Cryptic intron activation within the large exon of the mouse polymeric immunoglobulin receptor gene: cryptic splice sites correspond to protein domain boundaries

Abstract

The fourth exon of the mouse polymeric immuno-globulin receptor (pIgR) is 654 nt long and, despite being surrounded by large introns, is constitutively spliced into the mRNA. Deletion of an 84 nt sequence from this exon strongly activated both cryptic 5' and 3' splice sites surrounding a 78 nt cryptic intron. The 84 nt deletion is just upstream of the cryptic 3' splice site; the cryptic 3' splice site was likely activated because the deletion created a better 3' splice site. However, the cryptic 5' splice site was also required to activate the cryptic splice reaction; point mutations in either of the cryptic splice sites that decreased their match to the consensus splice site sequence inactivated the cryptic splice reaction. The activation and inactivation of these cryptic splice sites as a pair suggests that they are being co-recognized by the splicing machinery. Interestingly, the large fourth exon of the pIgR gene encodes two immunoglobulin-like extracellular protein domains; the cryptic 3' splice site coincides with the junction between these protein domains. The cryptic 5' splice site is located between protein subdomains where an intron is found in another gene of the immunoglobulin superfamily.

B-cell and plasma-cell splicing differences: A potential role in regulated immunoglobulin RNA processing

“…3C). We also monitored expression by RT-PCR (data not shown), which provides information on the size of the pIgR exon spliced into the D d RNA, as described previously (Bruce et al 1999;Bruce and Peterson 2001). The ratio of full-length to cryptic RNA expressed in the S194 plasma-cell line was similar to that seen previously in HepG2 cells; in pIgR, exon 4 was spliced intact, whereas the 5ЈSS mutation partially activated the previously identified upstream cryptic 5Ј splice site (Fig.…”

“…We have shown previously that the unusually large fourth exon from the mouse polymeric Ig receptor (pIgR) gene, when placed in the third intron of the mouse major histocom- Fig. 2A), is constitutively spliced into the mRNA in the human HepG2 liver-cell line (Bruce et al 1999;Bruce and Peterson 2001). However, when the 5Ј splice site of pIgR exon 4 was weakened by a point mutation (D d -pIgR 5ЈSS or 5ЈSS, Fig.…”

“…The Ig µ plasmid pSV5Cµs-m (Peterson and Perry 1986) and the D d -pIgR chimeric gene and its derivatives (Bruce et al 1999;Bruce and Peterson 2001) have been described previously. As with the Cµ construct, a 3.8-kb polyomavirus fragment that enables the plasmids to replicate was added to the D d -pIgR constructs (Peterson and Perry 1989).…”

The der(17)t(X;17)(p11;q25) of human alveolar soft part sarcoma fuses the TFE3 transcription factor gene to ASPL, a novel gene at 17q25

“…This 47 nt segment seem to represent a`cryptic intron' (Bruce et al, 1999;Haselo et al, 1997), yet it lacks canonical exon splice junctions. That both splice forms are present in cDNA rather than deriving from contaminating genomic DNA was con®rmed by RT ± PCR assays spanning exon boundaries.…”

Immunoglobulin Transport and Immunoglobulin Receptors

“…The preferential retention of exon 4 of pIgR mRNA in most species may therefore represent a novel mechanism that has evolved in the presence of functional selection. A detailed analysis of exon four from the mouse Pigr gene revealed the presence of a cryptic RNA splice site corresponding to the boundary of domains 3 and 4 in pIgR protein (Bruce et al, 1999). Multiple exonic and intronic features were found to suppress usage of this cryptic splice site and promote constitutive inclusion of exon 4 in pIgR mRNA (Bruce and Peterson, 2001).…”