Lee, T.-J., Pascuzzi, P.E., Settlage, S., Shultz, R., Tanurdzic, M., Rabinowicz, P.D., Menges, M., Zheng, P., Main, D., Murray, J.A.H., Sosinski, B., Allen, G.C., Martienssen, R.A., Hanley-Bowdoin, L., Vaughn, M.W., and Thompson, W.F. (2010). DNA replication of Arabidopsis chromosome 4 occurs in two phases that correlate with chromatin state. PLOS Genetics, submitted.



Allen, G.C. (2009). The role of nuclear matrix attachment regions (MARs) in plants. In Functional Organization of the Plant Nucleus I. Meier, ed (Germany: Plant Cell Monographs, Springer-Verlag Publishing Ltd), pp. 101-130.

Shultz, R.W., Lee, T.J., Allen, G.C., Thompson, W.F., and Hanley-Bowdoin, L. (2009). Dynamic localization of the DNA replication proteins MCM5 and MCM7 in plants. Plant Physiol. 150, 658-669. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=19357199



Ascencio-Ibanez, J.T., Sozzani, R., Lee, T.-J., Chu, T.-M., Wolfinger, R.D., Cella, R., and Hanley-Bowdoin, L. (2008). Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting the pathogen response and cell cycle controls during geminivirus infection. Plant Physiol. 148, 436-454. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18650403

Kloc, A., Zaratiegui, M., Nora, E., and Martienssen, R. (2008). RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490-495. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18394897

Tanurdzic, M., Vaughn, M.W., Jiang, H., Lee, T.-J., Slotkin, R.K., Sosinski, B., Thompson, W.F., Doerge, R.W., and Martienssen, R.A. (2008). Epigenomic consequences of immortalized plant cell suspension culture. PLoS Biol. 6, e302. http://dx.doi.org/10.1371%2Fjournal.pbio.0060302

Weil, C., and Martienssen, R. (2008). Epigenetic interactions between transposons and genes: lessons from plants. Curr. Opin. Genet. Dev. 18, 188-192. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18339541



Boccara, M., Sarazin, A., Billoud, B., Jolly, V., Martienssen, R., Baulcombe, D., and Colot, V. (2007). New approaches for the analysis of Arabidopsis thaliana small RNAs. Biochimie 89, 1252-1256. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17562352

Shultz, R.W., Tatineni, V.M., Hanley-Bowdoin, L., and Thompson, W.F. (2007). Genome-wide analysis of the core DNA replication machinery in the higher plants Arabidopsis and rice. Plant Physiol. 144, 1697-1714. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17556508

Slotkin, R.K., and Martienssen, R. (2007). Transposable elements and the epigenetic regulation of the genome. Nat. Rev. Genet. 8, 272-285. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17363976

Turck, F., Roudier, F.o., Farrona, S., Martin-Magniette, M.-L., Guillaume, E., Buisine, N., Gagnot, S., Martienssen, R.A., Coupland, G., and Colot, V. (2007). Arabidopsis TFL2/LHP1 Specifically Associates with Genes Marked by Trimethylation of Histone H3 Lysine 27. PLoS Genetics 3, e86. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17542647

Vaughn, M.W., Tanurdic;, M., Lippman, Z., Jiang, H., Carrasquillo, R., Rabinowicz, P.D., Dedhia, N., McCombie, W.R., Agier, N., Bulski, A.s., Colot, V., Doerge, R.W., and Martienssen, R.A. (2007). Epigenetic Natural Variation in Arabidopsis thaliana. PLoS Biology 5, e174. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17579518



Allen, G.C., Flores-Vergara, M.A., Krasynanski, S., Kumar, S., and Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyltrimethylammonium bromide (CTAB). Nat. Protocols 1, 2320-2325. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=17406474

Garcia, D., Collier, S.A., Byrne, M.E., and Martienssen, R.A. (2006). Specification of leaf polarity in Arabidopsis via the trans-acting siRNA pathway. Curr. Biol. 16, 933-938. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16682355

Kumar, S., Allen, G.C., and Thompson, W.F. (2006). Gene targeting in plants: fingers on the move. Trends Plant Sci. 11, 159-161. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16530459

Kumar, S., Franco, M., and Allen, G.C. (2006). Gene targeting: Development of novel systems for genome engineering in plants. In Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues, J.A.T.d. Silva, ed (London, UK Global Science Books).

Ronemus, M., Vaughn, M.W., and Martienssen, R.A. (2006). MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis. Plant Cell 18, 1559-1574. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16798886

Santos, A.P., Wegal, E., Allen, G.C., Thompson, W.F., Stoger, E., Shaw, P.J., and Abranches, R. (2006). In situ methods to localize transgenes and transcripts in interphase nuclei: A tool for transgenic plant research. Plant Methods 2, 1-18. http://www.ncbi.nlm.nih.gov/pubmed/17081287?dopt=Abstract&holding=f1000,f1000m,isrctn

Thompson, W.F., Allen, G.C., and Spiker, S. (2006). Matrix attachment regions. In Regulation of Transcription in Plants K.D. Grasser, ed (Oxford, UK Blackwell Publishing Ltd), pp. 136-158.



Gendrel, A.V., Lippman, Z., Martienssen, R., and Colot, V. (2005). Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2, 213-218. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16163802

Halweg, C., Thompson, W.F., and Spiker, S. (2005). The rb7 matrix attachment region increases the likelihood and magnitude of transgene expression in tobacco cells: a flow cytometric study. Plant Cell 17, 418-429. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15659622

Lippman, Z., Gendrel, A.V., Colot, V., and Martienssen, R. (2005). Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2, 219-224. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16163803

Martienssen, R.A., Doerge, R.W., and Colot, V. (2005). Epigenomic mapping in Arabidopsis using tiling microarrays. Chromosome Res. 13, 299-308. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=15868423

Rabinowicz, P.D., Citek, R., Budiman, M.A., Nunberg, A., Bedell, J.A., Lakey, N., O'Shaughnessy, A.L., Nascimento, L.U., McCombie, W.R., and Martienssen, R.A. (2005). Differential methylation of genes and repeats in land plants. Genome Res. 15, 1431-1440. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16204196

Shultz, R., S., Settlage, L., Hanley-Bowdoin, L., and Thompson, W.F. (2005). A trichloroacetic acid-acetone method greatly reduces infrared autofluorescence of protein extracts from plant tissue. Plant Mol. Biol. Rep. 23, 405-409. http://pubs.nrc-cnrc.gc.ca/ispmb/r06-006.html

Vaughn, M.W., and Martienssen, R. (2005). It's a small RNA world, after all. Science 309, 1525-1526. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16141062

Vaughn, M.W., Tanurdzic, M., and Martienssen, R. (2005). Replication, repair, and reactivation. Dev. Cell 9, 724-725. http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=16326383



Lee, T.-J., Shultz, R., Hanley-Bowdoin, L., and Thompson, W. (2004). Establishment of rapidly proliferating rice cell suspension culture and its characterization by fluorescence-activated cell sorting analysis. Plant Mol. Biol. Rep. 22, 259-267. http://pubs.nrc-cnrc.gc.ca/ispmb/r04-050.html