bioRxiv preprint doi: https://doi.org/10.1101/620062; this version posted April 29, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Functional effects of variation in transcription factor binding highlight long-range gene regulation by epromoters Joanna Mitchelmore1, Nastasiya Grinberg2, Chris Wallace2,3 and Mikhail Spivakov1,4,5,* 1 Nuclear Dynamics Programme, Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK 2 Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge Biomedical Campus, University of Cambridge, Cambridge, CB2 0AW, UK 3 MRC Biostatistics Unit, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0SR, UK 4 MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK 5 Institute of Clinical Sciences, Faculty of Medicine, Imperial College, Du Cane Road, London W12 0NN, UK * Corresponding author. Email
[email protected] Present address: Joanna Mitchelmore, Novartis Institutes of Biomedical Research, Fabrikstrasse 16, Novartis Campus Basel, 4056. Switzerland ABSTRACT Identifying DNA cis-regulatory modules (CRMs) that control the expression of specific genes is crucial for deciphering the logic of transcriptional control. Natural genetic variation can point to the possible gene regulatory function of specific sequences through their allelic associations with gene expression. However, comprehensive identification of causal regulatory sequences in brute- force association testing without incorporating prior knowledge is challenging due to limited statistical power and effects of linkage disequilibrium. Sequence variants affecting transcription factor (TF) binding at CRMs have a strong potential to influence gene regulatory function, which provides a motivation for prioritising such variants in association testing.