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Environmental and epigenetic regulation of Rider retrotransposons in tomato.

Benoit M, Drost HG, Catoni M, Gouil Q, Lopez-Gomollon S, Baulcombe D, Paszkowski J.

PLoS Genet. 2019 Sep 16;15(9):e1008370. doi: 10.1371/journal.pgen.1008370. eCollection 2019 Sep.


Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression.

Chung BY, Valli A, Deery MJ, Navarro FJ, Brown K, Hnatova S, Howard J, Molnar A, Baulcombe DC.

Sci Rep. 2019 Jul 31;9(1):11091. doi: 10.1038/s41598-019-47415-x.


How Virus Resistance Provided a Mechanistic Foundation for RNA Silencing.

Baulcombe DC.

Plant Cell. 2019 Jul;31(7):1395-1396. doi: 10.1105/tpc.19.00348. Epub 2019 May 8. No abstract available.


Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis.

Kirkbride RC, Lu J, Zhang C, Mosher RA, Baulcombe DC, Chen ZJ.

Proc Natl Acad Sci U S A. 2019 Feb 12;116(7):2761-2766. doi: 10.1073/pnas.1807621116. Epub 2019 Jan 28. Erratum in: Proc Natl Acad Sci U S A. 2019 Apr 23;116(17):8633.


Enhanced resistance to bacterial and oomycete pathogens by short tandem target mimic RNAs in tomato.

Canto-Pastor A, Santos BAMC, Valli AA, Summers W, Schornack S, Baulcombe DC.

Proc Natl Acad Sci U S A. 2019 Feb 12;116(7):2755-2760. doi: 10.1073/pnas.1814380116. Epub 2019 Jan 24.


miRNA-Mediated Regulation of Synthetic Gene Circuits in the Green Alga Chlamydomonas reinhardtii.

Navarro FJ, Baulcombe DC.

ACS Synth Biol. 2019 Feb 15;8(2):358-370. doi: 10.1021/acssynbio.8b00393. Epub 2019 Jan 24.


Birth of a Photosynthetic Chassis: A MoClo Toolkit Enabling Synthetic Biology in the Microalga Chlamydomonas reinhardtii.

Crozet P, Navarro FJ, Willmund F, Mehrshahi P, Bakowski K, Lauersen KJ, Pérez-Pérez ME, Auroy P, Gorchs Rovira A, Sauret-Gueto S, Niemeyer J, Spaniol B, Theis J, Trösch R, Westrich LD, Vavitsas K, Baier T, Hübner W, de Carpentier F, Cassarini M, Danon A, Henri J, Marchand CH, de Mia M, Sarkissian K, Baulcombe DC, Peltier G, Crespo JL, Kruse O, Jensen PE, Schroda M, Smith AG, Lemaire SD.

ACS Synth Biol. 2018 Sep 21;7(9):2074-2086. doi: 10.1021/acssynbio.8b00251. Epub 2018 Sep 5.


A novel DCL2-dependent miRNA pathway in tomato affects susceptibility to RNA viruses.

Wang Z, Hardcastle TJ, Canto Pastor A, Yip WH, Tang S, Baulcombe DC.

Genes Dev. 2018 Sep 1;32(17-18):1155-1160. doi: 10.1101/gad.313601.118. Epub 2018 Aug 27.


Towards annotating the plant epigenome: the Arabidopsis thaliana small RNA locus map.

Hardcastle TJ, Müller SY, Baulcombe DC.

Sci Rep. 2018 Apr 20;8(1):6338. doi: 10.1038/s41598-018-24515-8.


Paramutation-like features of multiple natural epialleles in tomato.

Gouil Q, Baulcombe DC.

BMC Genomics. 2018 Mar 20;19(1):203. doi: 10.1186/s12864-018-4590-4.


Maize chlorotic mottle virus exhibits low divergence between differentiated regional sub-populations.

Braidwood L, Quito-Avila DF, Cabanas D, Bressan A, Wangai A, Baulcombe DC.

Sci Rep. 2018 Jan 19;8(1):1173. doi: 10.1038/s41598-018-19607-4.


Endogenous miRNA in the green alga Chlamydomonas regulates gene expression through CDS-targeting.

Chung BY, Deery MJ, Groen AJ, Howard J, Baulcombe DC.

Nat Plants. 2017 Oct;3(10):787-794. doi: 10.1038/s41477-017-0024-6. Epub 2017 Oct 2.


Epigenetic and Genetic Contributions to Adaptation in Chlamydomonas.

Kronholm I, Bassett A, Baulcombe D, Collins S.

Mol Biol Evol. 2017 Sep 1;34(9):2285-2306. doi: 10.1093/molbev/msx166.


Improved Denaturation of Small RNA Duplexes and Its Application for Northern Blotting.

Harris CJ, Baulcombe DC, Molnar A.

Methods Mol Biol. 2017;1580:1-6. doi: 10.1007/978-1-4939-6866-4_1.


DNA Methylation Signatures of the Plant Chromomethyltransferases.

Gouil Q, Baulcombe DC.

PLoS Genet. 2016 Dec 20;12(12):e1006526. doi: 10.1371/journal.pgen.1006526. eCollection 2016 Dec.


Analysis of Small RNA Populations Using Hybridization to DNA Tiling Arrays.

Boccara M, Sarazin A, Billoud B, Bulski A, Chapell L, Baulcombe D, Colot V.

Methods Mol Biol. 2017;1456:127-139.


A Viral Movement Protein Prevents Spread of the Gene Silencing Signal in Nicotiana benthamiana.

Voinnet O, Lederer C, Baulcombe DC.

Cell. 2016 Jul 28;166(3):780. doi: 10.1016/j.cell.2016.07.015. No abstract available.


Systemic Spread of Sequence-Specific Transgene RNA Degradation in Plants Is Initiated by Localized Introduction of Ectopic Promoterless DNA.

Voinnet O, Vain P, Angell S, Baulcombe DC.

Cell. 2016 Jul 28;166(3):779. doi: 10.1016/j.cell.2016.07.014. No abstract available.


Most microRNAs in the single-cell alga Chlamydomonas reinhardtii are produced by Dicer-like 3-mediated cleavage of introns and untranslated regions of coding RNAs.

Valli AA, Santos BA, Hnatova S, Bassett AR, Molnar A, Chung BY, Baulcombe DC.

Genome Res. 2016 Apr;26(4):519-29. doi: 10.1101/gr.199703.115. Epub 2016 Mar 11.


SLTAB2 is the paramutated SULFUREA locus in tomato.

Gouil Q, Novák O, Baulcombe DC.

J Exp Bot. 2016 Apr;67(9):2655-64. doi: 10.1093/jxb/erw096. Epub 2016 Mar 8.


The P1N-PISPO trans-Frame Gene of Sweet Potato Feathery Mottle Potyvirus Is Produced during Virus Infection and Functions as an RNA Silencing Suppressor.

Mingot A, Valli A, Rodamilans B, San León D, Baulcombe DC, García JA, López-Moya JJ.

J Virol. 2016 Jan 20;90(7):3543-57. doi: 10.1128/JVI.02360-15.


Mobile small RNAs regulate genome-wide DNA methylation.

Lewsey MG, Hardcastle TJ, Melnyk CW, Molnar A, Valli A, Urich MA, Nery JR, Baulcombe DC, Ecker JR.

Proc Natl Acad Sci U S A. 2016 Feb 9;113(6):E801-10. doi: 10.1073/pnas.1515072113. Epub 2016 Jan 19.


Two classes of short interfering RNA in RNA silencing.

Hamilton A, Voinnet O, Chappell L, Baulcombe D.

EMBO J. 2015 Oct 14;34(20):2590. doi: 10.15252/embj.201570050. Epub 2015 Aug 19. No abstract available.


The use of duplex-specific nuclease in ribosome profiling and a user-friendly software package for Ribo-seq data analysis.

Chung BY, Hardcastle TJ, Jones JD, Irigoyen N, Firth AE, Baulcombe DC, Brierley I.

RNA. 2015 Oct;21(10):1731-45. doi: 10.1261/rna.052548.115. Epub 2015 Aug 18.


VIGS, HIGS and FIGS: small RNA silencing in the interactions of viruses or filamentous organisms with their plant hosts.

Baulcombe DC.

Curr Opin Plant Biol. 2015 Aug;26:141-6. doi: 10.1016/j.pbi.2015.06.007. Epub 2015 Aug 3. Review.


Standards for plant synthetic biology: a common syntax for exchange of DNA parts.

Patron NJ, Orzaez D, Marillonnet S, Warzecha H, Matthewman C, Youles M, Raitskin O, Leveau A, Farré G, Rogers C, Smith A, Hibberd J, Webb AA, Locke J, Schornack S, Ajioka J, Baulcombe DC, Zipfel C, Kamoun S, Jones JD, Kuhn H, Robatzek S, Van Esse HP, Sanders D, Oldroyd G, Martin C, Field R, O'Connor S, Fox S, Wulff B, Miller B, Breakspear A, Radhakrishnan G, Delaux PM, Loqué D, Granell A, Tissier A, Shih P, Brutnell TP, Quick WP, Rischer H, Fraser PD, Aharoni A, Raines C, South PF, Ané JM, Hamberger BR, Langdale J, Stougaard J, Bouwmeester H, Udvardi M, Murray JA, Ntoukakis V, Schäfer P, Denby K, Edwards KJ, Osbourn A, Haseloff J.

New Phytol. 2015 Oct;208(1):13-9. doi: 10.1111/nph.13532. Epub 2015 Jul 14. Erratum in: New Phytol. 2016 Jan;209(2):885.


FDF-PAGE: a powerful technique revealing previously undetected small RNAs sequestered by complementary transcripts.

Harris CJ, Molnar A, Müller SY, Baulcombe DC.

Nucleic Acids Res. 2015 Sep 3;43(15):7590-9. doi: 10.1093/nar/gkv604. Epub 2015 Jun 13.


RNA polymerase slippage as a mechanism for the production of frameshift gene products in plant viruses of the potyviridae family.

Rodamilans B, Valli A, Mingot A, San León D, Baulcombe D, López-Moya JJ, García JA.

J Virol. 2015 Jul;89(13):6965-7. doi: 10.1128/JVI.00337-15. Epub 2015 Apr 15. No abstract available.


Evolution of NBS-LRR gene copies among Dicot plants and its regulation by members of the miR482/2118 superfamily of miRNAs.

González VM, Müller S, Baulcombe D, Puigdomènech P.

Mol Plant. 2015 Feb;8(2):329-31. doi: 10.1016/j.molp.2014.11.013. Epub 2014 Dec 12. No abstract available.


Epigenetic transitions leading to heritable, RNA-mediated de novo silencing in Arabidopsis thaliana.

Bond DM, Baulcombe DC.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):917-22. doi: 10.1073/pnas.1413053112. Epub 2015 Jan 5.


Epigenetic regulation in plant responses to the environment.

Baulcombe DC, Dean C.

Cold Spring Harb Perspect Biol. 2014 Sep 2;6(9):a019471. doi: 10.1101/cshperspect.a019471. Review.


5' isomiR variation is of functional and evolutionary importance.

Tan GC, Chan E, Molnar A, Sarkar R, Alexieva D, Isa IM, Robinson S, Zhang S, Ellis P, Langford CF, Guillot PV, Chandrashekran A, Fisk NM, Castellano L, Meister G, Winston RM, Cui W, Baulcombe D, Dibb NJ.

Nucleic Acids Res. 2014 Aug;42(14):9424-35. doi: 10.1093/nar/gku656. Epub 2014 Jul 23.


Relationship between genome and epigenome--challenges and requirements for future research.

Almouzni G, Altucci L, Amati B, Ashley N, Baulcombe D, Beaujean N, Bock C, Bongcam-Rudloff E, Bousquet J, Braun S, Bressac-de Paillerets B, Bussemakers M, Clarke L, Conesa A, Estivill X, Fazeli A, Grgurević N, Gut I, Heijmans BT, Hermouet S, Houwing-Duistermaat J, Iacobucci I, Ilaš J, Kandimalla R, Krauss-Etschmann S, Lasko P, Lehmann S, Lindroth A, Majdič G, Marcotte E, Martinelli G, Martinet N, Meyer E, Miceli C, Mills K, Moreno-Villanueva M, Morvan G, Nickel D, Niesler B, Nowacki M, Nowak J, Ossowski S, Pelizzola M, Pochet R, Potočnik U, Radwanska M, Raes J, Rattray M, Robinson MD, Roelen B, Sauer S, Schinzer D, Slagboom E, Spector T, Stunnenberg HG, Tiligada E, Torres-Padilla ME, Tsonaka R, Van Soom A, Vidaković M, Widschwendter M.

BMC Genomics. 2014 Jun 18;15:487. doi: 10.1186/1471-2164-15-487.


Using a viral vector to reveal the role of microRNA159 in disease symptom induction by a severe strain of Cucumber mosaic virus.

Du Z, Chen A, Chen W, Westwood JH, Baulcombe DC, Carr JP.

Plant Physiol. 2014 Mar;164(3):1378-88. doi: 10.1104/pp.113.232090. Epub 2014 Feb 3.


Stepwise artificial evolution of a plant disease resistance gene.

Harris CJ, Slootweg EJ, Goverse A, Baulcombe DC.

Proc Natl Acad Sci U S A. 2013 Dec 24;110(52):21189-94. doi: 10.1073/pnas.1311134110. Epub 2013 Dec 9.


Plant science. Small RNA--the secret of noble rot.

Baulcombe D.

Science. 2013 Oct 4;342(6154):45-6. doi: 10.1126/science.1245010. No abstract available.


Standing up for GMOs.

Alberts B, Beachy R, Baulcombe D, Blobel G, Datta S, Fedoroff N, Kennedy D, Khush GS, Peacock J, Rees M, Sharp P.

Science. 2013 Sep 20;341(6152):1320. doi: 10.1126/science.1245017. No abstract available.


Small RNAs and heritable epigenetic variation in plants.

Bond DM, Baulcombe DC.

Trends Cell Biol. 2014 Feb;24(2):100-7. doi: 10.1016/j.tcb.2013.08.001. Epub 2013 Sep 3. Review.


Metastable differentially methylated regions within Arabidopsis inbred populations are associated with modified expression of non-coding transcripts.

Havecker ER, Wallbridge LM, Fedito P, Hardcastle TJ, Baulcombe DC.

PLoS One. 2012;7(9):e45242. doi: 10.1371/journal.pone.0045242. Epub 2012 Sep 20.


A PHABULOSA/cytokinin feedback loop controls root growth in Arabidopsis.

Dello Ioio R, Galinha C, Fletcher AG, Grigg SP, Molnar A, Willemsen V, Scheres B, Sabatini S, Baulcombe D, Maini PK, Tsiantis M.

Curr Biol. 2012 Sep 25;22(18):1699-704. doi: 10.1016/j.cub.2012.07.005. Epub 2012 Aug 16.


Maternal siRNAs as regulators of parental genome imbalance and gene expression in endosperm of Arabidopsis seeds.

Lu J, Zhang C, Baulcombe DC, Chen ZJ.

Proc Natl Acad Sci U S A. 2012 Apr 3;109(14):5529-34. doi: 10.1073/pnas.1203094109. Epub 2012 Mar 19.


A microRNA superfamily regulates nucleotide binding site-leucine-rich repeats and other mRNAs.

Shivaprasad PV, Chen HM, Patel K, Bond DM, Santos BA, Baulcombe DC.

Plant Cell. 2012 Mar;24(3):859-74. doi: 10.1105/tpc.111.095380. Epub 2012 Mar 9. Erratum in: Plant Cell. 2019 Jul;31(7):1665-1668.


Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs.

Shivaprasad PV, Dunn RM, Santos BA, Bassett A, Baulcombe DC.

EMBO J. 2012 Jan 18;31(2):257-66. doi: 10.1038/emboj.2011.458. Epub 2011 Dec 16.


Identifying small interfering RNA loci from high-throughput sequencing data.

Hardcastle TJ, Kelly KA, Baulcombe DC.

Bioinformatics. 2012 Feb 15;28(4):457-63. doi: 10.1093/bioinformatics/btr687. Epub 2011 Dec 9.


An atypical epigenetic mechanism affects uniparental expression of Pol IV-dependent siRNAs.

Mosher RA, Tan EH, Shin J, Fischer RL, Pikaard CS, Baulcombe DC.

PLoS One. 2011;6(10):e25756. doi: 10.1371/journal.pone.0025756. Epub 2011 Oct 7.


Mobile 24 nt small RNAs direct transcriptional gene silencing in the root meristems of Arabidopsis thaliana.

Melnyk CW, Molnar A, Bassett A, Baulcombe DC.

Curr Biol. 2011 Oct 11;21(19):1678-83. doi: 10.1016/j.cub.2011.08.065. Epub 2011 Sep 29.


Intercellular and systemic movement of RNA silencing signals.

Melnyk CW, Molnar A, Baulcombe DC.

EMBO J. 2011 Aug 31;30(17):3553-63. doi: 10.1038/emboj.2011.274. Review.


The specific binding to 21-nt double-stranded RNAs is crucial for the anti-silencing activity of Cucumber vein yellowing virus P1b and perturbs endogenous small RNA populations.

Valli A, Oliveros JC, Molnar A, Baulcombe D, García JA.

RNA. 2011 Jun;17(6):1148-58. doi: 10.1261/rna.2510611. Epub 2011 Apr 29.


Comparative functional genomics of the fission yeasts.

Rhind N, Chen Z, Yassour M, Thompson DA, Haas BJ, Habib N, Wapinski I, Roy S, Lin MF, Heiman DI, Young SK, Furuya K, Guo Y, Pidoux A, Chen HM, Robbertse B, Goldberg JM, Aoki K, Bayne EH, Berlin AM, Desjardins CA, Dobbs E, Dukaj L, Fan L, FitzGerald MG, French C, Gujja S, Hansen K, Keifenheim D, Levin JZ, Mosher RA, Müller CA, Pfiffner J, Priest M, Russ C, Smialowska A, Swoboda P, Sykes SM, Vaughn M, Vengrova S, Yoder R, Zeng Q, Allshire R, Baulcombe D, Birren BW, Brown W, Ekwall K, Kellis M, Leatherwood J, Levin H, Margalit H, Martienssen R, Nieduszynski CA, Spatafora JW, Friedman N, Dalgaard JZ, Baumann P, Niki H, Regev A, Nusbaum C.

Science. 2011 May 20;332(6032):930-6. doi: 10.1126/science.1203357. Epub 2011 Apr 21.

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