Evolution of tissue-specific expression of ancestral genes across vertebrates and insects.

Regulation of gene expression is arguably the main mechanism underlying the phenotypic diversity of tissues within and between species. Here we assembled an extensive transcriptomic dataset covering 8 tissues across 20 bilaterian species and performed analyses using a symmetric phylogeny that allowed the combined and parallel investigation of gene expression evolution between vertebrates and insects. We specifically focused on widely conserved ancestral genes, identifying strong cores of pan-bilaterian tissue-specific genes and even larger groups that diverged to define vertebrate and insect tissues. Systematic inferences of tissue-specificity gains and losses show that nearly half of all ancestral genes have been recruited into tissue-specific transcriptomes. This occurred during both ancient and, especially, recent bilaterian evolution, with several gains being associated with the emergence of unique phenotypes (for example, novel cell types). Such pervasive evolution of tissue specificity was linked to gene duplication coupled with expression specialization of one of the copies, revealing an unappreciated prolonged effect of whole-genome duplications on recent vertebrate evolution.

Health-Related Quality of Life in Mexican Children and Adolescents with Non-Syndromic Craniosynostosis.

OBJECTIVE: Assess the Health-Related Quality of Life in children and adolescents with non-syndromic craniosynostosis and compare it with participants without craniosynostosis. DESIGN: Non-experimental, cross-sectional design. SETTING: The assessment was done remotely and the instrument was sent via chat or email. PATIENTS/PARTICIPANTS: Participants (ages 8-17) with non-syndromic craniosynostosis (n = 27) and without craniosynostosis (n = 26). MAIN OUTCOME MEASURE(S): We used an adapted version for the Mexican population of the Health-Related Quality of Life Questionnaire for Children and Adolescents -KIDSCREEN-52. RESULTS: All scores were in the average clinical range and both groups scored similarly in all domains except those with craniosynostosis were significantly lower in the Social Support and Peers domain (rpb = 0.48). CONCLUSIONS: Children and adolescents with non-syndromic craniosynostosis reported similar Health-Related Quality of Life as the control group, except for the Social Support domain, which should be investigated in future studies.

Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads.

Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence whether or not an intron is spliced before its downstream neighbor, multiple questions related to adjacent introns' splicing order (AISO) remain unanswered. Here, we present Insplico, the first standalone software for quantifying AISO that works with both short and long read sequencing technologies. We first demonstrate its applicability and effectiveness using simulated reads and by recapitulating previously reported AISO patterns, which unveiled overlooked biases associated with long read sequencing. We next show that AISO around individual exons is remarkably constant across cell and tissue types and even upon major spliceosomal disruption, and it is evolutionarily conserved between human and mouse brains. We also establish a set of universal features associated with AISO patterns across various animal and plant species. Finally, we used Insplico to investigate AISO in the context of tissue-specific exons, particularly focusing on SRRM4-dependent microexons. We found that the majority of such microexons have non-canonical AISO, in which the downstream intron is spliced first, and we suggest two potential modes of SRRM4 regulation of microexons related to their AISO and various splicing-related features. Insplico is available on gitlab.com/aghr/insplico.

Fetal surgery for occipital encephalocele: A case report.

Background: Occipital encephalocele is a congenital defect of the neural tube at the level of the cranial midline, which results in herniation of meninges and brain tissue. The results of the management of myelomeningocele study determine the maternal and fetal risks for an open fetal surgery and have motivated the constant review of the concepts and strategies which the pediatric neurosurgeon can employ for the treatment of neural tube defects in the prenatal period. Case Description: We present a case of a female patient in utero of 26 gestational weeks with the diagnosis of an occipital encephalocele treated by open fetal surgery. During week 20 of gestation, the diagnosis of occipital encephalocele was made by ultrasound, which was corroborated by fetal magnetic resonance that showed cranial protrusion of neural and meningeal content in the occipital region, measuring 1.6 × 2.8 × 3.3 cm with an approximate volume of 7.7 cc through a bone defect of 6 mm. The closure of the defect was performed by the postnatal surgical technique adapted to the open fetal surgery. Later, the patient was born transabdominal with a 2.8 cm occipital wound, with suture points and approximated borders, normocephalic, without clinical signs of sepsis, hydrocephalus, or overt neurologic compromise. Conclusion: Open fetal surgery is a therapeutic option in the face of an isolated occipital encephalocele. This case report demonstrates the viability of the surgical procedure by the adaptation of a postnatal surgical technique to a prenatal surgery. Further studies are needed to evaluate the long-term functional results, comparing them with those seen in patients who undergo a postnatal procedure.

Mobile colistin resistance (MCR), extended-spectrum beta-lactamase (ESBL) and multidrug resistance monitoring in Escherichia coli (commensal and pathogenic) in pig farming: need of harmonized guidelines and clinical breakpoints.

Current data on antimicrobial resistance in pig production is essential for the follow-up strategic programs to eventually preserve the effectiveness of last-resort antibiotics for humans. Here, we characterized 106 Escherichia coli recovered in routine diagnosis (2020-2022) from fecal sample pigs, belonging to 74 Spanish industrial farms, affected by diarrhea. The analysis of virulence-gene targets associated with pathotypes of E. coli, determined 64 as pathogenic and 42 as commensal. Antimicrobial susceptibility testing (AST) performed by minimal inhibitory concentration (MIC) assay, was interpreted by applying breakpoints/cut-off values from the different standards EUCAST/TECOFF 2022, CLSI VET ED5:2020, and CASFM VET2020. Comparisons taking EUCAST as reference exhibited moderate to high correlation except for enrofloxacin, neomycin, and florfenicol. Of note, is the lack of clinical breakpoints for antibiotics of common use in veterinary medicine such as cefquinome, marbofloxacin, or florfenicol. AST results determined multidrug resistance (MDR) to ≥3 antimicrobial categories for 78.3% of the collection, without significant differences in commensal vs pathogenic isolates. Plasmid-mediated mobile colistin resistance gene (mcr) was present in 11.3% of 106 isolates, all of them pathogenic. This means a significant decrease compared to our previous data. Furthermore, 21.7% of the 106 E. coli were ESBL-producers, without differences between commensal and pathogenic isolates, and mcr/ESBL genes co-occurred in 3 isolates. Phylogenetic characterization showed a similar population structure (A, B1, C, D, and E), in both commensal and pathogenic E. coli, but with significant differences for B1, C, and E (38.1 vs 20.3%; 19 vs 1.6%; and 7.1 vs 25%, respectively). Additionally, we identified one B2 isolate of clone O4:H5-B2-ST12 (CH13-223), positive for the uropathogenic (UPEC) status, and in silico predicted as human pathogen. We suggest that a diagnosis workflow based on AST, detection of mcr and ESBL genes, and phylogenetic characterization, would be a useful monitoring tool under a "One-Health" perspective.

The Transcriptomic Landscape of Pediatric Astrocytoma.

Central nervous system tumors are the most common solid neoplasia during childhood and represent one of the leading causes of cancer-related mortality. Tumors arising from astrocytic cells (astrocytomas) are the most frequently diagnosed, and according to their histological and pathological characteristics, they are classified into four categories. However, an additional layer of molecular classification considering the DNA sequence of the tumorigenesis-associated genes IDH1/2 and H3F3A has recently been incorporated into the classification guidelines. Although mutations in H3F3A are found exclusively in a subtype of grade IV pediatric astrocytoma, mutations in IDH1/2 genes are very rare in children under 14 years of age. The transcriptomic profiles of astrocytoma in adults and children have been extensively studied. However, there is scarce information on these profiles in pediatric populations considering the status of tumorigenesis-associated genes. Therefore, here we report the transcriptomic landscape of the four grades of pediatric astrocytoma by RNA sequencing. We found several well-documented biological functions associated with the misregulated genes in the four grades of astrocytoma, as well as additional biological pathways. Among the four grades of astrocytoma, we found shared misregulated genes that could have implications in tumorigenesis. Finally, we identified a transcriptional signature for almost all grades of astrocytoma that could be used as a transcription-based identification method.

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals.

Alternative splicing increases neuronal transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal microexon program in Drosophila and compared it with that of mammals. In nonvertebrate bilaterians, this splicing program is restricted to neurons by the posttranscriptional processing of the enhancer of microexons (eMIC) domain in Srrm234. In Drosophila, this processing is dependent on regulation by Elav/Fne. eMIC deficiency or misexpression leads to widespread neurological alterations largely emerging from impaired neuronal activity, as revealed by a combination of neuronal imaging experiments and cell type-specific rescues. These defects are associated with the genome-wide skipping of short neural exons, which are strongly enriched in ion channels. We found no overlap of eMIC-regulated exons between flies and mice, illustrating how ancient posttranscriptional programs can evolve independently in different phyla to affect distinct cellular modules while maintaining cell-type specificity.

CroSR391 , an ortholog of the λ Cro repressor, plays a major role in suppressing polVR391 -dependent mutagenesis.

When subcloned into low-copy-number expression vectors, rumAB, encoding polVR391 (RumA'2 B), is best characterized as a potent mutator giving rise to high levels of spontaneous mutagenesis in vivo. This is in dramatic contrast to the poorly mutable phenotype when polVR391 is expressed from the native 88.5 kb R391, suggesting that R391 expresses cis-acting factors that suppress the expression and/or the activity of polVR391 . Indeed, we recently discovered that SetRR391 , an ortholog of λ cI repressor, is a transcriptional repressor of rumAB. Here, we report that CroSR391 , an ortholog of λ Cro, also serves as a potent transcriptional repressor of rumAB. Levels of RumA are dependent upon an interplay between SetRR391 and CroSR391 , with the greatest reduction of RumA protein levels observed in the absence of SetRR391 and the presence of CroSR391 . Under these conditions, CroSR391 completely abolishes the high levels of mutagenesis promoted by polVR391 expressed from low-copy-number plasmids. Furthermore, deletion of croSR391 on the native R391 results in a dramatic increase in mutagenesis, indicating that CroSR391 plays a major role in suppressing polVR391 mutagenesis in vivo. Inactivating mutations in CroSR391 therefore have the distinct possibility of increasing cellular mutagenesis that could lead to the evolution of antibiotic resistance of pathogenic bacteria harboring R391.

Silencing of SRRM4 suppresses microexon inclusion and promotes tumor growth across cancers.

RNA splicing is widely dysregulated in cancer, frequently due to altered expression or activity of splicing factors (SFs). Microexons are extremely small exons (3-27 nucleotides long) that are highly evolutionarily conserved and play critical roles in promoting neuronal differentiation and development. Inclusion of microexons in mRNA transcripts is mediated by the SF Serine/Arginine Repetitive Matrix 4 (SRRM4), whose expression is largely restricted to neural tissues. However, microexons have been largely overlooked in prior analyses of splicing in cancer, as their small size necessitates specialized computational approaches for their detection. Here, we demonstrate that despite having low expression in normal nonneural tissues, SRRM4 is further silenced in tumors, resulting in the suppression of normal microexon inclusion. Remarkably, SRRM4 is the most consistently silenced SF across all tumor types analyzed, implying a general advantage of microexon down-regulation in cancer independent of its tissue of origin. We show that this silencing is favorable for tumor growth, as decreased SRRM4 expression in tumors is correlated with an increase in mitotic gene expression, and up-regulation of SRRM4 in cancer cell lines dose-dependently inhibits proliferation in vitro and in a mouse xenograft model. Further, this proliferation inhibition is accompanied by induction of neural-like expression and splicing patterns in cancer cells, suggesting that SRRM4 expression shifts the cell state away from proliferation and toward differentiation. We therefore conclude that SRRM4 acts as a proliferation brake, and tumors gain a selective advantage by cutting off this brake.

Effects of the microtubule nucleator Mto1 on chromosomal movement, DNA repair, and sister chromatid cohesion in fission yeast.

Although the function of microtubules (MTs) in chromosomal segregation during mitosis is well characterized, much less is known about the role of MTs in chromosomal functions during interphase. In the fission yeast Schizosaccharomyces pombe, dynamic cytoplasmic MT bundles move chromosomes in an oscillatory manner during interphase via linkages through the nuclear envelope (NE) at the spindle pole body (SPB) and other sites. Mto1 is a cytoplasmic factor that mediates the nucleation and attachment of cytoplasmic MTs to the nucleus. Here, we test the function of these cytoplasmic MTs and Mto1 on DNA repair and recombination during interphase. We find that mto1Δ cells exhibit defects in DNA repair and homologous recombination (HR) and abnormal DNA repair factory dynamics. In these cells, sister chromatids are not properly paired, and binding of Rad21 cohesin subunit along chromosomal arms is reduced. Our findings suggest a model in which cytoplasmic MTs and Mto1 facilitate efficient DNA repair and HR by promoting dynamic chromosomal organization and cohesion in the nucleus.

Pediatric ependymoma: GNAO1, ASAH1, IMMT and IPO7 protein expression and 5-year prognosis correlation.

OBJECTIVE: The aim of this work was to evaluate a pediatric ependymoma protein expression that may be useful as a molecular biomarker candidate for prognosis, correlated with clinical features such as age, gender, histopathological grade, ependymal tumor recurrence and patient survival. PATIENTS AND METHODS: Immunohistochemistry assays were performed for GNAO1, ASAH1, IMMT, IPO7, Cyclin D1, P53 and Ki-67 proteins. Kaplan-Meier and Cox analysis were performed for age, gender, histopathological grade, relapse and survival correlation. RESULTS: We found that three proteins correlate with histopathological grade and relapse; two proteins correlate with survival; one protein does not correlate with any clinical feature. CONCLUSION: Our results suggest that, out of the proteins analyzed, five may be considered suitable prognostic biomarkers and one may be considered a predictive biomarker for response to treatment of pediatric ependymoma.

Srrm234, but not canonical SR and hnRNP proteins, drive inclusion of Dscam exon 9 variable exons.

Alternative splicing of pre-mRNA is a major mechanism to diversify protein functionality in metazoans from a limited number of genes. The Drosophila melanogaster Down syndrome cell adhesion molecule (Dscam) gene, which is important for neuronal wiring and phagocytosis of bacteria, can generate up to 38,016 isoforms by mutually exclusive alternative splicing in four clusters of variable exons. However, it is not understood how a specific exon is chosen from the many variables and how variable exons are prevented from being spliced together. A main role in the regulation of Dscam alternative splicing has been attributed to RNA binding proteins (RBPs), but how they impact on exon selection is not well understood. Serine-arginine rich (SR) proteins and hnRNP proteins are the two main types of RBPs with major roles in exon definition and splice site selection. Here, we analyzed the role of SR and hnRNP proteins in Dscam exon 9 alternative splicing in mutant Drosophila melanogaster embryos because of their essential function for development. Strikingly, loss or overexpression of canonical SR and hnRNP proteins even when multiple proteins are depleted together, does not affect Dscam alternative exon selection very dramatically. Conversely, noncanonical SR protein Serine-arginine repetitive matrix 2/3/4 (Srrm234) is a main determinant of exon inclusion in the Dscam exon 9 cluster. Since long-range base-pairings are absent in the exon 9 cluster, our data argue for a small complement of regulatory factors as main determinants of exon inclusion in the Dscam exon 9 cluster.

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons.

The mechanisms by which entire programmes of gene regulation emerged during evolution are poorly understood. Neuronal microexons represent the most conserved class of alternative splicing in vertebrates, and are critical for proper brain development and function. Here, we discover neural microexon programmes in non-vertebrate species and trace their origin to bilaterian ancestors through the emergence of a previously uncharacterized 'enhancer of microexons' (eMIC) protein domain. The eMIC domain originated as an alternative, neural-enriched splice isoform of the pan-eukaryotic Srrm2/SRm300 splicing factor gene, and subsequently became fixed in the vertebrate and neuronal-specific splicing regulator Srrm4/nSR100 and its paralogue Srrm3. Remarkably, the eMIC domain is necessary and sufficient for microexon splicing, and functions by interacting with the earliest components required for exon recognition. The emergence of a novel domain with restricted expression in the nervous system thus resulted in the evolution of splicing programmes that qualitatively expanded the neuronal molecular complexity in bilaterians.

Neurocirugía estereotáctica ablativa para trastorno neuroagresivo irreductible en pediátricos / Ablative stereotactic neurosurgery for irreducible neuroaggressive disorder in pediatric patients

Introducción y objetivos: El trastorno neuroagresivo irreductible (TNI) es una entidad bien descrita asociada con comportamiento impulsivo y agresivo. Es un dilema tanto para el tratamiento farmacológico como para el no farmacológico en la psiquiatría moderna, implicando un riesgo individual y social importante. A pesar de los avances en la terapia estereotáctica dirigida para TNI persiste una ausencia de información cuando se compara la eficacia de los diferentes blancos anatómicos validados. En el presente trabajo se describen los resultados quirúrgicos de los pacientes con TNI tratados con cirugía estereotáctica ablativa, con enfoque en los criterios de selección y métodos utilizados en nuestra institución. El objetivo es analizar la eficacia y seguridad de los diferentes blancos estereotácticos más utilizados para agresividad irreductible en niños. Materiales y métodos: Seleccionamos a 8 pacientes pediátricos con TNI bajo un estricto protocolo. Se les realizó electroencefalograma, videoelectroencefalograma y resonancia magnética previo a la cirugía. El síntoma neuroagresivo irreductible fue tratado con cirugía estereotáctica hacia los blancos cerebrales más descritos para agresividad, y posteriormente evaluado mediante la Overt Agressive Scale en el prequirúrgico y a los 6 meses de seguimiento, usando el test de Wilcoxon para el análisis estadístico. Resultados y conclusiones: La edad promedio de los pacientes fue de 13 años y 2 meses, 7 de los 8 pacientes incluidos tenían discapacidad intelectual, un paciente tenía secuelas neurológicas por síndrome de Dandy Walker y 7 pacientes no tenían alteraciones anatómicas preoperatorias. Después de la cirugía los pacientes mostraron mejoría en la escala Overt Agressive Scale con un promedio de 39,29% (p=0,0156), lo cual se encuentra dentro del rango descrito para TNI en adultos. Los resultados más satisfactorios tuvieron en común la inclusión del complejo nuclear amigdalino dentro de los blancos quirúrgicos. No hubo muertes ni secuelas permanentes atribuibles al procedimiento. La presente serie es la más grande descrita en la literatura hasta el momento para pacientes pediátricos con TNI tratados con ablación estereotáctica

Introduction and objectives: The irreducible neuroaggressive disorder (IND) is a well-described entity known to be associated with impulsive and aggressive behavior. While various studies have assessed available pharmacological and non-pharmacological treatment regimens, patients with IND continue to pose a major threat to themselves and society. While targeted stereotactic therapy for IND has gained traction in recent years, there is a paucity of information describing comparative effectiveness of different validated anatomic regions. In this paper, we discuss the surgical results for patients with IND following targeted lesional therapy with a special focus on selection criteria and operative methods. The objective is to analyze the efficacy and safety of the different described targets for this disorder in pediatric patients. Materials and methods: Eight pediatric patients met strict criteria for IND and were enrolled in this study. Electroencephalography (EEG), video electroencephalography (VEEG) and magnetic resonance imaging (MRI) were performed in all patients prior to surgery. Irreducible neuroagressive symptom was approached by lesional therapy based on most described targets for this disorder and assessed by The Overt Agressive Scale (OAS) pre-operatively and 6 months following surgery, using Wilcoxon test for statistical analysis. Results and conclusions: The average patient age was 13 years 2 months. 7 of the 8 patients enrolled had intellectual disabilities, 1 patient suffered neurologic sequelae referable to Dandy Walker syndrome and 7 patients had no preoperative anatomical alterations. Following surgery, patients with IND noted improvement in their OAS. On average, the OAS improved by 39.29% (P=.0156), a figure similar in comparison to studies assessing treatment of IND in adult patients. The most satisfactory results were achieved in patients whose ablative therapy involved the Amygdala in their targets. There were no deaths or permanent neurological deficits attributable to procedure. To the author's knowledge, this is the largest series described in the literature for pediatric patients with IND treated with lesional stereotactic therapy

Ablative stereotactic neurosurgery for irreducible neuroaggressive disorder in pediatric patients. / Neurocirugía estereotáctica ablativa para trastorno neuroagresivo irreductible en pediátricos.

INTRODUCTION AND OBJECTIVES: The irreducible neuroaggressive disorder (IND) is a well-described entity known to be associated with impulsive and aggressive behavior. While various studies have assessed available pharmacological and non-pharmacological treatment regimens, patients with IND continue to pose a major threat to themselves and society. While targeted stereotactic therapy for IND has gained traction in recent years, there is a paucity of information describing comparative effectiveness of different validated anatomic regions. In this paper, we discuss the surgical results for patients with IND following targeted lesional therapy with a special focus on selection criteria and operative methods. The objective is to analyze the efficacy and safety of the different described targets for this disorder in pediatric patients. MATERIALS AND METHODS: Eight pediatric patients met strict criteria for IND and were enrolled in this study. Electroencephalography (EEG), video electroencephalography (VEEG) and magnetic resonance imaging (MRI) were performed in all patients prior to surgery. Irreducible neuroagressive symptom was approached by lesional therapy based on most described targets for this disorder and assessed by The Overt Agressive Scale (OAS) pre-operatively and 6 months following surgery, using Wilcoxon test for statistical analysis. RESULTS AND CONCLUSIONS: The average patient age was 13 years 2 months. 7 of the 8 patients enrolled had intellectual disabilities, 1 patient suffered neurologic sequelae referable to Dandy Walker syndrome and 7 patients had no preoperative anatomical alterations. Following surgery, patients with IND noted improvement in their OAS. On average, the OAS improved by 39.29% (P=.0156), a figure similar in comparison to studies assessing treatment of IND in adult patients. The most satisfactory results were achieved in patients whose ablative therapy involved the Amygdala in their targets. There were no deaths or permanent neurological deficits attributable to procedure. To the author's knowledge, this is the largest series described in the literature for pediatric patients with IND treated with lesional stereotactic therapy.

A Rhamnose-Inducible System for Precise and Temporal Control of Gene Expression in Cyanobacteria.

Cyanobacteria are important for fundamental studies of photosynthesis and have great biotechnological potential. In order to better study and fully exploit these organisms, the limited repertoire of genetic tools and parts must be expanded. A small number of inducible promoters have been used in cyanobacteria, allowing dynamic external control of gene expression through the addition of specific inducer molecules. However, the inducible promoters used to date suffer from various drawbacks including toxicity of inducers, leaky expression in the absence of inducer and inducer photolability, the latter being particularly relevant to cyanobacteria, which, as photoautotrophs, are grown under light. Here we introduce the rhamnose-inducible rhaBAD promoter of Escherichia coli into the model freshwater cyanobacterium Synechocystis sp. PCC 6803 and demonstrate it has superior properties to previously reported cyanobacterial inducible promoter systems, such as a non-toxic, photostable, non-metabolizable inducer, a linear response to inducer concentration and crucially no basal transcription in the absence of inducer.

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes.

Epithelial-mesenchymal interactions are crucial for the development of numerous animal structures. Thus, unraveling how molecular tools are recruited in different lineages to control interplays between these tissues is key to understanding morphogenetic evolution. Here, we study Esrp genes, which regulate extensive splicing programs and are essential for mammalian organogenesis. We find that Esrp homologs have been independently recruited for the development of multiple structures across deuterostomes. Although Esrp is involved in a wide variety of ontogenetic processes, our results suggest ancient roles in non-neural ectoderm and regulating specific mesenchymal-to-epithelial transitions in deuterostome ancestors. However, consistent with the extensive rewiring of Esrp-dependent splicing programs between phyla, most developmental defects observed in vertebrate mutants are related to other types of morphogenetic processes. This is likely connected to the origin of an event in Fgfr, which was recruited as an Esrp target in stem chordates and subsequently co-opted into the development of many novel traits in vertebrates.

An Efficient FLP-Based Toolkit for Spatiotemporal Control of Gene Expression in Caenorhabditis elegans.

Site-specific recombinases are potent tools to regulate gene expression. In particular, the Cre (cyclization recombination) and FLP (flipase) enzymes are widely used to either activate or inactivate genes in a precise spatiotemporal manner. Both recombinases work efficiently in the popular model organism Caenorhabditis elegans, but their use in this nematode is still only sporadic. To increase the utility of the FLP system in C. elegans, we have generated a series of single-copy transgenic strains that stably express an optimized version of FLP in specific tissues or by heat induction. We show that recombination efficiencies reach 100% in several cell types, such as muscles, intestine, and serotonin-producing neurons. Moreover, we demonstrate that most promoters drive recombination exclusively in the expected tissues. As examples of the potentials of the FLP lines, we describe novel tools for induced cell ablation by expression of the PEEL-1 toxin and a versatile FLP-out cassette for generation of GFP-tagged conditional knockout alleles. Together with other recombinase-based reagents created by the C. elegans community, this toolkit increases the possibilities for detailed analyses of specific biological processes at developmental stages inside intact animals.

Major Roles for Pyrimidine Dimers, Nucleotide Excision Repair, and ATR in the Alternative Splicing Response to UV Irradiation.

We have previously found that UV irradiation promotes RNA polymerase II (RNAPII) hyperphosphorylation and subsequent changes in alternative splicing (AS). We show now that UV-induced DNA damage is not only necessary but sufficient to trigger the AS response and that photolyase-mediated removal of the most abundant class of pyrimidine dimers (PDs) abrogates the global response to UV. We demonstrate that, in keratinocytes, RNAPII is the target, but not a sensor, of the signaling cascade initiated by PDs. The UV effect is enhanced by inhibition of gap-filling DNA synthesis, the last step in the nucleotide excision repair pathway (NER), and reduced by the absence of XPE, the main NER sensor of PDs. The mechanism involves activation of the protein kinase ATR that mediates the UV-induced RNAPII hyperphosphorylation. Our results define the sequence UV-PDs-NER-ATR-RNAPII-AS as a pathway linking DNA damage repair to the control of both RNAPII phosphorylation and AS regulation.