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| Jeong, D-H., German, M.A., Rymarquis, L.A., Thatcher, S.R., and Green, P.J. Abiotic Stress-Associated miRNAs: Detection and Functional Analysis. | |
| Accerbi, M., Schmidt, S.A., De Paoli, E., Park, S., Jeong, D-H., and Green, P.J. Methods for Isolation of total RNA to Recover miRNAs and Other Small RNAs from Diverse Species. | In Meyers, B.C. and Green, P.J. (Eds.) Plant microRNA protocols. Humana Press, New York, NY. EPub 2009 Oct 3. |
| De Paoli, E., Dorantes-Acosta, A., Zhai, J., Accerbi, M., Jeong, D-H., Meyers, B.C., Jorgensen, R.A., Green, P.J. Distinct extremely abundant siRNAs associated with cosuppression in petunia. | RNA 15:1965-1970 (2009), EPub 2009 September 23 |
| Haas, B.J.*, Kamoun, S.*, Zody, M.C., Jiang, R.H.Y., Handsaker, R.E., Cano, L.M., Grabherr, M., Kodira, C.D., Raffaele, S., Torto-Alalibo, T., Bozkurt, T.O., Ah-Fong, A.M.V., Alvarado, L., Anderson, V.L., Armstrong, M.R., Avrova, A., Baxter, L., Beynon, J., Boevink, P.C., Bollmann, S.R., Bos, J.I.B., Broad Institute Genome Sequencing Platform, Bulone, V., Cai, G., Cakir, C., Carrington, J.C., Chawner, M., Conti, L., Costanzo, S., Ewan, R., Fahlgren, N., Fischbach, M.A., Fugelstad, J., Gilroy, E.M., Gnerre, S., Green, P.J., Grenville-Briggs, L.J., Griffith, J., Grünwald, N.J., Horn, K., Horner, N.R., Hu, C-H., Huitema, E., Jeong, D-H, Jones, A.M.E., Jones, J.D.G., Jones, R.W., Karlsson, E.K., Kunjeti, S.G., Lamour, K., Liu, Z., Ma, L., MacLean, D., Marcus, C., McDonald, H., McWalters, J., Meijer, H.J.G., Morgan, W., Morris, P.F., Munro, C.A., O’Neill, K., Ospina-Giraldo, M., Pinzón, A., Pritchard, L., Ramsahoye, B., Ren, Q., Restrepo, S., Roy, S., Sadanandom, A., Savidor, A., Schornack, S., Schwartz, D.C., Schumann, U.D., Schwessinger, B., Seyer, L., Sharpe, T., Silvar, C., Song, J., Studholme, D.J., Sykes, S., Thines, M., van de Vondervoort, P.J.I., Vipaporn, P., Wawra, S., Weide, R., Win, J., Young, C., Zhou, S., Fry, W., Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R.J., Whisson, S.C., Judelson, H.S. & Nusbaum, C. Genome sequence and comparative analysis of the Irish potato famine pathogen Phytophthora infestans. *These authors contributed equally to this work. | Nature 461:393-398 (2009), EPub 2009 September 9. |
| Waidner, L., Morgan, R., Anderson, A., Bernberg, E., Kamboj, S., Garcia, M., RIblet, S., Ouyang, M., Isaacs, G., Markis, M., Meyers, B.C., Green, P.J., and Burnside, J. MicroRNAs of Gallid and Meleagrid Herpesviruses show generally conserved genomic locations and are virus-specific. | Virology 388:128–136 (2009), EPub 2009 March 28 |
| Chiba, Y. and Green, P.J. mRNA Degradation Machinery in Plants. | J. Plant Biology 52:114-124 (2009), EPub 2009 March 25 |
| German, M.A., Luo, S., Schroth, G., Meyers, B.C., and Green, P.J. Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. | Nature Protocols 4:356-362 (2009), EPub 2009 Feb. 26 |
| Meyers, B.C., Axtell, M.J., Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., and Zhu, J-K. Criteria for annotation of plant microRNAs. | Plant Cell 20:3186-3190 (2008).EPub 2008 December 12. |
| Morgan, R., Anderson, A., Bernberg, E., Kamboj, S., Huang, E., Lagasse, G., Isaacs, G., Parcells, M., Meyers, B.C., Green, P.J., and Burnside, J. Sequence conservation and differential expression of Marek’s Disease Virus microRNAs. | J. Virol. 82:12213–12220 (2008). |
Nobuta, K., Lu, C., Shrivastava, R., Pillay, M., De Paoli, E., Accerbi, M., Arteaga-Vazquez, M., Sidorenko, L., Jeong, D-H., Yen, Y., Green, P.J., Chandler, V.L., and Meyers, B.C. A distinct size distribution of endogenous siRNAs in Maize: Evidence from deep sequencing in the mop1-1 mutant. |
Proc. Nat’l. Acad. Sci. 105:14958–14963 (2008), EPub 2008 September 24. |
| Thompson, D.M., Lu, C., Green, P.J. and Parker, R. tRNA cleavage is a conserved response to oxidative stress in eukaryotes. | RNA (2008); EPub 2008 August 21. |
| Hillwig, M.S., LeBrasseur, N.D., Green, P.J. and MacIntosh, G.C. Impact of transcriptional, ABA-dependent, 1 and ABA-independent pathways on wounding regulation of RNS1 expression. | Molecular Genetics and Genomics 280:249–261 (2008); EPub 2008 July 8. |
| German, M.A., Pillay, M., Jeong, D-H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L., Nobuta, K., German, R., De Paoli, E., Lu, C., Schroth, G., Meyers, B.C. and Green, P.J. Novel microRNA-target RNA pairs revealed by Parallel Analysis of RNA Ends (PARE). | Nature Biotechnology 26: 941-946 (2008); EPub 2008 June 9. |
| Rymarquis, L.A., Kastenmayer, J.P., Hüttenhofer, A.G., and Green, P.J. Diamonds in the rough: mRNA-like non-coding RNAs. | Trends in Plant Science 13:329-334 (2008); EPub 2008 April 28. |
| Burnside,J., Ouyang, M., Anderson, A., Bernberg, E., Lu, C., Meyers, B.C., Green, P.J., Markis, M., Isaacs, G.K., Huang, E. and Morgan, R.W. Deep Sequencing of Chicken microRNAs. | BMC Genomics 9:185 (2008); EPub 2008 April 22. |
| Lu, C., Jeong, D-H., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S., Maher, C., Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B.C., and Green, P.J. Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs) | Proc. Nat’l. Acad. Sci. 105: 4951-4956 (2008); EPub 2008 March 19. |
| Rice Annotation Project, Tanaka, T., Antonio, B.A., Kikuchi, S., Matsumoto, T., Nagamura, Y., Numa, H.,Sakai, H., Wu, J., Itoh, T., Sasaki, T., Aono, R., Fujii, Y., Habara, T., Harada, E., Kanno, M., Kawahara, Y., Kawashima, H., Kubooka, H., Matsuya, A., Nakaoka, H., Saichi, N., Sanbonmatsu, R., Sato, Y., Shinso, Y., Suzuki, M., Takeda, J., Tanino, M., Todokoro, F., Yamaguchi, K., Yamamoto, N., Yamasaki, C., Imanishi, T., Okido, T., Tada, M., Ikeo, K., Tateno, Y., Gojobori, T., Lin, Y.C., Wei, F.J., Hsing. Y.I., Zhao, Q., Han, B., Kramer, M.R., McCombie, R.W., Lonsdale, D., O'Donovan, C.C., Whitfield, E.J., Apweiler, R., Koyanagi, K.O., Khurana, J.P., Raghuvanshi, S., Singh, N.K., Tyagi, A.K., Haberer, G., Fujisawa, M., Hosokawa, S., Ito, Y., Ikawa, H., Shibata, M., Yamamoto, M., Bruskiewich, R.M., Hoen, D.R., Bureau, T.E., Namiki, N., Ohyanagi, H., Sakai, Y., Nobushima, S., Sakata, K., Barrero, R.A., Sato, Y., Souvorov, A., Smith-White, B., Tatusova, T., An, S., An, G., Oota, S., Fuks, G., Messing, J., Christie, K.R., Lieberherr, D., Kim, H., Zuccolo, A., Wing, R.A., Nobuta, K., Green, P.J., Lu, C., Meyers, B.C., Chaparro, C., Piegu, B., Panaud, O., Echeverria, M. 2008. The Rice Annotation Project Database (RAP-DB): 2008 update. | Nucleic Acids Res.36 (Database issue): D1028-33. Epub 2007 Dec 17 |
| Wachter, A., Tunc-Ozdemir, M., Grove, B.C., Green, P.J., Shintani, D.K., and Breaker, R.R. Riboswitch Control Gene Expression in Plants by Splicing and Alternative 3' End Processing of mRNAs. | Plant Cell (2007) 19:34737-3450 EPub 2007 Nov 9 |
| Merchant SS, Prochnik SE, Vallon O, Harris EH, Karpowicz SJ, Witman GB, Terry A, Salamov A, Fritz-Laylin LK, Marechal-Drouard L, Marshall WF, Qu LH, Nelson DR, Sanderfoot AA, Spalding MH, Kapitonov VV, Ren Q, Ferris P, Lindquist E, Shapiro H, Lucas SM, Grimwood J, Schmutz J, Cardol P, Cerutti H, Chanfreau G, Chen CL, Cognat V, Croft MT, Dent R, Dutcher S, Fernandez E, Fukuzawa H, Gonzalez-Ballester D, Gonzalez-Halphen D, Hallmann A, Hanikenne M, Hippler M, Inwood W, Jabbari K, Kalanon M, Kuras R, Lefebvre PA, Lemaire SD, Lobanov AV, Lohr M, Manuell A, Meier I, Mets L, Mittag M, Mittelmeier T, Moroney JV, Moseley J, Napoli C, Nedelcu AM, Niyogi K, Novoselov SV, Paulsen IT, Pazour G, Purton S, Ral JP, Riano-Pachon DM, Riekhof W, Rymarquis L, Schroda M, Stern D, Umen J, Willows R, Wilson N, Zimmer SL, Allmer J, Balk J, Bisova K, Chen CJ, Elias M, Gendler K, Hauser C, Lamb MR, Ledford H, Long JC, Minagawa J, Page MD, Pan J, Pootakham W, Roje S, Rose A, Stahlberg E, Terauchi AM, Yang P, Ball S, Bowler C, Dieckmann CL, Gladyshev VN, Green P, Jorgensen R, Mayfield S, Mueller-Roeber B, Rajamani S, Sayre RT, Brokstein P, Dubchak I, Goodstein D, Hornick L, Huang YW, Jhaveri J, Luo Y, Martinez D, Ngau WC, Otillar B, Poliakov A, Porter A, Szajkowski L, Werner G, Zhou K, Grigoriev IV, Rokhsar DS, Grossman AR. The Chlamydomonas genome reveals the evolution of key animal and plant functions. | Science (2007) 318(5848):245-50 |
| Lu, C., Meyers, B.C., Green, P.J. Construction of small RNA cDNA libraries for deep sequencing. | Methods, 43: 110-117 (2007) |
| Nobuta, K., Venu, R.C., Lu, C., Belo, A., Vemaraju, K., Kulkarni, K., Wang, W., Pillay, M., Green, P.J., Wang, G., Meyers, B.C. An expression atlas of rice mRNA and small RNA | Nature Biotechnology (2007) Published online March 2007 |
| Zhang, X., Henderson, I.R., Lu, C., Green, P.J., and Jacobsen, S.E. The role of RNA Polymerase IV in Plant Small RNA Metabolism. | Proc. Natl. Acad. Sci. (2007) 104:4536-4541 |
| Lers, A., Sonego, L., Green, P.J., and Burd, S. Suppression of LX Ribonuclease in Tomato Results in a Delay of Leaf Senescence and Abscission. | Plant Physiol. (2006) 142:710-721 |
| Lu, C., Kulkarni, K., Souret, F., MuthuValliappan, R., Tej, S.S., Poethig, S., Henderson, I.R., Jacobsen, S.E., Wang, W., Green, P.J.# and Meyers, B.C. # MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. # = "joint corresponding authors" | Genome Research, 16: 1276-1288 (2006) |
| Yan, H., Ito, H., Nobuta, K., Ouyang,S., Jin, W. Tian,S., Lu, C., Venu, R.C., Wang,G., Green, P.J., Wing, R.A., Buell, C.R., Meyers, B.C.,and Jianga, J. Genomic and Genetic Characterization of Rice Cen3 Reveals Extensive Transcription and Evolutionary Implications of a Complex Centromere. | Plant Cell 18: 2123-2133 (2006) |
| Burnside, J. Bernberg, E., Anderson, A., Lu, C., Meyers, B.C., Green, P.J., Jain, N. Isaacs, G. and Morgan, R. Marek’s Disease Virus Encodes MicroRNAs That Map to meq and the Latency-Associated Transcript. | J. Virology, 80: 8778–8786 (2006) |
| van Hoof, A. and Green, P.J. Nonsense-mediated mRNA decay in plants, in Nonsense-Mediated mRNA Decay, (L. Maquat, ed.) | |
| Meyers, B.C., Souret, F.S., Lu, C., Green, P.J. Sweating the small stuff: MicroRNA discovery in plants | Current Opinion in Biotechnology, 17:139-146. (2006) |
| Henderson, I.R., Zhang, X., Lu, C., Johnson, L.., Meyers, B.C., Green, P.J. and Jacobsen, S.E. Dissecting Arabidopsis DICER function in small RNA processing, gene silencing, and DNA methylation patterning. | Nature Genetics, 38: 721-725 (2006) |
| Lu, C., Tej, S.S., Luo, S., Haudenschild, Meyers, B.C., and Green, P.J. Elucidation of the small RNA component of the transcriptome. |
Science, 309:1567-1569 (2005) |
| Lidder, P., Gutierrez, R.A., Salome, P.A., McClung, C.R., and Green, P.J. Circadian control of mRNA stability. Association with a sequence-specific mRNA decay pathway. | Plant Phys. 138:2374-2385 (2005) |
| Lidder, P., Johnson, M.A., Sullivan, M.L., Thompson, D.M., Pérez-Amador, M.A., Howard, C.J., Green, P.J. Genetics of the DST-mediated mRNA decay pathway using a transgene-based selection Biochem. |
Soc. Trans. 32:575-577 (2004) |
| Souret, F.S., Kastenmayer, J.P., and Green, P.J. AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. | Molecular Cell , 15:173-183, (2004) |
| Gutierrez, R.G., Green, P.J., Keegstra, K., and Ohlrogge, J. B. Phlogenetic fingerprinting of the Arabidopsis thaliana proteome: What proteins distinguish plants from other organisms? | Genome Biology, 5, R53 (2004) |
| Chiba, Y., Johnson, M.A., Lidder, P., Vogel, J.T., van Erp. H.E.G., and Green, P.J. Identification and characterization of AtPARN, an essential poly (A) ribonuclease in Arabidopsis. | Gene 328:95-102 (2004). |
| Brown, J.W.S., Echeverria, M., Qu, L.H., Lowe, T.M., Bachellerie, J.P., Hüttenhofer, A., Kastenmayer, J.P., Green, P.J., Shaw, P., and Marshall, D.F. Plant snoRNA Database. | Nucleic Acids Res. 31:432-435 (2003) |
| Marker, C., Zemann, A., Terhörst, T., Kiefmann, M., Kastenmayer, J.P., Green, P., Bachellerie, J.P., Brosius, J., and Hüttenhofer, A. Experimental RNomics:identification of 140 candidates for small, non-messenger RNAs in the plant Arabidopsis thaliana. |
Curr. Biol. 12: 2002-2013 (2002) |
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Perez-Amador, M., Leon, J., Green, P., and Carbonell, J. Induction of the Arginine Decarboxylase ADC2 gene provides evidence for involvement of Polyamines in the wound response in Arabidopsis. |
Plant Physiol. 130: 1454-1463 (2002) |
| Rodrigo A. Gutiérrez, Rob M. Ewing, J. Michael Cherry and Pamela J. Green, Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: Rapid decay is associated with a group of touch- and specific clock-controlled genes. | Proc. Natl. Acad. Sci. USA 99: 11513-11518 (2002) |
| Nicole D. LeBrasseur, Gustavo C. MacIntosh, Miguel A. Pérez-Amador, Maki Saitoh and Pamela J. Green. Local and systemic wound-induction of RNase and nuclease activities in Arabidopsis: RNS1 as a marker for a JA-independent systemic signalling pathway. | Plant Journal. 29: 393-403 (2002) |
| Feldbrügge M., Arizti, P., Sullivan, M.L., Zamore, P.D., Belasco, J.G. and Green, P.J. Comparative analysis of the plant mRNA-destabilizing element, DST, in mammalian and tobacco cells. | Plant Mol. Biol. 49: 215-223 (2002) |
| Miguel A. Pérez-Amador, Preetmoninder Lidder, Mark A. Johnson, Jeff Landgraf, Ellen Wisman, Pamela J. Green. New Molecular Phenotypes in the dst Mutants of Arabidopsis Revealed by DNA Microarray Analysis. Supplemental Material |
Plant Cell 13,2703-2717 (2001) |
| Gustavo C. MacIntosh, Curtis Wilkerson and Pamela J. Green. Identification and analysis of Arabidopsis expressed sequence tags characteristic of noncoding RNAs. | Plant Physiol 127, 765-776 (2001). |
| Kastenmayer, J.P., Johnson, M.A., and Green, P.J. Analysis of XRN orthologs by complementation of yeast mutants and localization of XRN-GFP fusion proteins. | Methods in Enzymology 342: 269-282 (2001) |
| Gustavo C. MacIntosh, Pauline A. Bariola, Ed Newbigin, and Pamela J. Green. Characterization of Rny1, the Saccaromyces cerevisiae member of the T2 RNase family of RNases: Unexpected functions for ancient enzymes? | Proc. Natl. Acad. Sci. U S A 98: 1018-1023 (2001) |
| Mark A. Johnson, Miguel A. Pérez-Amador, Preetmoninder Lidder, and Pamela J. Green. Mutants of Arabidopsis defective in a sequence-specific mRNA degradation pathway. | Proc. Natl. Acad. Sci. U S A 97: 13991-13996 (2000) |
| J. P. Kastenmayer and P. J. Green. Novel features of the XRN-family in Arabidopsis: Evidence that AtXRN4, one of several orthologs of nuclear Xrn2p/Rat1p, functions in the cytoplasm. | Proc. Natl. Acad. Sci. U S A 97: 13985-13990 (2000) |
| M. A. Pérez-Amador, M. L. Abler, J. DeRocher, D. M. Thompson, A. van Hoof, N. LeBrasseur, A. Lers, and P. J. Green. Identification of BFN1, a bifunctional nuclease induced during leaf and stem senescence in Arabidopsis thaliana. | Plant Physiol.122: 169-180 (2000) |
| Gutiérrez, R. A., MacIntosh, G. C. and Green, P. J. Current perspectives on mRNA stability in plants: multiple levels and mechanisms of control. | Trends in Plant Science 4: 429-438 (1999). |
| P. A. Bariola, G. C. MacIntosh and P. J. Green. Regulation of S-like ribonuclease levels in Arabidopsis: Antisense inhibition of RNS1 or RNS2 elevates anthocyanin accumulation1. | Plant Physiol. 119: 331-342 (1999) |
| E. J. De Rocher, T. C. Vargo-Gogola, S. H. Diehn, and P. J. Green. Direct Evidence for Rapid Degradation of B.t. toxin mRNA as a Cause of Poor Expression in Plants. | Plant Physiol. 117: 1445-1461 (1998) |
| S. H. Diehn, W.-L. Chiu, E. J. De Rocher, and P. J. Green. Premature Polyadenylation at Multiple Sites within a B.t. toxin Gene Coding Region. | Plant Physiol. 117: 1433-1443 (1998) |
| A. Lers, A. Khaltchitski, E. Lomaniec, S. Burd, and P. J. Green. Senescence-induced RNases in Tomato. | Plant Mol Biol. 36: 439-449 (1998) |
| A. van Hoof and P. J. Green. Rare codons are not sufficient to destabilize a reporter gene transcript in tobacco. | Plant Mol. Biol. 35:383-387 (1997) |
| Ambro van Hoof and P.J. Green. Premature Nonsense Codons Decrease the Stability of Phytohemagglutinin in a Position-Dependent Manner. | Plant J. 10 (3):415-424 (1996) |
| M.L. Sullivan and P.J. Green. Mutational analysis of the DST element in tobacco cells and transgenic plants: Identification of residues critical for mRNA instability. | RNA 2:308-315 (1996) |
| T.C. Newman, F. deBruijn, P. Green, K. Keegstra, H. Kende, L. McIntosh, J. Ohlrogge, N. Raikhel, S. Somerville, M. Tomashow, E. Retzel, and C.R. Somerville. Genes Galore: A summary of methods for accessing results from partial sequencing of anonymous Arabidopsis cDNA clones. | Plant Physiol. 106:1241-1255 (1994) |
| P. A. Bariola, C. J. Howard, C. B. Taylor, M. T. Verburg, V. D. Jaglan & P. J. Green. The Arabidopsis ribonuclease gene RNS1 is tightly controlled in response to phosphate limitation. | Plant J 6: 673-685 (1994) |
| P.J. Green. The ribonucleases of higher plants. | Annual Review Plant Physiology Plant Molecular Biology 45:421-445 (1994) |
| P. Gil, Y. Liu, V. Orbovic, E. Verkamp, K. L. Poff & P. J. Green. Characterization of the auxin-inducible SAUR-AC1 gene for use as a molecular genetic tool in Arabidopsis. | Plant Physiol. 104: 777-84 (1994) |
| M. Ohme-Takagi, C. B. Taylor, T. C. Newman & P. J. Green. The effect of sequences with high AU content on mRNA stability in tobacco. | Proc. Natl. Acad. Sci. U S A 90: 11811-5 (1993) |
| P.J. Green. Control of mRNA stability in higher plants. | Plant Physiol. 102:1065-1070 (1993) |
| T. C. Newman, M. Ohme-Takagi, C. B. Taylor & P. J. Green. DST sequences, highly conserved among plant SAUR genes, target reporter transcripts for rapid decay in tobacco. | Plant Cell 5: 701-14 (1993) |
| C. B. Taylor, P. A. Bariola, S. B. delCardayre, R. T. Raines & P. J. Green. RNS2: a senescence-associated RNase of Arabidopsis that diverged from the S- RNases before speciation. | Proc. Natl. Acad. Sci. U S A 90: 5118-22 (1993) |
| Y. Yen and P.J. Green. Identification and properties of the major ribonucleases of Arabidopsis thaliana. | Plant Physiol. 97:1487-1493 (1991) |
| C.B. Taylor and P.J. Green. Genes with homology to fungal and S-gene RNases are expressed in Arabidopsis thaliana. | Plant Physiol. 96:980-984 (1991) |