Features of Arabidopsis genes and genome discovered using full-length cDNAs
Features of Arabidopsis genes and genome discovered using full-length cDNAs
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DOI：
10.1007/s11103-005-2564-9
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发表时间：
2006-01-01
影响因子：
5.1
通讯作者：
Feldmann, KA
中科院分区：
文献类型：
--
作者：
Alexandrov, NN;Troukhan, ME;Feldmann, KA
拟南芥是目前高等植物的参考基因组。一个新的，更详细的统计分析拟南芥基因结构，包括内含子和外显子的长度，基因间的距离，启动子的功能，从同一个转录单位转录的mRNA的5 '端的变化。我们还提供了拟南芥转录本大小、UTR长度、3 '端切割位点、剪接变体和编码潜力的统计特征。这些分析通过仔细检查我们收集的测序的全长cDNA和更大的5 '-EST集合，以及来自Salk/斯坦福大学/植物基因表达中心/RIKEN的另一组全长cDNA而得到促进。7%的基因的转录本中观察到选择性剪接的例子，这些基因中的许多显示出多种剪接异构体。大多数剪接变体位于转录本的非编码区。非典型剪接位点占所有剪接位点的不到1%。少于四个内含子的基因显示平均mRNA水平降低。在30%的高表达基因和50%以上的低表达基因中观察到了假定的交替转录起始位点。转录起始位点与DNA序列中的CG偏斜峰非常好地相关。基因间的距离变化很大，那些基因相互转录的距离明显更短。新的转录本，在目前的TIGR基因组注释和非编码EST中缺失，包括那些已知基因的反义，在补充材料中得到并编目。他们在拟南芥基因组中发现了148个新的基因座。得出的结论提供了一个更好的了解拟南芥基因组和基因转录是如何处理的。这些结果还可以更好地预测尚未明确定义的基因，并为与目前正在确定完整序列的其他植物基因组进行比较提供参考。本文包括与水稻的一些比较。
Arabidopsis is currently the reference genome for higher plants. A new, more detailed statistical analysis of Arabidopsis gene structure is presented including intron and exon lengths, intergenic distances, features of promoters, and variant 5'-ends of mRNAs transcribed from the same transcription unit. We also provide a statistical characterization of Arabidopsis transcripts in terms of their size, UTR lengths, 3'-end cleavage sites, splicing variants, and coding potential. These analyses were facilitated by scrutiny of our collection of sequenced full-length cDNAs and much larger collection of 5'-ESTs, together with another set of full-length cDNAs from Salk/Stanford/Plant Gene Expression Center/RIKEN. Examples of alternative splicing are observed for transcripts from 7% of the genes and many of these genes display multiple spliced isoforms. Most splicing variants lie in non-coding regions of the transcripts. Non-canonical splice sites constitute less than 1% of all splice sites. Genes with fewer than four introns display reduced average mRNA levels. Putative alternative transcription start sites were observed in 30% of highly expressed genes and in more than 50% of the genes with low expression. Transcription start sites correlate remarkably well with a CG skew peak in the DNA sequences. The intergenic distances vary considerably, those where genes are transcribed towards one another being significantly shorter. New transcripts, missing in the current TIGR genome annotation and ESTs that are non-coding, including those antisense to known genes, are derived and cataloged in the Supplementary Material. They identify 148 new loci in the Arabidopsis genome. The conclusions drawn provide a better understanding of the Arabidopsis genome and how the gene transcripts are processed. The results also allow better predictions to be made for, as yet, poorly defined genes and provide a reference for comparisons with other plant genomes whose complete sequences are currently being determined. Some comparisons with rice are included in this paper.