A5051979607- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Cellular transport and secretion
- Streptococcal Infections and Treatments
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- Microtubule and mitosis dynamics
- Gene expression and cancer classification
- Signaling Pathways in Disease
- Antimicrobial Resistance in Staphylococcus
- Machine Learning in Materials Science
- Infective Endocarditis Diagnosis and Management
- Pancreatic function and diabetes
- Chronic Lymphocytic Leukemia Research
- Genetic Mapping and Diversity in Plants and Animals
- Advanced Electron Microscopy Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- Botulinum Toxin and Related Neurological Disorders
- Genetic Associations and Epidemiology
- Genomics and Rare Diseases
- FOXO transcription factor regulation
- Clostridium difficile and Clostridium perfringens research
- Single-cell and spatial transcriptomics
Centre for Genomic Regulation
2017-2023
Italian Institute of Technology
2023
Institute of Structural and Molecular Biology
2011-2022
Birkbeck, University of London
2014-2022
Institute of Science and Technology
2019
Universitat Pompeu Fabra
2018
University College London
2011-2014
Chromosome organization is crucial for genome function. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome organization. Using the microscopy methods OligoSTORM OligoDNA-PAINT, trace 8 megabases human 19, structures ranging in size from few kilobases over megabase. Focusing on regions that contribute compartments, discover distinct that, spite considerable variability, can predict whether...
Abstract To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia mantle lymphoma patients, here we integrate situ Hi-C nine additional omics layers. Beyond conventional active (A) inactive (B) compartments, uncover a highly-dynamic intermediate compartment enriched poised polycomb-repressed chromatin. During development, 28% compartments change, mostly involving...
Abstract Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops generally studied a finer scale, the impact looping on proximal interactions remains enigmatic. Here, we critically examine nuclear and loop-proximal using combination in situ Hi-C unparalleled depth, algorithm development, biophysical modeling. Producing large map with 33 billion contacts conjunction an for performing...
The potassium-chloride co-transporter KCC2, encoded by SLC12A5, plays a fundamental role in fast synaptic inhibition maintaining hyperpolarizing gradient for chloride ions. KCC2 dysfunction has been implicated human epilepsy, but to date, no monogenic KCC2-related epilepsy disorders have described. Here we show recessive loss-of-function SLC12A5 mutations patients with severe infantile-onset pharmacoresistant syndrome, of infancy migrating focal seizures (EIMFS). Decreased surface...
Membrane attack complex/perforin/cholesterol-dependent cytolysin (MACPF/CDC) proteins constitute a major superfamily of pore-forming that act as bacterial virulence factors and effectors in immune defence. Upon binding to the membrane, they convert from soluble monomeric form oligomeric, membrane-inserted pores. Using real-time atomic force microscopy (AFM), electron (EM), structure fitting, we have mapped assembly pathways CDC unprecedented detail accuracy, focussing on suilysin...
Membrane attack complex/perforin-like (MACPF) proteins comprise the largest superfamily of pore-forming proteins, playing crucial roles in immunity and pathogenesis. Soluble monomers assemble into large transmembrane pores via conformational transitions that remain to be structurally mechanistically characterised. Here we present an 11 Å resolution cryo-electron microscopy (cryo-EM) structure two-part, fungal toxin Pleurotolysin (Ply), together with crystal structures both components (the...
Kinesins are a superfamily of microtubule-based ATP-powered motors, important for multiple, essential cellular functions. How microtubule binding stimulates their ATPase and controls force generation is not understood. To address this fundamental question, we visualized microtubule-bound kinesin-1 kinesin-3 motor domains at multiple steps in cycles--including nucleotide-free states--at ∼ 7 Å resolution using cryo-electron microscopy. In both promotes ordered conformations conserved loops...
Three-dimensional electron microscopy is currently one of the most promising techniques used to study macromolecular assemblies. Rigid and flexible fitting atomic models into density maps often essential gain further insights assemblies they represent. Currently, tools that facilitate assessment fitted are needed. TEMPy (template comparison using Python) a toolkit designed for this purpose. The library includes set methods assess fits in intermediate-to-low resolution maps, both globally...
Chromosome structure is a crucial regulatory factor for wide range of nuclear processes. conformation capture (3C)-based experiments combined with computational modelling are pivotal unveiling 3D chromosome structure. Here, we introduce TADdyn, tool that integrates time-course 3C data, restraint-based modelling, and molecular dynamics to simulate the structural rearrangements genomic loci in completely data-driven way. We apply TADdyn on situ Hi-C studying reprogramming murine B cells...
The rapid development of Chromosome Conformation Capture (3C-based techniques), as well imaging together with bioinformatics analyses, has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While TADs appear nested patterns in 3C-based interaction matrices, vast majority available TAD callers based on hypothesis individual and unrelated chromatin structures. Here we introduce TADpole, a computational tool designed to...
The Tyr402His polymorphism of complement factor H (FH) with 20 short regulator (SCR) domains is associated age-related macular degeneration (AMD). How FH contributes to disease pathology not clear. Both and high concentrations zinc are found in drusen deposits, the key feature AMD. Heterozygous inhibited by zinc, which causes aggregate. Here, binding homozygous was studied. By analytical ultracentrifugation, large amounts oligomers were observed both native Tyr402 AMD-risk His402 allotypes...
PapC ushers are outer-membrane proteins enabling assembly and secretion of P pili in uropathogenic E. coli. Their translocation domain is a large β-barrel occluded by plug domain, which displaced to allow the pilus subunits across membrane. Previous studies suggested that this gating mechanism controlled β-hairpin an α-helix. To investigate role these elements allosteric signal communication, we developed method combining evolutionary molecular dynamics native mutants lacking and/or Analysis...
Abstract Genetic studies promise to provide insight into the molecular mechanisms underlying type 2 diabetes (T2D). Variants associated with T2D are often located in tissue-specific enhancer regions (enhancer clusters, stretch enhancers or super-enhancers). So far, such domains have been defined through clustering of linear genome maps rather than 3D-space. Furthermore, their target genes generally unknown. We now created promoter capture Hi-C human pancreatic islets. This linked...
ABSTRACT Background Despite advances in next generation sequencing technologies, the identification of variants uncertain significance (VUS) can often hinder definitive diagnosis patients with complex neurodevelopmental disorders. Objective The objective this study was to identify and characterize underlying cause disease a family two children severe developmental delay associated generalized dystonia episodic status dystonicus, chorea, epilepsy, cataracts. Methods Candidate genes identified...
Abstract Chromosome structure is thought to be crucial for proper functioning of the nucleus. Here, we present a method visualizing chromosomal DNA at super-resolution and then integrating Hi-C data produce three-dimensional models chromosome organization. We begin by applying Oligopaint probes single-molecule localization microscopy methods OligoSTORM OligoDNA-PAINT image 8 megabases human 19, discovering that regions contributing compartments can form distinct structures. Intriguingly, our...
Abstract Despite recent advances, the dynamics of genome architecture and chromatin function during human cell differentiation its potential reorganization upon neoplastic transformation remains poorly characterized. Here, we integrate in situ Hi-C nine additional omic layers to define biologically characterize dynamic changes three-dimensional (3D) across normal B cells from different subtypes chronic lymphocytic leukemia (CLL) mantle lymphoma (MCL) patients. Beyond conventional active (A)...
Abstract Chromosome conformation capture (3C) technologies measure the interaction frequency between pairs of chromatin regions within nucleus in a cell or population cells. Some these 3C retrieve interactions involving non-contiguous sets loci, resulting sparse matrices. One such is Promoter Capture Hi-C (pcHi-C) that tailored to probe only gene promoters. As such, pcHi-C provides matrices are suitable characterize short- and long-range enhancer–promoter interactions. Here, we introduce new...