Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig

Zhang, Liang; Lin, Tao; Ye, Lin; He, Ling; Zhu, Yuanzhong; Zhu, Yue-Dong; Zhou, Yan

doi:10.1016/s1672-0229(07)60011-4

Cited by 4 publications

(3 citation statements)

References 31 publications

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“…Alternative splicing is a very frequent phenomenon in the mammalian transcriptome, and it is now considered one of the main mechanisms responsible for increasing the diversity and complexity of the mammalian proteome [11]. ESTs are currently the most important resources to infer gene structure and alternative splicing in humans [12] or in porcine species [13]. A comparative analysis of the porcine ESTs found in the Genbank dbEST division (Sus scrofa,…”

Section: Resultsmentioning

confidence: 99%

The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization

Robic¹,

Faraut²,

Liaubet³

et al. 2009

Cellular and Molecular Biology Letters

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Carnitine acetyltransferase (CRAT) is an important enzyme for energy homeostasis and fat metabolism. We characterized the predicted full length cDNA sequence of the porcine CRAT gene. Its structure is very similar to that in humans with respect to the size and organization of the 14 exons. We demonstrated the existence of a porcine alternative transcript resulting from a partial intron-retention at the 5’ end of exon 2. To perform a comparison of the 5’ end variants of the mammalian CRAT gene, we analyzed the Genbank data, and here we propose a new 5’ variant for dog, rat and mouse. In contrast to other mammals where this variant encodes a shorter protein (−21 aa in human, mouse and rat, and −14 aa in dog), the pig variant encodes for a longer protein (+18 aa). In all mammalian species, variant 1 has a high probability of a preferential mitochondrial sub-cellular localization. Nevertheless, it is not evident, in particular in porcine and dog species, that the second variant is associated with a different sub-cellular specificity.

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Section: Resultsmentioning

confidence: 99%

The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization

Robic¹,

Faraut²,

Liaubet³

et al. 2009

Cellular and Molecular Biology Letters

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show abstract

“…Various research groups have attempted to understand the role of AS in the pig by using expressed sequence tags (EST). A total of 1, 223 genes with average 2.8 splicing variants were detected among 16, 540 unique genes via EST data [28]. It was reported that more AS could be produced by RNA-seq than EST technology in human and plants [1,29].…”

Section: Introductionmentioning

confidence: 99%

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

Feng

Zhao

Zheng

et al. 2019

Preprint

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Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms (Exon skipping, Alternative acceptor site and Intron retention) are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events). Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.

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“…Various research groups have attempted to understand the role of AS in the pig by using expressed sequence tags (EST). A total of 1, 223 genes with average 2.8 splicing variants were detected among 16, 540 unique genes via EST data [25]. It was reported that more AS could be produced by RNA-seq than EST technology in human and plants [1,26].…”

Section: Introductionmentioning

confidence: 99%

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

Liu

Feng

Zhao

et al. 2019

Preprint

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Background Alternative splicing (AS) is a process that mRNA precursor splices intron to form the mature mRNA. AS plays important roles in contributing to transcriptome and proteome divert. However, to date there is no research about pig AS in genome-wide level by RNA sequencing. Results To characterize the AS in pigs, herein we detected genome-wide transcripts and events by RNA sequencing technology (RNA-seq) 34 different tissues in Duroc pigs. In total, we identified 138, 403 AS events and 29, 270 expressed genes. We found alternative donor site was the most common AS form, which is accounted for 44% of the total AS events. The percentage of the other 3 AS forms are all around 19%. The results showed that the most common AS events (alternative donor site) can produce different transcripts or different proteins which affect the biological process. Among these AS events, 109, 483 were novel AS events, and the number of alternative donor splice site has increased the most (Accounting for 44% of the novel AS events).Conclusions The expression of gene with tissue specific AS events showed that the functions of these genes were consistent with the tissue function. AS increased proteome diversity and resulted in novel proteins that gained and lost important functional domains. In summary, these findings extend genome annotation and highlight roles that AS acts in tissue identity in pig.Key words: Alternative splicing; transcript; protein; SNP

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Alternative Splicing and Expression Profile Analysis of Expressed Sequence Tags in Domestic Pig

Cited by 4 publications

References 31 publications

The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization

The carnitine acetyltransferase gene (CRAT): A characterization of porcine transcripts with insights into the 5’-end variants of mammalian transcripts and their possible sub-cellular localization

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

Profiling novel alternative splicing within multiple tissues puts insight into the porcine genome annotation

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