Regulation Mechanism of Gene Expression Mediated by Transposon

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Biochemistry, Biophysics and Computational Biology".

Deadline for manuscript submissions: closed (25 November 2022) | Viewed by 2039

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Guest Editor
School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
Interests: computational Biology; circular RNAs; long noncoding RNAs; alternative splicing; transposons
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Special Issue Information

Dear Colleagues,

Transposons are a rich source of transcriptional regulatory elements, including enhancers, promoters, splicing and termination sites, and regulatory non-coding RNAs. Increasing evidence has shown that TEs can mediate the rewiring of gene regulatory networks in the context of pluripotency, innate immunity, and placentation. In addition, due to the development of CRISPR-based genome-editing technologies, we can also test for causal relationships between TE insertions and gene regulation. However, because of the repetitive nature, deciphering the potential regulatory roles of transposons remains challenging, requiring the development of specialized experimental and computational tools. In this Special Issue, we present a series of articles laying out the current understanding in the field, discussing potential applications for future research.

Dr. Xiao-Ou Zhang
Guest Editor

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Keywords

  • transposons
  • gene regulation

Published Papers (1 paper)

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Research

12 pages, 1424 KiB  
Article
Two Retrotransposon Elements in Intron of Porcine BMPR1B Is Associated with Phenotypic Variation
by Chenglin Chi, Jia He, Zhanyu Du, Yao Zheng, Enrico D’Alessandro, Cai Chen, Ali Shoaib Moawad, Emmanuel Asare, Chengyi Song and Xiaoyan Wang
Life 2022, 12(10), 1650; https://doi.org/10.3390/life12101650 - 20 Oct 2022
Cited by 1 | Viewed by 1507
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Regulation Mechanism of Gene Expression Mediated by Transposon)
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