305: Human cis-regulatory variants dissected by MPRA at single-nucleotide resolution

Siraj L et al., Nature, doi:10.1038/s41586-026-10121-6 - Using MPRA in five human cell types, the authors assayed 221,412 fine-mapped variants and identified 13,121 trait-associated regulatory variants (TARVs), mapping mechanisms at single-nucleotide resolution. Key terms: massively parallel reporter assay, trait-associated regulatory variants, saturation mutagenesis, transcription factor motifs, regulatory epistasis.

Study Highlights:
The study assayed 221,412 fine-mapped human GWAS and eQTL variants using a massively parallel reporter assay (MPRA) across five cell lines and performed saturation mutagenesis on 136 TARVs. MPRA identified 13,121 trait-associated regulatory variants (TARVs) and showed that emVar status within endogenous CREs improves precision for causal-variant prioritization. Saturation mutagenesis defined activity blocks, assigned transcription factors for 91% of previously non-canonical TARVs, and revealed that only 69% of TARVs disrupt known TF motifs. The authors also detected regulatory epistasis in ~11% of nearby variant pairs, demonstrating non-additive effects between cis variants.

Conclusion:
Large-scale MPRA combined with saturation mutagenesis systematically identifies and mechanistically annotates thousands of human trait-associated regulatory variants at single-nucleotide resolution, revealing motif-disrupting and non-canonical TF mechanisms and local epistasis.

Music:
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Article title:
Functional dissection of complex trait variants at single-nucleotide resolution

First author:
Siraj L

Journal:
Nature, doi:10.1038/s41586-026-10121-6

DOI:
10.1038/s41586-026-10121-6

Reference:
Siraj L., Castro R.I., Dewey H.B., Kales S., Butts J.C., Nguyen T.T.L., Kanai M., et al. Functional dissection of complex trait variants at single-nucleotide resolution. Nature. https://doi.org/10.1038/s41586-026-10121-6

License:
This episode is based on an open-access article published under the Creative Commons Attribution 4.0 International License (CC BY 4.0) - https://creativecommons.org/licenses/by/4.0/

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QC:
This episode was checked against the original article PDF and publication metadata for the episode release published on 2026-03-02.

QC Scope:
- article metadata and core scientific claims from the narration
- excludes analogies, intro/outro, and music
- transcript coverage: Audited the transcript’s coverage of MPRA scale and variant coverage, TARV identification and counts, mechanistic categories (motif disruption and non-canonical mechanisms), saturation mutagenesis mapping, regulatory epistasis, recall/precision metrics, cell-type context, and translational HbA1c example.
- transcript topics: MPRA scale and variant coverage; TARV identification and counts; Motif disruption as mechanism; Saturation mutagenesis mapping and activity blocks; Non-canonical TARV mechanisms; Regulatory epistasis in nearby TARV pairs

QC Summary:
- factual score: 10/10
- metadata score: 10/10
- supported core claims: 7
- claims flagged for review: 0
- metadata checks passed: 4
- metadata issues found: 0

Metadata Audited:
- article_doi
- article_title
- article_journal
- license

Factual Items Audited:
- MPRA tested 221,412 fine-mapped trait-associated variants
- Identified 13,121 TARVs with high precision
- 69% of TARVs disrupt known transcription factor motifs
- Saturation mutagenesis assigned TFs for 91% of non-canonical TARVs
- Regulatory epistasis detected in ~11% of nearby TARV pairs
- Precision for causal-variant prioritization ~82–83%; recall ~15–20%

QC result: Pass.