Supplementary Material for: Genome-Wide Analysis of mRNAs and lncRNAs of Intramuscular Fat Related to Lipid Metabolism in Two Pig Breeds

Background/Aims: Long non-coding RNAs (lncRNAs) can regulate adipogenesis and lipid accumulation. Intramuscular fat deposition appears to vary in different pig breeds, and the regulation mechanism has not yet been fully elucidated at molecular level. Moreover, little is known about the function and profile of lncRNAs in intramuscular fat deposition and metabolism in pig. The aim of this study was thus to explore the regulatory functions of lncRNAs in intramuscular fat deposition. Methods: In this study, Laiwu (LW) pig and Large White (LY) pig with significant difference in fat deposition were selected for use. RNA-seq technology and bioinformatics methods were used to comparatively analyze the gene expression profiles of intramuscular fat between LW and LY pigs to identify key mRNAs and lncRNAs associated with lipid metabolism and adipogenesis. Real-time fluorescence-based quantitative PCR was applied to verify the expression level of the differentially expressed mRNAs and lncRNAs. Results: A total of 513 mRNAs and 55 lncRNAs were differentially expressed between two pig breeds. By co-expression network construction as well as cis- and trans-regulated target gene analysis, 31 key lncRNAs were identified. Gene Ontology and KEGG pathway analyses revealed that differentially expressed genes and lncRNAs were mainly involved in the biological processes and pathways related to adipogenesis and lipid metabolism. Conclusion: XLOC_046142, XLOC_004398 and XLOC_015408 may target MAPKAPK2, NR1D2 and AKR1C4, respectively, and play critical regulatory roles in intramuscular adipogenesis and lipid accumulation in pig. XLOC_064871 and XLOC_011001 may play a role in lipid metabolism-related disease via regulating TRIB3 and BRCA1. This study provides a valuable resource for lncRNA study and improves our understanding of the biological roles of lipid metabolism- related genes and molecular mechanism of intramuscular fat metabolism and deposition.

背景与研究目的：长链非编码RNA（Long non-coding RNAs，lncRNAs）可调控脂肪生成与脂质蓄积。不同猪品种间的肌内脂肪沉积存在显著差异，其调控机制在分子层面尚未完全阐明。此外，目前关于猪肌内脂肪沉积与代谢过程中lncRNAs的功能及表达谱的研究尚少。因此本研究旨在探究lncRNAs在猪肌内脂肪沉积中的调控功能。
研究方法：本研究选取肌内脂肪沉积存在显著差异的莱芜猪（Laiwu pig，LW）与大白猪（Large White pig，LY）作为实验材料。采用RNA测序（RNA-seq）技术与生物信息学方法，对莱芜猪与大白猪的肌内脂肪基因表达谱进行比较分析，以筛选与脂质代谢及脂肪生成相关的关键mRNA与lncRNAs。采用实时荧光定量聚合酶链反应（Real-time fluorescence-based quantitative PCR）对差异表达的mRNA及lncRNAs的表达水平进行验证。
研究结果：两猪品种间共筛选得到513个差异表达mRNA与55个差异表达lncRNAs。通过共表达网络构建以及顺式、反式调控靶基因分析，最终鉴定出31个关键lncRNAs。基因本体（Gene Ontology，GO）富集分析与京都基因与基因组百科全书（Kyoto Encyclopedia of Genes and Genomes，KEGG）通路富集分析结果显示，差异表达基因及lncRNAs主要参与脂肪生成与脂质代谢相关的生物学过程及通路。
研究结论：XLOC_046142、XLOC_004398及XLOC_015408可分别靶向MAPKAPK2、NR1D2与AKR1C4，并在猪肌内脂肪生成与脂质蓄积过程中发挥关键调控作用。XLOC_064871与XLOC_011001可通过调控TRIB3与BRCA1参与脂质代谢相关疾病的发生发展过程。本研究为lncRNAs相关研究提供了宝贵的资源，同时加深了我们对脂质代谢相关基因生物学功能以及猪肌内脂肪代谢与沉积分子机制的认知。