A5049519110- Genomics and Chromatin Dynamics
- Single-cell and spatial transcriptomics
- Immune Cell Function and Interaction
- Chronic Lymphocytic Leukemia Research
- Genetic Mapping and Diversity in Plants and Animals
- RNA Research and Splicing
- Advanced Fluorescence Microscopy Techniques
- Gene expression and cancer classification
- IL-33, ST2, and ILC Pathways
- Molecular Biology Techniques and Applications
- Ubiquitin and proteasome pathways
- Sarcoma Diagnosis and Treatment
- Cancer Genomics and Diagnostics
- Protein Degradation and Inhibitors
- Lymphoma Diagnosis and Treatment
- Multiple Myeloma Research and Treatments
- Genomic variations and chromosomal abnormalities
- RNA and protein synthesis mechanisms
- Epigenetics and DNA Methylation
- T-cell and B-cell Immunology
- Immunotherapy and Immune Responses
Consorci Institut D'Investigacions Biomediques August Pi I Sunyer
2020-2024
Centre for Genomic Regulation
2018-2021
Institute of Science and Technology
2019
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...
Palatine tonsils are secondary lymphoid organs (SLOs) representing the first line of immunological defense against inhaled or ingested pathogens. We generated an atlas human tonsil composed >556,000 cells profiled across five different data modalities, including single-cell transcriptome, epigenome, proteome, and immune repertoire sequencing, as well spatial transcriptomics. This census identified 121 cell types states, defined developmental trajectories, enabled understanding functional...
Abstract Palatine tonsils are secondary lymphoid organs representing the first line of immunological defense against inhaled or ingested pathogens. Here, we present a comprehensive census cell types forming human tonsil by applying single-cell transcriptome, epigenome, proteome and adaptive immune repertoire sequencing as well spatial transcriptomics, resulting in an atlas >357,000 cells. We provide glossary 121 annotated states, disentangle gene regulatory mechanisms that drive cells...
Abstract Single-cell assay for transposase-accessible chromatin by sequencing (scATAC-seq) has emerged as a powerful tool dissecting regulatory landscapes and cellular heterogeneity. However, an exploration of systemic biases among scATAC-seq technologies remained absent. In this study, we benchmark the performance eight methods across 47 experiments using human peripheral blood mononuclear cells (PBMCs) reference sample develop PUMATAC, universal preprocessing pipeline, to handle various...
Multiple myeloma (MM) is a plasma cell neoplasm associated with broad variety of genetic lesions. In spite this heterogeneity, MMs share characteristic malignant phenotype whose underlying molecular basis remains poorly characterized. the present study, we examined cells from MM using multi-epigenomics approach and demonstrated that, when compared to normal B cells, showed an extensive activation regulatory elements, in part affecting coregulated adjacent genes. Among target genes...
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...
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 The rapid development of chromosome conformation capture (3C-based) techniques as well super-resolution imaging together with bioinformatics analyses has been fundamental for unveiling that chromosomes are organized into the so-called topologically associating domains or TADs. While these TADs appear nested patterns in 3C-based interaction matrices, vast majority available computational methods based on hypothesis individual and unrelated chromatin structures. Here we introduce...