Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice
Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice
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DOI：
10.1016/s1673-8527(07)60026-5
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发表时间：
2007-03-01
影响因子：
5.9
通讯作者：
Guo, Rongfa
中科院分区：
文献类型：
--
作者：
Gu, Lianfeng;Guo, Rongfa
选择性剪接是基因组复杂性和蛋白质组多样性的重要组成部分，但对含有核苷酸结合位点和富含亮氨酸重复序列（NBS-LRR）结构域的水稻选择性剪接的研究尚未见报道。对NBS-LRR域进行隐马尔可夫模型（HMM）搜索。从基因组研究所（Institute for Genomic Research，TIGR）获得875个NBS-LRR编码序列。并将其应用于知识型水稻分子生物学百科全书的检索。（KOME）、TIGR rice gene index（TGI）和Universal Protein Resource（UniProt）中获得同源全长cDNA（FL-cDNA）、暂定共有序列和蛋白质序列。从FL-cDNA、暂定共有序列和蛋白质序列的基因组比对中检测到选择性剪接事件，这提供了关于基因剪接变体的有价值的信息。使用Spidey和Sim 4程序将这些序列与相应的BAC序列进行比对，并通过tBLASTn比对每种蛋白质。在875个NBS-LRR序列中，119个（13.6%）序列具有选择性剪接，其中多个FL-cDNA、TGI序列和蛋白质对应于同一基因。鉴定了71个内含子保留事件、20个外显子跳跃事件、16个选择性终止事件、25个选择性起始事件、12个选择性5'剪接事件和16个选择性3'剪接事件。大多数这些替代剪接支持两个或更多的成绩单。数据集可在http://www.bioinfor.org上获得。此外，剪接边界的生物信息学分析表明，外显子跳跃和内含子保留没有表现出强烈的一致性。这意味着不同的调控机制，指导剪接异构体的表达。本文还分析了内含子保留对蛋白质的影响。替代蛋白质的C-末端区域比N-末端区域更易变。最后，对选择性剪接的组织分布和蛋白定位进行了探讨。选择性剪接的组织分布的最大类别是芽和愈伤组织。超过三分之一的剪接形式的蛋白质定位在质膜和细胞质。所有剪接形式的NBS-LRR蛋白都可能在抗病过程中发挥重要作用，并激活下游信号通路。
Alternative splicing is a major contributor to genomic complexity and proteome diversity, yet the analysis of alternative splicing for the sequence containing nucleotide binding site and leucine-rich repeats (NBS-LRR) domain has not been explored in rice (Oryza sativa L.). Hidden Markov model (HMM) searches were performed for NBS-LRR domain. 875 NBS-LRR-encoding sequences were obtained from the Institute for Genomic Research (TIGR). All of them were used to blast Knowledge-based Oryza Molecular Biological Encyclopaedia. (KOME), TIGR rice gene index (TGI), and Universal Protein Resource (UniProt) to obtain homologous full-length cDNAs (FL-cDNAs), tentative consensus sequences, and protein sequences. Alternative splicing events were detected from genomic alignment of FL-cDNAs, tentative consensus sequences, and protein sequences, which provide valuable information on splice variants of genes. These sequences were aligned to the corresponding BAC sequences using the Spidey and Sim4 programs and each of the proteins was aligned by tBLASTn. Of the 875 NBS-LRR sequences, 119 (13.6%) sequences had alternative splicing where multiple FL-cDNAs, TGI sequences and proteins corresponded to the same gene. 71 intron retention events, 20 exon skipping events, 16 alternative termination events, 25 alternative initiation events, 12 alternative 5' splicing events, and 16 alternative 3' splicing events were identified. Most of these alternative splices were supported by two or more transcripts. The data sets are available at http://www.bioinfor.org. Furthermore, the bioinformatics analysis of splice boundaries showed that exon skipping and intron retention did not exhibit strong consensus. This implies a different regulation mechanism that guides the expression of splice isoforms. This article also presents the analysis of the effects of intron retention on proteins. The C-terminal regions of alternative proteins turned out to be more variable than the N-terminal regions. Finally, tissue distribution and protein localization of alternative splicing were explored. The largest categories of tissue distributions for alternative splicing were shoot and callus. More than one-thirds of protein localization for splice forms was plasma membrane and cytoplasm. All the NBS-LRR proteins for splice forms may have important function in disease resistance and activate downstream signaling pathways.