1. Academic Validation
  2. Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

Integrated multiplexed assays of variant effect reveal determinants of catechol-O-methyltransferase gene expression

  • Mol Syst Biol. 2024 Feb 14. doi: 10.1038/s44320-024-00018-9.
Ian Hoskins 1 Shilpa Rao 1 Charisma Tante 1 Can Cenik 2
Affiliations

Affiliations

  • 1 Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.
  • 2 Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. ccenik@austin.utexas.edu.
Abstract

Multiplexed assays of variant effect are powerful methods to profile the consequences of rare variants on gene expression and organismal fitness. Yet, few studies have integrated several multiplexed assays to map variant effects on gene expression in coding sequences. Here, we pioneered a multiplexed assay based on polysome profiling to measure variant effects on translation at scale, uncovering single-nucleotide variants that increase or decrease ribosome load. By combining high-throughput ribosome load data with multiplexed mRNA and protein abundance readouts, we mapped the cis-regulatory landscape of thousands of catechol-O-methyltransferase (COMT) variants from RNA to protein and found numerous coding variants that alter COMT expression. Finally, we trained machine learning models to map signatures of variant effects on COMT gene expression and uncovered both directional and divergent impacts across expression layers. Our analyses reveal expression phenotypes for thousands of variants in COMT and highlight variant effects on both single and multiple layers of expression. Our findings prompt future studies that integrate several multiplexed assays for the readout of gene expression.

Keywords

COMT; MAVE; Mutagenesis; RNA Secondary Structure; Ribosome Load.

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