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Transcription variants of SLA-7, a swine non classical MHC class I gene.

Hu R, Lemonnier G, Bourneuf E, Vincent-Naulleau S, Rogel-Gaillard C - BMC Proc (2011)

Bottom Line: Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant.An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon.In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR de Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France. claire.rogel-gaillard@jouy.inra.fr.

ABSTRACT
In pig, very little information is available on the non classical class I (Ib) genes of the Major Histocompatibility Complex (MHC) i.e. SLA-6, -7 and -8. Our aim was to focus on the transcription pattern of the SLA-7 gene. RT-PCR experiments were carried out with SLA-7 specific primers targeting either the full coding sequence (CDS) from exon 1 to the 3 prime untranslated region (3UTR) or a partial CDS from exon 4 to the 3UTR. We show that the SLA-7 gene expresses a full length transcript not yet identified that refines annotation of the gene with eight exons instead of seven as initially described from the existing RefSeq RNA. These two RNAs encode molecules that differ in cytoplasmic tail length. In this study, another SLA-7 transcript variant was characterized, which encodes a protein with a shorter alpha 3 domain, as a consequence of a splicing site within exon 4. Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant. An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon. In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.

No MeSH data available.


Related in: MedlinePlus

Multi-alignment of peptides encoded by the transcripts SLA-7-1465, SLA-7-1366 and SLA-7-001. The successive eight (SLA-7-1366 and SLA-7-1465) or seven (SLA-7-001) exons are alternatively indicated by black and blue font. Aminoacids at the junction between two exons are in grey boxes. Aminoacid similarities between two or three sequences are indicated below the sequence alignments by dots or stars, respectively.
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Figure 2: Multi-alignment of peptides encoded by the transcripts SLA-7-1465, SLA-7-1366 and SLA-7-001. The successive eight (SLA-7-1366 and SLA-7-1465) or seven (SLA-7-001) exons are alternatively indicated by black and blue font. Aminoacids at the junction between two exons are in grey boxes. Aminoacid similarities between two or three sequences are indicated below the sequence alignments by dots or stars, respectively.

Mentions: Full length SLA-7 transcripts were characterized by RT-PCR from the thymus of MeLiM pigs using the primers SLA-7-e1-F and SLA-7-3UTR-R (Table 1 and Figure 1). A 1465 nucleotides long transcript was obtained and further named SLA-7-1465 (Accession number: GU322918). Annotation was carried out by aligning the cDNA sequence to the genomic reference sequence (GenBank accession number AJ251914) and eight exons were detected in this new transcript, in contrast to the reference full-length transcript (Accession number NM_213768) that harbours only seven exons [12] (Figure 1) and is referred to as SLA-7-001 (OTTSUST00000000782) in the Vertebrate Genome Annotation database [19]. The two RNAs encode proteins that differ in the cytoplasmic tail (Figure 2). The SLA-7-001 encoded protein contains a cytoplasmic tail that is defined by exons 6 and 7 and is 68 aminoacids long. The SLA-7-1465 encoded protein is characterized by a cytoplasmic tail that is defined by exons 6 to 8 and is 55 aminoacids long. It has been demonstrated that the cytoplasmic tail of MHC class I molecules contributes to their expression on the cell surface [20] and that mutations of cysteine residues in the cytoplasmic tail of MHC class Ia molecules modify extracellular recognition by Leukocyte Ig-Like receptor 1 [21]. Moreover, it has been reported that HLA-F molecules are entirely dependent on the cytoplasmic tail for export from the endoplasmic reticulum to the Golgi apparatus [22]. Altogether, these reports strongly support a major role for the cytoplasmic tail of MHC class I molecules in transport and function. Further experiments are required to study whether the SLA-7 molecules encoded by SLA-7-001 or SLA-7-1465 transcripts have distinct properties due to their different cytoplasmic tails.


Transcription variants of SLA-7, a swine non classical MHC class I gene.

Hu R, Lemonnier G, Bourneuf E, Vincent-Naulleau S, Rogel-Gaillard C - BMC Proc (2011)

Multi-alignment of peptides encoded by the transcripts SLA-7-1465, SLA-7-1366 and SLA-7-001. The successive eight (SLA-7-1366 and SLA-7-1465) or seven (SLA-7-001) exons are alternatively indicated by black and blue font. Aminoacids at the junction between two exons are in grey boxes. Aminoacid similarities between two or three sequences are indicated below the sequence alignments by dots or stars, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3108204&req=5

Figure 2: Multi-alignment of peptides encoded by the transcripts SLA-7-1465, SLA-7-1366 and SLA-7-001. The successive eight (SLA-7-1366 and SLA-7-1465) or seven (SLA-7-001) exons are alternatively indicated by black and blue font. Aminoacids at the junction between two exons are in grey boxes. Aminoacid similarities between two or three sequences are indicated below the sequence alignments by dots or stars, respectively.
Mentions: Full length SLA-7 transcripts were characterized by RT-PCR from the thymus of MeLiM pigs using the primers SLA-7-e1-F and SLA-7-3UTR-R (Table 1 and Figure 1). A 1465 nucleotides long transcript was obtained and further named SLA-7-1465 (Accession number: GU322918). Annotation was carried out by aligning the cDNA sequence to the genomic reference sequence (GenBank accession number AJ251914) and eight exons were detected in this new transcript, in contrast to the reference full-length transcript (Accession number NM_213768) that harbours only seven exons [12] (Figure 1) and is referred to as SLA-7-001 (OTTSUST00000000782) in the Vertebrate Genome Annotation database [19]. The two RNAs encode proteins that differ in the cytoplasmic tail (Figure 2). The SLA-7-001 encoded protein contains a cytoplasmic tail that is defined by exons 6 and 7 and is 68 aminoacids long. The SLA-7-1465 encoded protein is characterized by a cytoplasmic tail that is defined by exons 6 to 8 and is 55 aminoacids long. It has been demonstrated that the cytoplasmic tail of MHC class I molecules contributes to their expression on the cell surface [20] and that mutations of cysteine residues in the cytoplasmic tail of MHC class Ia molecules modify extracellular recognition by Leukocyte Ig-Like receptor 1 [21]. Moreover, it has been reported that HLA-F molecules are entirely dependent on the cytoplasmic tail for export from the endoplasmic reticulum to the Golgi apparatus [22]. Altogether, these reports strongly support a major role for the cytoplasmic tail of MHC class I molecules in transport and function. Further experiments are required to study whether the SLA-7 molecules encoded by SLA-7-001 or SLA-7-1465 transcripts have distinct properties due to their different cytoplasmic tails.

Bottom Line: Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant.An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon.In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: INRA, UMR de Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France. claire.rogel-gaillard@jouy.inra.fr.

ABSTRACT
In pig, very little information is available on the non classical class I (Ib) genes of the Major Histocompatibility Complex (MHC) i.e. SLA-6, -7 and -8. Our aim was to focus on the transcription pattern of the SLA-7 gene. RT-PCR experiments were carried out with SLA-7 specific primers targeting either the full coding sequence (CDS) from exon 1 to the 3 prime untranslated region (3UTR) or a partial CDS from exon 4 to the 3UTR. We show that the SLA-7 gene expresses a full length transcript not yet identified that refines annotation of the gene with eight exons instead of seven as initially described from the existing RefSeq RNA. These two RNAs encode molecules that differ in cytoplasmic tail length. In this study, another SLA-7 transcript variant was characterized, which encodes a protein with a shorter alpha 3 domain, as a consequence of a splicing site within exon 4. Surprisingly, a cryptic non canonical GA-AG splicing site is used to generate this transcript variant. An additional SLA-7 variant was also identified in the 3UTR with a splicing site occurring 31 nucleotides downstream to the stop codon. In conclusion, the pig SLA-7 MHC class Ib gene presents a complex transcription pattern with two transcripts encoding various molecules and transcripts that do not alter the CDS and may be subject to post-transcriptional regulation.

No MeSH data available.


Related in: MedlinePlus