Manuel Irimia

The paper compares tissue-specific alternative splicing and gene expression across species to show they follow distinct evolutionary routes in repurposing ancestral genes, with TS-AS playing a key role in nervous system diversification.

This study defines the post-transcriptional RNA splicing landscape in fully grown mouse oocytes and identifies splicing events and regulatory programs essential for meiotic progression and oocyte division.

The paper investigates ZGA timing across 61 animal species and finds that genome size to cytoplasm volume ratio predicts ZGA onset.

This study identifies eukaryotic retrotransposons that encode prokaryotic-like DNA adenine methyltransferases and shows their adaptation to host 6mA-associated chromatin.

The paper uses RNA-seq and spatial transcriptomics in zebra finches to study the role of the germline-restricted chromosome (GRC) in germ cell development, identifying its involvement in oocyte maturation and gene expression regulation.

The paper investigates the phenotypic impact of individual conserved neuronal microexons and their regulators in zebrafish, finding that microexon deletions have mild effects while Srrm3/4 loss causes severe neurodevelopmental and behavioral changes.

This study identifies senescent cells as resembling developmental signaling centers by showing their SASP activates conserved developmental pathways across species.

The paper analyzes sequence and expression divergence of 7,000 conserved genes across vertebrates and insects to identify patterns of molecular diversification and lineage-specific evolution.

The paper identifies core splicing architecture and length constraints as factors determining microexon sensitivity to SRRM3/4 across vertebrates.

The paper investigates how arboviruses like chikungunya virus maintain persistent infections in mosquito cells through translational repression of viral RNA without affecting host cell fitness.

This study shows that srrm3 regulates arousal states in zebrafish via cAMP signaling, with mutations causing hyperarousal and transcriptional changes.

The paper identifies E93 as a repressor of broad (br) to enable adult differentiation in Drosophila by preventing premature activation of pupal-specific enhancers.

The paper investigates the evolution of tissue-specific gene expression across vertebrates and insects, finding that nearly half of ancestral genes have been recruited into tissue-specific transcriptomes.

The paper identifies an alternative splicing event in SUZ12 that generates two PRC2 subtypes, SUZ12-S and SUZ12-L, with distinct roles in PRC2 function and H3K27 methylation.

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

Insplico quantifies intron splicing order using short and long RNA-seq reads, revealing conserved patterns and novel features across species and tissues.

This study investigates the behavioral effects of rbfox1 deficiency in zebrafish, finding multiple behavioral changes that resemble those in Rbfox1-deficient mice and psychiatric patients.

The paper investigates day-night and seasonal gene expression variation across human tissues using GTEx data, finding unique patterns in different tissues and conserved clock gene differences across species.

The paper identifies splicing QTLs in human pancreatic islets that contribute to type 2 diabetes susceptibility by affecting gene splicing and revealing novel molecular mechanisms.

The paper identifies Srrm3-dependent microexons as critical for photoreceptor function and vision, showing their role in outer segment maintenance and their loss leading to blindness.

The paper identifies a microexon program in pancreatic islets regulated by SRRM3, which affects insulin secretion and is linked to type 2 diabetes risk.

The paper identifies a splicing program in neurons of Drosophila and mammals, showing how it evolves independently in different species to regulate ion channels and neuronal activity.

ExOrthist infers exon orthologies across species by analyzing exon sequences and their surrounding intron context, enabling analysis at any evolutionary distance.

This study shows environmental enrichment alters chromatin structure, transcription factor binding, and 3D genome organization in mice, affecting cognitive function and gene regulation.

The paper introduces ACME, a cell fixation-dissociation method for single-cell transcriptomics that preserves RNA integrity and enables cryopreservation and sorting, validated with SPLiT-seq in planarians.

The paper shows that during zygotic genome activation, embryos exhibit temporary splicing failures in DNA damage response genes, regulated by Snrpb and Snrpd2, which reduce DNA damage response.

The paper decodes the compact genome of Dimorphilus gyrociliatus, revealing a conservative route to genome compaction with features similar to vertebrates.

The paper identifies HD-specific mis-splicing using intersect-RNA-seq in human and mouse models, revealing pathogenic splicing factors and effector genes.

The paper identifies Srrm234 as a key regulator of Dscam exon 9 alternative splicing, showing that canonical SR and hnRNP proteins have minimal impact on this process.