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Identification and quantitative mRNA analysis of a novel splice variant of GPIHBP1 in dairy cattle.

Yang J, Liu X, Zhang Q, Jiang L - J Anim Sci Biotechnol (2014)

Bottom Line: However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.

ABSTRACT

Background: Identification of functional genes affecting milk production traits is very crucial for improving breeding efficiency in dairy cattle. Many potential candidate genes have been identified through our previous genome wide association study (GWAS). Of these, GPIHBP1 is an important novel candidate gene for milk production traits. However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.

Results: In this study, we identified a novel alternatively splice transcript variant (X5) which leads to a 31 bp insertion in exon 3 and also confirmed the other four existed transcripts (X1, X2, X3 and X4) of the bovine GPIHBP1 gene. We showed that transcript X5 with a 31 bp insertion and transcript X1 with an 8 bp deletion might have tremendous effect on the protein function and structure of GPIHBP1, respectively. With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.

Conclusions: Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

No MeSH data available.


Schematic representation of theGPIHBP1alternative splice variants. Transcripts X1 (XM_002692563.2), X2 (XM_005215283.1), X3 (XM_005215284.1) and X4 (XM_005215285.1) were obtained from NCBI. Transcript X5 was observed by RNA-seq (unpublished data). Transcript X1 contained a 8 bp deletion in exon 3. Transcript X5 contained a 31 bp insertion in exon 3. Although transcript X2, X3 and X4 had different 5′ untranslated region, they had the same translation initiation site (TIS).
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Fig2: Schematic representation of theGPIHBP1alternative splice variants. Transcripts X1 (XM_002692563.2), X2 (XM_005215283.1), X3 (XM_005215284.1) and X4 (XM_005215285.1) were obtained from NCBI. Transcript X5 was observed by RNA-seq (unpublished data). Transcript X1 contained a 8 bp deletion in exon 3. Transcript X5 contained a 31 bp insertion in exon 3. Although transcript X2, X3 and X4 had different 5′ untranslated region, they had the same translation initiation site (TIS).

Mentions: Currently, four transcript variants (X1, X2, X3 and X4) of GPIHBP1 are presented in NCBI. Transcript X1, which leads to colonies with a deletion of 8 bp nucleotides, was reported very recently. However, the colonies with an insertion of 31 bp nucleotides suggest that there may exist a novel transcript variant in the bovine GPIHBP1 gene. This novel transcript variant was named transcript variant X5 [GenBank accession number: KJ502292]. To further confirm that the 8 bp deletion and the 31 bp insertion were not a cloning artifact, we designed two pairs of primers (Additional file1: Table S3) specifically for the 8 bp deletion and the 31 bp insertion sequences, respectively, and performed PCR amplification. As a result, we obtained a fragment of 207 bp for transcript X1 and a fragment of 101 bp for transcript X5. The existence of transcript variants X1 and X5 were thus confirmed again. The structures of different splice forms of GPIHBP1 were shown in Figure 2. And there were notable differences in 5′ untranslated region (UTR) of different GPIHBP1 transcripts. Out of five different splice forms, three (X2,X3 and X4) have the same translation initiation site.Figure 2


Identification and quantitative mRNA analysis of a novel splice variant of GPIHBP1 in dairy cattle.

Yang J, Liu X, Zhang Q, Jiang L - J Anim Sci Biotechnol (2014)

Schematic representation of theGPIHBP1alternative splice variants. Transcripts X1 (XM_002692563.2), X2 (XM_005215283.1), X3 (XM_005215284.1) and X4 (XM_005215285.1) were obtained from NCBI. Transcript X5 was observed by RNA-seq (unpublished data). Transcript X1 contained a 8 bp deletion in exon 3. Transcript X5 contained a 31 bp insertion in exon 3. Although transcript X2, X3 and X4 had different 5′ untranslated region, they had the same translation initiation site (TIS).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4373091&req=5

Fig2: Schematic representation of theGPIHBP1alternative splice variants. Transcripts X1 (XM_002692563.2), X2 (XM_005215283.1), X3 (XM_005215284.1) and X4 (XM_005215285.1) were obtained from NCBI. Transcript X5 was observed by RNA-seq (unpublished data). Transcript X1 contained a 8 bp deletion in exon 3. Transcript X5 contained a 31 bp insertion in exon 3. Although transcript X2, X3 and X4 had different 5′ untranslated region, they had the same translation initiation site (TIS).
Mentions: Currently, four transcript variants (X1, X2, X3 and X4) of GPIHBP1 are presented in NCBI. Transcript X1, which leads to colonies with a deletion of 8 bp nucleotides, was reported very recently. However, the colonies with an insertion of 31 bp nucleotides suggest that there may exist a novel transcript variant in the bovine GPIHBP1 gene. This novel transcript variant was named transcript variant X5 [GenBank accession number: KJ502292]. To further confirm that the 8 bp deletion and the 31 bp insertion were not a cloning artifact, we designed two pairs of primers (Additional file1: Table S3) specifically for the 8 bp deletion and the 31 bp insertion sequences, respectively, and performed PCR amplification. As a result, we obtained a fragment of 207 bp for transcript X1 and a fragment of 101 bp for transcript X5. The existence of transcript variants X1 and X5 were thus confirmed again. The structures of different splice forms of GPIHBP1 were shown in Figure 2. And there were notable differences in 5′ untranslated region (UTR) of different GPIHBP1 transcripts. Out of five different splice forms, three (X2,X3 and X4) have the same translation initiation site.Figure 2

Bottom Line: However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

View Article: PubMed Central - PubMed

Affiliation: National Engineering Laboratory for Animal Breeding; Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture of China; College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China.

ABSTRACT

Background: Identification of functional genes affecting milk production traits is very crucial for improving breeding efficiency in dairy cattle. Many potential candidate genes have been identified through our previous genome wide association study (GWAS). Of these, GPIHBP1 is an important novel candidate gene for milk production traits. However, the mRNA structure of the bovine GPIHBP1 gene is not fully determined up to now.

Results: In this study, we identified a novel alternatively splice transcript variant (X5) which leads to a 31 bp insertion in exon 3 and also confirmed the other four existed transcripts (X1, X2, X3 and X4) of the bovine GPIHBP1 gene. We showed that transcript X5 with a 31 bp insertion and transcript X1 with an 8 bp deletion might have tremendous effect on the protein function and structure of GPIHBP1, respectively. With semi-quantitative PCR and quantitative real-time RT-PCR, we found that the mRNA expression of GPIHBP1, GPIHBP1-X1 and GPIHBP1-X5 in mammary gland of lactating cows were much higher than that in other tissues.

Conclusions: Our study reports a novel alternative splicing of GPIHBP1 in bovine for the first time and provide useful information for the further functional analyses of GPIHBP1 in dairy cattle.

No MeSH data available.