Pauws E, van Kampen A H, van de Graaf S A, de Vijlder J J, Ris-Stalpers C
Laboratory of Pediatric Endocrinology and Bioinformatics Laboratory, Academic Medical Center, University of Amsterdam, PO Box 22700, 1100 DE Amsterdam, The Netherlands. :
Nucleic Acids Res. 2001 Apr 15;29(8):1690-4. doi: 10.1093/nar/29.8.1690.
The analysis of a human thyroid serial analysis of gene expression (SAGE) library shows the presence of an abundant SAGE tag corresponding to the mRNA of thyroglobulin (TG). Additional, less abundant tags are present that can not be linked to any other known gene, but show considerable homology to the wild-type TG tag. To determine whether these tags represent TG mRNA molecules with alternative cleavage, 3'-RACE clones were sequenced. The results show that the three putative TG SAGE tags can be attributed to TG transcripts and reflect the use of alternative polyadenylation cleavage sites downstream of a single polyadenylation signal in vivo. By screening more than 300 000 sequences corresponding to human, mouse and rat transcripts for this phenomenon we show that a considerable percentage of mRNA transcripts (44% human, 22% mouse and 22% rat) show cleavage site heterogeneity. When analyzing SAGE-generated expression data, this phenomenon should be considered, since, according to our calculations, 2.8% of human transcripts show two or more different SAGE tags corresponding to a single gene because of alternative cleavage site selection. Both experimental and in silico data show that the selection of the specific cleavage site for poly(A) addition using a given polyadenylation signal is more variable than was previously thought.
对人类甲状腺基因表达序列分析（SAGE）文库的分析表明，存在一个与甲状腺球蛋白（TG）mRNA相对应的丰富SAGE标签。此外，还存在一些丰度较低的标签，它们无法与任何其他已知基因相关联，但与野生型TG标签具有相当的同源性。为了确定这些标签是否代表具有可变切割的TG mRNA分子，对3'-RACE克隆进行了测序。结果表明，三个假定的TG SAGE标签可归因于TG转录本，并反映了体内单个聚腺苷酸化信号下游可变聚腺苷酸化切割位点的使用情况。通过筛选超过300000条对应于人类、小鼠和大鼠转录本的序列以寻找这种现象，我们发现相当比例的mRNA转录本（人类为44%，小鼠和大鼠均为22%）表现出切割位点异质性。在分析SAGE产生的表达数据时，应考虑这种现象，因为根据我们的计算，由于可变切割位点选择，2.8%的人类转录本显示对应于单个基因的两个或更多不同SAGE标签。实验数据和计算机模拟数据均表明，使用给定聚腺苷酸化信号进行聚（A）添加的特定切割位点选择比以前认为的更具变异性。
