Genome-wide suppression of aberrant mRNA-like noncoding RNAs by NMD in Arabidopsis

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

Volumn 106, Issue 7, 2009, Pages 2453-2458

  Kurihara, Yukio ^a   Matsui, Akihiro ^a   Hanada, Kousuke ^a   Kawashima, Makiko ^a   Ishida, Junko ^a   Morosawa, Taeko ^a   Tanaka, Maho ^a   Kaminuma, Eli ^b   Mochizuki, Yoshiki ^b   Matsushima, Akihiro ^b   Toyoda, Tetsuro ^b   Shinozaki, Kazuo ^a   Seki, Motoaki ^a,c  

^a RIKEN   (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c YOKOHAMA CITY UNIVERSITY   (Japan)

Author keywords

ncRNA; Tiling array; UPF1; UPF3

Indexed keywords

ARABIDOPSIS PROTEIN; COMPLEMENTARY RNA; MESSENGER RNA; N METHYL DEXTRO ASPARTIC ACID; PROTEIN UPF1 1; PROTEIN UPF3 1; UNCLASSIFIED DRUG; UNTRANSLATED RNA;

ARABIDOPSIS; ARTICLE; CONTROLLED STUDY; GENOME ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN SYNTHESIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSLATION REGULATION; UPREGULATION;

ARABIDOPSIS; ARABIDOPSIS PROTEINS; CYCLOHEXIMIDE; EXONS; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; MODELS, BIOLOGICAL; MODELS, GENETIC; MUTATION; PROTEIN SYNTHESIS INHIBITORS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; RNA; RNA, MESSENGER; RNA, UNTRANSLATED;

ARABIDOPSIS; EUKARYOTA;

EID: 60549106018     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0808902106     Document Type: Article

References (30)

1. Yamada K, et al. (2003) Empirical analysis of transcriptional activity in the Arabidopsis genome. Science 302:842-846.
2. Zhang X, et al. (2006) Genome-wide high resolution mapping and functional analysis of DNA methylation in Arabidopsis. Cell 126:1189-1201.
3. Chekanova JA, et al. (2007) Genome-wide high resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome. Cell 131:1340-1353.
4. Matsui A, et al. (2008) Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array. Plant Cell Physiol 49:1135-1149.
5. Seki M, et al. (2002) Functional annotation of a full-length Arabidopsis cDNA collection. Science 296:141-145.
6. Lister R, et al. (2008) Highly integrated single-base resolution maps of the epigenome in Arabidopsis. Cell 133:523-536.
7. Gregory BD, et al. (2008) A link between RNA Metabolism and silencing affecting Arabidopsis development. Dev Cell 14:854-866.
8. Laubinger S, et al. (2008) Dual roles of the nuclear cap-binding complex and SERRATE in pre-mRNA splicing and microRNA processing in Arabidopsis thaliana. Proc Natl Acad Sci USA 105:8795-8800.
9. Maquat LE (2004) Nonsense-mediated mRNA decay: Splicing, translation and mRNP dynamics. Nat Rev Mol Cell Biol 5:89-99.
10. Behm-Ansmant I, et al. (2007) mRNA quality control: An ancient machinery recognizes and degrades mRNAs with nonsense codons. FEBS Lett 581:2845-2853.
11. Conti E, Izaurralde E (2005) Nonsense-mediated mRNA decay: Molecular insights and mechanistic variations across species. Curr Opin Cell Biol 17:316-325.
12. Culbertson MR, Leeds PF (2003) Looking atm RNA decay pathways through the window of molecular evolution. Curr Opin Genet Dev 13:207-214.
13. Rehwinkel J, Raes J, Izaurralde E (2006) Nonsense-mediated mRNA decay: Target genes and functional diversification of effectors. Trends Biochem Sci 31:639-646.
14. Mitchell P, Tollervey D (2003) An NMD pathway in yeast involving accelerated deadenylation and exosome-mediated 3′→5′ degradation. Mol Cell 11:1405-1413.
15. Lejeune F, Li X, Maquat LE (2003) Nonsense-mediated mRNA decay in mammalian cells involves decapping, deadenylating, and exonucleolytic activities. Mol Cell 12:675-687.
16. He F, et al. (2003) Genome-wide analysis of mRNAs regulated by the nonsense-mediated and 5′ to 3′ mRNA decay pathways in yeast. Mol Cell 12:1439-1452.
17. Hori K, Watanabe Y (2005) UPF3 suppresses aberrant spliced mRNA in Arabidopsis. Plant J 43:530-540.
18. Yoine M, et al. (2006) The lba1 mutation of UPF1 RNA helicase involved in nonsense-mediated mRNA decay cause pleiotropic phenotypic changes and altered sugar signaling in Arabidopsis. Plant J 47:49-62.
19. Arciga-Reyes L, Wootton L, Kieffer M, Davies B (2006) UPF1 is required for nonsense-mediated mRNA decay (NMD) and RNAi in Arabidopsis. Plant J 47:480-489.
20. Yoine M, Nishii T, Nakamura K (2006) Arabidopsis UPF1 RNA helicase for nonsense-mediated mRNA decay is involved in seed size control and is essential for growth. Plant Cell Physiol 47:572-580.
21. Kertesz S, et al. (2006) Both introns and long 3′-UTRs operate as cis-acting elements to trigger nonsense-mediated decay in plants. Nucleic Acids Res 34:6147-6157.
22. Schwartz AM, et al. (2006) Stability of plant mRNAs depends on the length of the 3′-untranslated region. Biochemistry (Moscow) 71:1377-1384.
23. Hori K, Watanabe Y (2007) Context analysis of termination codons in mRNA that are recognized by plant NMD. Plant Cell Physiol 48:1072-1078.
24. Kerenyi Z, et al. (2008) Inter-kingdom conservation of mechanism of nonsense-mediated mRNA decay. EMBO J 27:1585-1595.
25. Mendell JT, Dietz HC (2001) When the message goes awry: Disease-producing mutations that influence mRNA content and performance. Cell 107:411-414.
26. Mendell JT, et al. (2004) Nonsense surveillance regulates expression of diverse classes of mammalian transcripts and mutes genomic noise. Nat Genet 36:1073-1078.
27. Toyoda T, Shinozaki K (2005) Tiling array-driven elucidation of transcriptional structures based on maximum-likelihood and Markov models. Plant J 43:611-621.
28. Galindo MI, Pueyo JI, Fouix S, Bishop SA, Couso JP (2007) Peptides encoded by short ORFs control development and define a new eukaryotic gene family. PLoS Biol 5:e106.
29. Kondo T, et al. (2007) Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat Cell Biol 9:660-665.
30. Hosoda K, Kim YK, Lejeune F, Maquat LE (2005) CBP80 promotes interaction of Upf1 with Upf2 during nonsense-mediated mRNA decay in mammalian cells. Nat Struct Mol Biol 12:893-901.