title: Writ large: Genomic dissection of the effect of cellular environment on immune response.
abstract: Cells of the immune system routinely respond to cues from their local environment and feed back to their surroundings through transient responses, choice of differentiation trajectories, plastic changes in cell state, and malleable adaptation to their tissue of residence. Genomic approaches have opened the way for comprehensive interrogation of such orchestrated responses. Focusing on genomic profiling of transcriptional and epigenetic cell states, we discuss how they are applied to investigate immune cells faced with various environmental cues. We highlight some of the emerging principles on the role of dense regulatory circuitry, epigenetic memory, cell type fluidity, and reuse of regulatory modules in achieving and maintaining appropriate responses to a changing environment. These provide a first step toward a systematic understanding of molecular circuits in complex tissues.
authors.affiliation: Department of Electrical Engineering and Computer Science and Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA. niryosef@berkeley.edu aregev@broadinstitute.org.|Ragon Institute of Massachusetts General Hospital, MIT, and Harvard, Cambridge, MA 02139, USA.
authors.forename: Nir
authors.initials: N
authors.lastname: Yosef
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. niryosef@berkeley.edu aregev@broadinstitute.org.|Howard Hughes Medical Institute and Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.
authors.forename: Aviv
authors.initials: A
authors.lastname: Regev
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics / Q000276:immunology; D000818:Animals; D002454:Cell Differentiation; D000066670:Cell Plasticity / Q000235:genetics / Q000276:immunology; D004777:Environment; D044127:Epigenesis, Genetic; D059647:Gene-Environment Interaction; D023281:Genomics / Q000379:methods; D006412:Hematopoietic Stem Cells / Q000166:cytology / Q000276:immunology; D006706:Homeostasis / Q000235:genetics; D006801:Humans; D007107:Immune System / Q000166:cytology* / Q000378:metabolism*; D007111:Immunity, Cellular / Q000235:genetics*; D059467:Transcriptome