Genomics Inform.  2013 Sep;11(3):142-148. 10.5808/GI.2013.11.3.142.

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

• Kwon YJ
• Choi Y
• Eo J
• Noh YN
• Gim JA
• Jung YD
• Lee JR
• Kim HS

• KMID: 2009107
• DOI: http://doi.org/10.5808/GI.2013.11.3.142

Abstract

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.

Keyword

gene expression profiling; genomics; messenger RNA isoform; SVA; tissue specificity

MeSH Terms

3' Untranslated Regions
5' Untranslated Regions
Exons
Gene Expression Profiling
Genome, Human
Genomics
Humans
Lung
Organ Specificity
Poly A
Primates
Protein Isoforms
3' Untranslated Regions
5' Untranslated Regions
Poly A
Protein Isoforms