A5041402608- Genomics and Chromatin Dynamics
- Developmental Biology and Gene Regulation
- Epigenetics and DNA Methylation
- Chromosomal and Genetic Variations
- Congenital heart defects research
- RNA Research and Splicing
- Genomics and Phylogenetic Studies
- Animal Genetics and Reproduction
- Cancer-related Molecular Pathways
- Single-cell and spatial transcriptomics
- RNA modifications and cancer
- Retinal Development and Disorders
- interferon and immune responses
- Protist diversity and phylogeny
- Genetic and Kidney Cyst Diseases
- Genetics, Aging, and Longevity in Model Organisms
- IL-33, ST2, and ILC Pathways
- Cancer-related gene regulation
- Pancreatic function and diabetes
- Cancer Research and Treatments
- MicroRNA in disease regulation
- Asthma and respiratory diseases
- Renal and related cancers
- Cancer-related molecular mechanisms research
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
Centro Andaluz de Biología del Desarrollo
2016-2025
Universidad Pablo de Olavide
2016-2025
Junta de Andalucía
2016-2025
Consejo Superior de Investigaciones Científicas
2015-2024
Hospital General Mateu Orfila
2022
University of Geneva
2022
Weatherford College
2020
University of Chicago
2012
Universidad de Sevilla
2004-2009
Spanish Foundation for Science and Technology
2003
Vertebrates have greatly elaborated the basic chordate body plan and evolved highly distinctive genomes that been sculpted by two whole-genome duplications. Here we sequence genome of Mediterranean amphioxus (Branchiostoma lanceolatum) characterize DNA methylation, chromatin accessibility, histone modifications transcriptomes across multiple developmental stages adult tissues to investigate evolution regulation genome. Comparisons with vertebrates identify an intermediate stage in...
The generation of distinctive cell types that form different tissues and organs requires precise, temporal spatial control gene expression. This depends on specific cis -regulatory elements distributed in the noncoding DNA surrounding their target genes. Studies performed mammalian embryonic stem cells Drosophila embryos suggest active enhancers part a defined chromatin landscape marked by histone H3 lysine 4 mono-methylation (H3K4me1) 27 acetylation (H3K27ac). Nevertheless, little is known...
Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate origin phenotypic innovation by developing little skate Leucoraja erinacea as a genomically enabled model. Analysis high-quality chromosome-scale genome sequence for shows that it preserves many ancestral jawed vertebrate compared with other sequenced genomes,...
Recent studies of the genome architecture vertebrates have uncovered two unforeseen aspects its organization. First, large regions genome, called gene deserts, are devoid protein-coding sequences and no obvious biological role. Second, comparative genomics has highlighted existence an array highly conserved non-coding (HCNRs) in all vertebrates. Most surprisingly, these structural features strongly associated with genes that essential functions during development. Among these, vertebrate...
Heterozygous mutations in p63 are associated with split hand/foot malformations (SHFM), orofacial clefting, and ectodermal abnormalities. Elucidation of the gene network that includes target genes regulatory elements may reveal new for other malformation disorders. We performed genome-wide DNA-binding profiling by chromatin immunoprecipitation (ChIP), followed deep sequencing (ChIP-seq) primary human keratinocytes, identified potential controlled p63. show binds to an enhancer element SHFM1...
Abstract The identification and characterization of the regulatory activity genomic sequences is crucial for understanding how information contained in genomes translated into cellular function. cis ‐regulatory control when, where, much genes are transcribed can activate (enhancers) or repress (silencers) gene expression. Here, we describe a novel Tol2 transposon‐based vector assessing enhancer zebrafish ( Danio rerio ). This Zebrafish Enhancer Detector (ZED) harbors several key...
Significance Mammalian chromatin is compartmentalized in topologically associating domains (TADs), genomic regions within which sequences preferentially contact each other. This organization has been proposed to be essential organize the regulatory information contained mammalian genomes. We show that Six homeobox genes, developmental regulators organized gene clusters across different animal phyla, share a deeply conserved formed by two abutting TADs predates Cambrian explosion. required...
The order of genes in eukaryotic genomes has generally been assumed to be neutral, since gene is largely scrambled over evolutionary time. Only a handful exceptional examples are known, typically involving deeply conserved clusters tandemly duplicated (e.g., Hox and histones). Here we report the first systematic survey microsynteny conservation across metazoans, utilizing 17 genome sequences. We identified nearly 600 pairs unrelated that have remained tightly physically linked diverse...
Significance The fossil record shows that the wrist and digits have an aquatic origin, becoming recognizable in a group of (mostly extinct) fish contained robust fins. Do fins living fishes equivalent these structures? Because comparisons fin limb morphology been inconclusive, we sought to investigate this question using developmental molecular data. By utilizing nonmodel (the spotted gar), find regulatory networks control “wrist digit”-building genes ( Hox ) are deeply conserved between...
Genome-wide association studies (GWAS) identified the MEIS1 locus for Restless Legs Syndrome (RLS), but causal single nucleotide polymorphisms (SNPs) and their functional relevance remain unknown. This contains a large number of highly conserved noncoding regions (HCNRs) potentially functioning as cis -regulatory modules. We analyzed these HCNRs allele-dependent enhancer activity in zebrafish mice found that risk allele lead SNP rs12469063 reduces Meis1 expression domain murine embryonic...
Abstract Coordinated chromatin interactions between enhancers and promoters are critical for gene regulation. The architectural protein CTCF mediates looping is enriched at the boundaries of topologically associating domains (TADs), which sub-megabase structures. In vitro depletion leads to a loss TADs but has only limited effects over expression, challenging concept that CTCF-mediated structures fundamental requirement However, how perturbed structure impacts expression during development...
Deuterostomes are a monophyletic group of animals that includes Hemichordata, Echinodermata (together called Ambulacraria), and Chordata. The diversity deuterostome body plans has made it challenging to reconstruct their ancestral condition decipher the genetic changes drove diversification lineages. Here, we generate chromosome-level genome assemblies 2 hemichordate species, Ptychodera flava Schizocardium californicum , use comparative genomic approaches infer chromosomal architecture...
Neurotrophins, as target-derived factors, are essential for neuronal survival during development, but adulthood, their scope of actions widens to become also mediators synaptic and morphological plasticity. Target disconnection by axotomy produces an initial stripping ensued rearrangement upon target reinnervation. Using abducens motoneurons the oculomotor system a model axotomy, we report that trophic support brain-derived neurotrophic factor (BDNF), neurotrophin-3 (NT-3) or mixture both,...
Cardiac progenitors are specified early in development and progressively differentiate mature into fully functional cardiomyocytes. This process is controlled by an extensively studied transcriptional program. However, the regulatory events coordinating progression of such program from to maturation largely unknown. Here, we show that genome organizer CTCF essential for cardiogenesis it mediates genomic interactions coordinate cardiomyocyte differentiation developing heart. Inactivation Ctcf...
Human malaria is a devastating disease and major cause of poverty in resource-limited countries. To develop adapt within hosts Plasmodium falciparum undergoes drastic switches gene expression. identify regulatory regions the parasite genome, we performed genome-wide profiling chromatin accessibility two culture-adapted isogenic subclones at four developmental stages during intraerythrocytic cycle by using Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq). Tn5 transposase...