title: Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1.
abstract: The transcription factor PU.1 is crucial for the development of many hematopoietic lineages and its binding patterns significantly change during differentiation processes. However, the 'rules' for binding or not-binding of potential binding sites are only partially understood. To unveil basic characteristics of PU.1 binding site selection in different cell types, we studied the binding properties of PU.1 during human macrophage differentiation. Using in vivo and in vitro binding assays, as well as computational prediction, we show that PU.1 selects its binding sites primarily based on sequence affinity, which results in the frequent autonomous binding of high affinity sites in DNase I inaccessible regions (25-45% of all occupied sites). Increasing PU.1 concentrations and the availability of cooperative transcription factor interactions during lineage differentiation both decrease affinity thresholds for in vivo binding and fine-tune cell type-specific PU.1 binding, which seems to be largely independent of DNA methylation. Occupied sites were predominantly detected in active chromatin domains, which are characterized by higher densities of PU.1 recognition sites and neighboring motifs for cooperative transcription factors. Our study supports a model of PU.1 binding control that involves motif-binding affinity, PU.1 concentration, cooperativeness with neighboring transcription factor sites and chromatin domain accessibility, which likely applies to all PU.1 expressing cells.
authors: Department of Internal Medicine III, University Hospital Regensburg, F.-J.-Strauss Allee 11, D-93042 Regensburg, Germany.
authors: Thu-Hang
authors: TH
authors: Pham
authors: Julia
authors: J
authors: Minderjahn
authors: Christian
authors: C
authors: Schmidl
authors: Helen
authors: H
authors: Hoffmeister
authors: Sandra
authors: S
authors: Schmidhofer
authors: Wei
authors: W
authors: Chen
authors: Gernot
authors: G
authors: Längst
authors: Christopher
authors: C
authors: Benner
authors: Michael
authors: M
authors: Rehli
mesh_terms: D001483:Base Sequence; D001665:Binding Sites; D002843:Chromatin / Q000737:chemistry / Q000378:metabolism; D016384:Consensus Sequence; D004247:DNA / Q000378:metabolism; D003850:Deoxyribonuclease I; D006801:Humans; D008264:Macrophages / Q000378:metabolism; D009000:Monocytes / Q000378:metabolism; D059372:Nucleotide Motifs; D011485:Protein Binding; D011518:Proto-Oncogene Proteins / Q000378:metabolism*; D013234:Stem Cells / Q000378:metabolism; D015534:Trans-Activators / Q000378:metabolism*; D000099232:Proto-Oncogene Protein Spi-1
chemical_list: D002843:Chromatin; D004247:DNA; D003850:Deoxyribonuclease I; D011518:Proto-Oncogene Proteins; D015534:Trans-Activators; D000099232:Proto-Oncogene Protein Spi-1
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