数字农科院2.0

Genome-Wide Expression Profiling and Networking Reveals an Imperative Role of IMF-Associated Novel CircRNAs as ceRNA in Pigs

文献类型： 外文期刊

作者： Yousuf, Salsabeel;Li, Ai;Feng, Hui;Lui, Tianyi;Huang, Wanlong;Zhang, Xiuxiu;Xie, Lingli;Miao, Xiangyang

作者机构：

关键词： intramuscular adipose tissue;metabolic syndromes;transcriptome analysis;expression profiling;protein modeling;genomic organizations

期刊名称： CELLS

ISSN：

年卷期： 2022 年 11.0 卷 17 期

页码：

摘要： Intramuscular fat (IMF) deposition is a biological process that has a strong impact on the nutritional and sensorial properties of meat, with relevant consequences on human health. Pork loins determine the effects of marbling on the sensory attributes and meat quality properties, which differ among various pig breeds. This study explores the crosstalk of non-coding RNAs with mRNAs and analyzes the potential pathogenic role of IMF-associated competing endogenous RNA (ceRNA) in IMF tissues, which offer a framework for the functional validation of key/potential genes. A high-throughput whole-genome transcriptome analysis of IMF tissues from longissimus dorsi muscles of Large White (D_JN) and Laiwu (L_JN) pigs resulted in the identification of 283 differentially expressed circRNAs (DECs), including two key circRNAs (circRNA-23437, circRNA-08840) with potential binding sites for multiple miRNAs regulating the whole network. The potential ceRNA mechanism identified the DEC target miRNAs-mRNAs involved in lipid metabolism, fat deposition, meat quality, and metabolic syndrome via the circRNA-miRNA-mRNA network, concluding that ssc-mir-370 is the most important target miRNA shared by both key circRNAs. TGM2, SLC5A6, ECI1, FASN, PER1, SLC25A34, SOD1, and COL5A3 were identified as hub genes through an intensive protein-protein interaction (PPI) network analysis of target genes acquired from the ceRNA regulatory network. Functional enrichments, pathway examinations, and qRT-PCR analyses infer their implications in fat/cholesterol metabolism, insulin secretion, and fatty acid biosynthesis. Here, circRNAs and miRNA sequencing accompanied by computational techniques were performed to analyze their expressions in IMF tissues from the longissimus dorsi muscles of two pig breeds. Their target gene evolutionary trajectories, expression profiling, functional enrichments, subcellular localizations, and structural advances with high-throughput protein modeling, following genomic organizations, will provide new insights into the underlying molecular mechanisms of adipocyte differentiation and IMF deposition and a much-needed qualitative framework for future research to improve meat quality and its role as a biomarker to treat lipid metabolic syndromes.

分类号：

  • 相关文献

[1]Gene and protein expression profiling analysis of young spike development in large spike wheat germplasms. Chen Dan,Zhang Jin-peng,Liu Wei-hua,Wu Xiao-yang,Yang Xin-ming,Li Xiu-quan,Lu Yu-qing,Li Li-hui,Chen Dan. 2016

[2]Genome-wide characterization and expression profiling of the NAC genes under abiotic stresses in Cucumis sativus. Zhang, Xiao Meng,Yu, Hong Jun,Sun, Chao,Deng, Jie,Zhang, Xue,Liu, Peng,Li, Yun Yun,Li, Qiang,Jiang, Wei Jie,Sun, Chao,Jiang, Wei Jie.

[3]Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice. Venu, R. C.,Sreerekha, M. V.,Madhav, M. Sheshu,Chen, Songbiao,Wang, Guo-Liang,Wang, Guo-Liang,Nobuta, Kan,Meyers, Blake C.,Venu, R. C.,Jia, Yulin,Madhav, M. Sheshu,Mohan, K. Madhan,Chen, Songbiao.

[4]Genome-wide transcriptome analysis of two maize inbred lines under drought stress. Zheng, Jun,Liu, Yunjun,Wang, Guoying,Zheng, Jun,Liu, Yunjun,Wang, Guoying,Fu, Junjie,Gou, Mingyue,Huai, Junling,Jian, Min,Guo, Xiying,Dong, Zhigang,Wang, Guoying,Huang, Quansheng,Wang, Hongzhi.

[5]Identification, bioinformatic analysis and expression profiling of candidate mRNA-like non-coding RNAs in Sus scrofa. Xiao, Bang,Zhang, Xingju,Li, Yong,Tang, Zhonglin,Yang, Shulin,Mu, Yulian,Cui, Wentao,Ao, Hong,Li, Kui,Xiao, Bang. 2009

[6]Identification and characterization of the zinc-regulated transporters, iron-regulated transporter-like protein (ZIP) gene family in maize. Li, Suzhen,Huang, Yaqun,Zhu, Liying,Zhao, Yongfeng,Guo, Jinjie,Chen, Jingtang,Li, Suzhen,Zhou, Xiaojin,Zhang, Shaojun,Chen, Rumei. 2013

[7]Constitutive expression of the ZmZIP7 in Arabidopsis alters metal homeostasis and increases Fe and Zn content. Li, Suzhen,Zhao, Yongfeng,Li, Hongbo,Liu, Yuanfeng,Zhu, Liying,Guo, Jinjie,Huang, Yaqun,Chen, Jingtang,Li, Suzhen,Zhou, Xiaojin,Yang, Wenzhu,Fan, Yunliu,Chen, Rumei.

[8]Transcript profiling of a dominant male sterile mutant (Ms-cd1) in cabbage during flower bud development. Lou, Ping,Kang, Jungen,Zhang, Guoyu,Bonnema, Guusje,Fang, Zhiyuan,Wang, Xiaowu. 2007

[9]Genome-wide identification, classification and expression profiling of nicotianamine synthase (NAS) gene family in maize. Zhou, Xiaojin,Zhao, Qianqian,Liu, Xiaoqing,Zhang, Shaojun,Sun, Cheng,Fan, Yunliu,Zhang, Chunyi,Chen, Rumei,Zhou, Xiaojin,Zhao, Qianqian,Liu, Xiaoqing,Zhang, Shaojun,Sun, Cheng,Fan, Yunliu,Zhang, Chunyi,Chen, Rumei,Li, Suzhen. 2013

[10]Genome wide identification and characterization of fertility associated novel CircRNAs as ceRNA reveal their regulatory roles in sheep fecundity. Salsabeel Yousuf,Waqar Afzal Malik,Hui Feng,Tianyi Liu,Lingli Xie,Xiangyang Miao. 2023

[11]Transcriptomic analysis of short-term salt-stress response in mega hybrid rice seedlings. Noushin Jahan,Yang Lv,Mengqiu Song,Yu Zhang,Lianguang Shang,Ying Lu,Guoyou Ye,Qian Qian,Zhenyu Gao,Longbiao Guo. 2021

[12]Gene expression and DNA methylation altering lead to the high oil content in wild allotetraploid peanut (A. monticola). Liu N.,Wu B.,Pandey M.K.,Huang L.,Luo H.,Chen Y.,Zhou X.,Chen W.,Huai D.,Yu B.,Chen H.,Guo J.,Lei Y.,Liao B.,Varshney R.K.,Jiang H.. 2022

[13]Genome-wide identification and evolutionary analysis of leucine-rich repeat receptor-like protein kinase genes in soybean. Fulai Zhou,Yong Guo, Li-Juan Qiu. 2016

[14]Transcriptomic analysis of short-term salt-stress response in mega hybrid rice seedlings. Noushin Jahan,Yang Lv,Mengqiu Song,Yu Zhang,Lianguang Shang,Ying Lu,Guoyou Ye,Qian Qian,Zhenyu Gao,Longbiao Guo. 2021

[15]Genome-Wide Identification and Characterization of Growth Regulatory Factor Family Genes in Medicago. Wenxuan Du,Junfeng Yang,Qian Li,Qian Su,Dengxia Yi,Yongzhen Pang. 2022

[16]Genome-Wide Analysis of MADS-Box Genes in Foxtail Millet (Setaria italica L.) and Functional Assessment of the Role of SiMADS51 in the Drought Stress Response. Wan Zhao,Li Li Zhang,Zhao Shi Xu,Liang Fu,Hong Xi Pang,You Zhi Ma,Dong Hong Min. 2021

[17]Genome-wide identification and expression profiles of AP2/ERF transcription factor family in mung bean (Vigna radiata L.). 陈红霖, 胡亮亮, 王丽侠, 王素华, 程须珍. 2022

[18]Over-expression of Medicago Acyl-CoA-binding 2 genes enhance salt and drought tolerance in Arabidopsis. Wenxuan Du,Haijun Huang,Weiye Kong,Wenbo Jiang,Yongzhen Pang. 2024

[19]Identification and Analysis of WRKY Transcription Factors in Response to Cowpea Fusarium Wilt in Cowpea. Yali Hao,Rui Liu,Zhenchuan Mao,Qihong Yang,Shijie Zheng,Xiaofei Lu,Yuhong Yang,Bingyan Xie,Jianlong Zhao,Yan Li,Guohua Chen,Jian Ling. 2024

[20]Genome-Wide Identification of the DOG1 Gene Family in Pepper (Capsicum annuum) and Its Expression Profiles During Seed Germination. Zhao, Zhichao,Sun, Jingbo,Zhang, Feng,Dong, Chunjuan. 2025

作者其他论文 更多>>