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4. tRNA-derived small RNA dataset in multiple organs of intrauterine growth-restricted pig

Author

Ma Jianfeng, Gan Mailin, Yang Yitang, Chen Lei, Zhao Ye, Niu Lili, Wang Yan, Zhang Shunhua, Wang Jingyong, Zhu Li, and Shen Linyuan

Subjects
Science
Abstract

Abstract Intrauterine growth restriction (IUGR) impairs neonatal weight and causes multiple organ dysplasia. IUGR not only threatens human health but is also a significant constraint to the development of animal husbandry. However, the molecular mechanism underlying IUGR remains to be further elucidated. tRNA-derived small RNA (tsRNAs) is a regulative non-coding RNA, which has recently been reported to correlate with the onset and progression of several diseases. In this study, we investigated the tsRNAs expression profiles of IUGR pigs. A tsRNAs dataset for multiple organs in normal and IUGR pigs was generated, including muscle, liver, spleen and intestine. We further analyzed the characteristics of tsRNAs in different organs of pigs, and KEGG pathway analysis was performed to investigate possible pathways involved. This dataset will provide valuable information for further exploring the molecular mechanism of IUGR formation.

Published
2023
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7. Dynamic chromatin architecture of the porcine adipose tissues with weight gain and loss

Author

Jin, Long, Wang, Danyang, Zhang, Jiaman, Liu, Pengliang, Wang, Yujie, Lin, Yu, Liu, Can, Han, Ziyin, Long, Keren, Li, Diyan, Jiang, Yu, Li, Guisen, Zhang, Yu, Bai, Jingyi, Li, Xiaokai, Li, Jing, Lu, Lu, Kong, Fanli, Wang, Xun, Li, Hua, Huang, Zhiqing, Ma, Jideng, Fan, Xiaolan, Shen, Linyuan, Zhu, Li, Jiang, Yanzhi, Tang, Guoqing, Feng, Bin, Zeng, Bo, Ge, Liangpeng, Li, Xuewei, Tang, Qianzi, Zhang, Zhihua, and Li, Mingzhou

Published
2023
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9. tRF-Gly-GCC in Atretic Follicles Promotes Ferroptosis in Granulosa Cells by Down-Regulating MAPK1.

Author

Pan, Yuheng, Gan, Mailin, Wu, Shuang, He, Yuxu, Feng, Jinkang, Jing, Yunhong, Li, Jiaxin, Chen, Qian, Tong, Jiang, Kang, Lingfan, Chen, Lei, Zhao, Ye, Niu, Lili, Zhang, Shunhua, Wang, Yan, Zhu, Li, and Shen, Linyuan

Abstract

Follicle development refers to the process in which the follicles in the ovary gradually develop from the primary stage to a mature state, and most primary follicles fail to develop normally, without forming a dense granular cell layer and cell wall, which is identified as atretic follicles. Granulosa cells assist follicle development by producing hormones and providing support, and interference in the interaction between granulosa cells and oocytes may lead to the formation of atretic follicles. Ferroptosis, as a non-apoptotic form of death, is caused by cells accumulating lethal levels of iron-dependent phospholipid peroxides. Healthy follicles ranging from 4 to 5 mm were randomly divided into two groups: a control group (DMSO) and treatment group (10 uM of ferroptosis inducer erastin). Each group was sequenced after three repeated cultures for 24 h. We found that ferroptosis was associated with atretic follicles and that the in vitro treatment of healthy follicles with the ferroptosis inducer erastin produced a phenotype similar to that of atretic follicles. Overall, our study elucidates that tRF-1:30-Gly-GCC-2 is involved in the apoptosis and ferroptosis of GCs. Mechanistically, tRF-1:30-Gly-GCC-2 inhibits granulosa cell proliferation and promotes ferroptosis by inhibiting Mitogen-activated protein kinase 1 (MAPK1). tRF-1:30-Gly-GCC-2 may be a novel molecular target for improving the development of atretic follicles in ovarian dysfunction. In conclusion, our study provides a new perspective on the pathogenesis of granulosa cell dysfunction and follicular atresia. [ABSTRACT FROM AUTHOR]

Published
2024
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10. Whole-genome sequencing association analysis reveals the genetic architecture of meat quality traits in Chinese Qingyu pigs

Author

Wu, Pingxian, Wang, Kai, Zhou, Jie, Chen, Dejuan, Yang, Xidi, Jiang, Anan, Shen, Linyuan, Zhang, Shunhua, Xiao, Weihang, Jiang, Yanzhi, Zhu, Li, Zeng, Yangshuang, Xu, Xu, Li, Xuewei, and Tang, Guoqing

Subjects
Nucleotide sequencing -- Analysis, Genomics -- Analysis, Pork -- Analysis, Genes -- Analysis, DNA sequencing -- Analysis, Swine -- Analysis, Genomes -- Analysis, Muscles -- Analysis, Quality control -- Analysis, Quality control, Biological sciences
Abstract

The Chinese Qingyu pig breed is an invaluable indigenous genetic resource. However, few studies have investigated the genetic architecture of meat quality traits in Qingyu pigs. Here, 30 purebred Qingyu pigs were subjected to whole-genome sequencing. After quality control, 18 436 759 SNPs were retained. Genome-wide association studies (GWAS) were then performed for meat pH and color at three postmortem time points (45 min, 24 h, and 48 h) using single-marker regression analysis. In total, 11 and 69 SNPs were associated with meat pH and color of the longissimus thoracis muscle (LTM), respectively, while 54 and 29 SNPs were associated with meat pH and color of the semimembranosus muscle (SM), respectively. Seven SNPs associated with pork pH were shared by all three postmortem time points. Several candidate genes for meat traits were identified, including four genes (CXXC5, RYR3, BN1P3, and MYCT1) related to skeletal muscle development, regulation of [Ca.sup.2+] release in the muscle, and anaerobic respiration, which are promising candidates for selecting superior meat quality traits in Qingyu pigs. To our knowledge, this is the first study investigating the postmortem genetic architecture of pork pH and color in Qingyu pigs. Our findings further the current understanding of the genetic factors influencing meat quality. Keywords: pork color, pork pH, GWAS, SNPs, Qingyu pigs. La race porcine chinoise Qingyu est une ressource genetique de grande valeur. Cependant, peu d'etudes ont examine l'architecture des caracteres de la qualite de la viande chez le porc Qingyu. Dans ce travail, 30 porcs Qingyu de race pure ont ete assujettis a un sequencage du genome complet. Apres controle de qualite, 18 436 759 SNP ont ete retenus. Des analyses pangenomiques d'association (GWAS) ont ensuite ete realisees pour le pH et la couleur de la viande a trois temps post-mortem (45 min., 24 h et 48 h) au moyen d'une analyse de regression sur marqueurs individuels. Au total, 11 et 69 SNP etaient associes respectivement avec le pH et la couleur du muscle longissimus thoracis (LTM), tandis que 54 et 29 SNP etaient associes respectivement au pH et a la couleur du muscle semimembranosus (SM). Sept SNP associes au pH etaient communs aux trois temps etudies. Plusieurs genes candidats pour des proprietes de la viande ont ete identifies, incluant quatre genes (CXXC5, RYR3, BN1P3 et MYCT1) lies au developpement des muscles squelettiques, la regulation de la liberation intramusculaire du [Ca.sup.2+] et la respiration anaerobique, lesquels sont des candidats prometteurs pour ameliorer la qualite de la viande chez les porcs Qingyu. Ces resultats contribuent a ameliorer la connaissance des facteurs genetiques qui influencent la qualite de la viande. [Traduit par la Redaction] Mots-cles : couleur chez le porc, pH chez le porc, GWAS, SNP, porcs Qingyu., Introduction The Chinese Qingyu pig breed is an invaluable Chinese genetic resource. Qingyu pigs are mainly distributed in a narrow region within the mountainous areas of Sichuan Province, China. It [...]

Published
2020
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12. A pig BodyMap transcriptome reveals diverse tissue physiologies and evolutionary dynamics of transcription

Author

Jin, Long, Tang, Qianzi, Hu, Silu, Chen, Zhongxu, Zhou, Xuming, Zeng, Bo, Wang, Yuhao, He, Mengnan, Li, Yan, Gui, Lixuan, Shen, Linyuan, Long, Keren, Ma, Jideng, Wang, Xun, Chen, Zhengli, Jiang, Yanzhi, Tang, Guoqing, Zhu, Li, Liu, Fei, Zhang, Bo, Huang, Zhiqing, Li, Guisen, Li, Diyan, Gladyshev, Vadim N., Yin, Jingdong, Gu, Yiren, Li, Xuewei, and Li, Mingzhou

Published
2021
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13. Short-term dietary choline supplementation alters the gut microbiota and liver metabolism of finishing pigs

Author

Xie, Zhongwei, primary, Du, Junhua, additional, Gan, Mailin, additional, Zhou, Chengpeng, additional, Li, Menglin, additional, Liu, Chengming, additional, Wang, Meng, additional, Chen, Lei, additional, Zhao, Ye, additional, Wang, Yan, additional, Jiang, Yanzhi, additional, Cheng, Wenqiang, additional, Zhu, Kangping, additional, Luo, Yi, additional, Zhu, Li, additional, and Shen, Linyuan, additional

Published
2023
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16. Comparison of Growth Performance and Plasma Metabolomics between Two Sire-Breeds of Pigs in China

Author

Xie, Zhongwei, primary, Gan, Mailin, additional, Du, Junhua, additional, Du, Gao, additional, Luo, Yi, additional, Liu, Bin, additional, Zhu, Kangping, additional, Cheng, Wenqiang, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Wang, Yan, additional, Wang, Jingyong, additional, Zhu, Li, additional, and Shen, Linyuan, additional

Published
2023
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17. Effects of dietary L-Citrulline supplementation on growth performance, meat quality, and fecal microbial composition in finishing pigs

Author

Du, Junhua, primary, Gan, Mailin, additional, Xie, Zhongwei, additional, Zhou, Chengpeng, additional, Jing, Yunhong, additional, Li, Menglin, additional, Liu, Chengming, additional, Wang, Meng, additional, Dai, Haodong, additional, Huang, Zhiyang, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Wang, Yan, additional, Zhang, Shunhua, additional, Guo, Zongyi, additional, Shen, Linyuan, additional, and Zhu, Li, additional

Published
2023
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20. Estimation of genetic parameters of pig reproductive traits

Author

Yang, Yiting, primary, Gan, Mailin, additional, Yang, Xidi, additional, Zhu, Peng, additional, Luo, Yi, additional, Liu, Bin, additional, Zhu, Kangping, additional, Cheng, Wenqiang, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Wang, Yan, additional, Zhang, Hui, additional, Wang, Jingyong, additional, Shen, Linyuan, additional, and Zhu, Li, additional

Published
2023
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22. DNA Damage-Induced, S-Phase Specific Phosphorylation of Orc6 is Critical for the Maintenance of Genome Stability

Author

Lin, Yo-Chuen, primary, Liu, Dazhen, additional, Chakraborty, Arindam, additional, Macias, Virgilia, additional, Brister, Eileen, additional, Sonalkar, Jay, additional, Shen, Linyuan, additional, Mitra, Jaba, additional, Ha, Taekjip, additional, Kajdacsy-Balla, Andre, additional, Prasanth, Kannanganattu V., additional, and Prasanth, Supriya G., additional

Published
2023
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24. Haplotype-resolved 3D chromatin architecture of the hybrid pig

Author

Lin, Yu, Li, Jing, Gu, Yiren, Jin, Long, Bai, Jingyi, Zhang, Jiaman, Wang, Yujie, Liu, Pengliang, Long, Keren, He, Mengnan, Li, Diyan, Liu, Can, Han, Ziyin, Zhang, Yu, Li, Xiaokai, Zeng, Bo, Lu, Lu, Kong, Fanli, Sun, Ying, Fan, Yongliang, Wang, Xun, Wang, Tao, Jiang, An'an, Ma, Jideng, Shen, Linyuan, Zhu, Li, Jiang, Yanzhi, Tang, Guoqing, Fan, Xiaolan, Liu, Qingyou, Li, Hua, Wang, Jinyong, Chen, Li, Ge, Liangpeng, Li, Xuewei, Tang, Qianzi, and Li, Mingzhou

Abstract

In diploid mammals, allele-specific three-dimensional (3D) genome architecture may lead to imbalanced gene expression. Through ultradeep in situ Hi-C sequencing of three representative somatic tissues (liver, skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data revealed the tissue dependence of 3D chromatin conformation, suggesting that parent-of-origin-specific conformation may drive gene imprinting. We quantify the effects of genetic variations and histone modifications on allelic differences of long-range promoter–enhancer contacts, which likely contribute to the phenotypic differences between the parental pig breeds. We also observe the fine structure of somatically paired homologous chromosomes in the pig genome, which has a functional implication genome-wide. This work illustrates how allele-specific chromatin architecture facilitates concomitant shifts in allele-biased gene expression, as well as the possible consequential phenotypic changes in mammals.

Published
2024
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25. A Novel tRNA-Derived Fragment, tRF GlnCTG , Regulates Angiogenesis by Targeting Antxr1 mRNA.

Author

Chen, Qiuyang, Shen, Linyuan, Liao, Tianci, Qiu, Yanhao, Lei, Yuhang, Wang, Xingyu, Chen, Lei, Zhao, Ye, Niu, Lili, Wang, Yan, Zhang, Shunhua, Zhu, Li, and Gan, Mailin

Subjects
*VASCULAR endothelial cells, *NEOVASCULARIZATION, *GENE expression, *NON-coding RNA, *MESSENGER RNA, *TRANSFER RNA
Abstract

As a novel non-coding RNA with important functions corresponding to various cellular stresses, the function of tRFs in angiogenesis remains unclear. Firstly, small RNA sequencing was performed on normal and post-muscle injury mouse tibialis anterior muscle to identify and analyse differentially expressed tRF/tiRNA. tRNA GlnCTG-derived fragments (tRFGlnCTG) were found to be overexpressed in high abundance in the damaged muscle. Subsequent in vitro experiments revealed that the overexpression of tRFGlnCTG suppressed the vascular endothelial cells' viability, cell cycle G1/S transition, proliferation, migration, and tube-formation capacity. Similarly, in vivo experiments showed that the tRFGlnCTG decreased the relative mRNA levels of vascular endothelial cell markers and pro-angiogenic factors and reduced the proportion of CD31-positive cells. Finally, luciferase activity analysis confirmed that the tRFGlnCTG directly targeted the 3′UTR of Antxr1, leading to a significant reduction in the mRNA expression of the target gene. These results suggest that tRFGlnCTG is a key regulator of vascular endothelial cell function. The results provide a new idea for further exploration of the molecular mechanisms that regulate angiogenesis. [ABSTRACT FROM AUTHOR]

Published
2023
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27. tsRNA Landscape and Potential Function Network in Subcutaneous and Visceral Pig Adipose Tissue

Author

Wang, Linghui, primary, Gu, Hao, additional, Liao, Tianci, additional, Lei, Yuhang, additional, Qiu, Yanhao, additional, Chen, Qiuyang, additional, Chen, Lei, additional, Zhang, Shunhua, additional, Wang, Jinyong, additional, Hao, Xiaoxia, additional, Jiang, Dongmei, additional, Zhao, Ye, additional, Niu, Lili, additional, Li, Xuewei, additional, Shen, Linyuan, additional, Gan, Mailin, additional, and Zhu, Li, additional

Published
2023
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28. Regulation of SIRT1 in Ovarian Function: PCOS Treatment

Author

Li, Xinrong, primary, He, Yuxu, additional, Wu, Shuang, additional, Zhang, Peiwen, additional, Gan, Mailin, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Zhang, Shunhua, additional, Jiang, Yanzhi, additional, Guo, Zongyi, additional, Wang, Jinyong, additional, Shen, Linyuan, additional, and Zhu, Li, additional

Published
2023
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29. tRNA‐derived small RNA, 5'tiRNA‐Gly‐CCC, promotes skeletal muscle regeneration through the inflammatory response

Author

Shen, Linyuan, primary, Liao, Tianci, additional, Chen, Qiuyang, additional, Lei, Yuhang, additional, Wang, Linghui, additional, Gu, Hao, additional, Qiu, Yanhao, additional, Zheng, Ting, additional, Yang, Yiting, additional, Wei, Chenggang, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Zhang, Shunhua, additional, Zhu, Yan, additional, Li, Mingzhou, additional, Wang, Jinyong, additional, Li, Xuewei, additional, Gan, Mailin, additional, and Zhu, Li, additional

Published
2023
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32. Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs

Author

Gu, Hao, primary, Gan, Mailin, additional, Wang, Linghui, additional, Yang, Yiting, additional, Wang, Jinyong, additional, Chen, Lei, additional, Zhang, Shunhua, additional, Zhao, Ye, additional, Niu, Lili, additional, Jiang, Dongmei, additional, Chen, Yiwu, additional, Jiang, Anan, additional, Shen, Linyuan, additional, and Zhu, Li, additional

Published
2022
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33. Plasma Metabolomic Profiling Reveals Preliminary Biomarkers of Pork Quality Based on pH Value

Author

Shen, Linyuan, primary, Ma, Jianfeng, additional, Zhou, Haodi, additional, Chen, Lei, additional, Tang, Jie, additional, Zhang, Kaige, additional, Zhao, Ye, additional, Niu, Lili, additional, Zhang, Shunhua, additional, Jiang, Anan, additional, Wang, Jinyong, additional, Guo, Zongyi, additional, Li, Xuewei, additional, Chen, Yiwu, additional, Gan, Mailin, additional, and Zhu, Li, additional

Published
2022
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37. Identifying SNPs associated with birth weight and days to 100 kg traits in Yorkshire pigs based on genotyping-by-sequencing

Author

Xiao Wei-hang, Tang Guo-qing, Zhou Jie, Xu Xu, Jin Long, Li Mingzhou, Yang Xi-di, Liu Yihui, Shen Linyuan, Jiang An-an, Ping-xian Wu, Jiang Yanzhi, Wang Kai, Zhu Li, Li Xuewei, Chen De-juan, Qiu Xiao-tian, and Zeng Yang-shuang

Subjects
Genetics, Genotyping by sequencing, Ecology, Birth weight, Genome-wide association study, Single-nucleotide polymorphism, Plant Science, Biology, Quantitative trait locus, Biochemistry, Genetic architecture, Food Animals, Polygene, Genetic structure, Animal Science and Zoology, Agronomy and Crop Science, Food Science
Abstract

Birth weight (BW) and days to 100 kg (D100) are important economic traits that are both affected by polygenes. However, the genetic architecture of these quantitative traits is still elusive. Genotyping-by-sequencing (GBS) data containing a large number of single nucleotide polymorphisms (SNPs) have become a powerful tool in genomic analysis. To better understand their complex genetic structure, a total of 600 Yorkshire pigs were sequenced using GBS technology. After quality control, 279 787 SNPs were generated for subsequent genome-wide association study (GWAS). A total of 30 genome-wide SNPs (P

Published
2021

39. Characteristics of tRNA-Derived Small RNAs and microRNAs Associated with Immunocompromise in an Intrauterine Growth-Restricted Pig Model

Author

Ma, Jianfeng, primary, Gan, Mailin, additional, Chen, Jingyun, additional, Chen, Lei, additional, Zhao, Ye, additional, Zhu, Yan, additional, Niu, Lili, additional, Zhang, Shunhua, additional, Jiang, Yanzhi, additional, Guo, Zongyi, additional, Wang, Jinyong, additional, Zhu, Li, additional, and Shen, Linyuan, additional

Published
2022
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41. LncRNA-Mediated Adipogenesis in Different Adipocytes

Author

Zhang, Peiwen, primary, Wu, Shuang, additional, He, Yuxu, additional, Li, Xinrong, additional, Zhu, Yan, additional, Lin, Xutao, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Zhang, Shunhua, additional, Li, Xuewei, additional, Zhu, Li, additional, and Shen, Linyuan, additional

Published
2022
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44. Detection of Four Porcine Enteric Coronaviruses Using CRISPR-Cas12a Combined with Multiplex Reverse Transcriptase Loop-Mediated Isothermal Amplification Assay

Author

Liu, Jiajia, primary, Tao, Dagang, additional, Chen, Xinquan, additional, Shen, Linyuan, additional, Zhu, Li, additional, Xu, Bingrong, additional, Liu, Hailong, additional, Zhao, Shuhong, additional, Li, Xinyun, additional, Liu, Xiangdong, additional, Xie, Shengsong, additional, and Niu, Lili, additional

Published
2022
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47. l-Arginine Alleviates LPS-Induced Oxidative Stress and Apoptosis via Activating SIRT1-AKT-Nrf2 and SIRT1-FOXO3a Signaling Pathways in C2C12 Myotube Cells

Author

Zhao, Ye, primary, Jiang, Qin, additional, Zhang, Xuefei, additional, Zhu, Xiaoxiao, additional, Dong, Xia, additional, Shen, Linyuan, additional, Zhang, Shunhua, additional, Niu, Lili, additional, Chen, Lei, additional, Zhang, Ming, additional, Jiang, Jun, additional, Chen, Daiwen, additional, and Zhu, Li, additional

Published
2021
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48. miR-370-3p Regulates Adipogenesis through Targeting Mknk1

Author

Zhang, Peiwen, primary, Li, Xinrong, additional, Zhang, Shunhua, additional, Wu, Shuang, additional, Xiao, Qian, additional, Gu, Yang, additional, Guo, Xinyu, additional, Lin, Xutao, additional, Chen, Lei, additional, Zhao, Ye, additional, Niu, Lili, additional, Tang, Guoqing, additional, Jiang, Yanzhi, additional, Shen, Linyuan, additional, and Zhu, Li, additional

Published
2021
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50. Profiling of skeletal muscle tissue for long non-coding RNAs related to muscle metabolism in the QingYu pig at the growth inflection point

Author

Luo, Jia, primary, Shen, Linyuan, additional, Gan, Mailin, additional, Jiang, Anan, additional, Chen, Lei, additional, Ma, Jideng, additional, Jin, Long, additional, Liu, Yihui, additional, Tang, Guoqing, additional, Jiang, Yanzhi, additional, Li, Mingzhou, additional, Li, Xuewei, additional, Zhang, Shunhua, additional, and Zhu, Li, additional

Published
2021
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