A5034571954- Genomics and Chromatin Dynamics
- Advanced Fluorescence Microscopy Techniques
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- Pluripotent Stem Cells Research
- Genomics and Phylogenetic Studies
- Advanced Biosensing Techniques and Applications
- CRISPR and Genetic Engineering
- Plant Molecular Biology Research
- Monoclonal and Polyclonal Antibodies Research
- Chromosomal and Genetic Variations
- Advanced biosensing and bioanalysis techniques
- PI3K/AKT/mTOR signaling in cancer
- Click Chemistry and Applications
- Cancer Treatment and Pharmacology
- Single-cell and spatial transcriptomics
- Photosynthetic Processes and Mechanisms
- bioluminescence and chemiluminescence research
- Immunotherapy and Immune Responses
- RNA Interference and Gene Delivery
- Signaling Pathways in Disease
- Histone Deacetylase Inhibitors Research
- RNA modifications and cancer
- Colorectal Cancer Treatments and Studies
- Protein Degradation and Inhibitors
Wellcome/MRC Cambridge Stem Cell Institute
2016-2023
Stem Cell Institute
2023
Friedrich Miescher Institute
2021-2022
University of Cambridge
2017-2020
Medical Research Council
2016
Abstract Chromosome structure in mammals is thought to regulate transcription by modulating three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated loops topologically associating domains (TADs) 1–4 . However, how chromosome are actually translated into transcriptional outputs remains unclear. Here, address this question, we use an assay position enhancer at large numbers of densely spaced chromosomal locations relative a fixed promoter, measure promoter...
In mammals, interactions between sequences within topologically associating domains enable control of gene expression across large genomic distances. Yet it is unknown how frequently such contacts occur, long they last and depend on the dynamics chromosome folding loop extrusion activity cohesin. By imaging chromosomal locations at high spatial temporal resolution in living cells, we show that are transient occur during course a cell cycle. Interactions become more frequent longer presence...
The nucleosome remodeling deacetylase (NuRD) complex is a highly conserved regulator of chromatin structure and transcription. Structural studies have shed light on this other modifying machines, but much less known about how they assemble whether stable functional sub-modules exist that retain enzymatic activity. Purification the endogenous Drosophila NuRD shows it consists core subunits, while others, in particular remodeler CHD4, associate transiently. To dissect assembly activity NuRD,...
Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often found as multiple paralogous proteins vertebrate complexes. In some cases, these paralogues specify distinct biochemical and/or functional activities cells. Here, we set out to define the and diversity encoded by one such group within mammalian Nucleosome Remodelling Deacetylation (NuRD) complex: Mta1, Mta2 Mta3. We find that,...
Abstract Chromosome structure in mammals is thought to regulate transcription by modulating the three-dimensional interactions between enhancers and promoters, notably through CTCF-mediated topologically associating domains (TADs) 1–4 . However, how chromosome are actually translated into transcriptional outputs remains unclear. To address this question we use a novel assay position an enhancer at large number of densely spaced chromosomal locations relative fixed promoter, measure promoter...
Abstract To understand how the nucleosome remodeling and deacetylase (NuRD) complex regulates enhancers enhancer–promoter interactions, we have developed an approach to segment extract key biophysical parameters from live-cell three-dimensional single-molecule trajectories. Unexpectedly, this has revealed that NuRD binds chromatin for minutes, decompacts structure increases enhancer dynamics. We also uncovered a rare fast-diffusing state of found restricts time spent in state. Hi-C...
Abstract Physical proximity between genomic sequences in mammalian chromosomes controls key biological processes such as transcriptional regulation and DNA repair. Yet it is currently unknown if chromosomal contacts are rare stable or instead frequent dynamic, how they depend on the loop extrusion activity of cohesin barriers CTCF. By imaging locations at high spatial temporal resolution over several hours living cells, we show that within topological associating domains (TADs) frequently...
Abstract Gene expression in mammalian cells is controlled by enhancers that are often dispersed across large cis -regulatory landscapes around a promoter. Yet how determine transcription of their target genes, and this depends on relative position inside landscape remains unclear. Here we use live-cell imaging to track the activity promoter under control same enhancer, but inserted at different positions simplified regulatory with minimal complexity. Combined mathematical modeling, reveals...
A major challenge in single-molecule imaging is tracking the dynamics of proteins or complexes for long periods time dense environments found living cells. Here, we introduce concept using FRET to enhance photophysical properties photo-modulatable (PM) fluorophores commonly used such studies. By developing novel pairs, consisting a PM donor fluorophore (either mEos3.2 PA-JF549) next photostable acceptor dye JF646, demonstrate that competes with normal photobleaching kinetic pathways increase...
Abstract Enhancer-promoter dynamics are crucial for the spatiotemporal control of gene expression, but it remains unclear whether these controlled by chromatin regulators, such as nucleosome remodelling and deacetylase (NuRD) complex. The NuRD complex binds to all active enhancers modulate transcription here we use Hi-C experiments show that blurs TAD boundaries increases proximity intermediate-range (~1 Mb) genomic sequences enhancer-promoter interactions. To understand alters 3D genome...
Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The Nucleosome Remodelling Deacetylation (NuRD) complex is highly conserved remodeller which fine-tunes expression embryonic stem cells. While function NuRD mouse has been well defined, no study yet defined human Here we find while activity...
Abstract Multiprotein chromatin remodelling complexes show remarkable conservation of function amongst metazoans, even though components present in invertebrates are often as multiple paralogous proteins vertebrate complexes. In some cases these paralogues specify distinct biochemical and/or functional activities cells. Here we set out to define the and diversity encoded by one such group within mammalian Nucleosome Remodelling Deacetylation (NuRD) complex: Mta1, Mta2 Mta3. We find that,...
Abstract Differentiation of mammalian pluripotent cells involves large-scale changes in transcription and, among the molecules that orchestrate these changes, chromatin remodellers are essential to initiate, establish and maintain a new gene regulatory network. The NuRD complex is highly conserved remodeller which fine-tunes expression embryonic stem cells. While function mouse has been well defined, no study yet defined human We investigated structure induced (hiPSCs). Using...