Identification of novel alternative splicing transcript and expression analysis of bovine TMEM95 gene

Zhang, Sihuan; Cai, Hanfang; Yang, Qing; Shi, Tao; Pan, Chuanying; Lei, Chuzhao; Dang, Ruihua; Chen, Hong; Lan, Xianyong

doi:10.1016/j.gene.2015.09.026

Cited by 17 publications

(11 citation statements)

References 33 publications

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“…Numerous alternative splicing events occur during cell differentiation and tissue maturation, suggesting that alternative splicing supports proper development. Although the mechanisms and outcomes of alternative splicing of individual transcripts are relatively well-understood in dairy and beef cattle, such as angiopoietin like 6 (ANGPTL6) ( 23 ), transmembrane protein 95 (TMEM95) ( 24 ), and calpain 3 (CAPN3) ( 25 ), the scopes and exact functions of this regulatory mechanism still remain to be investigated on novel transcripts and alternative splicing networks.…”

Section: Discussionmentioning

confidence: 99%

Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Fang

Xia

et al. 2021

Front. Vet. Sci.

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Alternative splicing is a ubiquitous regulatory mechanism in gene expression that allows a single gene generating multiple messenger RNAs (mRNAs). Significant differences in fat deposition ability and meat quality traits have been reported between Japanese black cattle (Wagyu) and Chinese Red Steppes, which presented a unique model for analyzing the effects of transcriptional level on marbling fat in livestock. In previous studies, the differentially expressed genes (DGEs) in longissimus dorsi muscle (LDM) samples between Wagyu and other breeds of beef cattle have been reported. In this study, we further investigated the differences in alternative splicing in LDM between Wagyu and Chinese Red Steppes cattle. We identified several alternative splicing types including cassette exon, mutually exclusive exons, alternative 5′ splice site, alternative 3′ splice site, alternative start exon, and intron retention. In total, 115 differentially expressed alternatively spliced genes were obtained, of which 17 genes were enriched in the metabolic pathway. Among the 17 genes, 5 genes, including MCAT, CPT1B, HADHB, SIRT2, and DGAT1, appeared to be the novel spliced candidates that affect the lipid metabolism in cattle. Additionally, another 17 genes were enriched in the Gene Ontology (GO) terms related to muscle development, such as NR4A1, UQCC2, YBX3/CSDA, ITGA7, etc. Overall, altered splicing and expression levels of these novel candidates between Japanese black cattle and Chinese Red Steppes revealed by RNA-seq suggest their potential involvement in the muscle development and fat deposition of beef cattle.

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Section: Discussionmentioning

confidence: 99%

Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Fang

Xia

et al. 2021

Front. Vet. Sci.

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“…A recent study indicated that alternative transcription start and termination sites, rather than AS, encompasses most of tissue-dependent exon usage [ 1 ]. Transcripts produced by any of the mechanisms mentioned above might contribute to differences between tissues or cells by modifying protein structure and expression [ 3 – 5 ]. Indeed, the differential expression of mRNA isoforms has been associated with a broad array of physiological and pathological conditions in humans [ 3 , 4 ] and domestic species [ 5 , 6 ].…”

Section: Introductionmentioning

confidence: 99%

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

et al. 2018

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BackgroundThe identification of genes differentially expressed in the skeletal muscle of pigs displaying distinct growth and fatness profiles might contribute to identify the genetic factors that influence the phenotypic variation of such traits. So far, the majority of porcine transcriptomic studies have investigated differences in gene expression at a global scale rather than at the mRNA isoform level. In the current work, we have investigated the differential expression of mRNA isoforms in the gluteus medius (GM) muscle of 52 Duroc HIGH (increased backfat thickness, intramuscular fat and saturated and monounsaturated fatty acids contents) and LOW pigs (opposite phenotype, with an increased polyunsaturated fatty acids content).ResultsOur analysis revealed that 10.9% of genes expressed in the GM muscle generate alternative mRNA isoforms, with an average of 2.9 transcripts per gene. By using two different pipelines, one based on the CLC Genomics Workbench and another one on the STAR, RSEM and DESeq2 softwares, we have identified 10 mRNA isoforms that both pipelines categorize as differentially expressed in HIGH vs LOW pigs (P-value < 0.01 and ±0.6 log2fold-change). Only five mRNA isoforms, produced by the ITGA5, SEMA4D, LITAF, TIMP1 and ANXA2 genes, remain significant after correction for multiple testing (q-value < 0.05 and ±0.6 log2fold-change), being upregulated in HIGH pigs.ConclusionsThe increased levels of specific ITGA5, LITAF, TIMP1 and ANXA2 mRNA isoforms in HIGH pigs is consistent with reports indicating that the overexpression of these four genes is associated with obesity and metabolic disorders in humans. A broader knowledge about the functional attributes of these mRNA variants would be fundamental to elucidate the consequences of transcript diversity on the determinism of porcine phenotypes of economic interest.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4515-2) contains supplementary material, which is available to authorized users.

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“…Multiple studies have suggested that indel mutations located in coding or non-coding regions have notable effects on gene expression and phenotypes [21]; thus, this mutation might significantly affect the function of bovine TMEM95 , though that needs further verification. Furthermore, two alternative splicing variants of the TMEM95 gene have been identified in the brain and testicular tissue of fetal Qinchuan cattle [22]. Alternative splicing plays a critical role in regulating biological function and is viewed as a crucial factor in generating functional diversity proteins in metazoan organisms [23].…”

Section: Discussionmentioning

confidence: 99%

Detection of Bovine TMEM95 p.Cys161X Mutation in 13 Chinese Indigenous Cattle Breeds

Zhang

Peng

Zhang

et al. 2019

Animals

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Chinese indigenous cattle breeds have abundant genetic resources, which are valuable for the molecular breeding of cattle around the world. Thus, identifying important candidate genes and their genetic markers is very important for cattle molecular breeding. A previous study found that a nonsense mutation (rs378652941, c.483C > A, p.Cys161X) in the bovine transmembrane protein 95 gene (TMEM95) seriously reduced the reproductive performance in bulls, but few studies have detected this mutation in Chinese indigenous cattle breeds. Since the mutation c.483C > A may serve as a potential genetic marker for selecting higher fertility bulls, in the present study, using tetra-primer amplification refractory mutation system PCR (T-ARMS-PCR), forced PCR restriction fragment length polymorphism (forced PCR-RFLP), and DNA sequencing methods, the mutation c.483C > A was detected in 765 individuals from 13 Chinese cattle breeds. However, the results showed that this mutation did not exist at this locus in our analyzed breeds. Interestingly, we identified a newly frameshift insertion/deletion (indel) mutation (NC_037346.1: g.27056998_27057000delCT) in the bovine TMEM95 gene in 11 cattle breeds, which changed the location of the termination codon and changed the 16 amino acids in the C-terminal to 21 amino acids. Combined with previous studies, our study provides evidence that in Chinese cattle breeds the mutation c.483C > A cannot be used as a genetic marker in molecular breeding.

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Identification of novel alternative splicing transcript and expression analysis of bovine TMEM95 gene

Cited by 17 publications

References 33 publications

Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Comparative Genome-Wide Alternative Splicing Analysis of Longissimus Dorsi Muscles Between Japanese Black (Wagyu) and Chinese Red Steppes Cattle

Differential expression of mRNA isoforms in the skeletal muscle of pigs with distinct growth and fatness profiles

Detection of Bovine TMEM95 p.Cys161X Mutation in 13 Chinese Indigenous Cattle Breeds

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