Publications

An up to date full list of publications can be found on Google Scholar.

Bold text indicates Slotkin lab current member or alumni

Italic text indicates Slotkin lab undergraduate reseracher

2023

P. Liu, K. Panda, S.A. Edwards, H. Yi, P. Pandesha, Y.-H. Hung, R. Swanson, G. Klaas, X. Ye, V. Veena, L.A. Gilbertson, C.N. Hancock and R.K. Slotkin. CRISPR-targeted transposable element insertion for efficient plant genome engineering. In Review

S. Belanger, M.C. Kramer, H.A. Payne, A.Y. Hui, R.K. Slotkin, B.C. Meyers, J.M. Staub. Plastid double-strand RNA transgenes trigger small RNA-based gene silencing of nuclear-encoded genes The Plant Cell 35:2298-3412.

K. Panda, B. Mohanasundaram, J. Gutierrez, L. McLain, S.E. Castillo, H. Sheng, A. Casto, G. Gratacós, A. Chakrabarti, N. Fahlgren, S. Pandey, M.A. Gehan and R.K. Slotkin. The plant response to high CO2 levels is heritable and orchestrated by DNA methylation. New Phytologist 238:2427-2439.

K. Renken, S.M. Mendoza, S. Diaz, R.K. Slotkin, C.N. Hancock. Pol V produced RNA facilitates transposable element excision site repair in Arabidopsis. MicroPublication Biology 000793.

P. Zhang, A. Mbodj, A. Soundiramourtty, C. Llauro, A. Ghesquiere, M. Ingouff, R.K. Slotkin, F. Pontvianne, M. Catoni, M. Mirouze. Extrachromosomal circular DNA and structural variants highlight genome instability in Arabidopsis epigenetic mutants. Nature Communications 14:5236.

2022

P. Liu, D. Cuerda-Gil, S. Shahid and R.K. Slotkin. The Epigenetic Control of the Transposable Element Life Cycle in Plant Genomes and Beyond Annual Review of Genetics 56:63-87.

D. Cuerda-Gil, Y.-H. Hung, K. Panda and R.K. Slotkin. A plant tethering system for the functional study of protein-RNA interactions in vivo Plant Methods 18:75.

C. Oliver, M.L. Annacondia, Z. Wang, P.E. Jullien, R.K. Slotkin, C. Kohler and G. Martinez. The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation The Plant Cell 34:784-801.

2021

M. Sigman, K. Panda, R. Kirchner, L. McLain, H. Payne, J. Peasari, A. Husbands, R.K. Slotkin and A.D. McCue. An siRNA-guided ARGONAUTE protein directs RNA polymerase V to initiate DNA methylation Nature Plants 7:1461–1474.

Y.-H. Hung and R.K. Slotkin. The initiation of RNA interference (RNAi) in plants Current Opinion in Plant Biology v61:102014.

M.L. Annacondia, D. Markovic, J.L. Reig-Valiente, V. Scaltsoyiannes, C.M. Pieterse, V. Ninkovic, R.K. Slotkin and G. Martinez. Aphid feeding induces the relaxation of epigenetic control and the associated regulation of the defense response in Arabidopsis New Phytologist 230:1185-1200.

2020

K. Panda and R.K. Slotkin. Long-read cDNA Sequencing Enables a ‘Gene-Like’ Transcript Annotation of Transposable Elements. The Plant Cell v32: 2687-98.

S. Shahid and R.K. Slotkin. The current revolution in transposable element biology enabled by long reads. Current Opinion in Plant Biology v54: 49-56.

A.D. Yates-Stewart, J. Daron, S. Wijeratne, S. Shahid, H.A. Edgington, R.K. Slotkin and A. Michel. Soybean aphids adapted to host-plant resistance by down regulating putative effectors and up regulating transposable elements. Insect Biochemistry and Molecular Biology 121: 103363.

C. Warman, K. Panda, Z. Vejlupkova, S. Hokin, E. Unger-Wallace, R.A. Cole, A.M. Chettoor, D. Jiang, E. Vollbrecht, M. Evans, R.K. Slotkin, J.E. Fowler. Highly expressed maize pollen genes display coordinated expression with neighboring transposable elements and contribute to pollen fitness. PLoS Genetics 16:e1008462.

K. Panda, A.D. McCue and R.K. Slotkin. Arabidopsis 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 B 375: e0417.

Y. Lai, X.M. Lu, J. Daron, S. Pan, J. Wang, W. Wang, T. Tsuchiya, E. Holub, J.M. McDowell, R.K. Slotkin, K.G. LeRoch, T. Eulgem. The Arabidopsis PHD-finger protein EDM2 has multiple roles in balancing NLR immune receptor gene expression. PLoS Genetics 16:e1008993.

J. Antunez-Sanchez, M. Naish, J.S. Ramirez-Prado, S. Ohno, Y. Huang, A. Dawson, K. Opassathian, D. Manza-Mianza, F. Ariel, C. Raynaud, A. Wibowo, J. Daron, M. Ueda, D. Latrasse, R.K. Slotkin, D. Weigel, M. Benhamed, J. Gutierrez-Marcos. A new role for histone demethylases in the maintenance of genome integrity eLife 9:e58533.

P. Liu and R.K. Slotkin. Commentary: Cis-regulatory units of grass genomes identified by their DNA methylation Proceedings of the National Academy of Sciences v117: 24198-99.

G. Parry, N.J. Provart, S.M. Brady, B. Uzilday, The Multinational Arabidopsis Steering Committee. Current status of the multinational Arabidopsis community Plant Direct v4: 1-9.

2019

L. Ji, S.M. Mathioni, S. Johnson, D. Tucker, A.J. Bewick, K.D. Kim, J. Daron, R.K. Slotkin, S.A. Jackson, W.A. Parrot, B.C. Meyers, R.J. Schmitz. Genome-wide reinforcement of DNA methylation occurs during somatic embryogenesis in soybean. The Plant Cell 31: 2315-2331.

Y. Zhang, A. Ramming, L. Heinke, L. Altschmied, R.K. Slotkin, J.D. Becker, C. Kappel and M. Lenhard. The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA methylation pathway in sporophyte and pollen development. The Plant Journal 99: 655-672.

S.G. Choudury, S. Shahid, D. Cuerda-Gil, K. Panda, A. Cullen, Q. Ashraf, M. Sigman, A.D. McCue and R.K. Slotkin. The RNA export factor ALY1 enables genome-wide RNA-directed DNA methylation. The Plant Cell 31: 759-774.

C.S. Calhoun, D.K. Crist, E.M. Knee, C.G. Price, B.E. Lindsey, D.M. Castrejon, E. Nagy, J.W. Mann, J.A. Miller, E. Grotewold, R.K. Slotkin, J. Brkljacic. Chapter 2: The Genetic Resources of Arabidopsis thaliana. The Biological Resources of Model Organisms, Edited by R.L. Jarret and K. McCluskey. CRC Press.

International Arabidopsis Informatics Consortium. Arabidopsis Bioinformatics Resources: The Current State, Challenges, and Priorities for the Future Plant Direct v3: 1-7.

2018

G. Martinez, P. Wolff, Z. Wang, J. Moreno-Romero, J. Santos-González, L.L. Conze, C. DeFraia, R.K. Slotkin and C. Köhler. Paternal easiRNAs regulate parental genome dosage in Arabidopsis. Nature Genetics v50:193-198.

R.K. Slotkin. The case for not masking away repetitive DNA. Mobile DNA v9: 475.

2017

J. Daron and R.K. Slotkin. EpiTEome: Simultaneous detection of transposable element insertion sites and their DNA methylation levels. Genome Biology v18:7704.

D. Fultz and R.K. Slotkin. Exogenous Transposable Elements Circumvent Identity-Based Silencing Permitting the Dissection of Expression Dependent Silencing. The Plant Cell v29:360-376.

G. Martinez, S. Choudury and R.K. Slotkin. tRNA-derived small RNAs target transposable element transcripts. Nucleic Acids Research v45:5142-52.

2016

K. Panda, L. Ji, D.A. Neumann, J. Daron, R.J. Schmitz and R.K. Slotkin. Full-length autonomous transposable elements are preferentially targeted by expression-dependent forms of RNA-directed DNA methylation. Genome Biology v17: 170.

D. Cuerda-Gil and R.K. Slotkin. Non-Canonical RNA-directed DNA Methylation. Nature Plants v2: 16163.

M.J. Sigman and R.K. Slotkin. The First Rule of Plant Transposable Element Silencing: Location, Location, Location. The Plant Cell v28: 304-313.

G. Martinez, K. Panda, C. Köhler and R.K. Slotkin. Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nature Plants v2: 16030.

2015

A.D. McCue, K. Panda, S. Nuthikattu, S.G. Choudury, E.N. Thomas and R.K. Slotkin. ARGONAUTE6 bridges transposable element mRNA-derived siRNAs to the establishment of DNA methylation. EMBO Journal v34: 20-35.

D. Fultz, S.G. Choudury, and R.K. Slotkin. Silencing of Active Transposable Elements in Plants. Current Opinion in Plant Biology v27: 67-76.

2014

C. DeFraia and R.K. Slotkin. Analysis of Retrotransposon Activity in Plants. Plant Epigenetics and Epigenomics. Editors Charles Spillane & Peter McKeown, Methods in Molecular Biology, Springer Press, v1112: 195-210.

2013

S. Nuthikattu, A.D. McCue, K. Panda, D. Fultz, C. DeFraia, E.N. Thomas and R.K. Slotkin. The Initiation of Epigenetic Silencing of Active Transposable Elements is Triggered by RDR6 and 21-22 Nucleotide Small Interfering RNAs. Plant Physiology v162: 116-131.

A.D. McCue, S. Nuthikattu, and R.K. Slotkin. Genome-wide Identification of Genes Regulated in trans by Transposable Element Small Interfering RNAs. RNA Biology v10: 1379-1395.

K. Panda and R.K. Slotkin. Proposed Mechanism for the Initiation of Transposable Element Silencing by the RDR6-directed DNA Methylation Pathway. Plant Signaling & Behavior v8: e25206.

2012

A.D. McCue, S. Nuthikattu, S.H. Reeder and R.K. Slotkin.Gene Expression and Stress Response Mediated by the Epigenetic Regulation of a Transposable Element Small RNA. PLoS Genetics v8: e1002474.

G. Martinez and R.K. Slotkin. Developmental Reactivation of Transposable Element Silencing in Plants: Functional or Byproduct? Current Opinion in Plant Biology v15: 496-502.

A.D. McCue and R.K. Slotkin. Transposable Element Small RNAs as Regulators of Gene Expression. Trends in Genetics v28: 616-623.

R.K. Slotkin, S. Nuthikattu, and N. Jiang. The Evolutionary Impact of Transposable Elements on Gene and Genome Regulation. Molecular Biology and Evolution of the Plant Genome. Editors Johann Greilhuber and Jonathan Wendel, Springer Press, p35-58.

2011

A.D. McCue, M. Cresti, J.A. Feijo and R.K. Slotkin. Cytoplasmic connection of sperm cells to the pollen vegetative nucleus: the functional role of the male germ unit revisited. Journal of Experimental Botany v62: 1621-1631.

D. Lisch and R.K. Slotkin. Strategies for Silencing and Escape: The Ancient Struggle Between Transposable Elements and Their Hosts. International Review of Cell and Molecular Biology v292: 119-152.

2010

R.K. Slotkin. The Epigenetic Control of the Athila Family of Retrotransposons in Arabidopsis. Epigenetics v5: 483-490.