Prediction of trans-antisense transcripts in Arabidopsis thaliana

被引:66
作者
Wang, Huan
Chua, Nam-Hai
Wang, Xiu-Jie [1 ]
机构
[1] Chinese Acad Sci, State Key Lab Plant Genom, Inst Genet & Dev Biol, Beijing 100101, Peoples R China
[2] Grad Univ, Chinese Acad Sci, Beijing 100101, Peoples R China
[3] Rockefeller Univ, Plant Mol Biol Lab, New York, NY 10021 USA
关键词
D O I
10.1186/gb-2006-7-10-r92
中图分类号
Q81 [生物工程学(生物技术)]; Q93 [微生物学];
学科分类号
071005 ; 0836 ; 090102 ; 100705 ;
摘要
Background: Natural antisense transcripts (NATs) are coding or non-coding RNAs with sequence complementarity to other transcripts (sense transcripts). These RNAs could potentially regulate the expression of their sense partner(s) at either the transcriptional or post-transcriptional level. Experimental and computational methods have demonstrated the widespread occurrence of NATs in eukaryotes. However, most previous studies only focused on cis-NATs with little attention being paid to NATs that originate in trans. Results: We have performed a genome-wide screen of trans-NATs in Arabidopsis thaliana and identified 1,320 putative trans-NAT pairs. An RNA annealing program predicted that most trans-NATs could form extended double-stranded RNA duplexes with their sense partners. Among trans-NATs with available expression data, more than 85% were found in the same tissue as their sense partners; of these, 67% were found in the same cell as their sense partners at comparable expression levels. For about 60% of Arabidopsis trans-NATs, orthologs of at least one transcript of the pair also had trans-NAT partners in either Populus trichocarpa or Oryza sativa. The observation that 430 transcripts had both putative cis- and trans-NATs implicates multiple regulations by antisense transcripts. The potential roles of trans-NATs in inducing post-transcriptional gene silencing and in regulating alternative splicing were also examined. Conclusion: The Arabidopsis transcriptome contains a fairly large number of trans-NATs, whose possible functions include silencing of the corresponding sense transcripts or altering their splicing patterns. The interlaced relationships observed in some cis- and trans-NAT pairs suggest that antisense transcripts could be involved in complex regulatory networks in eukaryotes.
引用
收藏
页数:11
相关论文
共 34 条
  • [1] *AREX, 2005, AR GEN EXPR DAT
  • [2] Characterizing gene sets with FuncAssociate
    Berriz, GF
    King, OD
    Bryant, B
    Sander, C
    Roth, FP
    [J]. BIOINFORMATICS, 2003, 19 (18) : 2502 - 2504
  • [3] Specific interference with gene expression induced by long, double-stranded RNA in mouse embryonal teratocarcinoma cell lines
    Billy, E
    Brondani, V
    Zhang, HD
    Müller, U
    Filipowicz, W
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (25) : 14428 - 14433
  • [4] Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis
    Borsani, O
    Zhu, JH
    Verslues, PE
    Sunkar, R
    Zhu, JK
    [J]. CELL, 2005, 123 (07) : 1279 - 1291
  • [5] Expression and regulation of the Msx1 natural antisense transcript during development
    Coudert, AE
    Pibouin, L
    Vi-Fane, B
    Thomas, BL
    Macdougall, M
    Choudhury, A
    Robert, B
    Sharpe, PT
    Berdal, A
    Lezot, F
    [J]. NUCLEIC ACIDS RESEARCH, 2005, 33 (16) : 5208 - 5218
  • [6] Naturally occurring antisense: Transcriptional leakage or real overlap?
    Dahary, D
    Elroy-Stein, O
    Sorek, R
    [J]. GENOME RESEARCH, 2005, 15 (03) : 364 - 368
  • [7] Prediction of hybridization and melting for double-stranded nucleic acids
    Dimitrov, RA
    Zuker, M
    [J]. BIOPHYSICAL JOURNAL, 2004, 87 (01) : 215 - 226
  • [8] NATURALLY-OCCURRING ANTISENSE TRANSCRIPTS ARE PRESENT IN CHICK-EMBRYO CHONDROCYTES SIMULTANEOUSLY WITH THE DOWN-REGULATION OF THE ALPHA-1(I) COLLAGEN GENE
    FARRELL, CM
    LUKENS, LN
    [J]. JOURNAL OF BIOLOGICAL CHEMISTRY, 1995, 270 (07) : 3400 - 3408
  • [9] MicroRNA directs mRNA cleavage of the transcription factor NAC1 to downregulate auxin signals for Arabidopsis lateral root development
    Guo, HS
    Xie, Q
    Fei, JF
    Chua, NH
    [J]. PLANT CELL, 2005, 17 (05) : 1376 - 1386
  • [10] Dicing and slicing - The core machinery of the RNA interference pathway
    Hammond, SM
    [J]. FEBS LETTERS, 2005, 579 (26) : 5822 - 5829