Stadler Peter F, Chen Julian J-L, Hackermüller Jörg, Hoffmann Steve, Horn Friedemann, Khaitovich Phillip, Kretzschmar Antje K, Mosig Axel, Prohaska Sonja J, Qi Xiaodong, Schutt Katharina, Ullmann Kerstin
Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.
Mol Biol Evol. 2009 Sep;26(9):1975-91. doi: 10.1093/molbev/msp112. Epub 2009 Jun 2.
Vault RNAs (vtRNAs) are small, about 100 nt long, polymerase III transcripts contained in the vault particles of eukaryotic cells. Presumably due to their enigmatic function, they have received little attention compared with most other noncoding RNA (ncRNA) families. Their poor sequence conservation makes homology search a complex and tedious task even within vertebrates. Here we report on a systematic and comprehensive analysis of this rapidly evolving class of ncRNAs in deuterostomes, providing a comprehensive collection of computationally predicted vtRNA genes. We find that all previously described vtRNAs are located at a conserved genomic locus linked to the protocadherin gene cluster, an association that is conserved throughout gnathostomes. Lineage-specific expansions to small vtRNA gene clusters are frequently observed in this region. A second vtRNA locus is syntenically conserved across eutherian mammals. The vtRNAs at the two eutherian loci exhibit substantial differences in their promoter structures, explaining their differential expression patterns in several human cancer cell lines. In teleosts, expression of several paralogous vtRNA genes, most but not all located at the syntenically conserved protocadherin locus, was verified by reverse transcriptase-polymerase chain reaction.
穹窿体RNA（vtRNAs）是一类小分子RNA，长度约为100个核苷酸，由真核细胞的穹窿体颗粒中所含的RNA聚合酶III转录产生。可能由于其功能神秘，与大多数其他非编码RNA（ncRNA）家族相比，它们受到的关注较少。其序列保守性较差，即使在脊椎动物中，同源性搜索也是一项复杂而繁琐的任务。在此，我们报告了对后口动物中这一快速进化的ncRNA类群进行的系统全面分析，提供了通过计算预测的vtRNA基因的全面集合。我们发现，所有先前描述的vtRNAs都位于与原钙黏蛋白基因簇相关的保守基因组位点，这种关联在整个有颌类动物中都是保守的。在该区域经常观察到向小vtRNA基因簇的谱系特异性扩增。第二个vtRNA位点在真兽类哺乳动物中是共线性保守的。这两个真兽类位点的vtRNAs在启动子结构上表现出显著差异，这解释了它们在几种人类癌细胞系中的差异表达模式。在硬骨鱼中，通过逆转录聚合酶链反应验证了几个旁系同源vtRNA基因的表达，其中大多数但并非全部位于共线性保守的原钙黏蛋白位点。
