Dynamic transcriptional control of macrophage miRNA signature via inflammation responsive enhancers revealed using a combination of next generation sequencing-based approaches

• Published in: Biochimica et biophysica acta. Gene regulatory mechanisms 2018-01, Vol.1861 (1), p.14-28
• Main Authors: Czimmerer, Zsolt, Horvath, Attila, Daniel, Bence, Nagy, Gergely, Cuaranta-Monroy, Ixchelt, Kiss, Mate, Kolostyak, Zsuzsanna, Poliska, Szilard, Steiner, Laszlo, Giannakis, Nikolas, Varga, Tamas, Nagy, Laszlo
• Format: Article
• Language: English
• Subjects: Animals; Chromatin - drug effects; Chromatin - genetics; Chromatin looping; Enhancer; Gene Expression Regulation - drug effects; Gene Expression Regulation - genetics; Gene Regulatory Networks - genetics; High-Throughput Nucleotide Sequencing; Humans; Inflammation; Inflammation - chemically induced; Inflammation - genetics; Inflammation - pathology; Lipopolysaccharides - toxicity; Macrophage; Mice; MicroRNAs - genetics; pri-miRNA; Promoter Regions, Genetic - genetics; Regulatory Sequences, Nucleic Acid - genetics; Transcription Factor RelA - genetics; Transcription, Genetic
• ISSN: 1874-9399; 1876-4320
• DOI: 10.1016/j.bbagrm.2017.11.003

MicroRNAs are important components of the post-transcriptional fine-tuning of macrophage gene expression in physiological and pathological conditions. However, the mechanistic underpinnings and the cis-acting genomic factors of how macrophage polarizing signals induce miRNA expression changes are not well characterized. Therefore, we systematically evaluated the transcriptional basis underlying the inflammation-mediated regulation of macrophage microRNome using the combination of different next generation sequencing datasets. We investigated the LPS-induced expression changes at mature miRNA and pri-miRNA levels in mouse macrophages utilizing a small RNA-seq method and publicly available GRO-seq dataset, respectively. Next, we identified an enhancer set associated with LPS-responsive pri-miRNAs based on publicly available H3K4 mono-methylation-specific ChIP-seq and GRO-seq datasets. This enhancer set was further characterized by the combination of publicly available ChIP and ATAC-seq datasets. Finally, direct interactions between the miR-155-coding genomic region and its distal regulatory elements were identified using a 3C–seq approach. Our analysis revealed 15 robustly LPS-regulated miRNAs at the transcriptional level. In addition, we found that these miRNA genes are associated with an inflammation-responsive enhancer network. Based on NFκB-p65 and JunB transcription factor binding, we showed two distinct enhancer subsets associated with LPS-activated miRNAs that possess distinct epigenetic characteristics and LPS-responsiveness. Finally, our 3C–seq analysis revealed the LPS-induced extensive reorganization of the pri-miR-155-associated functional chromatin domain as well as chromatin loop formation between LPS-responsive enhancers and the promoter region. Our genomic approach successfully combines various genome-wide datasets and allows the identification of the putative regulatory elements controlling miRNA expression in classically activated macrophages. •Next generation sequencing-based approaches were applied to investigate the transcriptional regulation of miRNA expression.•15 transcriptionally regulated miRNAs were identified in LPS-activated macrophages.•LPS-regulated pri-miRNAs are associated with 33 induced and 11 repressed enhancers.•2 distinct LPS-activated enhancer subsets can be distinguished based on NFkB and JunB binding and epigenetic characteristics.•The architecture of pri-miR-155-associated topological domain undergoes LPS-induced spa