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Chi C, He J, Du Z, Zheng Y, D’Alessandro E, Chen C, Moawad AS, Asare E, Song C, Wang X. Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation. Life (Basel) 2022; 12:life12101650. [PMID: 36295085 PMCID: PMC9604734 DOI: 10.3390/life12101650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
It has been established that through binding to bone morphogenetic proteins (BMPs), bone morphogenetic protein receptor I B (BMPR1B) can mediate transforming growth factor β (TGF-β) signal transduction, and is involved in the regulation of several biological processes, such as bone and muscle formation and homeostasis, as well as folliculogenesis. Also known as FecB, BMPR1B has been reported as the major gene for sheep prolificacy. A number of previous studies have analyzed the relationship between single nucleotide polymorphisms (SNPs) in this gene and its related performance. In recent years, with the illustration of the effect of retrotransposon insertion on the expression of the proximal genes or phenotypic variation, retrotransposon insertion polymorphisms (RIPs) have been used as a novel type of molecular marker in the evaluation of evolution, population structure and breeding of plant and domestic animals. In this study, the RIPs in porcine BMPR1B gene were excavated, and thereafter verified using a comparative genome and polymerase chain reaction (PCR). The potential effects of phenotype, gene expression and functions related to RIPs were also explored. The results showed that 13 distinct RIPs were identified in introns of porcine BMPR1B. Among these, only BMPR1B-SINE-RIP9 and BMPR1B-LINE-RIP13 displayed a close relationship with the growth traits of Large White pigs. Moreover, the total number of BMPR1B-SINE+/+-RIP9 individuals born was found to be significantly higher than that of SINE−/− (p < 0.05). These two RIPs showed an obvious distribution pattern among Chinese indigenous breeds and Western commercial breeds. The expression of BMPR1B in ovaries of adult BMPR1B-SINE+/+-RIP9 Sushan pigs was found to be significantly higher in comparison to those of BMPR1B-SINE−/−-RIP9 (p < 0.05). SINE insertion of BMPR1B-SINE-RIP9 and LINE insertion of BMPR1B-LINE-RIP13 were observed to significantly increase the activity of Octamer binding transcription factor 4 (OCT4) minipromoter in CHO and C2C12 cells (p < 0.01). Therefore, these two RIPs could serve as useful molecular markers for modulating the growth or reproductive traits in assisted selection of pig breeding, while the mechanisms of the insertion function should be studied further.
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Affiliation(s)
- Chenglin Chi
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Jia He
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhanyu Du
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Yao Zheng
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Enrico D’Alessandro
- Department of Veterinary Science, Division of Animal Production, University of Messina, 98168 Messina, Italy
| | - Cai Chen
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Ali Shoaib Moawad
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
- Department of Animal Production, Faculty of Agriculture, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
| | - Emmanuel Asare
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Chengyi Song
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
| | - Xiaoyan Wang
- College of Animal Science & Technology, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel./Fax: +86-013511768881
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Kumar RD, Burns BA, Vandeventer PJ, Luna PN, Shaw CA. Selection for or against escape from nonsense mediated decay is a novel signature for the detection of cancer genes. Cancer Genet 2021; 258-259:80-84. [PMID: 34592632 DOI: 10.1016/j.cancergen.2021.09.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 08/18/2021] [Accepted: 09/20/2021] [Indexed: 01/02/2023]
Abstract
Escape from nonsense mediated mRNA decay (NMD-) can produce activated or inactivated gene products, and bias in rates of escape can identify functionally important genes in germline disease. We hypothesized that the same would be true of cancer genes, and tested for NMD- bias within The Cancer Genome Atlas pan-cancer somatic mutation dataset. We identify 29 genes that show significantly elevated or suppressed rates of NMD-. This novel approach to cancer gene discovery reveals genes not previously cataloged as potentially tumorigenic, and identifies many potential driver mutations in known cancer genes for functional characterization.
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Affiliation(s)
- Runjun D Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Briana A Burns
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Paul J Vandeventer
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Pamela N Luna
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States
| | - Chad A Shaw
- Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, MS225, Houston, TX 77030, United States; Baylor Genetics, Houston, TX, United States; Department of Statistics, Rice University, Houston, TX, United States.
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Neuronal Signaling: A reflection on the Biochemical Society's newest journal and an exciting outlook on its next steps. Neuronal Signal 2021; 5:NS20210007. [PMID: 33585040 PMCID: PMC7871031 DOI: 10.1042/ns20210007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 01/29/2021] [Accepted: 02/01/2021] [Indexed: 11/17/2022] Open
Abstract
The inaugural Editor-in-Chief of Neuronal Signaling, Aideen M. Sullivan, reflects on the journal's journey so far and welcomes the new Editor-in-Chief, Clare Stanford, as she shares some of the exciting initiatives and plans for its future.
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