De novo Reconstruction of Adipose Tissue Transcriptomes Reveals Novel Long Non-coding RNAs that Regulate Brown Adipocyte Development

Brown adipose tissue (BAT) protects against obesity by promoting energy expenditure via uncoupled respiration. To uncover BAT-specific long non-coding RNAs (lncRNAs), we used RNA-seq to reconstruct de novo transcriptomes of mouse brown, inguinal white, and epididymal white fat and identified ~1500 lncRNAs, including 127 BAT-restricted loci induced during differentiation and often targeted by key regulators PPARgamma, C/EBPalpha and C/EBPbeta. One of them, lnc-BATE1, is required for establishment and maintenance of BAT identity and thermogenic capacity. lnc-BATE1 inhibition impairs concurrent activation of brown fat and repression of white fat genes, and is partially rescued by exogenous lnc-BATE1 with mutated siRNA-targeting sites, demonstrating a function in trans. We show that lnc-BATE1 binds heterogeneous nuclear ribonucleoprotein U and that both are required for brown adipogenesis. Our work provides an annotated catalog for the study of fat depot-selective lncRNAs, available online, and establishes lnc-BATE1 as a novel regulator of BAT development and physiology. Total RNA profiles of BAT, iWAT and eWAT samples were sequenced on the Illumina HiSeq2000 platform棕色脂肪组织（Brown Adipose Tissue, BAT）可通过解偶联呼吸促进能量消耗，从而对抗肥胖。为了探究BAT特异性的长链非编码RNA（long non-coding RNAs, lncRNAs），我们利用RNA测序（RNA-seq）重构了小鼠棕色脂肪、腹股沟白色脂肪以及附睾白色脂肪的从头转录组，共鉴定出约1500条lncRNAs，其中包括127个在分化过程中被诱导表达的BAT特异性位点，且这些位点常受到关键调控因子过氧化物酶体增殖物激活受体γ（PPARγ）、CCAAT增强子结合蛋白α（C/EBPα）以及CCAAT增强子结合蛋白β（C/EBPβ）的靶向调控。其中lnc-BATE1对于棕色脂肪细胞特性的建立与维持以及产热能力不可或缺。抑制lnc-BATE1会同时损害棕色脂肪基因的激活与白色脂肪基因的抑制，而引入携带突变小干扰RNA（small interfering RNA, siRNA）靶向位点的外源性lnc-BATE1可部分挽救这一表型，证明其具备反式作用功能。我们证实lnc-BATE1可与异质性细胞核核糖蛋白U（heterogeneous nuclear ribonucleoprotein U, hnRNP U）结合，且二者均为棕色脂肪生成所必需。本研究为脂肪部位特异性lncRNAs的研究提供了带注释的目录（可在线获取），并确立了lnc-BATE1作为BAT发育与生理功能的新型调控因子的地位。本研究对BAT、iWAT以及eWAT样本的总RNA谱进行了Illumina HiSeq2000平台测序。