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Enhancer-Targeted Immunosuppression

Sci. Signal.  09 Jul 2013:
Vol. 6, Issue 283, pp. ec154
DOI: 10.1126/scisignal.2004486

The Rev-Erb family of nuclear receptors [also known as NR1D (nuclear receptor subfamily 1, group D)] repress the transcription of genes that encode proteins involved in many processes, including the immune response. Using genome-wide approaches, Lam et al. found that Rev-Erbα and Rev-Erbβ repressed gene transcription in mouse bone marrow–derived macrophages (BMDMs) by binding to enhancers and inhibiting the transcription of eRNAs, a type of noncoding RNA that enhances transcription. In cultured mouse RAW264.7, macrophages that contained biotin-labeled Rev-Erbα and Rev-Erbβ, Rev-Erb–bound DNA regions tended to have enhancer-like characteristics: They were located at least 1 kilobase (kb) away from transcriptional start sites, had a high abundance of monomethylated histone H3 at Lys4 (H3K4me1) and a low abundance of trimethylated H3K4 (H3K4me3), and contained binding sites for C/EBP (CCAAT/enhancer-binding protein) and AP-1 (activator protein 1), transcription factors that are critical for macrophage differentiation. Global run-on sequencing (GRO-seq) in BMDMs from wild-type or Rev-Erb–knockout mice revealed that the abundance of 142 mRNAs was increased in knockout mice. Only three of the corresponding genes showed binding sites within 2 kb of transcription start sites. The expression of Mmp9 (encoding matrix metalloproteinase 9) and Cxc3r1 (encoding CXC chemokine receptor 1), two genes involved in mounting an immune response, inversely correlated with the abundance of either Rev-Erb receptor in BMDMs and in RAW264.7 cells. Using a modified GRO-seq method, eRNA transcript initiation was detected at a majority of intergenic Rev-Erbα target sites in BMDMs, whereas none was substantially detected in liver-derived macrophages. Transcript initiation and the abundance of eRNAs also inversely correlated with Rev-Erb abundance, as did the acetylation of H3K9 in Rev-Erb target enhancers, a mark associated with transcriptional activation. Knockdown or mutation of Mmp9 and Cxc3r1 enhancer–associated eRNAs reduced the abundance of Mmp9 and Cxc3r1 mRNA in wild-type BMDMs and in vivo in peritoneal cells from mice induced with sterile peritonitis and blocked the derepression of these transcripts in Rev-Erb–knockout BMDMs. Together the findings suggest that Rev-Erbs repress macrophage gene expression by inhibiting distal eRNA transcription in a context-specific manner.

M. T. Y. Lam, H. Cho, H. P. Lesch, D. Gosselin, S. Heinz, Y. Tanaka-Oishi, C. Benner , M. U. Kaikkonen, A. S. Kim, M. Kosaka, C. Y. Lee, A. Watt, T. R. Grossman, M. G. Rosenfeld, R. M. Evans, C. K. Glass, Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. Nature 498, 511–515 (2013). [PubMed]