The transcriptional program controlled by the stem cell leukemia gene Scl/Tal1 during early embryonic hematopoietic development.
The basic helix-loop-helix transcription factor Scl/Tal1 controls the development and subsequent differentiation of hematopoietic stem cells (HSCs). However, because few Scl target genes have been validated to date, the underlying mechanisms have remained largely unknown. In this study, we have used ChIP-Seq technology (coupling chromatin immunoprecipitation with deep sequencing) to generate a genome-wide catalog of Scl-binding events in a stem/progenitor cell line, followed by validation using primary fetal liver cells and comprehensive transgenic mouse assays. Transgenic analysis provided in vivo validation of multiple new direct Scl target genes and allowed us to reconstruct an in vivo validated network consisting of 17 factors and their respective regulatory elements. By coupling ChIP-Seq in model cell lines with in vivo transgenic validation and sophisticated bioinformatic analysis, we have identified a widely applicable strategy for the reconstruction of stem cell regulatory networks in which biologic material is otherwise limiting. Moreover, in addition to revealing multiple previously unrecognized links to known HSC regulators, as well as novel links to genes not previously implicated in HSC function, comprehensive transgenic analysis of regulatory elements provided substantial new insights into the transcriptional control of several important hematopoietic regulators, including Cbfa2t3h/Eto2, Cebpe, Nfe2, Zfpm1/Fog1, Erg, Mafk, Gfi1b, and Myb.
University of Cambridge, Department of Haematology, Cambridge Institute for Medical Research, Cambridge, United Kingdom.
Nicola K
NK
Wilson
Diego
D
Miranda-Saavedra
Sarah
S
Kinston
Nicolas
N
Bonadies
Samuel D
SD
Foster
Fernando
F
Calero-Nieto
Mark A
MA
Dawson
Ian J
IJ
Donaldson
Stephanie
S
Dumon
Jonathan
J
Frampton
Rekin's
R
Janky
Xiao-Hong
XH
Sun
Sarah A
SA
Teichmann
Andrew J
AJ
Bannister
Berthold
B
Göttgens
D000818:Animals; D051792:Basic Helix-Loop-Helix Proteins / Q000378:metabolism / Q000502:physiology*; D001665:Binding Sites / Q000235:genetics; D002478:Cells, Cultured; D004622:Embryo, Mammalian / Q000098:blood supply; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D006410:Hematopoiesis / Q000235:genetics*; D006801:Humans; D051379:Mice; D008822:Mice, Transgenic; D008954:Models, Biological; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism / Q000502:physiology*; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; D014158:Transcription, Genetic
D051792:Basic Helix-Loop-Helix Proteins; D011518:Proto-Oncogene Proteins; D000073942:T-Cell Acute Lymphocytic Leukemia Protein 1; C067143:TAL1 protein, human