An alternative polyadenylation mechanism coopted to the Arabidopsis RPP7 gene through intronic retrotransposon domestication

Proceedings of the National Academy of Sciences of the United States of America

Volumn 110, Issue 37, 2013, Pages

  Tsuchiya, Tokuji ^a   Eulgem, Thomas ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

EDM2; Hyaloperonospora arabidopsidis; PHD finger; Post translational histone modification

Indexed keywords

HISTONE;

ADENYLATION; ARABIDOPSIS THALIANA; ARTICLE; CONTROLLED STUDY; DOMESTICATION; EPIGENETICS; GENE EXPRESSION; GENE FUNCTION; GENE LOCUS; GENETIC CODE; IN VIVO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT IMMUNITY; POLYADENYLATION; PRIORITY JOURNAL; RETROPOSON; RNA PROCESSING; TRANSPOSON;

EDM2; HYALOPERONOSPORA ARABIDOPSIDIS; PHD FINGER; POST TRANSLATIONAL HISTONE MODIFICATION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; BASE SEQUENCE; EPIGENESIS, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; HISTONE-LYSINE N-METHYLTRANSFERASE; HISTONES; INTRONS; MOLECULAR SEQUENCE DATA; PLANTS, GENETICALLY MODIFIED; POLYADENYLATION; RETROELEMENTS; RNA PRECURSORS; RNA, PLANT; TRANSCRIPTION FACTORS;

EID: 84883796284     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1312545110     Document Type: Article

References (41)

1. Rigal M, Mathieu O (2011) A "mille-feuille" of silencing: Epigenetic control of transposable elements. Biochim Biophys Acta 1809(8):452-458.
2. Jackson JP, Lindroth AM, Cao X, Jacobsen SE (2002) Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416(6880):556-560. (Pubitemid 34288860)
3. Johnson L, Cao X, Jacobsen S (2002) Interplay between two epigenetic marks: DNA methylation and histone H3 lysine 9 methylation. Curr Biol 12(16):1360-1367. (Pubitemid 34915537)
4. Ebbs ML, Bartee L, Bender J (2005) H3 lysine 9 methylation is maintained on a transcribed inverted repeat by combined action of SUVH6 and SUVH4 methyltransferases. Mol Cell Biol 25(23):10507-10515. (Pubitemid 41681971)
5. Ebbs ML, Bender J (2006) Locus-specific control of DNA methylation by the Arabidopsis SUVH5 histone methyltransferase. Plant Cell 18(5):1166-1176. (Pubitemid 43956123)
6. Jacob Y, et al. (2009) ATXR5 and ATXR6 are H3K27 monomethyltransferases required for chromatin structure and gene silencing. Nat Struct Mol Biol 16(7):763-768.
7. Bennetzen JL (2005) Transposable elements, gene creation and genome rearrangement in flowering plants. Curr Opin Genet Dev 15(6):621-627.
8. Weil C, Martienssen R (2008) Epigenetic interactions between transposons and genes: Lessons from plants. Curr Opin Genet Dev 18(2):188-192. (Pubitemid 351749827)
9. Dooner HK, Weil CF (2007) Give-and-take: Interactions between DNA transposons and their host plant genomes. Curr Opin Genet Dev 17(6):486-492. (Pubitemid 350184304)
10. Lisch D (2013) How important are transposons for plant evolution? Nat Rev Genet 14(1):49-61.
11. Orphanides G, Reinberg D (2002) A unified theory of gene expression. Cell 108(4):439-451. (Pubitemid 34260870)
12. Wu X, et al. (2011) Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci USA 108(30):12533-12538.
13. Di Giammartino DC, Nishida K, Manley JL (2011) Mechanisms and consequences of alternative polyadenylation. Mol Cell 43(6):853-866.
14. Millevoi S, Vagner S (2010) Molecular mechanisms of eukaryotic pre-mRNA 3′ end processing regulation. Nucleic Acids Res 38(9):2757-2774.
15. Pandya-Jones A, Black DL (2009) Co-transcriptional splicing of constitutive and alternative exons. RNA 15(10):1896-1908.
16. de la Mata M, Lafaille C, Kornblihtt AR (2010) First come, first served revisited: Factors affecting the same alternative splicing event have different effects on the relative rates of intron removal. RNA 16(5):904-912.
17. Moore MJ, Proudfoot NJ (2009) Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136(4):688-700.
18. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T (2011) Epigenetics in alternative pre-mRNA splicing. Cell 144(1):16-26.
19. Spies N, Nielsen CB, Padgett RA, Burge CB (2009) Biased chromatin signatures around polyadenylation sites and exons. Mol Cell 36(2):245-254.
20. Mavrich TN, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18(7):1073-1083. (Pubitemid 351931158)
21. Lian Z, et al. (2008) A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3′ end RNA polyadenylation. Genome Res 18(8):1224-1237.
22. Maekawa T, Kufer TA, Schulze-Lefert P (2011) NLR functions in plant and animal immune systems: So far and yet so close. Nat Immunol 12(9):817-826.
23. Eulgem T, et al. (2007) EDM2 is required for RPP7-dependent disease resistance in Arabidopsis and affects RPP7 transcript levels. Plant J 49(5):829-839. (Pubitemid 46279266)
24. Tsuchiya T, Eulgem T (2013) Mutations in EDM2 selectively affect silencing states of transposons and induce plant developmental plasticity. Sci Rep 3:1701.
25. Xiao S, Brown S, Patrick E, Brearley C, Turner JG (2003) Enhanced transcription of the Arabidopsis disease resistance genes RPW8.1 and RPW8.2 via a salicylic acid-dependent amplification circuit is required for hypersensitive cell death. Plant Cell 15(1):33-45. (Pubitemid 36137660)
26. Yi H, Richards EJ (2007) A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing. Plant Cell 19(9):2929-2939. (Pubitemid 350046238)
27. Holt BF, 3rd, Belkhadir Y, Dangl JL (2005) Antagonistic control of disease resistance protein stability in the plant immune system. Science 309(5736):929-932. (Pubitemid 41099928)
28. Li F, et al. (2012) MicroRNA regulation of plant innate immune receptors. Proc Natl Acad Sci USA 109(5):1790-1795.
29. Bomblies K, et al. (2007) Autoimmune response as a mechanism for a Dobzhansky-Muller-type incompatibility syndrome in plants. PLoS Biol 5(9):e236.
30. Tsuchiya T, Eulgem T (2011) EMSY-like genes are required for full RPP7-mediated race-specific immunity and basal defense in Arabidopsis. Mol Plant Microbe Interact 24(12):1573-1581.
31. Liu F, Marquardt S, Lister C, Swiezewski S, Dean C (2010) Targeted 3′ processing of antisense transcripts triggers Arabidopsis FLC chromatin silencing. Science 327(5961):94-97.
32. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33:479-532. (Pubitemid 30083131)
33. Cao J, et al. (2011) Whole-genome sequencing of multiple Arabidopsis thaliana populations. Nat Genet 43(10):956-963.
34. Tsuchiya T, Eulgem T (2010) Co-option of EDM2 to distinct regulatory modules in Arabidopsis thaliana development. BMC Plant Biol 10:203.
35. Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12(7):1075-1079. (Pubitemid 34785200)
36. Clough SJ, Bent AF (1998) Floral dip: A simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16(6):735-743.
37. Holub EB, Beynon JL, Crute IR (1994) Phenotypic and genotypic characterization of interactions between isolates of Peronospora parasitica and accessions of Arabidopsis thaliana. MPMI-Molecular Plant Microbe Interactions 7(2):223-239. (Pubitemid 2085746)
38. Parker JE, et al. (1993) Phenotypic characterization and molecular mapping of the Arabidopsis thaliana locus RPP5, determining disease resistance to Peronospora parasitica. Plant J 4(5):821-831. (Pubitemid 2017546)
39. McDowell JM, et al. (2000) Downy mildew (Peronospora parasitica) resistance genes in Arabidopsis vary in functional requirements for NDR1, EDS1, NPR1 and salicylic acid accumulation. Plant J 22(6):523-529. (Pubitemid 30427761)
40. Koch E, Slusarenko A (1990) Arabidopsis is susceptible to infection by a downy mildew fungus. Plant Cell 2(5):437-445. (Pubitemid 120029602)
41. Tsuchiya T, Eulgem T (2010) The Arabidopsis defense component EDM2 affects the floral transition in an FLC-dependent manner. Plant J 62(3):518-528.