Biology subjects

Vardy, L. A.

Publications and source records attributed to Vardy, L. A..

2 recordsLinked to original sources

bioRxiv2022

Synergistic Combined-proteomics Guided Mapping strategy identifies mTOR mediated phosphorylation of LARP1 in nutrient responsiveness and dilated cardiomyopathy

Increased activity of the mammalian target of rapamycin (mTOR) signalling pathway, a crucial nutrient sensor, exacerbates ageing and ageing-related diseases, including cancer and heart failure. To further elucidate the physiological role of the serine/threonine kinase mTOR, we devised a novel tractable proteomics strategy that combines interaction proteomics, proximity-based proteomics and quantitative phosphoproteomics to identify interactors with and potential substrates of mTOR. We identified 58 candidate mTOR substrates, several of which were further validated. Interestingly, several of these candidate mTOR substrates are involved in various aspects of RNA biology, including regulating stability and processing. We characterized in-depth one of the validated mTOR substrates, LARP1, an RNA binding protein. mTOR-dependent phosphorylation of LARP1 is nutrient-sensitive and controls the RNA-binding ability of LARP1. We show that mTOR activity and LARP1 and LARP1 phosphorylation levels are increased in a congenital mouse model of dilated cardiomyopathy (DCM) caused by a mutation in the Lamin A gene. This implicates LARP1 in the development of DCM.

molecular biology↗

bioRxiv2020

Direct RNA sequencing reveals structural differences between transcript isoforms

The ability to correctly assign structure information to an individual transcript in a continuous and phased manner is critical to understanding RNA function. RNA structure play important roles in every step of an RNAs lifecycle, however current short-read high throughput RNA structure mapping strategies are long, complex and cannot assign unique structures to individual gene-linked isoforms in shared sequences. To address these limitations, we present an approach that combines structure probing with SHAPE-like compound NAI-N3, nanopore direct RNA sequencing, and one-class support vector machines to detect secondary structures on near full-length RNAs (PORE-cupine). PORE-cupine provides rapid, direct, accurate and robust structure information along known RNAs and recapitulates global structural features in human embryonic stem cells. The majority of gene-linked isoforms showed structural differences in shared sequences both local and distal to the alternative splice site, highlighting the importance of long-read sequencing for phasing of structures. Structural differences between gene-linked isoforms are associated with differential translation efficiencies globally, highlighting the role of structure as a pervasive mechanism for regulating isoform-specific gene expression inside cells.

biochemistry↗