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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.


Schematic representation of the SLA-7 transcripts. Exons are numbered E1 to E8 and the three prime non coding region is indicated as 3UTR. Sizes of exons and 3UTR are given in nucleotides within the boxes. The number of aminoacids for each exon is indicated above the exon number. Exons represented by a dark blue box (E1) correspond to the leader sequences. Exons represented by orange boxes (E2 to E4) stand for the alpha1, 2 and 3 domains of the molecules. Exons represented in bright blue (E5) correspond to the transmembrane domain. Exons represented by green boxes encode the cytoplasmic tail of the molecule. The 3UTR is represented by a grey box. Positions of the primers used for RT-PCRs are indicated by arrows on top of the figure on E1 (SLA-7-e1-F), E4 (SLA-7-e4-F) and 3UTR (SLA-7-3UTR-R). The donor and acceptor splice sequences are positioned by arrows on E4 and 3UTR boxes.
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Figure 1: Schematic representation of the SLA-7 transcripts. Exons are numbered E1 to E8 and the three prime non coding region is indicated as 3UTR. Sizes of exons and 3UTR are given in nucleotides within the boxes. The number of aminoacids for each exon is indicated above the exon number. Exons represented by a dark blue box (E1) correspond to the leader sequences. Exons represented by orange boxes (E2 to E4) stand for the alpha1, 2 and 3 domains of the molecules. Exons represented in bright blue (E5) correspond to the transmembrane domain. Exons represented by green boxes encode the cytoplasmic tail of the molecule. The 3UTR is represented by a grey box. Positions of the primers used for RT-PCRs are indicated by arrows on top of the figure on E1 (SLA-7-e1-F), E4 (SLA-7-e4-F) and 3UTR (SLA-7-3UTR-R). The donor and acceptor splice sequences are positioned by arrows on E4 and 3UTR boxes.

Mentions: Three primers were designed from the SLA-7 reference cDNA [12] and genomic [9,10] sequences, using the Primer3 online program [16]. The primer combinations were suitable to amplify the full coding sequence from exon 1 to the three prime untranslated region (3UTR) or a partial coding sequence from exon 4 to the 3UTR (Table 1 and Figure 1). Primers were also designed to amplify cDNAs of the RPL32 gene that has been used as control gene for expression levels (Table 1 and Figure 1).


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)

Schematic representation of the SLA-7 transcripts. Exons are numbered E1 to E8 and the three prime non coding region is indicated as 3UTR. Sizes of exons and 3UTR are given in nucleotides within the boxes. The number of aminoacids for each exon is indicated above the exon number. Exons represented by a dark blue box (E1) correspond to the leader sequences. Exons represented by orange boxes (E2 to E4) stand for the alpha1, 2 and 3 domains of the molecules. Exons represented in bright blue (E5) correspond to the transmembrane domain. Exons represented by green boxes encode the cytoplasmic tail of the molecule. The 3UTR is represented by a grey box. Positions of the primers used for RT-PCRs are indicated by arrows on top of the figure on E1 (SLA-7-e1-F), E4 (SLA-7-e4-F) and 3UTR (SLA-7-3UTR-R). The donor and acceptor splice sequences are positioned by arrows on E4 and 3UTR boxes.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 1: Schematic representation of the SLA-7 transcripts. Exons are numbered E1 to E8 and the three prime non coding region is indicated as 3UTR. Sizes of exons and 3UTR are given in nucleotides within the boxes. The number of aminoacids for each exon is indicated above the exon number. Exons represented by a dark blue box (E1) correspond to the leader sequences. Exons represented by orange boxes (E2 to E4) stand for the alpha1, 2 and 3 domains of the molecules. Exons represented in bright blue (E5) correspond to the transmembrane domain. Exons represented by green boxes encode the cytoplasmic tail of the molecule. The 3UTR is represented by a grey box. Positions of the primers used for RT-PCRs are indicated by arrows on top of the figure on E1 (SLA-7-e1-F), E4 (SLA-7-e4-F) and 3UTR (SLA-7-3UTR-R). The donor and acceptor splice sequences are positioned by arrows on E4 and 3UTR boxes.
Mentions: Three primers were designed from the SLA-7 reference cDNA [12] and genomic [9,10] sequences, using the Primer3 online program [16]. The primer combinations were suitable to amplify the full coding sequence from exon 1 to the three prime untranslated region (3UTR) or a partial coding sequence from exon 4 to the 3UTR (Table 1 and Figure 1). Primers were also designed to amplify cDNAs of the RPL32 gene that has been used as control gene for expression levels (Table 1 and Figure 1).

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.