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sRNA-FISH: versatile fluorescent in situ detection of small RNAs in plants.

Huang K, Baldrich P, Meyers BC, Caplan JL.

Plant J. 2018 Dec 21. doi: 10.1111/tpj.14210. [Epub ahead of print]


The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon.

Wittmeyer K, Cui J, Chatterjee D, Lee TF, Tan Q, Xue W, Jiao Y, Wang PH, Gaffoor I, Ware D, Meyers BC, Chopra S.

Plant Cell. 2018 Dec 18. pii: tpc.00546.2018. doi: 10.1105/tpc.18.00546. [Epub ahead of print]


Efficiency and precision of microRNA biogenesis modes in plants.

Moro B, Chorostecki U, Arikit S, Suarez IP, Höbartner C, Rasia RM, Meyers BC, Palatnik JF.

Nucleic Acids Res. 2018 Nov 16;46(20):10709-10723. doi: 10.1093/nar/gky853.


Characterizing Small RNAs in Filamentous Fungi Using the Rice Blast Fungus, Magnaporthe oryzae, as an Example.

Raman V, Meyers BC, Dean RA, Donofrio NM.

Methods Mol Biol. 2018;1848:53-66. doi: 10.1007/978-1-4939-8724-5_5.


Reproductive phasiRNAs in grasses are compositionally distinct from other classes of small RNAs.

Patel P, Mathioni S, Kakrana A, Shatkay H, Meyers BC.

New Phytol. 2018 Nov;220(3):851-864. doi: 10.1111/nph.15349. Epub 2018 Jul 18.


Biogenesis of a 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation.

Fei Q, Yu Y, Liu L, Zhang Y, Baldrich P, Dai Q, Chen X, Meyers BC.

Proc Natl Acad Sci U S A. 2018 Jul 31;115(31):8037-8042. doi: 10.1073/pnas.1807403115. Epub 2018 Jul 16.


Molecular mechanisms that limit the costs of NLR-mediated resistance in plants.

Richard MMS, Gratias A, Meyers BC, Geffroy V.

Mol Plant Pathol. 2018 Nov;19(11):2516-2523. doi: 10.1111/mpp.12723. Epub 2018 Sep 28. Review.


Plant 24-nt reproductive phasiRNAs from intramolecular duplex mRNAs in diverse monocots.

Kakrana A, Mathioni SM, Huang K, Hammond R, Vandivier L, Patel P, Arikit S, Shevchenko O, Harkess AE, Kingham B, Gregory BD, Leebens-Mack JH, Meyers BC.

Genome Res. 2018 Sep;28(9):1333-1344. doi: 10.1101/gr.228163.117. Epub 2018 Jul 12.


Cis-directed cleavage and nonstoichiometric abundances of 21-nucleotide reproductive phased small interfering RNAs in grasses.

Tamim S, Cai Z, Mathioni SM, Zhai J, Teng C, Zhang Q, Meyers BC.

New Phytol. 2018 Nov;220(3):865-877. doi: 10.1111/nph.15181. Epub 2018 Apr 30.


Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana.

He J, Xu M, Willmann MR, McCormick K, Hu T, Yang L, Starker CG, Voytas DF, Meyers BC, Poethig RS.

PLoS Genet. 2018 Apr 19;14(4):e1007337. doi: 10.1371/journal.pgen.1007337. eCollection 2018 Apr.


Brassicales phylogeny inferred from 72 plastid genes: A reanalysis of the phylogenetic localization of two paleopolyploid events and origin of novel chemical defenses.

Edger PP, Hall JC, Harkess A, Tang M, Coombs J, Mohammadin S, Schranz ME, Xiong Z, Leebens-Mack J, Meyers BC, Sytsma KJ, Koch MA, Al-Shehbaz IA, Pires JC.

Am J Bot. 2018 Mar;105(3):463-469. doi: 10.1002/ajb2.1040. Epub 2018 Mar 25.


Pathogen Trojan Horse Delivers Bioactive Host Protein to Alter Maize Anther Cell Behavior in Situ.

van der Linde K, Timofejeva L, Egger RL, Ilau B, Hammond R, Teng C, Meyers BC, Doehlemann G, Walbot V.

Plant Cell. 2018 Mar;30(3):528-542. doi: 10.1105/tpc.17.00238. Epub 2018 Feb 15.


Despacito: the slow evolutionary changes in plant microRNAs.

Baldrich P, Beric A, Meyers BC.

Curr Opin Plant Biol. 2018 Apr;42:16-22. doi: 10.1016/j.pbi.2018.01.007. Epub 2018 Feb 12. Review.


Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data.

Axtell MJ, Meyers BC.

Plant Cell. 2018 Feb;30(2):272-284. doi: 10.1105/tpc.17.00851. Epub 2018 Jan 17.


Coupling of microRNA-directed phased small interfering RNA generation from long noncoding genes with alternative splicing and alternative polyadenylation in small RNA-mediated gene silencing.

Ma W, Chen C, Liu Y, Zeng M, Meyers BC, Li J, Xia R.

New Phytol. 2018 Mar;217(4):1535-1550. doi: 10.1111/nph.14934. Epub 2017 Dec 8.


The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

Friesner J, Assmann SM, Bastow R, Bailey-Serres J, Beynon J, Brendel V, Buell CR, Bucksch A, Busch W, Demura T, Dinneny JR, Doherty CJ, Eveland AL, Falter-Braun P, Gehan MA, Gonzales M, Grotewold E, Gutierrez R, Kramer U, Krouk G, Ma S, Markelz RJC, Megraw M, Meyers BC, Murray JAH, Provart NJ, Rhee S, Smith R, Spalding EP, Taylor C, Teal TK, Torii KU, Town C, Vaughn M, Vierstra R, Ware D, Wilkins O, Williams C, Brady SM.

Plant Physiol. 2017 Dec;175(4):1499-1509. doi: 10.1104/pp.17.01490. No abstract available.


Overlapping RdDM and non-RdDM mechanisms work together to maintain somatic repression of a paramutagenic epiallele of maize pericarp color1.

Wang PH, Wittmeyer KT, Lee TF, Meyers BC, Chopra S.

PLoS One. 2017 Nov 7;12(11):e0187157. doi: 10.1371/journal.pone.0187157. eCollection 2017.


The asparagus genome sheds light on the origin and evolution of a young Y chromosome.

Harkess A, Zhou J, Xu C, Bowers JE, Van der Hulst R, Ayyampalayam S, Mercati F, Riccardi P, McKain MR, Kakrana A, Tang H, Ray J, Groenendijk J, Arikit S, Mathioni SM, Nakano M, Shan H, Telgmann-Rauber A, Kanno A, Yue Z, Chen H, Li W, Chen Y, Xu X, Zhang Y, Luo S, Chen H, Gao J, Mao Z, Pires JC, Luo M, Kudrna D, Wing RA, Meyers BC, Yi K, Kong H, Lavrijsen P, Sunseri F, Falavigna A, Ye Y, Leebens-Mack JH, Chen G.

Nat Commun. 2017 Nov 2;8(1):1279. doi: 10.1038/s41467-017-01064-8.


GC-rich coding sequences reduce transposon-like, small RNA-mediated transgene silencing.

Sidorenko LV, Lee TF, Woosley A, Moskal WA, Bevan SA, Merlo PAO, Walsh TA, Wang X, Weaver S, Glancy TP, Wang P, Yang X, Sriram S, Meyers BC.

Nat Plants. 2017 Nov;3(11):875-884. doi: 10.1038/s41477-017-0040-6. Epub 2017 Oct 30.


Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple.

Wai CM, VanBuren R, Zhang J, Huang L, Miao W, Edger PP, Yim WC, Priest HD, Meyers BC, Mockler T, Smith JAC, Cushman JC, Ming R.

Plant J. 2017 Oct;92(1):19-30. doi: 10.1111/tpj.13630. Epub 2017 Aug 21.


FASTmiR: an RNA-based sensor for in vitro quantification and live-cell localization of small RNAs.

Huang K, Doyle F, Wurz ZE, Tenenbaum SA, Hammond RK, Caplan JL, Meyers BC.

Nucleic Acids Res. 2017 Aug 21;45(14):e130. doi: 10.1093/nar/gkx504.


Small RNA Functions Are Required for Growth and Development of Magnaporthe oryzae.

Raman V, Simon SA, Demirci F, Nakano M, Meyers BC, Donofrio NM.

Mol Plant Microbe Interact. 2017 Jul;30(7):517-530. doi: 10.1094/MPMI-11-16-0236-R. Epub 2017 May 15.


The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants.

Xia R, Xu J, Meyers BC.

Plant Cell. 2017 Jun;29(6):1232-1247. doi: 10.1105/tpc.17.00185. Epub 2017 Apr 24.


Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce.

Reyes-Chin-Wo S, Wang Z, Yang X, Kozik A, Arikit S, Song C, Xia L, Froenicke L, Lavelle DO, Truco MJ, Xia R, Zhu S, Xu C, Xu H, Xu X, Cox K, Korf I, Meyers BC, Michelmore RW.

Nat Commun. 2017 Apr 12;8:14953. doi: 10.1038/ncomms14953.


ARGONAUTE10 promotes the degradation of miR165/6 through the SDN1 and SDN2 exonucleases in Arabidopsis.

Yu Y, Ji L, Le BH, Zhai J, Chen J, Luscher E, Gao L, Liu C, Cao X, Mo B, Ma J, Meyers BC, Chen X.

PLoS Biol. 2017 Feb 23;15(2):e2001272. doi: 10.1371/journal.pbio.2001272. eCollection 2017 Feb.


PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice.

Fan Y, Yang J, Mathioni SM, Yu J, Shen J, Yang X, Wang L, Zhang Q, Cai Z, Xu C, Li X, Xiao J, Meyers BC, Zhang Q.

Proc Natl Acad Sci U S A. 2016 Dec 27;113(52):15144-15149. doi: 10.1073/pnas.1619159114. Epub 2016 Dec 13.


MS23, a master basic helix-loop-helix factor, regulates the specification and development of the tapetum in maize.

Nan GL, Zhai J, Arikit S, Morrow D, Fernandes J, Mai L, Nguyen N, Meyers BC, Walbot V.

Development. 2017 Jan 1;144(1):163-172. doi: 10.1242/dev.140673. Epub 2016 Dec 2.


Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways.

Fei Q, Yang L, Liang W, Zhang D, Meyers BC.

J Exp Bot. 2016 Nov;67(21):6037-6049. Epub 2016 Oct 4.


The Influence of Genotype and Environment on Small RNA Profiles in Grapevine Berry.

Paim Pinto DL, Brancadoro L, Dal Santo S, De Lorenzis G, Pezzotti M, Meyers BC, Pè ME, Mica E.

Front Plant Sci. 2016 Oct 5;7:1459. eCollection 2016.


The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them.

Zhang Y, Xia R, Kuang H, Meyers BC.

Mol Biol Evol. 2016 Oct;33(10):2692-705. doi: 10.1093/molbev/msw154. Epub 2016 Aug 10.


An Agrobacterium-delivered CRISPR/Cas9 system for high-frequency targeted mutagenesis in maize.

Char SN, Neelakandan AK, Nahampun H, Frame B, Main M, Spalding MH, Becraft PW, Meyers BC, Walbot V, Wang K, Yang B.

Plant Biotechnol J. 2017 Feb;15(2):257-268. doi: 10.1111/pbi.12611. Epub 2016 Sep 5.


Regulatory Role of a Receptor-Like Kinase in Specifying Anther Cell Identity.

Yang L, Qian X, Chen M, Fei Q, Meyers BC, Liang W, Zhang D.

Plant Physiol. 2016 Jul;171(3):2085-100. doi: 10.1104/pp.16.00016. Epub 2016 May 20.


Evolution of plant genome architecture.

Wendel JF, Jackson SA, Meyers BC, Wing RA.

Genome Biol. 2016 Mar 1;17:37. doi: 10.1186/s13059-016-0908-1. Review.


Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses.

Fei Q, Zhang Y, Xia R, Meyers BC.

Mol Plant Microbe Interact. 2016 Mar;29(3):165-9. doi: 10.1094/MPMI-09-15-0212-FI. Epub 2016 Feb 11. Review.


High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs.

Khatabi B, Arikit S, Xia R, Winter S, Oumar D, Mongomake K, Meyers BC, Fondong VN.

BMC Genomics. 2016 Jan 28;17:85. doi: 10.1186/s12864-016-2391-1.


MicroRNA Maturation and MicroRNA Target Gene Expression Regulation Are Severely Disrupted in Soybean dicer-like1 Double Mutants.

Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Hammond R, Gutierrez-Gonzalez JJ, Donohue RC, Kantar MB, Eamens AL, Meyers BC, Voytas DF, Stupar RM.

G3 (Bethesda). 2015 Dec 17;6(2):423-33. doi: 10.1534/g3.115.022137.


miTRATA: a web-based tool for microRNA Truncation and Tailing Analysis.

Patel P, Ramachandruni SD, Kakrana A, Nakano M, Meyers BC.

Bioinformatics. 2016 Feb 1;32(3):450-2. doi: 10.1093/bioinformatics/btv583. Epub 2015 Oct 10.


A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis.

Zhai J, Bischof S, Wang H, Feng S, Lee TF, Teng C, Chen X, Park SY, Liu L, Gallego-Bartolome J, Liu W, Henderson IR, Meyers BC, Ausin I, Jacobsen SE.

Cell. 2015 Oct 8;163(2):445-55. doi: 10.1016/j.cell.2015.09.032.


Editorial overview: Cell signalling and gene regulation-communication and control as the twin pillars of systems biology.

Cao X, Meyers BC.

Curr Opin Plant Biol. 2015 Oct;27:v-viii. doi: 10.1016/j.pbi.2015.09.001. Epub 2015 Sep 30. No abstract available.


Extensive Families of miRNAs and PHAS Loci in Norway Spruce Demonstrate the Origins of Complex phasiRNA Networks in Seed Plants.

Xia R, Xu J, Arikit S, Meyers BC.

Mol Biol Evol. 2015 Nov;32(11):2905-18. doi: 10.1093/molbev/msv164. Epub 2015 Aug 28.


Evolution, functions, and mysteries of plant ARGONAUTE proteins.

Zhang H, Xia R, Meyers BC, Walbot V.

Curr Opin Plant Biol. 2015 Oct;27:84-90. doi: 10.1016/j.pbi.2015.06.011. Epub 2015 Jul 17. Review.


Novel and Recently Evolved MicroRNA Clusters Regulate Expansive F-BOX Gene Networks through Phased Small Interfering RNAs in Wild Diploid Strawberry.

Xia R, Ye S, Liu Z, Meyers BC, Liu Z.

Plant Physiol. 2015 Sep;169(1):594-610. doi: 10.1104/pp.15.00253. Epub 2015 Jul 4.


Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances.

Fei Q, Li P, Teng C, Meyers BC.

Plant J. 2015 Aug;83(3):451-65. doi: 10.1111/tpj.12900. Epub 2015 Jun 30.


miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing.

Belli Kullan J, Lopes Paim Pinto D, Bertolini E, Fasoli M, Zenoni S, Tornielli GB, Pezzotti M, Meyers BC, Farina L, Pè ME, Mica E.

BMC Genomics. 2015 May 16;16:393. doi: 10.1186/s12864-015-1610-5.


Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection.

Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Brechenmacher L, Findley S, Joshi T, Qiu L, Sherrier DJ, Ji T, Meyers BC, Xu D, Stacey G.

Plant Biotechnol J. 2016 Jan;14(1):332-41. doi: 10.1111/pbi.12387. Epub 2015 May 14.


Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis.

Tu B, Liu L, Xu C, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ramachandran V, Ren G, Yu B, Li S, Meyers BC, Mo B, Chen X.

PLoS Genet. 2015 Apr 30;11(4):e1005119. doi: 10.1371/journal.pgen.1005119. eCollection 2015 Apr.


A new approach for annotation of transposable elements using small RNA mapping.

El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA.

Nucleic Acids Res. 2015 Jul 27;43(13):e84. doi: 10.1093/nar/gkv257. Epub 2015 Mar 26.


Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation.

Yan Z, Hossain MS, Arikit S, Valdés-López O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC, Stacey G.

New Phytol. 2015 Aug;207(3):748-59. doi: 10.1111/nph.13365. Epub 2015 Mar 17.


Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean.

Zhao M, Meyers BC, Cai C, Xu W, Ma J.

Plant Cell. 2015 Mar;27(3):546-62. doi: 10.1105/tpc.15.00048. Epub 2015 Mar 6.


Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers.

Zhai J, Zhang H, Arikit S, Huang K, Nan GL, Walbot V, Meyers BC.

Proc Natl Acad Sci U S A. 2015 Mar 10;112(10):3146-51. doi: 10.1073/pnas.1418918112. Epub 2015 Feb 23.

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