Research ???Area main objective of the research activity in this unit is to understand how macrophage identity, functional specialization and plasticity are controlled by their specialized genomic organization, which is encoded in mammalian genomes, controlled by specific transcription factors, and modulated by the microenvironment. Within this area we provided the first genome-wide characterization of the genomic regulatory elements (enhancers) controlling inflammatory gene expression in macrophages. This activity involved the extensive use of chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-Seq) and allowed us to determine a general organizational principle of these enhancers, which consists in the combination of binding sites for ubiquitous, stimulus-responsive TFs and binding sites for constitutive cell type-restricted and lineage-determining TFs. Specifically, we have found that in macrophages genomic regulatory elements that control inflammatory gene expression contain two minimal elements, namely a binding site for one or more of the TFs activated in response to stimulation (e.g. NF-kB and AP-1), and a binding site for the major macrophage lineage-determining TF (Pu.1). This combination allows creating a cell type-specific context within which transcription of inflammatory genes is regulated, thus explaining variability among cell types in the inflammatory gene expression program induced by identical stimuli. Interestingly, part of the enhancers controlling inflammatory gene expression were found to undergo transcription, which may be instrumental to the maintenance of an open chromatin configuration and/ or to the production of non-coding RNAs that signal downstream transcriptional events. Ongoing research in the lab is mainly focused on the characterization of the impact of different environmental stimuli on the functional organization of macrophage genome using both in vitro models and ex-vivo analyses on macrophages obtained from tissues and primary tumors.
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As part of this effort we are characterizing the role of a panel of chromatin modifying enzymes, which represent potential drug targets, in the control of inflammatory responses. In this area we have reported a few years ago the first description of a histone demethylase involved in inflammatory gene expression. More recent work allowed us to identify a required role of a histone methyltransferase, MLL4, in the control of macrophage responsiveness to inflammatory stimuli. Publications The histone methyltransferase Wbp7 (MLL4) controls macrophage function through GPI anchor synthesis (L. Austenaa, I. Barozzi, A. Chronowska, A. Termanini, R. Ostuni, E. Prosperini, A. F. Stewart, G Testa, G Natoli) Immunity (36, 572–585, April 20 2012) Transcriptional control of macrophage polarization: enabling diversity with identity (T. Lawrence, G. Natoli) Nature Reviews Immunology 11, 750-761 (2011). The genomic landscapes of inflammation (G. Natoli, S. Ghisletti, I. Barozzi) Genes & Development 25, 101106 (2011). Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages (S. Ghisletti, I. Barozzi, F. Mietton, S. Polletti, F. De Santa, E. Venturini, L. Gregory, L. Lonie, A. Chew, C.L. Wei, J. Ragoussis, G. Natoli) Immunity, 32:31728. Epub 2010 Mar 4 (2010).
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