Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk

PLOS ONE, Dec 2019

MicroRNAs (miRNAs) are non-coding small RNA ∼22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNA-sequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f-5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders.

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Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk

et al. (2013) Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk. PLoS ONE 8(11): e80041. doi:10.1371/journal.pone.0080041 Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk Jideng Ma 0 Zhi Jiang 0 Shen He 0 Yingkai Liu 0 Lei Chen 0 Keren Long 0 Long Jin 0 An'an Jiang 0 Li Zhu 0 Jinyong Wang 0 Mingzhou Li 0 Xuewei Li 0 Roberto Amendola, ENEA, Italy 0 1 Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University , Ya'an, Sichuan, China, 2 Novogene Bioinformatics Institute, Beijing , China , 3 Chongqing Academy of Animal Science , Chongqing , China MicroRNAs (miRNAs) are non-coding small RNA ,22 nucleotides in length that can regulate the expression of a wide range of coding genes at the post-transcriptional level. Visceral adipose tissues (VATs) and subcutaneous adipose tissues (SATs), the two main fat compartments in mammals, are anatomically, physiologically, metabolically, and clinically distinct. Various studies of adipose tissues have focused mainly on DNA methylation, and mRNA and protein expression, nonetheless little research sheds directly light on the miRNA transcriptome differences between these two distinct adipose tissue types. Here, we present a comprehensive investigation of miRNA transcriptomes across six variant porcine adipose tissues by small RNAsequencing. We identified 219 known porcine miRNAs, 97 novel miRNA*s, and 124 miRNAs that are conserved to other mammals. A set of universally abundant miRNAs (i.e., miR-148a-3p, miR-143-3p, miR-27b-3p, miR-let-7a-1-5p, and miR-let-7f5p) across the distinct adipose tissues was found. This set of miRNAs may play important housekeeping roles that are involved in adipogenesis. Clustering analysis indicated significant variations in miRNA expression between the VATs and SATs, and highlighted the role of the greater omentum in responding to potential metabolic risk because of the observed enrichment in this tissue of the immune- and inflammation-related miRNAs, such as the members of miR-17-92 cluster and miR-181 family. Differential expression of the miRNAs between the VATs and SATs, and miRNA target prediction analysis revealed that the VATs-specific enriched miRNAs were associated mainly with immune and inflammation responses. In summary, the differences of miRNA expression between the VATs and SATs revealed some of their intrinsic differences and indicated that the VATs might be closely associated with increased risk of metabolic disorders. - Funding: This work was supported by grants from the National High Technology Research and Development Program of China (863 Program) (2013AA102502) to M.L., the Specialized Research Fund of Ministry of Agriculture of China (NYCYTX-009), the Project of Provincial Twelfth Five Years Animal Breeding of Sichuan Province (2011YZGG15), and the National Special Foundation for Transgenic Species of China (2011ZX08006-003) to X.L. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. . These authors contributed equally to this work. MicroRNAs (miRNAs) are a family of small single-stranded non-coding RNAs, which are known to function in a sequencespecific manner to silence specific protein-coding genes at the posttranscriptional level by targeting the 39 untranslated region of mRNAs [1]. With the rapid increase in knowledge that has accumulated over the last decade, various miRNAs have been shown to play vital regulatory roles in adipose deposition and adipogenesis. Typically, miR-143 is a potent pro-adipogenic regulator during pre-adipocyte differentiation [2,3,4], and the miR-17-92 cluster [5] and miR-103 [6] can accelerate adipocyte differentiation, while miR-27a [7], miR-27b [8] and miR-15a [9] can suppress adipogenic differentiation. In addition, miR-519d [10], miR-335 and miR-377 [11] are strongly associated with lipid metabolism disorders. Adipose tissues (ATs) are currently recognized as an endocrine organ, and the number of adipokines that have been identified in ATs is expanding rapidly. ATs are deeply involved in the development of metabolic disorders, such as cardiovascular disease and type 2 diabetes mellitus, which are connected to obesity [12,13,14]. Nonetheless, the different fat compartments may be associated with differential metabolic risk. Visceral adipose tissues (VATs), which are located within the abdominal and thoracic cavities, have been recognized to be more strongly associated with metabolic risk factors than the subcutaneous adipose tissues (SATs) [15,16,17]. It was suggested that the different impacts that VATs and SATs have on metabolic risk may be because of diverse gene expression profiles that lead to differences in lipolys (...truncated)


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Jideng Ma, Zhi Jiang, Shen He, Yingkai Liu, Lei Chen, Keren Long, Long Jin, An'an Jiang, Li Zhu, Jinyong Wang, Mingzhou Li, Xuewei Li. Intrinsic Features in MicroRNA Transcriptomes Link Porcine Visceral Rather than Subcutaneous Adipose Tissues to Metabolic Risk, PLOS ONE, 2013, Volume 8, Issue 11, DOI: 10.1371/journal.pone.0080041