SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

Zheng, Yao; Muráni, Eduard; D’Alessandro, Enrico; Moawad, Ali Shoaib; Wang, Xiaoyan; Wimmers, Klaus; Song, Chengyi

doi:10.3390/ani11071871

Cited by 6 publications

(10 citation statements)

References 62 publications

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“…We found that the number of the confirmed RIPs are much less than predicted. Similar result were found in our previous studies [44,57]. We believe that the number of differences between the predicted RIPs and the verified RIPs are due to the assembled levels and quality of genomes, although some genomes were not well-assembled, resulting in false positive RIP prediction.…”

Section: Discussionsupporting

confidence: 89%

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Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

D’Alessandro

Zheng

Wang

et al. 2022

Animals

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The diversity of livestock coat color results from human positive selection and represents an indispensable part of breed identity. As an important biodiversity resource, pigs have many special characteristics, including the most visualized feature, coat color, and excellent adaptation, and the coat color represents an important phenotypic characteristic of the pig breed. Exploring the genetic mechanisms of phenotypic characteristics and the melanocortin system is of considerable interest in domestic animals because their energy metabolism and pigmentation have been under strong selection. In this study, 20 genes related to coat color in mammals were selected, and the structural variations (SVs) in these genic regions were identified by sequence alignment across 17 assembled pig genomes, from representing different types of pigs (miniature, lean, and fat type). A total of 167 large structural variations (>50 bp) of coat-color genes, which overlap with retrotransposon insertions (>50 bp), were obtained and designated as putative RIPs. Finally, 42 RIPs were confirmed by PCR detection. Additionally, eleven RIP sites were further evaluated for their genotypic distributions by PCR in more individuals of eleven domesticated breeds representing different coat color groups. Differential distributions of these RIPs were observed across populations, and some RIPs may be associated with breed differences.

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Section: Discussionsupporting

confidence: 89%

“…Four RIPs in the GHR (growth hormone receptor) gene and one RIP in the IGF1 (insulin-like growth factor 1) gene was identified in pigs. Further analysis revealed that one RIP in the first intron of GHR might play a role in the regulation of GHR expression by acting as a repressor [44].…”

Section: Introductionmentioning

confidence: 99%

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

D’Alessandro

Zheng

Wang

et al. 2022

Animals

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“…The genomes of livestock and poultry contain active and functional TE. For example, the insertion of short interspersed nuclear elements (SINE) into the intron of the porcine growth hormone receptor ( GHR ) gene can reduce its expression by acting as a repressor [ 22 ]. Moreover, the insertion of a long interspersed nuclear element (LINE) into the 5′UTR of the agouti signaling protein ( ASIP ) gene promotes a nearly 10-fold increase in its expression and leads to white coat color in buffalo [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

Taming transposable elements in livestock and poultry: a review of their roles and applications

et al. 2023

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Livestock and poultry play a significant role in human nutrition by converting agricultural by-products into high-quality proteins. To meet the growing demand for safe animal protein, genetic improvement of livestock must be done sustainably while minimizing negative environmental impacts. Transposable elements (TE) are important components of livestock and poultry genomes, contributing to their genetic diversity, chromatin states, gene regulatory networks, and complex traits of economic value. However, compared to other species, research on TE in livestock and poultry is still in its early stages. In this review, we analyze 72 studies published in the past 20 years, summarize the TE composition in livestock and poultry genomes, and focus on their potential roles in functional genomics. We also discuss bioinformatic tools and strategies for integrating multi-omics data with TE, and explore future directions, feasibility, and challenges of TE research in livestock and poultry. In addition, we suggest strategies to apply TE in basic biological research and animal breeding. Our goal is to provide a new perspective on the importance of TE in livestock and poultry genomes.

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“…Recently, research works from our laboratory have indicated RIPs distribution in the pig genome [ 27 , 28 ]; their role in evaluating population structure [ 29 , 30 ]; and their insertion function on protein-coding genes and pig phenotypic variations such as GH , TLR1 , and TLR6 [ 31 , 32 , 33 ]. Therefore, considering the importance of LEPTIN , LEPR , and LEPROT on mammalian metabolism and growth, the RIPs in these three genes were identified, and the correlation between the RIPs and some pig economic performance was investigated in this study.…”

Section: Introductionmentioning

confidence: 99%

SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits

Wang

Chi

et al. 2022

Genes

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Retrotransposon is an important component of the mammalian genome. Previous studies have shown that the expression of protein-coding genes was affected by the insertion of retrotransposon into the proximal genes, and the phenotype variations would be related to the retrotransposon insertion polymorphisms (RIPs). In this study, leptin (LEP), leptin receptor (LEPR), and leptin receptor overlapping transcript (LEPROT), which play important roles in the regulation of fat synthesis and body weight, were screened to search for the RIPs and their effect on phenotype and gene expression, as well as to further study the function of the insertion. The results showed that three RIPs located in intron 1 of LEPROT and intron 2 and 21 of LEPR were identified, and they were all SINEA1, which was one type of retrotransposon. The SINE insertion at the LEPROT was the dominant allele in native pig breeds. The age of 100 kg body weight of SINE+/+ Large White individuals was significantly higher than those of SINE+/− and SINE−/− individuals (p < 0.05). The LEPROT gene expression in the liver and suet of 30-day-old SINE−/− Sujiang piglets were significantly higher than those of SINE+/+ and SINE+/− piglets (p < 0.01). The dual-luciferase reporter gene assay showed that SINE insertion in PK15 and 3T3-L1 cells significantly reduced the promoter activity of the LEPROT gene (p < 0.01). Therefore, SINE insertion can be a repressor to reduce the expression of LEPROT and could be a useful molecular marker for assisted selection of growth traits in pig breeding.

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SINE Insertion in the Intron of Pig GHR May Decrease Its Expression by Acting as a Repressor

Cited by 6 publications

References 62 publications

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

Retrotransposon Insertion Polymorphisms (RIPs) in Pig Coat Color Candidate Genes

Taming transposable elements in livestock and poultry: a review of their roles and applications

SINE Insertion May Act as a Repressor to Affect the Expression of Pig LEPROT and Growth Traits

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