Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.
Title | Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells. |
Publication Type | Journal Article |
Year of Publication | 2014 |
Authors | Ng, F. S. L., Schütte J., Ruau D., Diamanti E., Hannah R., Kinston S. J., & Göttgens B. |
Journal | Nucleic Acids Res |
Volume | 42 |
Issue | 22 |
Pagination | 13513-24 |
Date Published | 2014 Dec 16 |
ISSN | 1362-4962 |
Keywords | Animals, Binding Sites, Blood Cells, Chromatin Immunoprecipitation, DNA, Hematopoiesis, Mice, Nucleotide Motifs, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Transcription Factors, Transcription, Genetic |
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. |
DOI | 10.1093/nar/gku1254 |
Alternate Journal | Nucleic Acids Res. |
PubMed ID | 25428352 |
PubMed Central ID | PMC4267662 |
Grant List | 097922/Z/11/Z / / Wellcome Trust / United Kingdom 100140/Z/12/Z / / Wellcome Trust / United Kingdom BB/I00050X/1 / / Biotechnology and Biological Sciences Research Council / United Kingdom G0900951 / / Medical Research Council / United Kingdom c1163/A12765 / / Cancer Research UK / United Kingdom g0900951 / / Medical Research Council / United Kingdom |