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Constrained transcription factor spacing is prevalent and important for transcriptional control of mouse blood cells.


Type

Article

Change log

Authors

Ng, Felicia SL 
Ruau, David 
Diamanti, Evangelia 
Hannah, Rebecca 

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.

Description

Keywords

Animals, Binding Sites, Blood Cells, Chromatin Immunoprecipitation, DNA, Hematopoiesis, Mice, Nucleotide Motifs, Regulatory Elements, Transcriptional, Sequence Analysis, DNA, Transcription Factors, Transcription, Genetic

Journal Title

Nucleic Acids Res

Conference Name

Journal ISSN

0305-1048
1362-4962

Volume Title

42

Publisher

Oxford University Press (OUP)
Sponsorship
Wellcome Trust (097922/Z/11/Z)
Wellcome Trust (100140/Z/12/Z)
Medical Research Council (G0900951)
Biotechnology and Biological Sciences Research Council (BB/I00050X/1)
Cancer Research Uk (None)
Leukaemia & Lymphoma Research (12029)
Medical Research Council (MC_PC_12009)
Leukemia & Lymphoma Society (7001-12)
Medical Research Council (G0900951/1)
CCF (None)
Leukaemia and Lymphoma Research [12029]; the Medical Research Council [g0900951]; Cancer Research UK [c1163/A12765]; National Institute for Health Research Cambridge Biomedical Research Centre [RP-PG-0310- 1002]; Biotechnology and Biological Sciences Research Council [BB/I00050X/1]; Wellcome Trust to the Cambridge Institute for MedicalResearch [100140/Z/12/Z] and Wellcome Trust & MRC Cambridge Stem Cell Institute [097922/Z/11/Z]; Yousef Jameel scholarship [to F.S.L.N.]. Funding for open access charge: Wellcome Trust & MRC Cambridge Stem Cell Institute.