A5061569924- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Gene Regulatory Network Analysis
- CRISPR and Genetic Engineering
- Molecular Biology Techniques and Applications
- Single-cell and spatial transcriptomics
- Bacteriophages and microbial interactions
- Genomics and Phylogenetic Studies
- Mycobacterium research and diagnosis
- Antibiotic Resistance in Bacteria
- Microbial Fuel Cells and Bioremediation
- Protist diversity and phylogeny
- DNA Repair Mechanisms
- Evolution and Genetic Dynamics
- Gene expression and cancer classification
- Scientific Computing and Data Management
- MicroRNA in disease regulation
- Fungal and yeast genetics research
- Genomics and Chromatin Dynamics
University of Edinburgh
2016-2025
The Francis Crick Institute
2021-2025
Quantitative BioSciences
2024-2025
UK Dementia Research Institute
2023-2024
King's College London
2023-2024
Institut de Biologie systémique et synthétique
2020
Abstract RNA-binding proteins play a key role in shaping gene expression profiles during stress, however, little is known about the dynamic nature of these interactions and how this influences kinetics expression. To address this, we developed kinetic cross-linking analysis cDNAs (χCRAC), an ultraviolet method that enabled us to quantitatively measure dynamics protein–RNA vivo on minute time-scale. Here, using χCRAC global yeast transcription termination factor Nab3 response glucose...
By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to efficiently adapt changes in their environment. To better understand how Escherichia coli acclimatizes nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) uncover Hfq-associated RNA-RNA interactions at specific growth stages. We demonstrate that Hfq CLASH robustly captures bona fide interactions. identified hundreds novel sRNA base-pairing interactions, including many...
Pre-mRNA splicing is kinetically coupled to transcription as shown by the widespread effects of speed on alternative outcomes. The molecular basis for such kinetic coupling incompletely understood, but one potential mechanism through elongation rate dependent folding pathways nascent pre-mRNA. To search RNA structures in pre-mRNA, we modified SPLASH (1) (Sequencing Psoralen Crosslinked, Ligated And Selected Hybrids) use with Chromatin Associated RNA. We applied this new method called...
All living organisms have developed strategies to respond chromosomal damage and preserve genome integrity. One such response is the repair of DNA double-strand breaks (DSBs), one most toxic forms lesions. In Escherichia coli , DSBs are repaired via RecBCD-dependent homologous recombination. RecBCD essential for accurate chromosome maintenance, but its over-expression can lead reduced ability. This apparent paradox suggests that copy numbers may need be tightly controlled within an optimal...
Previous high-throughput studies in Gram-negative bacteria identified a large number of 3ʹUTR fragments that potentially function as sRNAs. Here we extensively characterize the MalH sRNA. We show is stable degradation intermediate derived from 3ʹ end malG, which part maltose uptake operon transcript malEFG. Unlike majority bacterial sRNAs, transiently expressed during transition exponential to stationary growth phase, suggesting it contributes adaptation changes nutrient availability....
Abstract The structure of mRNA molecules plays an important role in its interactions with trans-acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences this interplay. However, current transcriptome-wide experimental methods chart these are limited by their poor sensitivity. Here we extend hiCLIP atlas duplexes bound Staufen1 (STAU1) ∼10-fold, through careful consideration assumptions, and development bespoke computational which apply existing...
All living organisms have developed strategies to respond chromosomal damage and preserve genome integrity. One such response is the repair of DNA double-strand breaks (DSBs), one most toxic forms lesions. In Escherichia coli , DSBs are repaired via RecBCD-dependent homologous recombination. RecBCD essential for accurate chromosome maintenance, but its over-expression can lead reduced ability. This apparent paradox suggests that copy numbers may need be tightly controlled within an optimal...
Abstract Ever-increasing volumes of sequencing data offer potential for large-scale meta-analyses to address significant biological questions. However, challenges such as insufficient processing information, quality concerns, and issues related accessibility curation often present obstacles. Additionally, most experimental biologists lack the time expertise needed independently analyse, manage share their own data. To overcome these hurdles, we Flow, a web-based platform that links...
Abstract By shaping gene expression profiles, small RNAs (sRNAs) enable bacteria to very efficiently adapt constant changes in their environment. To better understand how Escherichia coli acclimatizes nutrient availability, we performed UV cross-linking, ligation and sequencing of hybrids (CLASH) uncover sRNA-target interactions. Strikingly, uncovered hundreds novel Hfq-mediated interactions at specific growth stages, involving many 3’UTR-derived sRNAs a plethora sRNA-sRNA We discovered...
<ns3:p>Ribosome profiling is a powerful technique to study translation at transcriptome-wide level. However, ensuring good data quality paramount for accurate interpretation, as that the analyses are reproducible. We introduce new Nextflow DSL2 pipeline, riboseq-flow, designed processing and comprehensive control of ribosome experiments. Riboseq-flow user-friendly, versatile upholds high standards in reproducibility, scalability, portability, version continuous integration. It enables users...
All living organisms have developed strategies to respond chromosomal damage and preserve genome integrity. One such response is the repair of DNA double-strand breaks (DSBs), one most toxic forms lesions. In Escherichia coli , DSBs are repaired via RecBCD-dependent homologous recombination. RecBCD essential for accurate chromosome maintenance, but its over-expression can lead reduced ability. This apparent paradox suggests that copy numbers may need be tightly controlled within an optimal...
Abstract In the crowded cellular environment, transcriptome is highly organised with a network of interactions between proteins and RNA molecules that are crucial for formation biomolecular condensates. While role in this process has been extensively studied, contribution remained underexplored. study, we identify distinct set RNAs prone to condensation during early embryonic development apply an integrative deep learning approach deconvolve sequence structural determinants, trans-acting...
Abstract Protein dosage is regulated to maintain cellular homeostasis and health. The of proteins containing disordered low complexity domains (LCDs) must be particularly well-controlled prevent aberrant disease, yet no mechanism has been identified 1, 2 . Here we report a mutual homeostatic that controls the concentration such proteins, termed ’interstasis’, in which with similar LCDs co-regulate their combined through collective negative feedback. We focused on exploits fundamental...
Abstract All living organisms have developed strategies to respond chromosomal damage and preserve genome integrity. One such response is the repair of DNA double-strand breaks (DSBs), one most toxic forms lesions. In Escherichia coli , DSBs are repaired via RecBCD-dependent homologous recombination. RecBCD essential for accurate chromosome maintenance, but its over-expression can lead reduced ability. This apparent paradox suggests that copy numbers may need be tightly controlled within an...
ABSTRACT The structure of mRNA molecules plays an important role in its interactions with trans -acting factors, notably RNA binding proteins (RBPs), thus contributing to the functional consequences this interplay. However, current transcriptome-wide experimental methods chart these are limited by their poor sensitivity. Here we extend hiCLIP atlas duplexes bound Staufen1 (STAU1) ∼10-fold, through careful consideration assumptions, and development bespoke computational which apply existing...