A5030044037- RNA Research and Splicing
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Ferroptosis and cancer prognosis
- CRISPR and Genetic Engineering
- Lymphoma Diagnosis and Treatment
- Immune Cell Function and Interaction
- RNA and protein synthesis mechanisms
- Cancer, Lipids, and Metabolism
- CAR-T cell therapy research
- Chromatin Remodeling and Cancer
- Cell Image Analysis Techniques
- Peptidase Inhibition and Analysis
- Muscle Physiology and Disorders
- RNA regulation and disease
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- Gene Regulatory Network Analysis
- Telomeres, Telomerase, and Senescence
- Single-cell and spatial transcriptomics
- Viral-associated cancers and disorders
- DNA Repair Mechanisms
- Genetic Neurodegenerative Diseases
Clinica Universidad de Navarra
2023-2025
Universidad de Navarra
2020-2025
Navarre Institute of Health Research
2023-2025
Queen Elizabeth II Medical Centre
2022
Harry Perkins Institute of Medical Research
2022
The University of Western Australia
2022
Human brain development is underpinned by cellular and molecular reconfigurations continuing into the third decade of life. To reveal cell dynamics orchestrating neural maturation, we profiled human prefrontal cortex gene expression chromatin accessibility at single-cell resolution from gestation to adulthood. Integrative analyses define dynamic trajectories each type, revealing major reconfiguration prenatal-to-postnatal transition in all types followed continuous adulthood identifying...
LncRNAs have been shown to be direct players in chromatin regulation, but little is known about their role at active genomic loci. We investigate the of lncRNAs gene activation by profiling RNA interactome SMARCB1-containing SWI/SNF complexes proliferating and senescent conditions. The isolation SMARCB1-associated transcripts, together with profiling, shows prevalent association regions where SMARCB1 differentially binds locally transcribed RNAs. identify SWINGN, a lncRNA interacting...
Abstract Cells must coordinate the activation of thousands replication origins dispersed throughout their genome. Active transcription is known to favor formation mammalian origins, although role that RNA plays in this process remains unclear. We show ORC1 subunit human Origin Recognition Complex interacts with RNAs transcribed from genes start sites (TSSs), displaying a positive correlation between binding and origin activity. depletion, or use RNA-binding mutant, result inefficient...
ABSTRACT Besides the well-characterized protein network involved in replication stress response, several regulatory RNAs have been shown to play a role this critical process. However, it has remained elusive whether they act locally at stressed forks. Here, by investigating localizing on chromatin upon induced hydroxyurea, we identified set of lncRNAs upregulated S-phase and controlled transcription factors. Among them, demonstrate that previously uncharacterized lncRNA lncREST (long...
Abstract Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study single-cell (sc) level has been challenging due to less accurate annotation low compared protein-coding genes. To identify the important, albeit widely overlooked, specific lncRNAs from scRNA-seq data, here, we develop a computational framework, ELATUS, based on pseudoaligner Kallisto that...
Abstract Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding its impact on fully efficient remains limited. Here, through targeted CRISPR-knockout screen, we identify RNA-binding proteins modifiers that participate in p53 response. Among top hits, find m 6 A reader YTHDC1 as master regulator expression. binds transcription start sites TP53 other...
Long non-coding RNAs (lncRNAs) play fundamental roles in cellular processes and pathologies, regulating gene expression at multiple levels. Despite being highly cell type-specific, their study single-cell (sc) level is challenging due to less accurate annotation low compared protein-coding genes. Here, we systematically benchmark different preprocessing methods develop a computational framework, named ELATUS, based on the combination of pseudoaligner Kallisto with selective functional...
Abstract Whole tissue transcriptomic analyses have been helpful to characterize molecular subtypes of hepatocellular carcinoma (HCC). Metabolic human HCC defined, yet whether these different metabolic classes are clinically relevant or derive in actionable cancer vulnerabilities is still an unanswered question. Publicly available gene sets signatures used infer functional changes through set enrichment methods. However, metabolism-related poorly coexpressed when applied a biological context....
Whole-tissue transcriptomic analyses have been helpful to characterize molecular subtypes of hepatocellular carcinoma (HCC). Metabolic human HCC defined, yet whether these different metabolic classes are clinically relevant or derive in actionable cancer vulnerabilities is still an unanswered question. Publicly available gene sets signatures used infer functional changes through set enrichment methods. However, metabolism-related poorly co-expressed when applied a biological context. Here,...
Abstract Huntingtin-lowering strategies are central to therapeutic approaches for Huntington’s disease. Recent studies reported the induction of age- and cell type-specific phenotypes by conditional huntingtin knockout, but these experimental conditions did not precisely mimic huntingtin-lowering or gene-editing in terms cells targeted brain distribution, no transcriptional profiles were provided. Here, we used adeno-associated delivery system commonly CNS gene therapy programmes...
Despite the classical view of senescence as passive growth arrest, it is an active process with profound implications for cellular homeostasis. Senescent cells remain metabolically to be able cope energetic demand program, although precise mechanisms underlying this metabolic reprogramming are just beginning emerge. Here we have identified sin-lncRNA, a previously uncharacterized lncRNA, highly specific senescent cells, and transcriptionally induced by C/EBPβ, master regulator...
Cells have evolved a robust and highly regulated DNA damage response to preserve their genomic integrity. Although increasing evidence highlights the relevance of RNA regulation, our understanding its impact on fully efficient remains limited. Here, through targeted CRISPR-knockout screen, we identified binding proteins modifiers that participate in mediating p53 response. Among top hits, m6A reader YTHDC1 was as master regulator expression. binds transcription start sites TP53 other genes...
Abstract Cells must coordinate the activation of thousands replication origins dispersed throughout their genome. Active transcription is known to favor formation mammalian origins, although role that RNA plays in this process remains unclear. We show ORC1 subunit human Origin Recognition Complex interacts with RNAs transcribed from genes start sites (TSSs), displaying a positive correlation between binding and origin activity. depletion, or use RNA-binding mutant, result inefficient...