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R. Keith Slotkin - Publications

Affiliations: 
Ohio State University, Columbus, Columbus, OH 
 2005 University of California, Berkeley, Berkeley, CA, United States 
Area:
Genetics, Molecular Biology, Plant Physiology
Website:
https://molgen.osu.edu/people/slotkin.2
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61 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Liu P, Panda K, Edwards SA, Swanson R, Yi H, Pandesha P, Hung YH, Klaas G, Ye X, Collins MV, Renken KN, Gilbertson LA, Veena V, Hancock CN, Slotkin RK. Transposase-assisted target-site integration for efficient plant genome engineering. Nature. PMID 38926583 DOI: 10.1038/s41586-024-07613-8  0.784
2024 Kramer MC, Swanson R, Slotkin RK. Reading banned regions of genomes. Nature Plants. PMID 38225351 DOI: 10.1038/s41477-023-01600-z  0.761
2023 Bélanger S, Kramer MC, Payne HA, Hui AY, Slotkin RK, Meyers BC, Staub JM. Plastid double-stranded RNA transgenes trigger phased small RNA-based gene silencing of nuclear-encoded genes. The Plant Cell. PMID 37309669 DOI: 10.1093/plcell/koad165  0.836
2023 Renken K, Mendoza SM, Diaz S, Slotkin RK, Hancock CN. Pol V produced RNA facilitates transposable element excision site repair in . Micropublication Biology. 2023. PMID 37273575 DOI: 10.17912/micropub.biology.000793  0.39
2023 Panda K, Mohanasundaram B, Gutierrez J, McLain L, Castillo SE, Sheng H, Casto A, Gratacós G, Chakrabarti A, Fahlgren N, Pandey S, Gehan MA, Slotkin RK. The plant response to high CO levels is heritable and orchestrated by DNA methylation. The New Phytologist. PMID 36918471 DOI: 10.1111/nph.18876  0.806
2023 Edwards SA, Slotkin RK. Broken up but still living together: how ARGONAUTE's retention of cleaved fragments explains its role during chromatin modification. Genes & Development. 37: 69-71. PMID 36754778 DOI: 10.1101/gad.350424.123  0.868
2022 Liu P, Cuerda-Gil D, Shahid S, Slotkin RK. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond. Annual Review of Genetics. 56: 63-87. PMID 36449356 DOI: 10.1146/annurev-genet-072920-015534  0.798
2022 Cuerda-Gil D, Hung YH, Panda K, Slotkin RK. A plant tethering system for the functional study of protein-RNA interactions in vivo. Plant Methods. 18: 75. PMID 35658900 DOI: 10.1186/s13007-022-00907-w  0.832
2021 Sigman MJ, Panda K, Kirchner R, McLain LL, Payne H, Peasari JR, Husbands AY, Slotkin RK, McCue AD. An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation. Nature Plants. 7: 1461-1474. PMID 34750500 DOI: 10.1038/s41477-021-01008-7  0.836
2021 Hung YH, Slotkin RK. The initiation of RNA interference (RNAi) in plants. Current Opinion in Plant Biology. 61: 102014. PMID 33657510 DOI: 10.1016/j.pbi.2021.102014  0.514
2021 Annacondia ML, Markovic D, Reig-Valiente JL, Scaltsoyiannes V, Pieterse CMJ, Ninkovic V, Slotkin RK, Martinez G. Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis. The New Phytologist. PMID 33475147 DOI: 10.1111/nph.17226  0.434
2020 Antunez-Sanchez J, Naish M, Ramirez-Prado JS, Ohno S, Huang Y, Dawson A, Opassathian K, Manza-Mianza D, Ariel F, Raynaud C, Wibowo A, Daron J, Ueda M, Latrasse D, Slotkin RK, et al. A new role for histone demethylases in the maintenance of plant genome integrity. Elife. 9. PMID 33107825 DOI: 10.7554/eLife.58533  0.784
2020 Lai Y, Lu XM, Daron J, Pan S, Wang J, Wang W, Tsuchiya T, Holub E, McDowell JM, Slotkin RK, Le Roch KG, Eulgem T. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. Plos Genetics. 16: e1008993. PMID 32925902 DOI: 10.1371/Journal.Pgen.1008993  0.799
2020 Panda K, Slotkin RK. Long-read cDNA Sequencing Enables a 'Gene-Like' Transcript Annotation of Transposable Elements. The Plant Cell. PMID 32647069 DOI: 10.1105/Tpc.20.00115  0.843
2020 Warman C, Panda K, Vejlupkova Z, Hokin S, Unger-Wallace E, Cole RA, Chettoor AM, Jiang D, Vollbrecht E, Evans MMS, Slotkin RK, Fowler JE. High expression in maize pollen correlates with genetic contributions to pollen fitness as well as with coordinated transcription from neighboring transposable elements. Plos Genetics. 16: e1008462. PMID 32236090 DOI: 10.1371/Journal.Pgen.1008462  0.809
2020 Yates-Stewart AD, Daron J, Wijeratne S, Shahid S, Edgington HA, Slotkin RK, Michel A. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. Insect Biochemistry and Molecular Biology. 103363. PMID 32201218 DOI: 10.1016/J.Ibmb.2020.103363  0.809
2020 Panda K, McCue AD, Slotkin RK. RNA Polymerase IV generates 21-22 nucleotide small RNAs that can participate in RNA-directed DNA methylation and may regulate genes. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 375: 20190417. PMID 32075560 DOI: 10.1098/Rstb.2019.0417  0.867
2020 Shahid S, Slotkin RK. The current revolution in transposable element biology enabled by long reads. Current Opinion in Plant Biology. 54: 49-56. PMID 32007731 DOI: 10.1016/J.Pbi.2019.12.012  0.731
2019 Ji L, Mathioni S, Johnson S, Tucker D, Bewick AJ, Kim KD, Daron J, Slotkin RK, Jackson SA, Parrott WA, Meyers BC, Schmitz R. Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. The Plant Cell. PMID 31439802 DOI: 10.1105/Tpc.19.00255  0.805
2019 Zhang Y, Ramming A, Heinke L, Altschmied L, Slotkin RK, Becker JD, Kappel C, Lenhard M. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development. The Plant Journal : For Cell and Molecular Biology. PMID 31009115 DOI: 10.1111/tpj.14348  0.502
2019 Choudury SG, Shahid S, Cuerda-Gil D, Panda K, Cullen A, Ashraf QUA, Sigman MJ, McCue AD, Slotkin RK. The RNA export factor ALY1 enables genome-wide RNA-directed DNA methylation. The Plant Cell. PMID 30814259 DOI: 10.1105/Tpc.18.00624  0.808
2019 Jupe F, Rivkin AC, Michael TP, Zander M, Motley ST, Sandoval JP, Slotkin RK, Chen H, Castanon R, Nery JR, Ecker JR. The complex architecture and epigenomic impact of plant T-DNA insertions. Plos Genetics. 15: e1007819. PMID 30657772 DOI: 10.1371/Journal.Pgen.1007819  0.349
2018 Slotkin RK. The case for not masking away repetitive DNA. Mobile Dna. 9: 15. PMID 29743957 DOI: 10.1186/S13100-018-0120-9  0.412
2018 Martinez G, Wolff P, Wang Z, Moreno-Romero J, Santos-González J, Conze LL, DeFraia C, Slotkin RK, Köhler C. Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nature Genetics. PMID 29335548 DOI: 10.1038/S41588-017-0033-4  0.856
2017 Daron J, Slotkin RK. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biology. 18: 91. PMID 28499400 DOI: 10.1186/S13059-017-1232-0  0.794
2017 Martinez G, Choudury SG, Slotkin RK. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Research. PMID 28335016 DOI: 10.1093/Nar/Gkx103  0.867
2017 Fultz D, Slotkin RK. Exogenous Transposable Elements Circumvent Identity-Based Silencing Permitting the Dissection of Expression Dependent Silencing. The Plant Cell. PMID 28193737 DOI: 10.1105/Tpc.16.00718  0.861
2016 Gautheret D, Taube JH, Mani SA, Santulli G, Cuerda-Gil D, Slotkin RK, Zhang B, Wang Y, Salzman DW, Weidhaas JB. Erratum: The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding RNA 2016, 2, 9. Non-Coding Rna. 2. PMID 29657269 DOI: 10.3390/Ncrna2040010  0.816
2016 Gautheret D, Taube JH, Mani SA, Santulli G, Cuerda-Gil D, Slotkin RK, Zhang B, Wang Y, Salzman DW, Weidhaas JB. The Non-Coding RNA Journal Club: Highlights on Recent Papers-4. Non-Coding Rna. 2. PMID 29657267 DOI: 10.3390/Ncrna2030009  0.807
2016 Cuerda-Gil D, Slotkin RK. Corrigendum: Non-canonical RNA-directed DNA methylation. Nature Plants. 3: 16211. PMID 27941819 DOI: 10.1038/Nplants.2016.211  0.853
2016 Cuerda-Gil D, Slotkin RK. Non-canonical RNA-directed DNA methylation. Nature Plants. 2: 16163. PMID 27808230 DOI: 10.1038/Nplants.2016.163  0.85
2016 Panda K, Ji L, Neumann DA, Daron J, Schmitz RJ, Slotkin RK. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology. 17: 170. PMID 27506905 DOI: 10.1186/S13059-016-1032-Y  0.864
2016 Martínez G, Panda K, Köhler C, Slotkin RK. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants. 2: 16030. PMID 27249563 DOI: 10.1038/Nplants.2016.30  0.816
2016 Slotkin RK. Plant epigenetics: from genotype to phenotype and back again. Genome Biology. 17: 57. PMID 27025922 DOI: 10.1186/S13059-016-0920-5  0.35
2016 Sigman MJ, Slotkin RK. The First Rule of Plant Transposable Element Silencing: Location, Location, Location. The Plant Cell. 28: 304-13. PMID 26869697 DOI: 10.1105/Tpc.15.00869  0.719
2015 Fultz D, Choudury SG, Slotkin RK. Silencing of active transposable elements in plants. Current Opinion in Plant Biology. 27: 67-76. PMID 26164237 DOI: 10.1016/J.Pbi.2015.05.027  0.808
2015 McCue AD, Panda K, Nuthikattu S, Choudury SG, Thomas EN, Slotkin RK. ARGONAUTE 6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. The Embo Journal. 34: 20-35. PMID 25388951 DOI: 10.15252/Embj.201489499  0.827
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. Mobile genetic elements and genome evolution 2014. Mobile Dna. 5: 26. PMID 30117500 DOI: 10.1186/1759-8753-5-26  0.367
2014 Defraia C, Slotkin RK. Analysis of retrotransposon activity in plants. Methods in Molecular Biology (Clifton, N.J.). 1112: 195-210. PMID 24478016 DOI: 10.1007/978-1-62703-773-0_13  0.86
2013 McCue AD, Nuthikattu S, Slotkin RK. Genome-wide identification of genes regulated in trans by transposable element small interfering RNAs. Rna Biology. 10: 1379-95. PMID 23863322 DOI: 10.4161/Rna.25555  0.856
2013 Dunoyer P, Melnyk C, Molnar A, Slotkin RK. Plant mobile small RNAs. Cold Spring Harbor Perspectives in Biology. 5. PMID 23818501 DOI: 10.1101/Cshperspect.A017897  0.562
2013 Panda K, Slotkin RK. Proposed mechanism for the initiation of transposable element silencing by the RDR6-directed DNA methylation pathway. Plant Signaling & Behavior. 8. PMID 23759554 DOI: 10.4161/psb.25206  0.838
2013 Nuthikattu S, McCue AD, Panda K, Fultz D, DeFraia C, Thomas EN, Slotkin RK. The initiation of epigenetic silencing of active transposable elements is triggered by RDR6 and 21-22 nucleotide small interfering RNAs. Plant Physiology. 162: 116-31. PMID 23542151 DOI: 10.1104/Pp.113.216481  0.828
2012 Borges F, Gardner R, Lopes T, Calarco JP, Boavida LC, Slotkin RK, Martienssen RA, Becker JD. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods. 8: 44. PMID 23075219 DOI: 10.1186/1746-4811-8-44  0.676
2012 McCue AD, Slotkin RK. Transposable element small RNAs as regulators of gene expression. Trends in Genetics : Tig. 28: 616-23. PMID 23040327 DOI: 10.1016/J.Tig.2012.09.001  0.866
2012 Martínez G, Slotkin RK. Developmental relaxation of transposable element silencing in plants: functional or byproduct? Current Opinion in Plant Biology. 15: 496-502. PMID 23022393 DOI: 10.1016/J.Pbi.2012.09.001  0.383
2012 McCue AD, Nuthikattu S, Reeder SH, Slotkin RK. Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA. Plos Genetics. 8: e1002474. PMID 22346759 DOI: 10.1371/Journal.Pgen.1002474  0.855
2011 Lisch D, Slotkin RK. Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts. International Review of Cell and Molecular Biology. 292: 119-52. PMID 22078960 DOI: 10.1016/B978-0-12-386033-0.00003-7  0.732
2011 McCue AD, Cresti M, Feijó JA, Slotkin RK. Cytoplasmic connection of sperm cells to the pollen vegetative cell nucleus: potential roles of the male germ unit revisited. Journal of Experimental Botany. 62: 1621-31. PMID 21357775 DOI: 10.1093/Jxb/Err032  0.775
2011 Borges F, Pereira PA, Slotkin RK, Martienssen RA, Becker JD. MicroRNA activity in the Arabidopsis male germline. Journal of Experimental Botany. 62: 1611-20. PMID 21357774 DOI: 10.1093/Jxb/Erq452  0.661
2011 Jiang N, Ferguson AA, Slotkin RK, Lisch D. Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition. Proceedings of the National Academy of Sciences of the United States of America. 108: 1537-42. PMID 21220310 DOI: 10.1073/Pnas.1010814108  0.684
2010 Slotkin RK. The epigenetic control of the Athila family of retrotransposons in Arabidopsis. Epigenetics. 5: 483-90. PMID 20484989 DOI: 10.4161/Epi.5.6.12119  0.505
2010 Olmedo-Monfil V, Durán-Figueroa N, Arteaga-Vázquez M, Demesa-Arévalo E, Autran D, Grimanelli D, Slotkin RK, Martienssen RA, Vielle-Calzada JP. Control of female gamete formation by a small RNA pathway in Arabidopsis. Nature. 464: 628-32. PMID 20208518 DOI: 10.1038/nature08828  0.73
2009 Slotkin RK, Vaughn M, Borges F, Tanurdzić M, Becker JD, Feijó JA, Martienssen RA. Epigenetic reprogramming and small RNA silencing of transposable elements in pollen. Cell. 136: 461-72. PMID 19203581 DOI: 10.1016/j.cell.2008.12.038  0.792
2009 Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH, Jiang N. The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. The Plant Cell. 21: 25-38. PMID 19136648 DOI: 10.1105/Tpc.108.063206  0.705
2008 Martienssen RA, Kloc A, Slotkin RK, Tanurdzić M. Epigenetic inheritance and reprogramming in plants and fission yeast. Cold Spring Harbor Symposia On Quantitative Biology. 73: 265-71. PMID 19329575 DOI: 10.1101/Sqb.2008.73.062  0.792
2008 Tanurdzic M, Vaughn MW, Jiang H, Lee TJ, Slotkin RK, Sosinski B, Thompson WF, Doerge RW, Martienssen RA. Epigenomic consequences of immortalized plant cell suspension culture. Plos Biology. 6: 2880-95. PMID 19071958 DOI: 10.1371/Journal.Pbio.0060302  0.76
2008 Gruntman E, Qi Y, Slotkin RK, Roeder T, Martienssen RA, Sachidanandam R. Kismeth: analyzer of plant methylation states through bisulfite sequencing. Bmc Bioinformatics. 9: 371. PMID 18786255 DOI: 10.1186/1471-2105-9-371  0.709
2007 Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nature Reviews. Genetics. 8: 272-85. PMID 17363976 DOI: 10.1038/Nrg2072  0.75
2005 Slotkin RK, Freeling M, Lisch D. Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication. Nature Genetics. 37: 641-4. PMID 15908951 DOI: 10.1038/Ng1576  0.861
2003 Slotkin RK, Freeling M, Lisch D. Mu killer causes the heritable inactivation of the Mutator family of transposable elements in Zea mays. Genetics. 165: 781-97. PMID 14573488  0.851
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