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Items: 40

1.

The complex architecture and epigenomic impact of plant T-DNA insertions.

Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR.

PLoS Genet. 2019 Jan 18;15(1):e1007819. doi: 10.1371/journal.pgen.1007819. eCollection 2019 Jan.

2.

The case for not masking away repetitive DNA.

Slotkin RK.

Mob DNA. 2018 May 1;9:15. doi: 10.1186/s13100-018-0120-9. eCollection 2018.

3.

Paternal easiRNAs regulate parental genome dosage in Arabidopsis.

Martinez G, Wolff P, Wang Z, Moreno-Romero J, Santos-González J, Conze LL, DeFraia C, Slotkin RK, Köhler C.

Nat Genet. 2018 Feb;50(2):193-198. doi: 10.1038/s41588-017-0033-4. Epub 2018 Jan 15.

PMID:
29335548
4.

EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels.

Daron J, Slotkin RK.

Genome Biol. 2017 May 12;18(1):91. doi: 10.1186/s13059-017-1232-0.

5.

tRNA-derived small RNAs target transposable element transcripts.

Martinez G, Choudury SG, Slotkin RK.

Nucleic Acids Res. 2017 May 19;45(9):5142-5152. doi: 10.1093/nar/gkx103.

6.

Exogenous Transposable Elements Circumvent Identity-Based Silencing, Permitting the Dissection of Expression-Dependent Silencing.

Fultz D, Slotkin RK.

Plant Cell. 2017 Feb;29(2):360-376. doi: 10.1105/tpc.16.00718. Epub 2017 Feb 13.

7.

Corrigendum: Non-canonical RNA-directed DNA methylation.

Cuerda-Gil D, Slotkin RK.

Nat Plants. 2016 Dec 12;3:16211. doi: 10.1038/nplants.2016.211. No abstract available.

PMID:
27941819
8.

Non-canonical RNA-directed DNA methylation.

Cuerda-Gil D, Slotkin RK.

Nat Plants. 2016 Nov 3;2(11):16163. doi: 10.1038/nplants.2016.163. Review. Erratum in: Nat Plants. 2016 Dec 12;3:16211.

PMID:
27808230
9.

Erratum: The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding RNA 2016, 2, 9.

Gautheret D, Taube JH, Mani SA, Santulli G, Cuerda-Gil D, Slotkin RK, Zhang B, Wang Y, Salzman DW, Weidhaas JB.

Noncoding RNA. 2016 Sep 30;2(4). pii: E10. doi: 10.3390/ncrna2040010.

10.

The Non-Coding RNA Journal Club: Highlights on Recent Papers-4.

Gautheret D, Taube JH, Mani SA, Santulli G, Cuerda-Gil D, Slotkin RK, Zhang B, Wang Y, Salzman DW, Weidhaas JB.

Noncoding RNA. 2016 Sep 21;2(3). pii: E9. doi: 10.3390/ncrna2030009.

11.

Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation.

Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK.

Genome Biol. 2016 Aug 9;17(1):170. doi: 10.1186/s13059-016-1032-y.

12.

Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell.

Martínez G, Panda K, Köhler C, Slotkin RK.

Nat Plants. 2016 Mar 21;2:16030. doi: 10.1038/nplants.2016.30.

PMID:
27249563
13.

Plant epigenetics: from genotype to phenotype and back again.

Slotkin RK.

Genome Biol. 2016 Mar 29;17:57. doi: 10.1186/s13059-016-0920-5.

14.

The First Rule of Plant Transposable Element Silencing: Location, Location, Location.

Sigman MJ, Slotkin RK.

Plant Cell. 2016 Feb;28(2):304-13. doi: 10.1105/tpc.15.00869. Epub 2016 Feb 11. Review.

15.

Silencing of active transposable elements in plants.

Fultz D, Choudury SG, Slotkin RK.

Curr Opin Plant Biol. 2015 Oct;27:67-76. doi: 10.1016/j.pbi.2015.05.027. Epub 2015 Jul 8. Review.

PMID:
26164237
16.

Mobile genetic elements and genome evolution 2014.

Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL.

Mob DNA. 2014 Nov 18;5:26. doi: 10.1186/1759-8753-5-26. eCollection 2014.

17.

ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation.

McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN, Slotkin RK.

EMBO J. 2015 Jan 2;34(1):20-35. doi: 10.15252/embj.201489499. Epub 2014 Nov 11.

18.

Analysis of retrotransposon activity in plants.

Defraia C, Slotkin RK.

Methods Mol Biol. 2014;1112:195-210. doi: 10.1007/978-1-62703-773-0_13.

PMID:
24478016
19.

Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs.

McCue AD, Nuthikattu S, Slotkin RK.

RNA Biol. 2013 Aug;10(8):1379-95. doi: 10.4161/rna.25555. Epub 2013 Jul 2.

20.

Plant mobile small RNAs.

Dunoyer P, Melnyk C, Molnar A, Slotkin RK.

Cold Spring Harb Perspect Biol. 2013 Jul 1;5(7). pii: a017897. doi: 10.1101/cshperspect.a017897. Review.

21.

Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway.

Panda K, Slotkin RK.

Plant Signal Behav. 2013 Aug;8(8). pii: e25206. doi: 10.4161/psb.25206. Epub 2013 Jun 5.

22.

The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs.

Nuthikattu S, McCue AD, Panda K, Fultz D, DeFraia C, Thomas EN, Slotkin RK.

Plant Physiol. 2013 May;162(1):116-31. doi: 10.1104/pp.113.216481. Epub 2013 Mar 29.

23.

FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei.

Borges F, Gardner R, Lopes T, Calarco JP, Boavida LC, Slotkin RK, Martienssen RA, Becker JD.

Plant Methods. 2012 Oct 17;8(1):44. doi: 10.1186/1746-4811-8-44.

24.

Transposable element small RNAs as regulators of gene expression.

McCue AD, Slotkin RK.

Trends Genet. 2012 Dec;28(12):616-23. doi: 10.1016/j.tig.2012.09.001. Epub 2012 Oct 3. Review.

PMID:
23040327
25.

Developmental relaxation of transposable element silencing in plants: functional or byproduct?

Martínez G, Slotkin RK.

Curr Opin Plant Biol. 2012 Nov;15(5):496-502. doi: 10.1016/j.pbi.2012.09.001. Epub 2012 Sep 27. Review.

PMID:
23022393
26.

Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA.

McCue AD, Nuthikattu S, Reeder SH, Slotkin RK.

PLoS Genet. 2012 Feb;8(2):e1002474. doi: 10.1371/journal.pgen.1002474. Epub 2012 Feb 9.

27.

Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts.

Lisch D, Slotkin RK.

Int Rev Cell Mol Biol. 2011;292:119-52. doi: 10.1016/B978-0-12-386033-0.00003-7. Review.

PMID:
22078960
28.

Cytoplasmic connection of sperm cells to the pollen vegetative cell nucleus: potential roles of the male germ unit revisited.

McCue AD, Cresti M, Feijó JA, Slotkin RK.

J Exp Bot. 2011 Mar;62(5):1621-31. doi: 10.1093/jxb/err032. Review.

PMID:
21357775
29.

MicroRNA activity in the Arabidopsis male germline.

Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD.

J Exp Bot. 2011 Mar;62(5):1611-20. doi: 10.1093/jxb/erq452. Review. Erratum in: J Exp Bot. 2011 Jun;62(10):3699.

30.

Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition.

Jiang N, Ferguson AA, Slotkin RK, Lisch D.

Proc Natl Acad Sci U S A. 2011 Jan 25;108(4):1537-42. doi: 10.1073/pnas.1010814108. Epub 2011 Jan 10.

31.

The epigenetic control of the Athila family of retrotransposons in Arabidopsis.

Slotkin RK.

Epigenetics. 2010 Aug 16;5(6):483-90. Epub 2010 Aug 16. Review.

PMID:
20484989
32.

Control of female gamete formation by a small RNA pathway in Arabidopsis.

Olmedo-Monfil V, Durán-Figueroa N, Arteaga-Vázquez M, Demesa-Arévalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA, Vielle-Calzada JP.

Nature. 2010 Mar 25;464(7288):628-32. doi: 10.1038/nature08828. Epub 2010 Mar 7.

33.

Epigenetic inheritance and reprogramming in plants and fission yeast.

Martienssen RA, Kloc A, Slotkin RK, Tanurdzić M.

Cold Spring Harb Symp Quant Biol. 2008;73:265-71. doi: 10.1101/sqb.2008.73.062. Epub 2009 Mar 27. Review.

PMID:
19329575
34.

Epigenetic reprogramming and small RNA silencing of transposable elements in pollen.

Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA.

Cell. 2009 Feb 6;136(3):461-72. doi: 10.1016/j.cell.2008.12.038.

35.

The functional role of pack-MULEs in rice inferred from purifying selection and expression profile.

Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH, Jiang N.

Plant Cell. 2009 Jan;21(1):25-38. doi: 10.1105/tpc.108.063206. Epub 2009 Jan 9.

36.

Epigenomic consequences of immortalized plant cell suspension culture.

Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA.

PLoS Biol. 2008 Dec 9;6(12):2880-95. doi: 10.1371/journal.pbio.0060302.

37.

Kismeth: analyzer of plant methylation states through bisulfite sequencing.

Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R.

BMC Bioinformatics. 2008 Sep 11;9:371. doi: 10.1186/1471-2105-9-371.

38.

Transposable elements and the epigenetic regulation of the genome.

Slotkin RK, Martienssen R.

Nat Rev Genet. 2007 Apr;8(4):272-85. Review.

PMID:
17363976
39.

Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication.

Slotkin RK, Freeling M, Lisch D.

Nat Genet. 2005 Jun;37(6):641-4. Epub 2005 May 22.

PMID:
15908951
40.

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