A5068739694- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Cancer-related molecular mechanisms research
- Biosensors and Analytical Detection
- SARS-CoV-2 detection and testing
- Endoplasmic Reticulum Stress and Disease
- SARS-CoV-2 and COVID-19 Research
- RNA regulation and disease
MRC Toxicology Unit
2019-2024
Centre for Genomic Regulation
2023-2024
University of Cambridge
2018-2024
Abstract Although the subcellular dynamics of RNA and proteins are key determinants cell homeostasis, their characterization is still challenging. Here we present an integrative framework to simultaneously interrogate transcriptome proteome at resolution by combining two methods: localization (LoRNA) a streamlined density-based isotope tagging (dLOPIT) map protein organelles (nucleus, endoplasmic reticulum mitochondria) membraneless compartments (cytosol, nucleolus cytosolic granules)....
Abstract Existing methods to analyse RNA localisation are constrained specific RNAs or subcellular niches, precluding the cell-wide mapping of RNA. We present Localisation (LoRNA), which maps, at once, membranous (nucleus, ER and mitochondria) membraneless compartments (cytosol, nucleolus phase-separated granules). Simultaneous interrogation all locations allows system-wide quantification proportional distribution comprehensive analysis dynamics. Moreover, we have re-engineered LOPIT...
Diagnostic testing continues to be an integral component of the strategy contain Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) global pandemic, causative agent Disease 2019 (COVID-19). The SARS-CoV-2 genome encodes 3C-like protease (3CLpro) which is essential for coronavirus replication. This study adapts in vitro colorimetric gold nanoparticle (AuNP) based assay specifically detect activity 3CLpro as a purified recombinant protein and cellular exogenously expressed HEK293T...
Abstract Current methods for the identification of RNA–protein interactions require a quantity and quality sample that hinders their application, especially dynamic biological systems or when material is limiting. Here, we present new approach to enrich RNA-Binding Proteins (RBPs): Orthogonal Organic Phase Separation (OOPS), which compatible with downstream proteomics RNA sequencing. OOPS enables recovery RBPs free protein, protein-bound RNA, from single in an unbiased manner. By applying...
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree redundancy and extensive modifications. As such, no method has become well established, while various approaches have been proposed quantify tRNAs from reads. Here, we use realistic simulations benchmark quantification approaches, including two novel approaches. We demonstrate that these are consistently the most accurate, data simulated mimic five different methods. This...
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated by their degree redundancy and extensive modifications. As such, no method has become well established, while various approaches have been proposed to quantify tRNAs from reads. Here, we use realistic simulations benchmark quantification approaches, including two novel approaches. We demonstrate that these are consistently the most accurate, data simulated mimic five different methods. This...
Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree redundancy and extensive modifications. As such, no method has become well established, while various approaches have been proposed quantify tRNAs from reads. Here, we use realistic simulations benchmark quantification approaches, including two novel approaches. We demonstrate that these are consistently the most accurate, data simulated mimic five different methods. This...
Abstract Quantification of transfer RNA (tRNA) using illumina sequencing based tRNA-Seq is complicated due to their degree redundancy and extensive modifications. As such, no method has become well established, while various approaches have been proposed quantify tRNAs from reads. Here, we use realistic simulations benchmark quantification approaches, including two novel approaches. We demonstrate that these are consistently the most accurate, data simulated mimic five different methods....
Abstract Characterising RNA-protein interaction dynamics is fundamental to understand how bacteria respond their environment. In this study, we have analysed the of 91% Escherichia coli expressed proteome and RNA-interaction properties 271 RNA-binding proteins (RBPs) at different growth phases. We find that 68% RBPs differentially bind RNA across phases characterise 17 previously unannotated as bacterial including YfiF, a ncRNA-binding protein. While these new are mostly present in...