A5085584582- RNA Research and Splicing
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Phylogenetic Studies
- Plant Molecular Biology Research
- Chromosomal and Genetic Variations
- Molecular Biology Techniques and Applications
- Plant Reproductive Biology
- Genetic Neurodegenerative Diseases
- Fungal and yeast genetics research
- Genetic diversity and population structure
- Developmental Biology and Gene Regulation
- Language and cultural evolution
- DNA Repair Mechanisms
- Protist diversity and phylogeny
- Mitochondrial Function and Pathology
- interferon and immune responses
- Evolution and Paleontology Studies
- Image Processing and 3D Reconstruction
- Genetics, Aging, and Longevity in Model Organisms
- Signaling Pathways in Disease
- Cancer-related gene regulation
- Legume Nitrogen Fixing Symbiosis
- Research Data Management Practices
- Neurogenetic and Muscular Disorders Research
Max Perutz Labs
2012-2025
Centre for Genomic Regulation
2016-2024
Barcelona Institute for Science and Technology
2017-2021
Universitat Pompeu Fabra
2017
Medical University of Vienna
2012-2016
Universidad Nacional Autónoma de México
2010-2011
University of Veterinary Medicine Vienna
2011
Alternative splicing (AS) is a key regulatory mechanism that contributes to transcriptome and proteome diversity. As very few genome-wide studies analyzing AS in plants are available, we have performed high-throughput sequencing of normalized cDNA library which resulted high coverage map Arabidopsis . We detect ∼150,000 splice junctions derived mostly from typical plant introns, including an eightfold increase the number U12 introns (2069). Around 61% multiexonic genes alternatively spliced...
Alternative splicing (AS) coupled to nonsense-mediated decay (NMD) is a post-transcriptional mechanism for regulating gene expression. We have used high-resolution AS RT–PCR panel identify endogenous isoforms which increase in abundance when NMD impaired the Arabidopsis factor mutants, upf1-5 and upf3-1 . Of 270 genes (950 transcripts) on panel, 102 transcripts from 97 (32%) were identified as targets. Extrapolating these data around 13% of intron-containing genome are potentially regulated...
Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, programs regulated remain to be identified. To address these challenges, we describe Vertebrate Splicing Transcription Database (VastDB), largest resource genome-wide, quantitative profiles assembled date. VastDB provides readily accessible information on inclusion levels functional associations detected RNA-seq data from diverse vertebrate...
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...
Alternative splicing generates multiple transcript and protein isoforms from the same gene thus is important in expression regulation. To date, RNA-sequencing (RNA-seq) standard method for quantifying changes alternative on a genome-wide scale. Understanding current limitations of RNA-seq crucial reliable analysis lack high quality, comprehensive transcriptomes most species, including model organisms such as Arabidopsis, major constraint accurate quantification isoforms. address this, we...
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...
Alternative splicing (AS) diversifies transcriptomes and proteomes is widely recognized as a key mechanism for regulating gene expression. Previously, in an analysis of intron retention events Arabidopsis , we found unusual AS inside annotated protein-coding exons. Here, also identify such human use these two sets to analyse their features, regulation, functional impact, evolutionary origin. As involve introns with features both exons, name them exitrons ( ex onic i n trons ). Though were...
Abstract The causes and consequences of genome reduction in animals are unclear because our understanding this process mostly relies on lineages with often exceptionally high rates evolution. Here, we decode the compact 73.8-megabase Dimorphilus gyrociliatus , a meiobenthic segmented worm. D. retains traits classically associated larger slower-evolving genomes, such as an ordered, intact Hox cluster, generally conserved developmental toolkit traces ancestral bilaterian linkage. Unlike some...
Accurate and comprehensive annotation of transcript sequences is essential for quantification differential gene expression analysis. Single-molecule long-read sequencing technologies provide improved integrity structures including alternative splicing, transcription start polyadenylation sites. However, accuracy significantly affected by errors, mRNA degradation, or incomplete cDNA synthesis.We present a new Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over...
Correction of mis-splicing events is a growing therapeutic approach for neurological diseases such as spinal muscular atrophy or neuronal ceroid lipofuscinosis 7, which are caused by splicing-affecting mutations. Mis-spliced effector genes that do not harbour mutations also good candidate targets in with more complex aetiologies cancer, autism, dystrophies neurodegenerative diseases. Next-generation RNA sequencing (RNA-seq) has boosted investigation global diseased tissue to identify key...
Summary RNA ‐sequencing ( ‐seq) allows global gene expression analysis at the individual transcript level. Accurate quantification of variants generated by alternative splicing AS ) remains a challenge. We have developed comprehensive, nonredundant Arabidopsis reference dataset (At RTD containing over 74 000 transcripts for use with algorithms to quantify isoforms in ‐seq. The At was formed merging from TAIR 10 and novel identified an discovery project. estimated abundance ‐seq data using...
Transcript annotation in plant databases is incomplete and often inaccurate, leading to misinterpretation. As more RNA-seq data are generated, scientists need be aware of potential pitfalls understand the nature impact specific alternative splicing transcripts on protein production. A primary area concern topic this article (mis)annotation open reading frames premature termination codons. The basic message that adequately address expression functions transcript isoforms, it necessary able...
Abstract Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools recruited in different lineages to control interplays between these tissues is key understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and essential mammalian organogenesis. We find that homologs have been independently multiple structures across deuterostomes. Although involved a wide variety...
AtCyp59 is a multidomain cyclophilin containing peptidyl-prolyl cis/trans isomerase (PPIase) domain and an evolutionarily highly conserved RRM domain. Deregulation of this class cyclophilins has been shown to affect transcription influence phosphorylation the C-terminal repeat largest subunit RNA polymerase II. We used genomic SELEX method for identifying targets AtCyp59. Analysis selected RNAs revealed RNA-binding motif (G[U/C]N[G/A]CC[A/G]) we show that it conserved. Binding was verified...
Summary Alternative splicing is essential for plants, enabling a single gene to produce multiple transcript variants boost functional diversity and fine‐tune responses environmental developmental cues. Arabidopsis thaliana At‐RS31, plant‐specific factor in the Serine/Arginine‐rich (SR) protein family, responds light Target of Rapamycin (TOR) signalling pathway, yet its downstream targets regulatory impact remain unknown. To identify At‐RS31 targets, we applied individual‐nucleotide...
The formation of RNA–DNA hybrids, referred to as R-loops, can promote genome instability and cancer development. Yet the mechanisms by which R-loops compromise are poorly understood. Here, we establish roles for evolutionarily conserved Nrl1 protein in pre-mRNA splicing regulation, R-loop suppression maintaining stability. nrl1Δ mutants exhibit endogenous DNA damage, sensitive exogenous have defects homologous recombination (HR) repair. Concomitantly, cells display significant changes gene...
Abstract Background The legume-rhizobium symbiosis requires the formation of root nodules, specialized organs where nitrogen fixation process takes place. Nodule development is accompanied by induction specific plant genes, referred to as nodulin genes. Important roles in processes such morphogenesis and metabolism have been assigned nodulins during symbiosis. Results Here we report purification biochemical characterization a novel from common bean ( Phaseolus vulgaris L.) nodules. This...
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...
Identical sequences with a minimal length of about 300 base pairs (bp) have been involved in the generation various meiotic/mitotic genomic rearrangements through non-allelic homologous recombination (NAHR) events. Genomic disorders and structural variation, together gene remodelling processes associated many these rearrangements. Based on observations, we identified integrated all 100% identical repeats at least bp NCBI version 36.2 human genome reference assembly into non-overlapping...
Abstract Background Alternative splicing is the major post-transcriptional mechanism by which gene expression regulated and affects a wide range of processes responses in most eukaryotic organisms. RNA-sequencing (RNA-seq) can generate genome-wide quantification individual transcript isoforms to identify changes alternative splicing. RNA-seq an essential modern tool but its ability accurately quantify depends on diversity, completeness quality information. Results We have developed new...
Summary The causes and consequences of genome reduction in animals are unclear, because our understanding this process mostly relies on lineages with often exceptionally high rates evolution. Here, we decode the compact 73.8 Mb Dimorphilus gyrociliatus , a meiobenthic segmented worm. D. retains traits classically associated larger slower-evolving genomes, such as an ordered, intact Hox cluster, generally conserved developmental toolkit, traces ancestral bilaterian linkage. Unlike some other...