Ali S, Azfer M A, Bashamboo A, Mathur P K, Malik P K, Mathur V B, Raha A K, Ansari S
Molecular Genetics Laboratory, National Institute of Immunology, Aruna Asaf Ali Marg, New Delhi 110 067, India.
Gene. 1999 Mar 4;228(1-2):33-42. doi: 10.1016/s0378-1119(99)00015-3.
We have cloned and sequenced a 906bp EcoRI repeat DNA fraction from Rhinoceros unicornis genome. The contig pSS(R)2 is AT rich with 340 A (37.53%), 187 C (20.64%), 173 G (19.09%) and 206 T (22.74%). The sequence contains MALT box, NF-E1, Poly-A signal, lariat consensus sequences, TATA box, translational initiation sequences and several stop codons. Translation of the contig showed seven different types of protein motifs, among which, EGF-like domain cysteine pattern signatures and Bowman-Birk serine protease inhibitor family signatures were prominent. The presence of eukaryotic transcriptional elements, protein signatures and analysis of subset sequences in the 5' region from 1 to 165nt indicating coding potential (test code value=0.97) suggest possible regulatory and/or functional role(s) of these sequences in the rhino genome. Translation of the complementary strand from 906 to 706nt and 190 to 2nt showed proteins of more than 7kDa rich in non-polar residues. This suggests that pSS(R)2 is either a part of, or adjacent to, a functional gene. The contig contains mostly non-consecutive simple repeat units from 2 to 17nt with varying frequencies, of which four base motifs were found to be predominant. Zoo-blot hybridization revealed that pSS(R)2 sequences are unique to R. unicornis genome because they do not cross-hybridize, even with the genomic DNA of South African black rhino Diceros bicornis. Southern blot analysis of R. unicornis genomic DNA with pSS(R)2 and other synthetic oligo probes revealed a high level of genetic homogeneity, which was also substantiated by microsatellite associated sequence amplification (MASA). Owing to its uniqueness, the pSS(R)2 probe has a potential application in the area of conservation biology for unequivocal identification of horn or other body tissues of R. unicornis. The evolutionary aspect of this repeat fraction in the context of comparative genome analysis is discussed.
我们从印度犀基因组中克隆并测序了一个906bp的EcoRI重复DNA片段。重叠群pSS(R)2富含AT，其中有340个A（37.53%）、187个C（20.64%）、173个G（19.09%）和206个T（22.74%）。该序列包含MALT框、NF-E1、多聚腺苷酸信号、套索状共有序列、TATA框、翻译起始序列和几个终止密码子。对该重叠群的翻译显示出七种不同类型的蛋白质基序，其中，表皮生长因子样结构域半胱氨酸模式特征和鲍曼-伯克丝氨酸蛋白酶抑制剂家族特征较为突出。真核转录元件、蛋白质特征的存在以及对1至165nt的5'区域子集序列的分析表明具有编码潜力（测试编码值=0.97），这表明这些序列在犀牛基因组中可能具有调控和/或功能作用。从906至706nt以及190至2nt的互补链翻译显示出富含非极性残基的超过7kDa的蛋白质。这表明pSS(R)2要么是一个功能基因的一部分，要么与一个功能基因相邻。该重叠群主要包含2至17nt的非连续简单重复单元，频率各异，其中发现四种碱基基序占主导。动物印迹杂交显示pSS(R)2序列是印度犀基因组所特有的，因为它们甚至不与南非黑犀双角犀的基因组DNA发生交叉杂交。用pSS(R)2和其他合成寡核苷酸探针对印度犀基因组DNA进行Southern印迹分析显示出高度的遗传同质性，微卫星相关序列扩增（MASA）也证实了这一点。由于其独特性，pSS(R)2探针在保护生物学领域具有潜在应用，可用于明确鉴定印度犀的角或其他身体组织。本文讨论了在比较基因组分析背景下该重复片段的进化方面。
