A5050078564- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- Erythrocyte Function and Pathophysiology
- RNA modifications and cancer
- interferon and immune responses
- Chromosomal and Genetic Variations
- Cancer, Hypoxia, and Metabolism
- Hemoglobinopathies and Related Disorders
- Single-cell and spatial transcriptomics
- CRISPR and Genetic Engineering
- Plant Molecular Biology Research
- Plant Virus Research Studies
- Genomics and Phylogenetic Studies
- Epigenetics and DNA Methylation
- Zebrafish Biomedical Research Applications
- Virus-based gene therapy research
- Blood groups and transfusion
- Pluripotent Stem Cells Research
- Immune cells in cancer
- Genetics and Neurodevelopmental Disorders
- Metabolism, Diabetes, and Cancer
- Blood disorders and treatments
- Genomic variations and chromosomal abnormalities
- Acute Myeloid Leukemia Research
Centre for Human Genetics
2022-2025
University of Oxford
2019-2025
MRC Weatherall Institute of Molecular Medicine
2017-2024
Max Delbrück Center
2016-2023
John Radcliffe Hospital
2019-2023
The University of Texas Southwestern Medical Center
2022
Children's Medical Center
2022
Medical Research Council
2019-2020
MRC Laboratory of Molecular Biology
2019
MRC Molecular Haematology Unit
2019
Abstract Mammalian gene expression patterns are controlled by regulatory elements, which interact within topologically associating domains (TADs). The relationship between activation of formation structural chromatin interactions and during development is unclear. Here, we present Tiled-C, a low-input chromosome conformation capture (3C) technique. We use this approach to study architecture at high spatial temporal resolution through in vivo mouse erythroid differentiation. Integrated...
Abstract Technology for measuring 3D genome topology is increasingly important studying gene regulation, assembly and mapping of rearrangements. Hi-C other ligation-based methods have become routine but specific biases. Here, we develop multiplex-GAM, a faster more affordable version architecture (GAM), ligation-free technique that maps chromatin contacts genome-wide. We perform detailed comparison multiplex-GAM using mouse embryonic stem cells. When examining the strongest detected by...
Abstract Chromosome conformation capture (3C) provides an adaptable tool for studying diverse biological questions. Current 3C methods generally provide either low-resolution interaction profiles across the entire genome, or high-resolution at limited numbers of loci. Due to technical limitations, generation reproducible has not been achieved genome-wide scale. Here, overcome this barrier, we systematically test each step and report two improvements over current methods. We show that up 30%...
Hypoxia is a common phenomenon in solid tumors and strongly linked to hallmarks of cancer. Recent evidence has shown that hypoxia promotes local immune suppression. Type I IFN supports cytotoxic T lymphocytes by stimulating the maturation dendritic cells enhancing their capacity process present antigens. However, little known about relationship between type pathway, which comprises sensing double-stranded RNA DNA (dsRNA/dsDNA) followed IFNα/β secretion transcriptional activation...
Abstract The α- and β-globin loci harbor developmentally expressed genes, which are silenced throughout post-natal life. Reactivation of these genes may offer therapeutic approaches for the hemoglobinopathies, most common single gene disorders. Here, we address mechanisms regulating embryonically α-like globin, termed ζ-globin. We show that in embryonic erythroid cells, ζ-gene lies within a ~65 kb sub-TAD (topologically associating domain) open, acetylated chromatin interacts with α-globin...
Red blood cell development from erythroid progenitors requires profound reshaping of metabolism and gene expression. How these transcriptional metabolic alterations are coupled is unclear. Nprl3 (an inhibitor mTORC1) has remained in synteny with the α-globin genes for >500 million years, harbours most a-globin enhancers. However, whether serves an role unknown. We found that while haematopoietic require basal expression, expression further boosted by This lineage-specific upregulation...
Although certain human genetic variants are conspicuously loss of function, decoding the impact many is challenging. Previously, we described a patient with leukemia predisposition syndrome (GATA2 deficiency) germline GATA2 variant that inserts 9 amino acids between 2 zinc fingers (9aa-Ins). Here, conducted mechanistic analyses using genomic technologies and rescue system Gata2 enhancer-mutant hematopoietic progenitor cells to compare how 9aa-Ins function genome-wide. Despite nuclear...
ABSTRACT Enhancers and their target promoters often come into close physical proximity when activated. This may be explained by a variety of mechanisms; most recently via cohesin-mediated chromatin loop extrusion. Despite this compelling hypothesis, acute depletion cohesin does not cause widespread changes in gene expression. We have tested the role extrusion on expression at mouse alpha-globin locus during erythropoiesis. Acute downregulates early but late stages differentiation. When...
Summary Technologies for measuring 3D genome topology are increasingly important studying mechanisms of gene regulation, assembly and mapping rearrangements. Hi-C other ligation-based methods have become routine but specific biases. Here, we develop multiplex-GAM, a faster more affordable version Genome Architecture Mapping (GAM), ligation-free technique to map chromatin contacts genome-wide. We perform detailed comparison obtained by multiplex-GAM using mouse embryonic stem (mES) cells....
Mouse embryonic stem cells (mESCs) can be manipulated in vitro to recapitulate the process of erythropoiesis, during which multipotent undergo lineage specification, differentiation and maturation produce erythroid cells. Although useful for identifying specific progenitors precursors, this system has not been fully exploited as a source analyse erythropoiesis. Here, we establish protocol characterised erythroblasts isolated scalable manner from differentiated embryoid bodies (EBs). Using...
The investigation of inherited disorders erythropoiesis has elucidated many the principles underlying production normal red blood cells and how this is perturbed in human disease. Congenital dyserythropoietic anemia type 1 (CDA-I) a rare form caused by mutations two genes unknown function: CDAN1 CDIN1 (previously called C15orf41), whilst some cases, genetic abnormality completely unknown. Consequently, pathways affected CDA-I remain to be discovered. In order enable detailed analysis...
Abstract Mammalian gene expression patterns are controlled by regulatory elements, which interact within Topologically Associating Domains (TADs). The relationship between activation of formation structural chromatin interactions and during development is unclear. We developed Tiled-C, a low-input Chromosome Conformation Capture (3C) approach, to study architecture at high spatial temporal resolution through in vivo mouse erythroid differentiation. Integrated analysis matched accessibility...
Abstract A substantial proportion of mutations underlying rare Mendelian diseases remain unknown, potentially because they lie in the non-coding genome. Here, we report mapping causal mutation an autosomal dominant cardiac arrhythmia syndrome, ST Depression Syndrome, which is associated with widespread ST-depression on electrocardiogram together risk sudden death and heart failure, to region KCNB1 locus. Using genetic linkage analysis, narrowed 1cM genome then a editing approach, show that...
Abstract Genome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As new approach, datasets require specialized analytical tools and approaches. Here we present GAMtools, pipeline analysing datasets. GAMtools covers the automated raw next-generation data generated by GAM, detection regions in each nuclear slice, calculation quality control metrics,...
Abstract Hypoxia is a common phenomenon in solid tumours and considered hallmark of cancer. Increasing evidence shows that hypoxia promotes local immune suppression. Type I IFN involved supporting cytotoxic T lymphocytes by stimulating the maturation dendritic cells (DCs) enhancing their capacity to process present antigens. However, there little information about relationship between type interferon (IFN) pathway, which comprises sensing double-stranded RNA DNA (dsRNA/dsDNA), followed...
Abstract We employ and extensively characterise an ex vivo culture system to study terminal erythroid maturation of CD34 + progenitors from the peripheral blood normal individuals patients with Congenital Dyserythropoietic Anaemia type 1 (CDA-I). Using morphological analysis, FACS analysis proteomic approach CyTOF, we analysed patient-derived erythroblasts stage-matched those healthy donors during expansion phase into early differentiation. In patient cells, aspects disordered erythropoiesis...