Prediction of trans-antisense transcripts in Arabidopsis thaliana.
Prediction of trans-antisense transcripts in Arabidopsis thaliana.
复制标题
拟南芥反义转录本的预测。
DOI：
10.1186/gb-2006-7-10-r92
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发表时间：
2006
期刊：
影响因子：
12.3
通讯作者：
Wang XJ
中科院分区：
文献类型：
--
作者：
Wang H;Chua NH;Wang XJ
对拟南芥中反义反义转录物的全基因组筛选表明，反义转录物可能参与了真核生物中复杂的调控网络。天然反义转录本(NAT)是与其他转录本(正义转录本)具有序列互补性的编码或非编码RNA。这些RNA可能在转录或转录后水平上调节其正义伴侣(S)的表达。实验和计算方法已经证明NAT在真核生物中广泛存在。然而，以前的研究大多只关注顺式NAT，而对源于反式NAT的研究很少。我们已经在拟南芥中进行了全基因组范围的反式NAT筛选，并鉴定了1320个假定的反式NAT对。一个RNA退火程序预测，大多数反式NAT可以与它们的正义伙伴形成扩展的双链RNA双链。在已有表达数据的反式NAT中，超过85%的反式NAT与其正义伙伴位于同一组织中；其中67%的反式NAT与其正义伙伴在同一细胞中具有类似的表达水平。在大约60%的拟南芥中，至少有一个转录本的直系同源基因在三果杨或水稻中也有反式NAT伙伴。观察到430个转录本同时具有假定的顺式和反式NAT，这暗示了反义转录物的多种调控作用。还研究了反式NAT在诱导转录后基因沉默和调节选择性剪接中的潜在作用。拟南芥转录组含有相当数量的反式NAT，其可能的功能包括沉默相应的正义转录本或改变其剪接模式。在一些顺式和反式NAT对中观察到的交错关系表明，反义转录本可能参与了真核生物中复杂的调控网络。
A genome-wide screen for trans-natural antisense transcripts in Arabidopsis thaliana suggests that antisense transcripts could be involved in complex regulatory networks in eukaryotes. 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. 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. 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.
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