A5091149401- RNA Research and Splicing
- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Genetic diversity and population structure
- Genomics and Chromatin Dynamics
- Zebrafish Biomedical Research Applications
- Cancer-related molecular mechanisms research
- Developmental Biology and Gene Regulation
- Animal Genetics and Reproduction
- Chromosomal and Genetic Variations
- Retinal Development and Disorders
- Language and cultural evolution
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Neurobiology and Insect Physiology Research
- Physiological and biochemical adaptations
- Plant Reproductive Biology
- Photoreceptor and optogenetics research
- Genetic and Kidney Cyst Diseases
- Advanced Fluorescence Microscopy Techniques
- Insect behavior and control techniques
- Image Processing and 3D Reconstruction
- interferon and immune responses
- Plant Molecular Biology Research
- Research Data Management Practices
Centre for Genomic Regulation
2020-2025
Universitat Pompeu Fabra
2024-2025
Barcelona Institute for Science and Technology
2022
University of Turin
2017-2018
Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies plants have investigated AS response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, comprehensive study contrasting stress-response tissue-specific patterns directly comparing them with those animal models still missing. Results We...
Regulation of gene expression is arguably the main mechanism underlying phenotypic diversity tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 across 20 bilaterian species performed analyses using a symmetric phylogeny that allowed combined parallel investigation evolution vertebrates insects. We specifically focused on widely conserved ancestral genes, identifying strong cores pan-bilaterian tissue-specific genes even larger groups diverged...
Retinal photoreceptors have a distinct transcriptomic profile compared to other neuronal subtypes, likely reflecting their unique cellular morphology and function in the detection of light stimuli by way ciliary outer segment. We discovered layer this molecular specialization revealing that vertebrate retina expresses largest number tissue-enriched microexons all tissue types. A subset these is included exclusively photoreceptor transcripts, particularly genes involved cilia biogenesis...
Abstract Background Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan genome organization with vertebrates but lack their 2R whole-genome duplications developmental complexity. For these reasons, amphioxus frequently used as an outgroup to study vertebrate evolution Evo-Devo. Aside from duplications, genes continuously duplicate on smaller scale. Small-scale duplicated can be found in both genomes,...
Insects are capable of extraordinary feats long-distance movement that have profound impacts on the function terrestrial ecosystems. The ability to undertake these movements arose multiple times through evolution a suite traits make up migratory syndrome, however underlying genetic pathways involved remain poorly understood. Migratory hoverflies (Diptera: Syrphidae) an emerging model group for studies migration. They seasonal in huge numbers across large parts globe and important...
Microexons exhibit striking evolutionary conservation and are subject to precise, switch-like regulation in neurons, orchestrated by the splicing factors Srrm3 Srrm4 . Disruption of these regulators mice leads severe neurological phenotypes, their misregulation is linked human disease. However, specific microexons involved phenotypes effects individual microexon deletions on neurodevelopment, physiology, behavior remain poorly understood. To explore this, we generated zebrafish lines with 18...
Abstract Actin cytoskeleton dynamics is critical for nervous system development and function, yet the role of alternative splicing in controlling these processes poorly understood. A highly conserved subset neuronal-specific microexons coordinates fundamental aspects biology. exons enriched genes involved actin cytoskeleton, their functions are unknown. Here, we focus on a microexon DAAM1, member formin-homology-2 (FH2) domain class proteins, which have diverse associated with reorganization...
Abstract Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection exon homology relationships. Here, we present ExOrthist , a fully reproducible Nextflow -based software enabling inference homologs orthogroups, visualization evolution exon-intron structures, assessment conservation alternative splicing patterns. evaluates sequence considers surrounding context to derive...
Abstract Background Vertebrates and insects diverged approximately 700 million years ago, yet they retain a large core of conserved genes from their last common ancestor. These ancient present strong evolutionary constraints, which limit overall sequence expression divergence. However, these constraints can greatly vary across ancestral gene families and, in at least some cases, changes have functional consequences. Importantly, patterns divergence potential outcomes never been explored...
Abstract Regulation of gene expression is arguably the main mechanism contributing to tissue phenotypic diversity within and between species. Here, we assembled an extensive transcriptomic dataset covering twenty bilaterian species eight tissues, selecting a specular phylogeny that allowed both combined parallel investigation evolution vertebrates insects. We specifically focused on widely conserved ancestral genes, identifying strong cores pan-bilaterian tissue-specific genes even larger...
Microexons exhibit striking evolutionary conservation and are subject to precise, switch-like regulation in neurons, orchestrated by the splicing factors Srrm3 Srrm4 . Disruption of these regulators mice leads severe neurological phenotypes, their misregulation is linked human disease. However, specific microexons involved phenotypes effects individual microexon deletions on neurodevelopment, physiology, behavior remain poorly understood. To explore this, we generated zebrafish lines with 18...
Microexons exhibit striking evolutionary conservation and are subject to precise, switch-like regulation in neurons, orchestrated by the splicing factors Srrm3 Srrm4 . Disruption of these regulators mice leads severe neurological phenotypes, their misregulation is linked human disease. However, specific microexons involved phenotypes effects individual microexon deletions on neurodevelopment, physiology, behavior remain poorly understood. To explore this, we generated zebrafish lines with 18...
Abstract Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes among species. However, no existing tool allows the detection orthologous/paralogous exons. Here, we present ExOrthist , a fully reproducible Nextflow -based software enabling to (i) infer exon homologs orthogroups, (ii) visualize evolution exon-intron structures, (iii) assess conservation alternative splicing patterns. not only evaluates sequence but also considers...
ABSTRACT Retinal photoreceptors differ in their transcriptomic profiles from other neuronal subtypes, likely as a reflection of unique cellular morphology and function the detection light thorough ciliary outer segment. We discovered new layer this molecular specialization by revealing that vertebrate retina expresses largest number tissue-enriched microexons all tissue types. A subset these is included exclusively photoreceptor transcripts, particularly genes involved cilia biogenesis...
Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies plants have investigated AS response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, comprehensive study contrasting stress-response tissue-specific patterns directly comparing them with those animal models still missing. Results We...
Abstract Background Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan genome organization with vertebrates but lack their 2 R whole-genome duplications developmental complexity. For these reasons, amphioxus frequently used as an outgroup to study vertebrate evolution Evo-Devo. Aside from duplications, genes continuously duplicate on smaller scale. Small-scale duplicated can be found in both genomes,...
Abstract Genome expansion is believed to be an important driver of the evolution gene regulation. To investigate role newly arising sequence in rewiring regulatory network we estimated age each region human genome by applying maximum parsimony genome-wide alignments with 100 vertebrates. We then studied distribution several types functional regions, a focus on elements. The elements reveals extensive use formed genomic interactions. Many transcription factors have expanded their repertoire...