Polyribosomal RNA-seq reveals the decreased complexity and diversity of the arabidopsis translatome

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Zhang, Xingtan ^a,b   Rosen, Benjamin D ^a   Tang, Haibao ^a   Krishnakumar, Vivek ^a   Town, Christopher D ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

^b CHONGQING UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

POLYRIBOSOMAL RNA; RIBOSOME RNA; TRANSCRIPTOME; UNCLASSIFIED DRUG; ARABIDOPSIS PROTEIN; MESSENGER RNA; PLANT RNA;

AFC2 GENE; ALTERNATIVE RNA SPLICING; ARABIDOPSIS; ARABIDOPSIS THALIANA; ARTICLE; ATGSTF11 GENE; GENE; GENETIC VARIABILITY; INTRON; NONHUMAN; RNA SEQUENCE; RNA TRANSCRIPTION; TRANSCRIPTOMICS; GENETIC VARIATION; GENETICS; POLYSOME; PROCEDURES; SEQUENCE ANALYSIS;

ANIMALIA; ARABIDOPSIS; ARABIDOPSIS THALIANA;

ALTERNATIVE SPLICING; ARABIDOPSIS; ARABIDOPSIS PROTEINS; GENETIC VARIATION; INTRONS; POLYRIBOSOMES; RNA, MESSENGER; RNA, PLANT; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84923356695     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0117699     Document Type: Article

References (28)

1. Campbell MA, Haas BJ, Hamilton JP, Mount SM, Buell CR (2006) Comprehensive analysis of alternative splicing in rice and comparative analyses with Arabidopsis. BMC Genomics 7: 327. PMID: 17194304
2. Iida K, Go M (2006) Survey of conserved alternative splicing events of mRNAs encoding SR proteins in land plants. Mol Biol Evol 23: 1085-1094. PMID: 16520337
3. Marquez Y, Brown JW, Simpson C, Barta A, Kalyna M (2012) Transcriptome survey reveals increased complexity of the alternative splicing landscape in Arabidopsis. Genome Res 22: 1184-1195. doi: 10.1101/gr.134106.111 PMID: 22391557
4. Syed NH, Kalyna M, Marquez Y, Barta A, Brown JW (2012) Alternative splicing in plants - coming of age. Trends Plant Sci 17: 616-623. doi: 10.1016/j.tplants.2012.06.001 PMID: 22743067
5. Lewis BP, Green RE, Brenner SE (2003) Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A 100: 189-192. PMID: 12502788
6. Filichkin SA, Priest HD, Givan SA, Shen R, Bryant DW, et al. (2010) Genome-wide mapping of alternative splicing in Arabidopsis thaliana. Genome Res 20: 45-58. doi: 10.1101/gr.093302.109 PMID: 19858364
7. Hori K, Watanabe Y (2007) Context analysis of termination codons in mRNA that are recognized by plant NMD. Plant Cell Physiol 48: 1072-1078. PMID: 17567637
8. Pickrell JK, Pai AA, Gilad Y, Pritchard JK (2010) Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet 6: e1001236. doi: 10.1371/journal.pgen.1001236 PMID: 21151575
9. Ingolia NT (2014) Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet 15: 205-213. doi: 10.1038/nrg3645 PMID: 24468696
10. Gerashchenko MV, Lobanov AV, Gladyshev VN (2012) Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress. Proc Natl Acad Sci U S A 109: 17394-17399. doi: 10.1073/pnas.1120799109 PMID: 23045643
11. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS (2009) Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223. doi: 10.1126/science.1168978 PMID: 19213877
12. Juntawong P, Girke T, Bazin J, Bailey-Serres J (2014) Translational dynamics revealed by genomewide profiling of ribosome footprints in Arabidopsis. Proc Natl Acad Sci U S A 111: E203-212. doi: 10.1073/pnas.1317811111 PMID: 24367078
13. Shalgi R, Hurt JA, Krykbaeva I, Taipale M, Lindquist S, et al. (2013) Widespread regulation of translation by elongation pausing in heat shock. Mol Cell 49: 439-452. doi: 10.1016/j.molcel.2012.11.028 PMID: 23290915
14. Zanetti ME, Chang IF, Gong F, Galbraith DW, Bailey-Serres J (2005) Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression. Plant Physiol 138: 624-635. PMID: 15955926
15. Reynoso MA, Blanco FA, Bailey-Serres J, Crespi M, Zanetti ME (2012) Selective recruitment of mRNAs and miRNAs to polyribosomes in response to rhizobia infection in Medicago truncatula. Plant J. doi: 10.1111/tpj.12055 PMID: 23227895
16. Aubry S, Smith-Unna RD, Boursnell CM, Kopriva S, Hibberd JM (2014) Transcript residency on ribosomes reveals a key role for the Arabidopsis thaliana bundle sheath in sulfur and glucosinolate metabolism. Plant J 78: 659-673. doi: 10.1111/tpj.12502 PMID: 24617819
17. Liu J, Jung C, Xu J, Wang H, Deng S, et al. (2012) Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24: 4333-4345. doi: 10.1105/tpc.112.102855 PMID: 23136377
18. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25 PMID: 19261174
19. Grabherr MG, Haas BJ, Yassour M, Levin JZ, Thompson DA, et al. (2011) Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29: 644-652. doi: 10.1038/nbt.1883 PMID: 21572440
20. Martin JA, Wang Z (2011) Next-generation transcriptome assembly. Nat Rev Genet 12: 671-682. doi: 10.1038/nrg3068 PMID: 21897427
21. Haas BJ, Delcher AL, Mount SM, Wortman JR, Smith RK Jr, et al. (2003) Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res 31: 5654-5666. PMID: 14500829
22. Wang BB, Brendel V (2006) Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A 103: 7175-7180. PMID: 16632598
23. Ner-Gaon H, Halachmi R, Savaldi-Goldstein S, Rubin E, Ophir R, et al. (2004) Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J 39: 877-885. PMID: 15341630
24. Hayes JD, Flanagan JU, Jowsey IR (2005) Glutathione transferases. Annu Rev Pharmacol Toxicol 45: 51-88. PMID: 15822171
25. Krajewski MP, Kanawati B, Fekete A, Kowalski N, Schmitt-Kopplin P, et al. (2013) Analysis of Arabidopsis glutathione-transferases in yeast. Phytochemistry 91: 198-207. doi: 10.1016/j.phytochem.2012.04.016 PMID: 22633844
26. Sonderby IE, Geu-Flores F, Halkier BA (2010) Biosynthesis of glucosinolates-gene discovery and beyond. Trends Plant Sci 15: 283-290. doi: 10.1016/j.tplants.2010.02.005 PMID: 20303821
27. Savaldi-Goldstein S, Sessa G, Fluhr R (2000) The ethylene-inducible PK12 kinase mediates the phosphorylation of SR splicing factors. Plant J 21: 91-96. PMID: 10652154
28. Li B, Dewey CN (2011) RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12: 323. doi: 10.1186/1471-2105-12-323 PMID: 21816040