Genome-wide identification of long noncoding natural antisense transcripts and their responses to light in Arabidopsis

Genome Research

Volumn 24, Issue 3, 2014, Pages 444-453

  Wang, Huan ^a   Chung, Pil Joong ^a,b   Liu, Jun ^a   Jang, In Cheol ^a,c   Kean, Michelle J ^a   Xu, Jun ^a   Chua, Nam Hai ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b Seoul National University   (South Korea)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; LONG UNTRANSLATED RNA; MESSENGER RNA;

ARABIDOPSIS; ARTICLE; DNA STRAND; GENE EXPRESSION PROFILING; GENE IDENTIFICATION; GENETIC TRANSCRIPTION; HISTONE ACETYLATION; HISTONE MODIFICATION; LIGHT; LONG NONCODING NATURAL ANTISENSE TRANSCRIPT; NONHUMAN; PLANT GENOME; PRIORITY JOURNAL; PROMOTER REGION; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE;

ACETYLATION; ARABIDOPSIS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; GENOME, PLANT; HISTONES; LIGHT; NUCLEIC ACID HYBRIDIZATION; RNA, ANTISENSE; RNA, LONG NONCODING; RNA, PLANT;

EID: 84893620730     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.165555.113     Document Type: Article

References (54)

1. Beiter T, Reich E, Williams RW, Simon P. 2009. Antisense transcription: A critical look in both directions. Cell Mol Life Sci 66: 94-112.
2. Borsani O, Zhu J, Verslues PE, Sunkar R, Zhu JK. 2005. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123: 1279-1291.
3. Bovre K, Szybalski W. 1969. Patterns of convergent and overlapping transcription within the b2 region of coliphage l. Virology 38: 614-626.
4. Burge C, Karlin S. 1997. Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94.
5. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL. 2011. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25: 1915-1927.
6. Camblong J, Iglesias N, Fickentscher C, Dieppois G, Stutz F. 2007. Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell 131: 706-717.
7. Camblong J, Beyrouthy N, Guffanti E, Schlaepfer G, Steinmetz LM, Stutz F. 2009. Trans-acting antisense RNAs mediate transcriptional gene cosuppression in S. cerevisiae. Genes Dev 23: 1534-1545.
8. Charon C, Moreno AB, Bardou F, CrespiM. 2010. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. Mol Plant 3: 729-739.
9. Charron JB, He H, Elling AA, Deng XW. 2009. Dynamic landscapes of four histone modifications during deetiolation in Arabidopsis. Plant Cell 21: 3732-3748.
10. Cheetham SW, Gruhl F, Mattick JS, Dinger ME. 2013. Long noncoding RNAs and the genetics of cancer. Br J Cancer 108: 2419-2425.
11. Chellappan P, Xia J, Zhou X, Gao S, Zhang X, Coutino G, Vazquez F, Zhang W, Jin H. 2010. siRNAs from miRNA sites mediate DNA methylation of target genes. Nucleic Acids Res 38: 6883-6894.
12. Chen J, Sun M, Kent WJ, Huang X, Xie H,WangW, Zhou G, Shi RZ, Rowley JD. 2004. Over 20% of human transcripts might form sense-antisense pairs. Nucleic Acids Res 32: 4812-4820.
13. Cheng J, Kapranov P, Drenkow J, Dike S, Brubaker S, Patel S, Long J, Stern D, Tammana H, Helt G, et al. 2005. Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science 308: 1149-1154.
14. Chua YL, Channelière S, Mott E, Gray JC. 2005. The bromodomain protein GTE6 controls leaf development in Arabidopsis by histone acetylation at ASYMMETRIC LEAVES1. Genes Dev 19: 2245-2254.
15. Faghihi MA, Wahlestedt C. 2009. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 10: 637-643.
16. Guell M, van Noort V, Yus E, Chen WH, Leigh-Bell J, Michalodimitrakis K, Yamada T, Arumugam M, Doerks T, Kuhner S, et al. 2009. Transcriptome complexity in a genome-reduced bacterium. Science 326: 1268-1271.
17. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, et al. 2009. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458: 223-227.
18. Hazen SP, Naef F, Quisel T, Gendron JM, Chen H, Ecker JR, Borevitz JO, Kay SA. 2009. Exploring the transcriptional landscape of plant circadian rhythms using genome tiling arrays. Genome Biol 10: R17.
19. Henz SR, Cumbie JS, Kasschau KD, Lohmann JU, Carrington JC, Weigel D, Schmid M. 2007. Distinct expression patterns of natural antisense transcripts in Arabidopsis. Plant Physiol 144: 1247-1255.
20. Ietswaart R, Wu Z, Dean C. 2012. Flowering time control: Another window to the connection between antisense RNA and chromatin. Trends Genet 28: 445-453.
21. Jang IC, Chung PJ, Hemmes H, Jung C, Chua NH. 2011. Rapid and reversible light-mediated chromatin modifications of Arabidopsis phytochrome A locus. Plant Cell 23: 459-470.
22. Ji H, Jiang H, Ma W, Wong WH. 2011. Using CisGenome to analyze ChIPchip and ChIP-seq data. Curr Protoc Bioinformatics 33: 2.13.1-2.13.45.
23. Jiao Y, Ma L, Strickland E, Deng XW. 2005. Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis. Plant Cell 17: 3239-3256.
24. Jiao Y, Lau OS, Deng XW. 2007. Light-regulated transcriptional networks in higher plants. Nat Rev Genet 8: 217-230.
25. Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M, Nishida H, Yap CC, Suzuki M, Kawai J, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309: 1564-1566.
26. Kurihara Y, Kaminuma E, Matsui A, Kawashima M, Tanaka M, Morosawa T, Ishida J, Mochizuki Y, Shinozaki K, Toyoda T, et al. 2009. Transcriptome analyses revealed diverse expression changes in ago1 and hyl1 Arabidopsis mutants. Plant Cell Physiol 50: 1715-1720.
27. Lavorgna G, Dahary D, Lehner B, Sorek R, Sanderson CM, Casari G. 2004. In search of antisense. Trends Biochem Sci 29: 88-94.
28. Lee JT, Davidow LS,Warshawsky D. 1999. Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21: 400-404.
29. Leung A, Trac C, Jin W, Lanting L, Akbany A, Saetrom P, Schones DE, Natarajan R. 2013. Novel long noncoding RNAs are regulated by angiotensin II in vascular smooth muscle cells. Circ Res 113: 266-278.
30. Li S, Liberman L, Mukherjee N, Benfey P, Ohler U. 2013. Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data. Genome Res 23: 1730-1739.
31. Liu J, Jung C, Xu J,Wang H, Deng S, Bernad L, Arenas-Huertero C, Chua NH. 2012. Genome-wide analysis uncovers regulation of long intergenic noncoding RNAs in Arabidopsis. Plant Cell 24: 4333-4345.
32. Loidl P. 2004. A plant dialect of the histone language. Trends Plant Sci 9: 84-90.
33. Lu F, Cui X, Zhang S, Jenuwein T, Cao X. 2011. Arabidopsis REF6 is a histone H3 lysine 27 demethylase. Nat Genet 43: 715-719.
34. Luo C, Sidote DJ, Zhang Y, Kerstetter RA, Michael TP, Lam E. 2013. Integrative analysis of chromatin states in Arabidopsis identified potential regulatory mechanisms for natural antisense transcript production. Plant J 73: 77-90.
35. Matsui A, Ishida J, Morosawa T, Mochizuki Y, Kaminuma E, Endo TA, Okamoto M, Nambara E, Nakajima M, Kawashima M, 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.
36. Ng SY, Bogu GK, Soh BS, Stanton LW. 2013a. The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis. Mol Cell 51: 349-359.
37. Ng SY, Lin L, Soh BS, Stanton LW. 2013b. Long noncoding RNAs in development and disease of the central nervous system. Trends Genet 29: 461-468.
38. Okamoto M, Tatematsu K, Matsui A, Morosawa T, Ishida J, Tanaka M, Endo TA, Mochizuki Y, Toyoda T, Kamiya Y, et al. 2010. Genome-wide analysis of endogenous abscisic acid-mediated transcription in dry and imbibed seeds of Arabidopsis using tiling arrays. Plant J 62: 39-51.
39. Shah JC, Clancy MJ. 1992. IME4, a gene that mediates MAT and nutritional control of meiosis in Saccharomyces cerevisiae. Mol Cell Biol 12: 1078-1086.
40. Smalheiser NR, Lugli G, Thimmapuram J, Cook EH, Larson J. 2011. Endogenous siRNAs and noncoding RNA-derived small RNAs are expressed in adult mouse hippocampus and are up-regulated in olfactory discrimination training. RNA 17: 166-181.
41. Spiegelman WG, Reichardt LF, Yaniv M, Heinemann SF, Kaiser AD, Eisen H. 1972. Bidirectional transcription and the regulation of phage l repressor synthesis. Proc Natl Acad Sci 69: 3156-3160.
42. Swiezewski S, Liu F, Magusin A, Dean C. 2009. Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycombtarget. Nature 462: 799-802.
43. Trapnell C, Pachter L, Salzberg SL. 2009. TopHat: Discovering splice junctions with RNA-Seq. Bioinformatics 25: 1105-1111.
44. Ulitsky I, Bartel DP. 2013. lincRNAs: Genomics, evolution, and mechanisms. Cell 154: 26-46.
45. Wang XJ, Gaasterland T, Chua NH. 2005. Genome-wide prediction and identification of cis-natural antisense transcripts in Arabidopsis thaliana. Genome Biol 6: R30.
46. Wang H, Zhang X, Liu J, Kiba T,Woo J, Ojo T, Hafner M, Tuschl T, Chua NH, Wang XJ. 2011. Deep sequencing of small RNAs specifically associated with Arabidopsis AGO1 and AGO4 uncovers new AGO functions. Plant J 67: 292-304.
47. Wek RC, Hatfield GW. 1986. Nucleotide sequence and in vivo expression ofthe ilvY and ilvC genes in Escherichia coli K12. Transcription from divergent overlapping promoters. J Biol Chem 261: 2441-2450.
48. Werner A. 2005. Natural antisense transcripts. RNA Biol 2: 53-62.
49. Wong F, Yuh ZT, Schaefer EL, Roop BC, Ally AH. 1987. Overlapping transcription units in the transient receptor potential locus of Drosophila melanogaster. Somat Cell Mol Genet 13: 661-669.
50. Wu X, LiuM, Downie B, Liang C, Ji G, Li QQ, Hunt AG. 2011. Genome-wide landscape of polyadenylation in Arabidopsis provides evidence for extensive alternative polyadenylation. Proc Natl Acad Sci 108: 12533-12538.
51. Yin Y, Zhao Y, Wang J, Liu C, Chen S, Chen R, Zhao H. 2007. antiCODE: Anatural sense-antisense transcripts database. BMC Bioinformatics 8: 319.
52. Zhang Y, Liu XS, Liu QR, Wei L. 2006. Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res 34: 3465-475.
53. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, Goodrich J,Jacobsen SE. 2007. Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129.
54. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, LiW, et al. 2008. Model-based analysis of ChIPSeq (MACS). Genome Biol 9: R137.