Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription

Rev-Erba and Rev-Erbb are nuclear receptors that regulate the expression of genes involved in the control of circadian rhythm, metabolism, and inflammatory responses. Rev-Erbs function as transcriptional repressors by recruiting NCoR/HDAC3 co-repressor complexes to Rev-Erb response elements in enhancers and promoters of target genes, but the molecular basis for cell-specific programs of repression is not known. Here, we present evidence that in macrophages, Rev-Erbs regulate target gene expression by inhibiting the functions of distal enhancers that are selected by macrophage lineage-determining factors, thereby establishing a macrophage-specific program of repression. Remarkably, the repressive functions of Rev-Erbs are associated with their ability to inhibit the transcription of enhancer-derived RNAs (eRNAs). Furthermore, targeted degradation of eRNAs at two enhancers subject to negative regulation by Rev-Erbs resulted in reduced expression of nearby mRNAs, implying a direct role of these eRNAs in enhancer function. By precisely defining eRNA start sites using a method that quantifies nascent 5' ends (5'-GRO-Seq), we show that transfer of full enhancer activity to a target promoter requires both the sequences mediating transcription factor binding and the specific sequences encoding the eRNA transcript. These studies provide evidence for direct roles of eRNAs in contributing to enhancer functions and suggest that Rev-Erbs act to suppress gene expression at a distance by repressing eRNA transcription. Using ChIPseq, GRO-seq, and 5'GRO-seq to determine mechanism of RevErb in transcriptional regulation in macrophagesRev-Erbα（Rev-Erba）与Rev-Erbβ（Rev-Erbb）是核受体（nuclear receptor），可调控参与昼夜节律调控、代谢及炎症反应的基因的表达。Rev-Erb家族蛋白作为转录阻遏因子，通过招募NCoR/HDAC3共阻遏复合物，结合至靶基因增强子及启动子区域的Rev-Erb应答元件，但目前其介导细胞特异性阻遏程序的分子基础仍不明晰。本研究证实，在巨噬细胞中，Rev-Erb家族通过抑制由巨噬细胞谱系决定因子所选定的远端增强子的功能，从而调控靶基因表达，进而建立巨噬细胞特异性的阻遏程序。值得注意的是，Rev-Erb的阻遏功能与其抑制增强子来源RNA（enhancer-derived RNAs, eRNAs）转录的能力紧密相关。进一步研究发现，在两个受Rev-Erb负调控的增强子区域靶向降解eRNAs，可导致邻近mRNA的表达水平降低，这暗示此类eRNAs在增强子功能中发挥直接作用。研究人员通过可定量新生5'端的5'-GRO-Seq技术，精确确定了eRNA的转录起始位点，实验证实，将完整的增强子活性转移至靶启动子，同时需要介导转录因子结合的序列与编码eRNA转录本的特定序列。本研究为eRNAs在增强子功能中的直接作用提供了实验证据，并表明Rev-Erb家族可通过抑制eRNA转录，在远距离范围内实现基因表达的阻遏。本研究借助ChIP-seq、GRO-seq及5'-GRO-seq技术，解析了Rev-Erb在巨噬细胞中转录调控的分子机制。