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
IntroductionHematopoiesis has long served as a model system for adult stem cells, with many paradigms of stem cell biology first being established as a result of studying hematopoietic stem cells (HSCs). A large body of work over the past 25 years has established that transcription factors (TFs) play critical roles during the specification, maintenance, and/or differentiation of HSCs. However, the underlying mechanisms have remained largely obscure because of a lack of comprehensive data on target genes, as well as very limited information on the way key TFs interact to form the regulatory networks that control blood stem cell development and subsequent behavior.The basic helix-loop-helix (bHLH) TF Scl (also known as Tal1) is required for the specification of HSCs as well as their subsequent differentiation into erythroid and megakaryocytic lineages. 1,2 Sclnull embryos do not survive beyond embryonic day (E) 9.5 due to a complete absence of hematopoiesis, 3,4 a more striking phenotype than seen with other important regulators of early hematopoiesis such as Runx1 or Gata2. [5][6][7] Moreover, together with its paralogue Lyl1, Scl was recently shown to be essential for the survival of adult HSCs, thus emphasizing critical functions for Scl at multiple stages of hematopoietic ontogeny. 8 In addition to its pleiotropic roles in hematopoiesis, Scl is also required for vascular and central nervous system development. [9][10][11] Within the blood system, Scl is thought to be a key component of the regulatory networks controlling the specification and subsequent differentiation of HSCs. 12,13 Studies on the transcriptional regulation of the murine Scl gene identified Ets and Gata factors as well as an autoregulatory loop as key upstream inputs. [14][15][16] However, to fully understand how Scl functions within hematopoietic regulatory networks, comprehensive information on downstream target genes will also be required. Scl has been found to regulate a handful of genes, including Gata1, 17 Runx1, 18 c-kit, 19 and ␣-globin 20 in different hematopoietic lineages. However, to date, no systematic genome-scale approach has been taken to interrogate Scl target genes at early developmental time points in which Scl function is critical.Together with bHLH class I proteins, such as E47, Scl binds DNA as a heterodimer to the so-called E-box sequence motif CANNTG. In addition to its bHLH DNA-binding partners, Scl can interact with various proteins, including the lim-only protein Lmo2 and Gata factors Gata1/Gata2 in multimeric ...