MATN and LAPTM Are Parts of Larger Transcription Units Produced by Intergenic Splicing: Intergenic Splicing May Be a Common Phenomenon

Intergenic splicing, the joining of exons from separate genes, has been observed only rarely in mammals. While the matrilin (MATN) and lysosomal-associated protein transmembrane (LAPTM) genes comprise distinct gene families, we have demonstrated intergenic splicing between two sets of family genes, the matrilin-3 (MATN3) and lysosomal-associated protein transmembrane 4alpha (LAPTM4A), and the matrilin-2 (MATN2) and lysosomal-associated protein transmembrane 4beta (LAPTM4B). The expression pattern and sub-cellular localization of the MATN-LAPTM hybrid transcripts differ from those of the original genes, suggesting unique functions for the products. Our observations indicate that intergenic splicing is a common and well-regulated phenomenon and underscore the fundamental challenges in defining the gene (transcriptional unit). Given these findings, the number of gene in the human genome may be smaller than present estimates suggest.