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

02 Mar 2026

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Siraj L et al., Nature - 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. 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:Enjoy the music based on this article at the end of the episode. 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/ Support:Base by Base – Stripe donations: https://donate.stripe.com/7sY4gz71B2sN3RWac5gEg00 Official website https://basebybase.com On PaperCast Base by Base you’ll discover the latest in genomics, functional genomics, structural genomics, and proteomics. Episode link: https://basebybase.com/episodes/mpra-human-regulatory-variants

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3ª PARTE | 17 DIC 2025 | EL PARTIDAZO DE COPE

01 Jan 1970

El Partidazo de COPE

13:00H | 21 DIC 2025 | Fin de Semana

01 Jan 1970

Fin de Semana

12:00H | 21 DIC 2025 | Fin de Semana

01 Jan 1970

Fin de Semana

10:00H | 21 DIC 2025 | Fin de Semana

01 Jan 1970

Fin de Semana

13:00H | 20 DIC 2025 | Fin de Semana

01 Jan 1970

Fin de Semana

12:00H | 20 DIC 2025 | Fin de Semana

01 Jan 1970

Fin de Semana

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

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3ª PARTE | 17 DIC 2025 | EL PARTIDAZO DE COPE

13:00H | 21 DIC 2025 | Fin de Semana

12:00H | 21 DIC 2025 | Fin de Semana

10:00H | 21 DIC 2025 | Fin de Semana

13:00H | 20 DIC 2025 | Fin de Semana

12:00H | 20 DIC 2025 | Fin de Semana

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