title: Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.
abstract: Combinatorial transcription factor (TF) binding is essential for cell-type-specific gene regulation. However, much remains to be learned about the mechanisms of TF interactions, including to what extent constrained spacing and orientation of interacting TFs are critical for regulatory element activity. To examine the relative prevalence of the 'enhanceosome' versus the 'TF collective' model of combinatorial TF binding, a comprehensive analysis of TF binding site sequences in large scale datasets is necessary. We developed a motif-pair discovery pipeline to identify motif co-occurrences with preferential distance(s) between motifs in TF-bound regions. Utilizing a compendium of 289 mouse haematopoietic TF ChIP-seq datasets, we demonstrate that haematopoietic-related motif-pairs commonly occur with highly conserved constrained spacing and orientation between motifs. Furthermore, motif clustering revealed specific associations for both heterotypic and homotypic motif-pairs with particular haematopoietic cell types. We also showed that disrupting the spacing between motif-pairs significantly affects transcriptional activity in a well-known motif-pair-E-box and GATA, and in two previously unknown motif-pairs with constrained spacing-Ets and Homeobox as well as Ets and E-box. In this study, we provide evidence for widespread sequence-specific TF pair interaction with DNA that conforms to the 'enhanceosome' model, and furthermore identify associations between specific haematopoietic cell-types and motif-pairs.
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: Felicia S L
authors.initials: FS
authors.lastname: Ng
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: Judith
authors.identifier: http://orcid.org/0000-0001-6335-711X
authors.initials: J
authors.lastname: Schütte
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: David
authors.initials: D
authors.lastname: Ruau
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: Evangelia
authors.initials: E
authors.lastname: Diamanti
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Hannah
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK.
authors.forename: Sarah J
authors.initials: SJ
authors.lastname: Kinston
authors.affiliation: Department of Haematology, Wellcome Trust and MRC Cambridge Stem Cell Institute & Cambridge Institute for Medical Research, Cambridge University, Cambridge CB2 0XY, UK bg200@cam.ac.uk.
authors.forename: Berthold
authors.initials: B
authors.lastname: Göttgens
mesh_terms: D000818:Animals; D001665:Binding Sites; D001773:Blood Cells / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D006410:Hematopoiesis / Q000235:genetics*; D051379:Mice; D059372:Nucleotide Motifs; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D014157:Transcription Factors / Q000378:metabolism*; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors; D004247:DNA