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	Systematic analysis of alternative first exons in plant genomes
	Chen, Wei-Hua1,4; Lv, Guanting1,2; Lv, Congying3; Zeng, Changqing1; Hu, Songnian1
刊名	Bmc plant biology
	2007-10-17
卷号	7页码:13
ISSN号	1471-2229
DOI	10.1186/1471-2229-7-55
通讯作者	Hu, songnian(husn@genomics.org.cn)
英文摘要	Background: alternative splicing (as) contributes significantly to protein diversity, by selectively using different combinations of exons of the same gene under certain circumstances. one particular type of as is the use of alternative first exons (afes), which can have consequences far beyond the fine-tuning of protein functions. for example, afes may change the n-termini of proteins and thereby direct them to different cellular compartments. when alternative first exons are distant, they are usually associated with alternative promoters, thereby conferring an extra level of gene expression regulation. however, only few studies have examined the patterns of afes, and these analyses were mainly focused on mammalian genomes. recent studies have shown that afes exist in the rice genome, and are regulated in a tissue-specific manner. our current understanding of afes in plants is still limited, including important issues such as their regulation, contribution to protein diversity, and evolutionary conservation. results: we systematically identified 1,378 and 645 afe-containing clusters in rice and arabidopsis, respectively. from our data sets, we identified two types of afes according to their genomic organisation. in genes with type i afes, the first exons are mutually exclusive, while most of the downstream exons are shared among alternative transcripts. conversely, in genes with type ii afes, the first exon of one gene structure is an internal exon of an alternative gene structure. the functionality analysis indicated about half and similar to 19% of the afes in arabidopsis and rice could alter n-terminal protein sequences, and similar to 5% of the functional alteration in type ii afes involved protein domain addition/deletion in both genomes. expression analysis indicated that 20 similar to 66% of rice afe clusters were tissue- and/or development- specifically transcribed, which is consistent with previous observations; however, a much smaller percentage of arabidopsis afes was regulated in this manner, which suggests different regulation mechanisms of afes between rice and arabidopsis. statistical analysis of some features of afe clusters, such as splice-site strength and secondary structure formation further revealed differences between these two species. orthologous search of afe-containing gene pairs detected only 19 gene pairs conserved between rice and arabidopsis, accounting only for a few percent of afe- containing clusters. conclusion: our analysis of afe-containing genes in rice and arabidopsis indicates that afes have multiple functions, from regulating gene expression to generating protein diversity. comparisons of afe clusters revealed different features in the two plant species, which indicates that afes may have evolved independently after the separation of rice (a model monocot) and arabidopsis (a model dicot).
WOS关键词	MESSENGER-RNA ; GENE STRUCTURE ; PROMOTER ; IDENTIFICATION ; ORGANIZATION ; PREDICTION ; DATABASE ; BIOLOGY ; WIDE ; TOOL
WOS研究方向	Plant Sciences
WOS类目	Plant Sciences
语种	英语
出版者	BIOMED CENTRAL LTD
WOS记录号	WOS:000252376200001
内容类型	期刊论文
URI标识	http://www.corc.org.cn/handle/1471x/2381458
专题	中国科学院大学
通讯作者	Hu, Songnian
作者单位	1.Chinese Acad Sci, Beijing Inst Genom, Key Lab Genome Sci & Informat, Beijing, Peoples R China 2.Chinese Acad Sci, Grad Sch, Beijing, Peoples R China 3.Nanyang Inst Technol, Henan, Peoples R China 4.Univ Dusseldorf, Dusseldorf, Germany
推荐引用方式 GB/T 7714	Chen, Wei-Hua,Lv, Guanting,Lv, Congying,et al. Systematic analysis of alternative first exons in plant genomes[J]. Bmc plant biology,2007,7:13.
APA	Chen, Wei-Hua,Lv, Guanting,Lv, Congying,Zeng, Changqing,&Hu, Songnian.(2007).Systematic analysis of alternative first exons in plant genomes.Bmc plant biology,7,13.
MLA	Chen, Wei-Hua,et al."Systematic analysis of alternative first exons in plant genomes".Bmc plant biology 7(2007):13.

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