1. Identification of transcriptional regulators in the mouse immune system
- Author
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Jojic, V, Shay, T, Sylvia, K, Zuk, O, Sun, X, Kang, J, Regev, A, Koller, D, Best, AJ, Knell, J, Goldrath, A, Joic, V, Cohen, N, Brennan, P, Brenner, M, Kim, F, Rao, TN, Wagers, A, Heng, T, Ericson, J, Rothamel, K, Ortiz-Lopez, A, Mathis, D, Benoist, C, Bezman, NA, Sun, JC, Min-Oo, G, Kim, CC, Lanier, LL, Miller, J, Brown, B, Merad, M, Gautier, EL, Jakubzick, C, Randolph, GJ, Monach, P, Blair, DA, Dustin, ML, Shinton, SA, Hardy, RR, Laidlaw, D, Collins, J, Gazit, R, Rossi, DJ, Malhotra, N, Kreslavsky, T, Fletcher, A, Elpek, K, Bellemarte-Pelletier, A, Malhotra, D, and Turley, S
- Subjects
Cell type ,Transcription, Genetic ,T-Lymphocytes ,Immunology ,Computational biology ,Biology ,Article ,03 medical and health sciences ,Mice ,0302 clinical medicine ,Immune system ,Gene expression ,Immunology and Allergy ,Animals ,Humans ,Cell Lineage ,Gene Regulatory Networks ,Gene ,030304 developmental biology ,Oligonucleotide Array Sequence Analysis ,Genetics ,0303 health sciences ,Gene Expression Profiling ,Cell Differentiation ,Receptors, Antigen, T-Cell, gamma-delta ,Genome project ,DNA-Binding Proteins ,Repressor Proteins ,Haematopoiesis ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,Immune System ,Trans-Activators ,Identification (biology) ,Stem cell ,Transcriptome ,Algorithms ,Transcription Factors - Abstract
The differentiation of hematopoietic stem cells into cells of the immune system has been studied extensively in mammals, but the transcriptional circuitry that controls it is still only partially understood. Here, the Immunological Genome Project gene-expression profiles across mouse immune lineages allowed us to systematically analyze these circuits. To analyze this data set we developed Ontogenet, an algorithm for reconstructing lineage-specific regulation from gene-expression profiles across lineages. Using Ontogenet, we found differentiation stage-specific regulators of mouse hematopoiesis and identified many known hematopoietic regulators and 175 previously unknown candidate regulators, as well as their target genes and the cell types in which they act. Among the previously unknown regulators, we emphasize the role of ETV5 in the differentiation of γδ T cells. As the transcriptional programs of human and mouse cells are highly conserved, it is likely that many lessons learned from the mouse model apply to humans.
- Published
- 2013