baal-nf identifies motif-disrupting variants that decrease transcription factor binding affinity.

Breeshey Roskams-Hieter, Øyvind Almelid, Chris P Ponting

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In one paragraph

Article in Genome biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

Epistatic contributions to human traits via transcription factor mechanisms.medRxiv : the preprint server for health sciences · 2025
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5 · Who and what money

Authors and funding

3 authors.

Breeshey Roskams-HieterInstitute of Genetics and Cancer, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK. b.j.roskams-hieter@sms.ed.ac.uk.

Øyvind AlmelidInstitute of Genetics and Cancer, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK.

Chris P PontingInstitute of Genetics and Cancer, MRC Human Genetics Unit, Western General Hospital, University of Edinburgh, Edinburgh, EH4 2XU, UK. chris.ponting@ed.ac.uk.

Funding

Alan Turing Institute 218529/Z/19/ZAlan Turing Institute TU/ASG/R-SPEH-102Health Data Research UK 218529/Z/19/ZMedical Research Council MC_UU_00007/15Wellcome TrustWellcome Trust 218529/Z/19/Z

6 · The paper itself

Abstract

Human traits vary in part due to genetically-determined change of transcription factor binding affinity within gene regulatory regions. However, few trait-causal variants or mechanisms are known. Here we propose 1,935 variants as strong candidates for causally altering human traits. We discover these through baal-nf which uses chromatin immunoprecipitation-sequencing data to identify allelic imbalance at heterozygous sites for affinity-concordant positions within transcription factor- and co-factor binding motifs. These allele-specific binding sites are evolutionarily conserved and enriched for trait and gene expression associations. baal-nf and these high-quality allele-specific binding sites allow trait variation due to altered transcription factor binding to be investigated.

Indexed as

Nucleotide MotifsTranscription FactorsAllelesAllelic ImbalanceBinding SitesChromatin ImmunoprecipitationChromatin Immunoprecipitation SequencingGenetic VariationHumansProtein BindingTranscription FactorsAllele-specific bindingAllelic imbalanceChIP-sequencingMotifsTranscription factors

Identifiers

PMID41526967

DOI10.1186/s13059-025-03916-9

PMCPMC12888418

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.