Biology subjects

Thao, K.

Publications and source records attributed to Thao, K..

2 recordsLinked to original sources

bioRxiv2024

Helicase-assisted continuous editing for programmable mutagenesis of endogenous genomes

A major challenge in human genomics is to decipher the context specific relationship of sequence to function. However, existing tools for locus specific hypermutation and evolution in the native genome context are limited. Here we present a novel programmable platform for long-range, locus-specific hypermutation called helicase-assisted continuous editing (HACE). HACE leverages CRISPR-Cas9 to target a processive helicase-deaminase fusion that incurs mutations across large (>1000 bp) genomic intervals. We applied HACE to identify mutations in MEK1 that confer kinase inhibitor resistance, to dissect the impact of individual variants in SF3B1-dependent mis-splicing, and to evaluate noncoding variants in a stimulation-dependent immune enhancer of CD69. HACE provides a powerful tool for investigating coding and noncoding variants, uncovering combinatorial sequence-to-function relationships, and evolving new biological functions. One Sentence SummaryWe developed a tool for continuous, long-range, targeted diversification of endogenous mammalian genomes and used it to explore the function of genetic variants in both coding and non-coding regions.

genetics↗

bioRxiv2020

mTOR-driven widespread exon skipping renders multifaceted gene regulation and proteome complexity

The mammalian target of rapamycin (mTOR) pathway is crucial in cell proliferation. Previously, we reported transcriptome-wide 3’-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon-skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: alternative splicing (AS) in the 5’-UTR controls translation efficiency while AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.Competing Interest StatementThe authors have declared no competing interest.View Full Text

biochemistry↗