title: Regulation of early T-lineage gene expression and developmental progression by the progenitor cell transcription factor PU.1.
abstract: The ETS family transcription factor PU.1 is essential for the development of several blood lineages, including T cells, but its function in intrathymic T-cell precursors has been poorly defined. In the thymus, high PU.1 expression persists through multiple cell divisions in early stages but then falls sharply during T-cell lineage commitment. PU.1 silencing is critical for T-cell commitment, but it has remained unknown how PU.1 activities could contribute positively to T-cell development. Here we employed conditional knockout and modified antagonist PU.1 constructs to perturb PU.1 function stage-specifically in early T cells. We show that PU.1 is needed for full proliferation, restricting access to some non-T fates, and controlling the timing of T-cell developmental progression such that removal or antagonism of endogenous PU.1 allows precocious access to T-cell differentiation. Dominant-negative effects reveal that this repression by PU.1 is mediated indirectly. Genome-wide transcriptome analysis identifies novel targets of PU.1 positive and negative regulation affecting progenitor cell signaling and cell biology and indicating distinct regulatory effects on different subsets of progenitor cell transcription factors. Thus, in addition to supporting early T-cell proliferation, PU.1 regulates the timing of activation of the core T-lineage developmental program.
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
authors.forename: Ameya
authors.initials: A
authors.lastname: Champhekar
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
authors.forename: Sagar S
authors.initials: SS
authors.lastname: Damle
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA;
authors.forename: George
authors.initials: G
authors.lastname: Freedman
authors.affiliation: Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Sebastian
authors.initials: S
authors.lastname: Carotta
authors.affiliation: Division of Molecular Immunology, Walter and Eliza Hall Institute of Medical Research, Melbourne, Victoria 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia.
authors.forename: Stephen L
authors.initials: SL
authors.lastname: Nutt
authors.affiliation: Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, USA; evroth@its.caltech.edu.
authors.forename: Ellen V
authors.initials: EV
authors.lastname: Rothenberg
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002470:Cell Survival; D002478:Cells, Cultured; D018507:Gene Expression Regulation, Developmental; D008810:Mice, Inbred C57BL; D011518:Proto-Oncogene Proteins / Q000235:genetics / Q000378:metabolism*; D051880:Receptors, Notch / Q000378:metabolism; D013234:Stem Cells; D013601:T-Lymphocytes / Q000166:cytology* / Q000378:metabolism*; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism*; D059467:Transcriptome; D000099232:Proto-Oncogene Protein Spi-1
chemical_list: D011518:Proto-Oncogene Proteins; D051880:Receptors, Notch; D015534:Trans-Activators; D000099232:Proto-Oncogene Protein Spi-1
keywords: Notch; RNA-seq; conditional knockout; hematopoiesis; in vitro development; obligate repressor
references.citation: Mol Cell. 2001 Sep;8(3):705-11
references.pmid: 11583631
references.citation: Nat Immunol. 2013 Jun;14(6):619-32
references.pmid: 23644507
references.citation: Immunity. 2002 Feb;16(2):297-309
references.pmid: 11869689
references.citation: Mol Cell Biol. 2003 Nov;23(21):7460-74
references.pmid: 14559995
references.citation: EMBO J. 1993 Jul;12(7):2723-33
references.pmid: 8334991
references.citation: Science. 1994 Sep 9;265(5178):1573-7
references.pmid: 8079170
references.citation: EMBO J. 1996 Oct 15;15(20):5647-58
references.pmid: 8896458
references.citation: Genes Dev. 1997 Nov 15;11(22):3072-82
references.pmid: 9367988
references.citation: Mol Cell Biol. 1998 May;18(5):2804-14
references.pmid: 9566899
references.citation: Development. 1999 Jun;126(14):3131-48
references.pmid: 10375504
references.citation: J Immunol. 1999 Sep 1;163(5):2681-7
references.pmid: 10453009
references.citation: Science. 2013 Aug 9;341(6146):670-3
references.pmid: 23868921
references.citation: Genome Biol. 2013;14(9):R99
references.pmid: 24028770
references.citation: Nat Rev Immunol. 2014 Aug;14(8):529-45
references.pmid: 25060579
references.citation: J Immunol. 2014 Oct 1;193(7):3470-91
references.pmid: 25172496
references.citation: Bioinformatics. 2015 Jan 15;31(2):166-9
references.pmid: 25260700
references.citation: J Exp Med. 2005 Jan 17;201(2):221-31
references.pmid: 15657291
references.citation: Exp Hematol. 2005 Apr;33(4):395-402
references.pmid: 15781329
references.citation: J Exp Med. 2005 May 2;201(9):1487-502
references.pmid: 15867096
references.citation: J Immunol. 2005 May 15;174(10):6184-94
references.pmid: 15879115
references.citation: Dev Biol. 2005 Apr 15;280(2):448-66
references.pmid: 15882585
references.citation: Blood. 2005 Sep 1;106(5):1590-600
references.pmid: 15914556
references.citation: EMBO J. 2005 Nov 2;24(21):3712-23
references.pmid: 16222338
references.citation: Nat Genet. 2006 Jan;38(1):27-37
references.pmid: 16311598
references.citation: J Exp Med. 2006 May 15;203(5):1329-42
references.pmid: 16682500
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11993-8
references.pmid: 16880393
references.citation: Immunity. 2006 Nov;25(5):731-44
references.pmid: 17088084
references.citation: Immunity. 2007 Jun;26(6):690-702
references.pmid: 17582342
references.citation: Nat Immunol. 2007 Aug;8(8):845-55
references.pmid: 17603486
references.citation: Leukemia. 2008 Jun;22(6):1214-25
references.pmid: 18354487
references.citation: J Exp Med. 2008 Oct 27;205(11):2507-13
references.pmid: 18824583
references.citation: PLoS Genet. 2009 Dec;5(12):e1000778
references.pmid: 20019798
references.citation: Immunity. 2010 Mar 26;32(3):317-28
references.pmid: 20206554
references.citation: Genome Biol. 2010;11(2):R14
references.pmid: 20132535
references.citation: Nat Immunol. 2010 Jun;11(6):527-34
references.pmid: 20431622
references.citation: Immunity. 2010 May 28;32(5):628-41
references.pmid: 20510871
references.citation: Mol Cell. 2010 May 28;38(4):576-89
references.pmid: 20513432
references.citation: J Immunol. 2010 Jul 1;185(1):284-93
references.pmid: 20543111
references.citation: Science. 2010 Jul 2;329(5987):89-93
references.pmid: 20595614
references.citation: Immunol Rev. 2010 Nov;238(1):150-68
references.pmid: 20969591
references.citation: Genome Biol. 2010;11(10):R106
references.pmid: 20979621
references.citation: Blood. 2011 Jun 16;117(24):6498-508
references.pmid: 21518930
references.citation: PLoS Genet. 2011 Jun;7(6):e1001392
references.pmid: 21695229
references.citation: PLoS One. 2011;6(7):e22189
references.pmid: 21779390
references.citation: Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3832-7
references.pmid: 22357756
references.citation: Cell. 2012 Apr 13;149(2):467-82
references.pmid: 22500808
references.citation: Nucleic Acids Res. 2012 Oct;40(18):8927-41
references.pmid: 22790984
references.citation: J R Soc Interface. 2013 Jan 6;10(78):20120774
references.pmid: 23152106
references.citation: Cell. 2013 Jan 17;152(1-2):157-71
references.pmid: 23332752
references.citation: Development. 2013 Mar;140(6):1207-19
references.pmid: 23444353
references.citation: Mol Cell. 2013 Mar 7;49(5):934-46
references.pmid: 23395001
references.citation: Immunity. 2002 Feb;16(2):285-96
references.pmid: 11869688