Accurate, sensitive, and efficient chromatin accessibility quantification at target loci using UNIChro-seq

Area of Science:

• Genomics
• Molecular Biology
• Immunology

Background:

• Fine-mapping studies identify numerous disease risk variants, necessitating efficient functional validation.
• Current genetic analysis tools lack the precision for detailed target-loci investigation.

Purpose of the Study:

• To introduce UNIChro-seq, a digital counting method for accessible chromatin molecules at specific genetic loci.
• To enable accurate, sensitive, and efficient quantification of allelic effects for functional genomics.

Main Methods:

• Development and application of UNIChro-seq for digital chromatin molecule counting.
• Investigation of 57 autoimmunity risk alleles and 20 genome-edited variants.
• Utilizing bi-directional genome editing to distinguish true causal effects from false positives.

Main Results:

• UNIChro-seq provides accurate and sensitive allelic effect quantification compared to conventional methods.
• Functional dissection of a LEF1 locus variant reveals its role in T cell dysregulation in rheumatoid arthritis.
• Identified a fraction of edited alleles showing false positive chromatin accessibility effects, distinguishable by bi-directional editing.

Conclusions:

• UNIChro-seq combined with genome editing offers a precise and scalable approach for functional analysis of disease-associated loci.
• This methodology advances the understanding of genetic variants in autoimmune diseases like rheumatoid arthritis.