8.

Montgomery TA, Yoo SJ, Fahlgren N, Gilbert SD, Howell MD, Sullivan CM, Alexander A, Nguyen G, Allen E, Ahn JH, Carrington JC. (2008) Inaugural Article: AGO1-miR173 complex initiates phased siRNA formation in plants. Proc Natl Acad Sci U S A 105, 20055-62.

Preuss SB, Costa-Nunes P, Tucker S, Pontes O, Lawrence RJ, Mosher R, Kasschau KD, Carrington JC, Baulcombe DC, Viegas W, Pikaard CS. (2008) Multimegabase silencing in nucleolar dominance involves siRNA-directed DNA methylation and specific methylcytosine-binding proteins. Mol Cell 32, 673-84.

Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK. (2008) Criteria for Annotation of Plant MicroRNAs. Plant Cell 20, 3186-90.

Montgomery TA, Carrington JC. (2008) Splicing and dicing with a SERRATEd edge. Proc Natl Acad Sci U S A 105, 8489-90.

Batista PJ, Ruby JG, Claycomb JM, Chiang R, Fahlgren N, Kasschau KD, Chaves DA, Gu W, Vasale JJ, Duan S, Conte D Jr, Luo S, Schroth GP, Carrington JC, Bartel DP, Mello CC. (2008) PRG-1 and 21U-RNAs interact to form the piRNA complex required for fertility in C. elegans. Mol Cell 31, 67-78.

Montgomery TA, Howell MD, Cuperus JT, Li D, Hansen JE, Alexander AL, Chapman EJ, Fahlgren N, Allen E, Carrington JC. (2008) Specificity of ARGONAUTE7-miR390 interaction and dual functionality in TAS3 trans-acting siRNA formation. Cell 133, 128-41.

Backman TW, Sullivan CM, Cumbie JS, Miller ZA, Chapman EJ, Fahlgren N, Givan SA, Carrington JC, Kasschau KD. (2008) Update of ASRP: the Arabidopsis Small RNA Project database. Nucleic Acids Res 36, D982-5.

Liu PP, Montgomery TA, Fahlgren N, Kasschau KD, Nonogaki H, Carrington JC. (2007) Repression of AUXIN RESPONSE FACTOR10 by microRNA160 is critical for seed germination and post-germination stages. Plant J 52, 133-46.

Henz SR, Cumbie JS, Kasschau KD, Lohmann JU, Carrington JC, Weigel D, Schmid M. (2007) Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol 144, 1247-55.

Palatnik JF, Wollmann H, Schommer C, Schwab R, Boisbouvier J, Rodriguez R, Warthmann N, Allen E, Dezulian T, Huson D, Carrington JC, Weigel D. (2007) Sequence and expression differences underlie functional specialization of arabidopsis microRNAs miR159 and miR319. Dev Cell 13, 115-25.

Howell MD, Fahlgren N, Chapman EJ, Cumbie JS, Sullivan CM, Givan SA, Kasschau KD, Carrington JC. (2007) Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting. Plant Cell 19, 926-942.

Kasschau KD, Fahlgren N, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Carrington JC. (2007) Genome-wide profiling and analysis of Arabidopsis siRNAs. PLoS Biol 5, e57.

Givan SA, Sullivan CM, Carrington JC. (2007) The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases. BMC Bioinformatics 8, 479.

Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangl JL, Carrington JC. (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS ONE 2, e219.

Chapman EJ, Carrington JC. (2007) Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet 8, 884-96.

Yu B, Chapman EJ, Yang Z, Carrington JC, Chen X. (2006) Transgenically expressed viral RNA silencing suppressors interfere with microRNA methylation in Arabidopsis. FEBS Lett 580, 3117-20.

Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC. (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 16, 939-44.

Chiba M, Reed JC, Prokhnevsky AI, Chapman EJ, Mawassi M, Koonin EV, Carrington JC, Dolja VV. (2006) Diverse suppressors of RNA silencing enhance agroinfection by a viral replicon. Virology 346, 7-14.

Lakatos L, Csorba T, Pantaleo V, Chapman EJ, Carrington JC, Liu YP, Dolja VV, Calvino LF, Lopez-Moya JJ, Burgyan J. (2006) Small RNA binding is a common strategy to suppress RNA silencing by several viral suppressors. EMBO J 25, 2768-80.

Deleris A, Gallego-Bartolome J, Bao J, Kasschau KD, Carrington JC, Voinnet O. (2006) Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense. Science 313, 68-71.

Xie Z, Allen E, Wilken A, Carrington JC. (2005) DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. Proc Natl Acad Sci U S A 102, 12984-9.

Grey F, Antoniewicz A, Allen E, Saugstad J, McShea A, Carrington JC, Nelson J. (2005) Identification and characterization of human cytomegalovirus-encoded microRNAs. J Virol 79, 12095-9.

Carrington JC. (2005) Small RNAs and Arabidopsis. A Fast Forward Look. Plant Physiol 138, 565-6.