Structure and Expression Analyses of SVA Elements in Relation to Functional Genes

• Published in: Genomics & informatics Vol. 11; no. 3; pp. 142 - 148
• Main Authors: Kwon, Yun-Jeong, Choi, Yuri, Eo, Jungwoo, Noh, Yu-Na, Gim, Jeong-An, Jung, Yi-Deun, Lee, Ja-Rang, Kim, Heui-Soo
• Format: Journal Article
• Language: English
• Published: Korea (South) Korea Genome Organization 01.09.2013; BioMed Central; 한국유전체학회
• Subjects: gene expression profiling; genomics; messenger RNA isoform; Original; SVA; tissue specificity; 자연과학일반; genomics; messenger RNA isoform; gene expression profiling; tissue specificity; SVA
• ISSN: 1598-866X; 2234-0742
• DOI: 10.5808/GI.2013.11.3.142

SINE-VNTR-Alu (SVA) elements are present in hominoid primates and are divided into 6 subfamilies (SVA-A to SVA-F) and active in the human population. Using a bioinformatic tool, 22 SVA element-associated genes are identified in the human genome. In an analysis of genomic structure, SVA elements are detected in the 5' untranslated region (UTR) of HGSNAT (SVA-B), MRGPRX3 (SVA-D), HYAL1 (SVA-F), TCHH (SVA-F), and ATXN2L (SVA-F) genes, while some elements are observed in the 3'UTR of SPICE1 (SVA-B), TDRKH (SVA-C), GOSR1 (SVA-D), BBS5 (SVA-D), NEK5 (SVA-D), ABHD2 (SVA-F), C1QTNF7 (SVA-F), ORC6L (SVA-F), TMEM69 (SVA-F), and CCDC137 (SVA-F) genes. They could contribute to exon extension or supplying poly A signals. LEPR (SVA-C), ALOX5 (SVA-D), PDS5B (SVA-D), and ABCA10 (SVA-F) genes also showed alternative transcripts by SVA exonization events. Dominant expression of HYAL1_SVA appeared in lung tissues, while HYAL1_noSVA showed ubiquitous expression in various human tissues. Expression of both transcripts (TDRKH_SVA and TDRKH_noSVA) of the TDRKH gene appeared to be ubiquitous. Taken together, these data suggest that SVA elements cause transcript isoforms that contribute to modulation of gene regulation in various human tissues.