@article{ddeb8d2a9aa24431b272ce11d7b1edcf,
title = "Characterization of Transcriptional Regulatory Networks that Promote and Restrict Identities and Functions of Intestinal Innate Lymphoid Cells",
abstract = "Innate lymphoid cells contribute to tissue homeostasis and defense against pathogens, processes that require coordinated transcription of thousands of genes. Pokrovskii and colleagues construct and experimentally validate a genome-scale transcriptional regulatory network describing how intestinal ILC gene expression programs and their plasticity are controlled by transcription factors.",
keywords = "ATAC-seq, Inferelator, gene regulation, lineage commitment, lymphocyte development",
author = "Maria Pokrovskii and Hall, {Jason A.} and Ochayon, {David E.} and Ren Yi and Chaimowitz, {Natalia S.} and Harsha Seelamneni and Nicholas Carriero and Aaron Watters and Waggoner, {Stephen N.} and Littman, {Dan R.} and Richard Bonneau and Miraldi, {Emily R.}",
note = "Funding Information: We thank the Flatiron Institute Scientific Computing Core (I. Fisk) and the NYU School of Medicine Genome Technology Core (GTC) (A. Heguy and P. Zappile). This work was supported by the Cincinnati Children's Research Foundation (Trustee Award to E.R.M. Research Innovation Award to S.N.W. Research In Residency Award to N.S.C. and Arnold P. Strauss Fellowship to D.O.), the Simons Foundation (E.R.M. A.W. N.D. N.C. and R.B.), the NIH (5T32AI100853 to M.P.; R01-DK103358-01 to R.B. and D.R.L.; DA038017 to S.N.W.; and R01-GM112192-01 to R.B. and T32 CA009161 [Levy] to J.A.H.), Howard Hughes Medical Institute (D.R.L.), Damon Runyon Cancer Research Foundation (Dale and Betty Frey Fellowship to J.A.H.), and the Colton Center for Autoimmunity (D.R.L). The NYU GTC was supported by NIH cancer center support grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. Cell sorting and flow cytometric data acquired at Cincinnati Children's relied on equipment maintained by the Research Flow Cytometry Core, which is supported in part by NIH grants AR47363, DK78392, and DK90971. E.R.M. M.P. J.A.H. D.R.L. and R.B. designed and contributed to analysis throughout the study. M.P. and J.A.H. generated ILC genomics data. M.P. contributed c-MAF data. S.N.W. conceived of BCL6 experiments and generated the mouse model. E.R.M. M.P. J.A.H. D.E.O. S.N.W. and D.R.L. designed BCL6 experiments. D.E.O. N.S.C. and H.S. performed BCL6 experiments. E.R.M. built the ILC TRNs and computational analyses. E.R.M. and R.Y. compiled public ILC genomics data. N.C. mapped RNA-seq and ATAC-seq data. A.W. designed interactive network visualization software with input from E.R.M. M.P. and R.B. E.R.M. and M.P. wrote the manuscript with input from J.A.H. D.E.O. S.N.W. D.R.L. and R.B. The authors declare no competing interests. Funding Information: We thank the Flatiron Institute Scientific Computing Core (I. Fisk) and the NYU School of Medicine Genome Technology Core (GTC) (A. Heguy and P. Zappile). This work was supported by the Cincinnati Children{\textquoteright}s Research Foundation (Trustee Award to E.R.M., Research Innovation Award to S.N.W., Research In Residency Award to N.S.C., and Arnold P. Strauss Fellowship to D.O.), the Simons Foundation (E.R.M., A.W., N.D., N.C., and R.B.), the NIH ( 5T32AI100853 to M.P.; R01-DK103358-01 to R.B. and D.R.L.; DA038017 to S.N.W.; and R01-GM112192-01 to R.B., and T32 CA009161 [Levy] to J.A.H.), Howard Hughes Medical Institute (D.R.L.), Damon Runyon Cancer Research Foundation (Dale and Betty Frey Fellowship to J.A.H.), and the Colton Center for Autoimmunity (D.R.L). The NYU GTC was supported by NIH cancer center support grant P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. Cell sorting and flow cytometric data acquired at Cincinnati Children{\textquoteright}s relied on equipment maintained by the Research Flow Cytometry Core, which is supported in part by NIH grants AR47363 , DK78392 , and DK90971 . Publisher Copyright: {\textcopyright} 2019 Elsevier Inc. Copyright: Copyright 2019 Elsevier B.V., All rights reserved.",
year = "2019",
month = jul,
day = "16",
doi = "10.1016/j.immuni.2019.06.001",
language = "English (US)",
volume = "51",
pages = "185--197.e6",
journal = "Immunity",
issn = "1074-7613",
publisher = "Cell Press",
number = "1",
}