Genomic organization of Tropomodulins 2 and 4 and unusual intergenic and intraexonic splicing of YL-1 and Tropomodulin 4

Abstract

Background: The tropomodulins (TMODs) are a family of proteins that cap the pointed ends of actin filaments. Four TMODs have been identified in humans, with orthologs in mice. Mutations in actin or actin-binding proteins have been found to cause several human diseases, ranging from hypertrophic cardiomyopathy to immunodeficiencies such as Wiskott-Aldrich syndrome. We had previously mapped Tropomodulin 2 (TMOD2) to the genomic region containing the gene for amyotrophic lateral sclerosis 5 (ALS5). We determined the genomic structure of Tmod2 in order to better analyze patient DNA for mutations; we also determined the genomic structure of Tropomodulin 4 (TMOD4).

Results: In this study, we determined the genomic structure of TMOD2 and TMOD4 and found the organization of both genes to be similar. Sequence analysis of TMOD2 revealed no mutations or polymorphisms in ALS5 patients or controls. Interestingly, we discovered that another gene, YL-1, intergenically splices into TMOD4. YL-1 encodes six exons, the last of which is 291 bp from a 5' untranslated exon of TMOD4. We used 5' RACE and RT-PCR from TMOD4 to identify several intergenic RACE products. YL-1 was also found to undergo unconventional splicing using non-canonical splice sites within exons (intraexonic splicing) to produce several alternative transcripts.

Conclusions: The genomic structure of TMOD2 and TMOD4 have been delineated. This should facilitate future mutational analysis of these genes. In addition, intergenic splicing at TMOD4/YL-1 was discovered, demonstrating yet another level of complexity of gene organization and regulation.

Figure 1

Genomic structure of TMOD2, TMOD4, and YL-1. Numbered rectangles represent coding exons, E0 represents 5' UTR exons. ATG represents the start codon of each gene and TAA or TAG represent the termination codon of each gene. Scale below is in kilobases (kb).

Figure 2

Summary of RACE products: Hatched rectangles represent YL-1 exons. Diagonal striped rectangles represent TMOD4 exons. Numbers in parentheses represent the number of amino acids produced from each ORF. Black rectangles represent introns, and horizontally striped rectangles represent exons which used a cryptic splice site.

Figure 3

Hatched rectangles represent YL-1 exons. Thick black lines represent the intraexonic splice events. The number of amino acids produced by each ORF is in parentheses. Asteriks represent the positions of intraexonic non-canonical splice sites used in multiple ESTs.

Figure 4

Human multiple tissue Northern blot probed with YL-1 RT-PCR product revealed a single highly expressed transcript between 1.4–1.6 kb in all tissues.