A5091493092- Genomics and Chromatin Dynamics
- Epigenetics and DNA Methylation
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Cancer-related gene regulation
- Pluripotent Stem Cells Research
- Bioinformatics and Genomic Networks
- Simulation Techniques and Applications
- Genetic Associations and Epidemiology
- Acute Lymphoblastic Leukemia research
- interferon and immune responses
- Chromosomal and Genetic Variations
- Single-cell and spatial transcriptomics
- SARS-CoV-2 and COVID-19 Research
- Wildlife-Road Interactions and Conservation
- Plant Virus Research Studies
- Animal Genetics and Reproduction
- Gene expression and cancer classification
- Immune Cell Function and Interaction
- Eosinophilic Esophagitis
- Autoimmune and Inflammatory Disorders Research
- Lymphoma Diagnosis and Treatment
- Chronic Myeloid Leukemia Treatments
- RNA and protein synthesis mechanisms
- Health, Environment, Cognitive Aging
VIB-UAntwerp Center for Molecular Neurology
2022-2025
University of Antwerp
2022-2025
Imperial College London
2018-2024
MRC London Institute of Medical Sciences
2018-2024
Institute of Clinical Research
2023
Babraham Institute
2018-2020
Genomics (United Kingdom)
2018-2019
La Ligue Contre le Cancer
2016-2019
Institut de génétique et de biologie moléculaire et cellulaire
2016-2018
Inserm
2018
It is currently assumed that 3D chromosomal organization plays a central role in transcriptional control. However, depletion of cohesin and CTCF affects the steady-state levels only minority transcripts. Here, we use high-resolution Capture Hi-C to interrogate dynamics contacts all annotated human gene promoters upon degradation CTCF. We show majority promoter-anchored are lost these conditions, but many with distinct properties maintained, some new ones gained. The rewiring between active...
Abstract Gene enhancers often form long-range contacts with promoters, but it remains unclear if the activity of and their chromosomal are mediated by same DNA sequences recruited factors. Here, we study effects expression quantitative trait loci (eQTLs) on enhancer promoter in primary monocytes isolated from 34 male individuals. Using eQTL-Capture Hi-C a Bayesian approach considering both intra- inter-individual variation, initially detect 19 eQTLs associated enhancer-eGene contacts, most...
Cell lineages, which shape the body architecture and specify cell functions, derive from integration of a plethora intrinsic extrinsic signals. These signals trigger multiplicity decisions at several levels to modulate activity dynamic gene regulatory networks (GRNs), ensure both general cell-specific functions within given lineage, thereby establishing fates. Significant knowledge about these events involved key drivers comes homogeneous differentiation models. Even single chemical trigger,...
Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package robust detection differential in data. Chicdiff enhances state-of-the-art testing count data with bespoke normalization and multiple procedures that account specific statistical properties Hi-C. validate published Promoter human Monocytes CD4+ T cells, identifying multitudes cell type-specific...
Alterations in genetic and epigenetic landscapes are known to contribute the development of different types cancer. However, mechanistic links between transcription factors epigenome which coordinate deregulation gene networks during cell transformation largely unknown.We used an isogenic model stepwise tumorigenic human primary cells monitor progressive upon immortalization oncogene-induced transformation. We applied a systems biology approach by combining transcriptome data for each step...
Abstract It is currently assumed that 3D chromosomal organisation plays a central role in transcriptional control. However, recent evidence shows steady-state transcription of only minority genes affected by depletion architectural proteins such as cohesin and CTCF. Here, we have used Capture Hi-C to interrogate the dynamics contacts all human gene promoters upon rapid protein degradation. We show promoter lost these conditions tend be long-range, with at least one interaction partner...
Abstract Gene enhancers often form long-range contacts with promoters, but it remains unclear if enhancer activity and their chromosomal are mediated by the same DNA sequences recruited factors. We studied effects of expression quantitative trait loci (eQTLs) on promoter in primary monocytes isolated from 34 individuals. Using eQTL-Capture Hi-C a Bayesian approach considering both intra- inter-individual variation, we initially detected 19 eQTLs associated enhancer-eGene contacts, most which...
SUMMARY The ongoing pandemic caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is currently affecting millions of lives worldwide. Large retrospective studies indicate that an elevated level inflammatory cytokines and pro-inflammatory factors are associated with both increased disease severity mortality. Here, using multidimensional epigenetic, transcriptional, in vitro vivo analyses, we report Topoisomerase 1 (Top1) inhibition suppresses lethal inflammation induced...
Abstract Innate lymphoid cells (ILCs) are rare tissue-resident “helper” lymphocytes that do not express diversified antigen receptors. Type 3 ILCs (ILC3s) an important class of these enriched in the respiratory and intestinal mucosa, where they regulate inflammation mucosal homeostasis. To gain insight into cis-regulatory circuitries underlying ILC3 function, we used high-resolution Capture Hi-C to profile promoter-anchored chromosomal contacts human primary ILC3s. Combining significant...
Abstract Lineage commitment is a fundamental process that enables the morphogenesis of multicellular organisms from single pluripotent cell. While many genes involved in to specific lineages are known, logic their joint action incompletely understood, and predicting effects genetic perturbations on lineage still challenging. Here, we devised gene regulatory network analysis approach, GRN-loop, identify key cis -regulatory DNA elements transcription factors drive commitment. GRN-loop based...
The enormous amount of freely accessible functional genomics data is an invaluable resource for interrogating the biological function multiple DNA-interacting players and chromatin modifications by large-scale comparative analyses. However, in practice, large collections public requires major efforts (i) reprocessing available raw reads, (ii) incorporating quality assessments to exclude artefactual low-quality data, (iii) processing using high-performance computation. Here, we present...
Proximity ligation-mediated methods are essential to study the impact of three-dimensional chromatin organization on gene programming. Albeit significant progress has been made in development computational tools that assess long-range interactions, next nothing is known about quality generated datasets. We have developed LOGIQA ( www.ngs-qc.org/logiqa ), a database hosting scores for genome interaction assays, accessible through user-friendly web-based environment. Currently, harbors QC >900...
<title>Abstract</title> B-lineage acute-lymphoblastic leukemia (B-ALL) is driven by genomic lesions and distinct transcriptional programs. Both are often directly linked as most B-ALLs caused genetic at transcription factor (TF)-encoding genes. TFs largely mediate their function through gene regulatory ‘enhancer’ elements enhancer deregulation known to promote cancer initiation progression. Consecutively, enhancer-targeting drugs currently in clinical trials for advanced hematologic cancers...
Abstract Gonadal sex determination relies on tipping a delicate balance involving the activation and repression of several transcription factors signalling pathways. This is likely mediated by numerous non-coding regulatory elements that shape sex-specific transcriptomic programs. To explore dynamics these in detail, we performed paired time-series chromatin accessibility assays pre-granulosa Sertoli cells throughout their development embryo, making use new existing mouse reporter lines....
Abstract Summary Capture Hi-C is a powerful approach for detecting chromosomal interactions involving, at least on one end, DNA regions of interest, such as gene promoters. We present Chicdiff, an R package robust detection differential in data. ChiScdiff enhances state-of-the-art testing count data with bespoke normalisation and multiple procedures that account specific statistical properties Hi-C. validate Chicdiff published Promoter human Monocytes CD4+ T cells, identifying multitudes...