Research article

Regulation of expression of two LY-6 family genes by intron retention and transcription induced chimerism

Vincenzo Calvanese^1,5 , Meera Mallya^2,4 , R Duncan Campbell^2,3 and Begoña Aguado^1,2

¹  Centro de Biología Molecular Severo Ochoa (CBMSO), CSIC, Madrid, 28804, Spain

²  MRC Rosalind Franklin Centre for Genomics Research, Cambridge, CB10 1SB, UK

³  Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3QX, UK

⁴  Department of Medicine, University of Cambridge, Wolfson College, CB3 9BB, UK

⁵  Centro Nacional de Investigaciones Oncológicas (CNIO), Madrid 28029, Spain

author email corresponding author email

BMC Molecular Biology 2008, 9:81doi:10.1186/1471-2199-9-81

Published:	25 September 2008

Abstract

Background

Regulation of the expression of particular genes can rely on mechanisms that are different from classical transcriptional and translational control. The LY6G5B and LY6G6D genes encode LY-6 domain proteins, whose expression seems to be regulated in an original fashion, consisting of an intron retention event which generates, through an early premature stop codon, a non-coding transcript, preventing expression in most cell lines and tissues.

Results

The MHC LY-6 non-coding transcripts have shown to be stable and very abundant in the cell, and not subject to Nonsense Mediated Decay (NMD). This retention event appears not to be solely dependent on intron features, because in the case of LY6G5B, when the intron is inserted in the artificial context of a luciferase expression plasmid, it is fully spliced but strongly stabilises the resulting luciferase transcript. In addition, by quantitative PCR we found that the retained and spliced forms are differentially expressed in tissues indicating an active regulation of the non-coding transcript. EST database analysis revealed that these genes have an alternative expression pathway with the formation of Transcription Induced Chimeras (TIC). This data was confirmed by RT-PCR, revealing the presence of different transcripts that would encode the chimeric proteins CSNKβ-LY6G5B and G6F-LY6G6D, in which the LY-6 domain would join to a kinase domain and an Ig-like domain, respectively.

Conclusion

In conclusion, the LY6G5B and LY6G6D intron-retained transcripts are not subjected to NMD and are more abundant than the properly spliced forms. In addition, these genes form chimeric transcripts with their neighbouring same orientation 5' genes. Of interest is the fact that the 5' genes (CSNKβ or G6F) undergo differential splicing only in the context of the chimera (CSNKβ-LY6G5B or G6F-LY6G6C) and not on their own.