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Polymorphic tandem repeats influence cell type-specific gene expression across the human immune landscape
Hope A Tanudisastro1,2,3,4, Anna S E Cuomo1,2,3,5,6, Ben Weisburd7,8
1Centre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Biorxiv : the Preprint Server for Biology
|April 28, 2025
Summary
Tandem repeats (TRs) significantly impact gene expression across various blood cell types. This study reveals TRs as key regulators, influencing genetic traits and rare diseases.
Area of Science:
- Genomics
- Human Genetics
- Molecular Biology
Background:
- Tandem repeats (TRs) are polymorphic genomic regions that regulate gene expression but are historically challenging to analyze.
- Their role in cell type-specific gene regulation and complex traits remains underexplored.
Purpose of the Study:
- To investigate the impact of TR variation on gene expression across diverse blood cell types.
- To identify TRs that causally influence gene expression and are associated with human traits and diseases.
Main Methods:
- Utilized whole genome and single-cell RNA sequencing from 1,925 individuals (over 5.4 million cells).
- Analyzed over 1.7 million polymorphic TR loci.
- Applied fine-mapping and colocalization to identify causal TRs and their associations.
Main Results:
- Identified over 62,000 single-cell expression quantitative trait TR loci (sc-eTRs), with 16.6% cell type-specific.
- Uncovered 4,283 sc-eTRs as candidate causal drivers for 13.6% of tested genes.
- Demonstrated TRs as likely mediators for genetic associations in over 700 genes related to immune and hematological traits.
Conclusions:
- Tandem repeats are critical, overlooked contributors to cell type-specific gene expression.
- TRs have significant implications for understanding the genetic basis of complex traits and rare disease pathogenesis.
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