DDR complex facilitates global association of RNA polymerase V to promoters and evolutionarily young transposons (original) (raw)

References

  1. Law, J.A. & Jacobsen, S.E. Establishing, maintaining and modifying DNA methylation patterns in plants and animals. Nat. Rev. Genet. 11, 204–220 (2010).
    Article CAS Google Scholar
  2. Cokus, S.J. et al. Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452, 215–219 (2008).
    Article CAS Google Scholar
  3. Haag, J.R. & Pikaard, C.S. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat. Rev. Mol. Cell Biol. 12, 483–492 (2011).
    Article CAS Google Scholar
  4. Mosher, R.A., Schwach, F., Studholme, D. & Baulcombe, D.C. PolIVb influences RNA-directed DNA methylation independently of its role in siRNA biogenesis. Proc. Natl. Acad. Sci. USA 105, 3145–3150 (2008).
    Article CAS Google Scholar
  5. Wierzbicki, A.T., Haag, J.R. & Pikaard, C.S. Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes. Cell 135, 635–648 (2008).
    Article CAS Google Scholar
  6. Kanno, T. et al. Involvement of putative SNF2 chromatin remodeling protein DRD1 in RNA-directed DNA methylation. Curr. Biol. 14, 801–805 (2004).
    Article CAS Google Scholar
  7. Kanno, T. et al. A structural-maintenance-of-chromosomes hinge domain-containing protein is required for RNA-directed DNA methylation. Nat. Genet. 40, 670–675 (2008).
    Article CAS Google Scholar
  8. Ausin, I., Mockler, T.C., Chory, J. & Jacobsen, S.E. IDN1 and IDN2 are required for de novo DNA methylation in Arabidopsis thaliana. Nat. Struct. Mol. Biol. 16, 1325–1327 (2009).
    Article CAS Google Scholar
  9. Law, J.A. et al. A protein complex required for polymerase V transcripts and RNA- directed DNA methylation in Arabidopsis. Curr. Biol. 20, 951–956 (2010).
    Article CAS Google Scholar
  10. Gao, Z. et al. An RNA polymerase II- and AGO4-associated protein acts in RNA-directed DNA methylation. Nature 465, 106–109 (2010).
    Article CAS Google Scholar
  11. Zheng, B. et al. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 23, 2850–2860 (2009).
    Article CAS Google Scholar
  12. El-Shami, M. et al. Reiterated WG/GW motifs form functionally and evolutionarily conserved ARGONAUTE-binding platforms in RNAi-related components. Genes Dev. 21, 2539–2544 (2007).
    Article CAS Google Scholar
  13. Rowley, M.J., Avrutsky, M.I., Sifuentes, C.J., Pereira, L. & Wierzbicki, A.T. Independent chromatin binding of ARGONAUTE4 and SPT5L/KTF1 mediates transcriptional gene silencing. PLoS Genet. 7, e1002120 (2011).
    Article CAS Google Scholar
  14. Huang, L. et al. An atypical RNA polymerase involved in RNA silencing shares small subunits with RNA polymerase II. Nat. Struct. Mol. Biol. 16, 91–93 (2009).
    Article CAS Google Scholar
  15. Wierzbicki, A.T., Ream, T.S., Haag, J.R. & Pikaard, C.S. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 41, 630–634 (2009).
    Article CAS Google Scholar
  16. Lee, T.F. et al. RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics 7, 798–795 (2012).
    Article Google Scholar
  17. Ausin, I. et al. An IDN2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc. Natl. Acad. Sci. USA 109, 8374–8381 (2012).
    Article CAS Google Scholar
  18. Zhang, X., Bernatavichute, Y.V., Cokus, S., Pellegrini, M. & Jacobsen, S.E. Genome-wide analysis of mono-, di- and trimethylation of histone H3 lysine 4 in Arabidopsis thaliana. Genome Biol. 10, R62 (2009).
    Article Google Scholar
  19. Slotkin, R., Nuthikattu, S. & Jiang, N. The impact of transposable elements on gene and genome evolution, in Plant Genome Diversity Vol. 1 (ed. Wendel, J.F.) Ch. 3, 35–55 (Springer Wien, 2012).
  20. Lisch, D. Epigenetic regulation of transposable elements in plants. Annu. Rev. Plant Biol. 60, 43–66 (2009).
    Article CAS Google Scholar
  21. Hollister, J.D. & Gaut, B.S. Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression. Genome Res. 19, 1419–1428 (2009).
    Article CAS Google Scholar
  22. Hu, T.T. et al. The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat. Genet. 43, 476–481 (2011).
    Article Google Scholar
  23. Hollister, J.D. et al. Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc. Natl. Acad. Sci. USA 108, 2322–2327 (2011).
    Article CAS Google Scholar
  24. Pontier, D. et al. Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. Genes Dev. 19, 2030–2040 (2005).
    Article CAS Google Scholar
  25. Herr, A.J., Jensen, M.B., Dalmay, T. & Baulcombe, D.C. RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118–120 (2005).
    Article CAS Google Scholar
  26. Johnson, L., Cao, X. & Jacobsen, S. Interplay between two epigenetic marks. DNA methylation and histone H3 lysine 9 methylation. Curr. Biol. 12, 1360–1367 (2002).
    Article CAS Google Scholar
  27. Stroud, H. et al. Genome-wide analysis of histone H3.1 and H3.3 variants in Arabidopsis thaliana. Proc. Natl. Acad. Sci. USA 109, 5370–5375 (2012).
    Article CAS Google Scholar
  28. Lu, C., Meyers, B.C. & Green, P.J. Construction of small RNA cDNA libraries for deep sequencing. Methods 43, 110–117 (2007).
    Article Google Scholar
  29. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
    Article Google Scholar
  30. Chen, P.Y., Cokus, S.J. & Pellegrini, M.B.S. Seeker: precise mapping for bisulfite sequencing. BMC Bioinformatics 11, 203 (2010).
    Article CAS Google Scholar
  31. Spyrou, C., Stark, R., Lynch, A.G. & Tavare, S. BayesPeak: Bayesian analysis of ChIP-seq data. BMC Bioinformatics 10, 299 (2009).
    Article Google Scholar
  32. Cairns, J. et al. BayesPeak—an R package for analysing ChIP-seq data. Bioinformatics 27, 713–714 (2011).
    Article CAS Google Scholar

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