Autoimmune non-coding variants perturb transcription factor-cofactor complex assembly linked to enhancer activity.

Area of Science:

• Genetics
• Immunology
• Molecular Biology

Background:

• Autoimmune disease-associated variants are primarily in non-coding DNA.
• Mechanisms linking these variants to gene regulation are poorly understood.
• Determining how disease alleles affect transcription factor (TF) binding, cofactor (COF) recruitment, and enhancer activity at scale is a challenge.

Purpose of the Study:

• To profile differential TF and COF binding to autoimmune disease-associated variants.
• To link altered TF/COF binding to enhancer activity and gene regulation.
• To identify specific TFs, COFs, and regulatory modules involved in autoimmune disease pathogenesis.

Main Methods:

• Utilized the CASCADE method to profile TF and COF binding to 2,901 autoimmune disease-associated variants in Jurkat T cells.
• Integrated biochemical binding data with MPRA (Massively Parallel Reporter Assay) and allele-specific reporter expression data.
• Analyzed binding patterns of five major TF families (ETS, RUNX, SP/KLF, OVOL/MYBL, bHLH) and associated cofactors.

Main Results:

• Identified 516 variants that modulate TF/COF binding.
• Found strong concordance between binding-modulating variants and expression-modulating variants.
• Observed distinct binding enrichment for ETS and RUNX factors and identified allele-dependent regulator switching.
• Discovered a recurrent regulatory module involving FOXM1 and cofactors (TIP60, BRD4, NCOA3, NCOA1) at ETS sites.

Conclusions:

• Established a framework linking allele-specific TF/COF binding mechanisms to enhancer activity for prioritizing autoimmune disease variants.
• Demonstrated that variants perturbing TF/COF binding are functionally relevant to gene regulation in T cells.
• Highlighted the roles of specific TF families and cofactor complexes in autoimmune disease mechanisms.