A5075122495- RNA modifications and cancer
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- RNA and protein synthesis mechanisms
- Logic, Reasoning, and Knowledge
- Formal Methods in Verification
- Distributed systems and fault tolerance
- Epigenetics and DNA Methylation
- Logic, programming, and type systems
- Advanced Software Engineering Methodologies
- Plant Disease Resistance and Genetics
- Service-Oriented Architecture and Web Services
- Multi-Agent Systems and Negotiation
- Genomics and Phylogenetic Studies
- Adipose Tissue and Metabolism
- Software Testing and Debugging Techniques
- Histone Deacetylase Inhibitors Research
- Software Reliability and Analysis Research
- Petri Nets in System Modeling
Wellcome Centre for Cell Biology
2015-2024
University of Edinburgh
2015-2024
Imperial College London
2005-2009
Abstract Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by two of largest complexes—UtpA and UtpB—interact nascent are poorly understood. Here, we combined biochemical structural biology approaches ensembles RNA–protein cross-linking data elucidate essential functions both complexes. We show that UtpA contains a composite RNA-binding site...
Epigenetic processes involving long non-coding RNAs regulate endothelial gene expression. However, the underlying regulatory mechanisms causing dysfunction remain to be elucidated. Enhancer of zeste homolog 2 (EZH2) is an important rheostat histone H3K27 trimethylation (H3K27me3) that represses targets, but EZH2 RNA binding capacity and EZH2:RNA functional interactions have not been explored in post-ischemic angiogenesis. We used formaldehyde/UV-assisted crosslinking ligation sequencing...
Yeast Npl3 is a highly abundant, nuclear-cytoplasmic shuttling, RNA-binding protein, related to metazoan SR proteins. Reported functions of include transcription elongation, splicing and RNA 3’ end processing. We used UV crosslinking analysis cDNA (CRAC) map precise binding sites, strand-specific tiling arrays look at the effects loss on all transcripts across genome. found that binds diverse species, both coding non-coding, sites indicative roles in early pre-mRNA processing formation....
<ns4:p><ns4:bold>Background:</ns4:bold> Recent analyses implicate changes in the expression of box C/D class small nucleolar RNAs (snoRNAs) several human diseases.</ns4:p><ns4:p> <ns4:bold>Methods:</ns4:bold> Here we report identification potential novel RNA targets for snoRNAs budding yeast, using approach UV crosslinking and sequencing hybrids (CLASH) with snoRNP proteins Nop1, Nop56 Nop58. We also developed a bioinformatics to filter snoRNA-target interactions bona fide methylation guide...
Current representations of interaction protocols either concentrate on ease understanding and neglect the need to specify unambiguously (e.g. [B. Bauer, J.P. Muller, J.Odell, Agent UML: A Formalism for Specifying Multiagent Software Systems, AOSE (2000) 91–104]), or formal rigour usability issues [S. Paurobally, Rational Agents Processes States Negotiation, Ph.D. thesis, Imperial College, London, 2002, N. Fornara, M. Colombetti, Defining Interaction Protocols using a Commitment Based...
<ns4:p><ns4:bold>Background:</ns4:bold> Recent analyses implicate changes in the expression of box C/D class small nucleolar RNAs (snoRNAs) several human diseases.</ns4:p><ns4:p> <ns4:bold>Methods:</ns4:bold> Here we report identification potential novel RNA targets for snoRNAs budding yeast, using approach UV crosslinking and sequencing hybrids (CLASH) with snoRNP proteins Nop1, Nop56 Nop58. We also developed a bioinformatics to filter snoRNA-target interactions bona fide methylation guide...
ABSTRACT Altered expression of box C/D small nucleolar RNAs (snoRNAs) is implicated in human diseases, including cancer. Box snoRNAs canonically direct site-specific, 2’- O -methylation but the extent to which they participate other functions remains unclear. To identify RNA targets cells, we applied two techniques based on UV crosslinking, proximity ligation and sequencing hybrids (CLASH FLASH). These identified hundreds novel snoRNA interactions with rRNA, mRNAs. We developed an informatic...
Summary Enhancer of Zeste Homologue 2 (EZH2) modulates gene transcription during endothelial cell (EC) dysfunction, via interaction with non-coding RNAs (ncRNAs). Thus, EZH2 can act as a rheostat in deposition histone H3K27 trimethylation (H3K27me3) to repress many genes. We profiled EZH2-RNA interactions using f ormaldehyde/UV assisted cross-linking l igation nd s equencing h ybrids (FLASH-seq) primary human ECs. Transcriptome-wide EZH2-associated ncRNAs and RNA–RNA interactome were...
Diagrammatic methodologies for the representation of agent interaction protocols can be classified as joint representations that describe an in terms a single sequential process, or agent-centred provide distinct description protocol each (or role) interaction. Here we discuss process deriving centred from and vice versa, using variant UML statecharts.
In order to prevent misunderstandings within groups of interacting agents, it is necessary ensure that the agents' beliefs regarding overall state interaction are consistent with each other at all times. [7], Paurobally et al. proposed these could be synchronized by adding a specialized protocol layer incorporates protocols specifically designed synchronize beliefs. Here we define problem such would need solve in worst case, and prove insoluble. We then consider possibility synchronizing...