Resultados de investigación

Expression profiling by high throughput sequencing, We dissected hippocampus from WT and Daam1-MIC_KO adult mice and perform RNA-seq, To investigate the impact of Daam1 microexon removal on hippocampal function, we have generated RNA-seq data from adult male mice. Actin cytoskeleton dynamics is crucial for neurogenesis and neuronal function. Precise quantitative and qualitative regulation of actin polymerization is achieved by multiple actin-binding proteins, among which formins are particularly versatile. Here, we investigate how neuronal-specific splicing expands formin's functional diversity in the brain. We uncovered a highly conserved microexon in DAAM1 that extends the linker region of its FH2 domain, leading to remarkable changes in actin polymerization rates and structure. Microexon deletion causes neuritogenesis defects and increased calcium influx in in vitro differentiated mouse neurons, and mice carrying this deletion exhibit deficient long-term memory formation. These memory defects were associated with higher activity of DAAM1's interactor RhoA, increased ARC protein levels, postsynaptic deficiencies, fewer dendritic spines and impaired long-term potentiation. In summary, precise post-transcriptional regulation of DAAM1's FH2 domain is a novel mechanism for modulating actin polymerization in neural spinesneurons and is essential for proper brain function., Peer reviewed

Sampled and measured for AMS using the KLY-3S Kappabridge (AGICO, Czech Republic) and processed with the Anisoft 5.1.01 software (Chadima et al., 2018)., This study was funded by Project UKRIA-4D (PID2019-104693GB-I00) of the Spanish Ministry of Science and Innovation,, Peer reviewed

Sampling, stepwise demagnetization and measurement of the natural remanent magnetization. - Methods for processing the data: Characteristic components directions (ChRM) were calculated by principal component analyses (PCA, Kirschvink, 1980) after they were identified through visual inspection of orthogonal demagnetization plots (Zijderveld, 1967) using the VPD software (Ramón et al., 2017)., Peer reviewed

Kdm1af/f, Kdm5cf/f and CamKIIα-CreERT2 mouse strains have been previously described , they are available at public repositories (Jackson Lab stock #23969; MMRRC stock 066789-UCD; and EMMA EM:02125, respectively). Mice were maintained on a C57BL/6J genetic background. The recombinant protein CreERT2 is dependent on tamoxifen (TMX) administration, and its expression is restricted to principal neurons of the forebrain, where CamKIIα is expressed. CaMKIIα–driven, TMX induced Cre recombination results in the elimination of exons 5 and 6 in Kdm1af/f and exons 11 and 12 in Kdm5cf/f . Mice were 2 to 3-month-old at the time of TMX administration., Loss or reduced expression of lysine demethylases (KDMs) is linked to neurodevelopmental disorders and intellectual disability. Given the phenotypic similarities between KDM1A and KDM5C deficient mice, and the convergence of both enzymes in maintaining a repressive state via H3K4 demethylation, we examined their functional interaction using double-inducible, forebrain-specific knockouts (dKDM-ifKOs). These mice showed transcriptional and epigenetic dysregulation beyond the additive effects of individual knockouts, including stronger ectopic expression of non-neuronal genes in hippocampal neurons. Thousands of de novo H3K4me3-enriched regions emerged, indicating synergistic disruption of chromatin regulation. In line with these molecular changes, dKDM-ifKOs displayed more severe behavioral impairments than the single ifKOs, along with altered hippocampal expression of ion channels and increased excitability of CA1 pyramidal neurons. These findings underscore the joint role of ID-linked KDMs in regulating cell-type-specific gene silencing and H3K4 methylation levels to safeguard neuronal identity and responsiveness, as well as cognitive function, Peer reviewed

Kdm1af/f, Kdm5cf/f and CamKIIα-CreERT2 mouse strains have been previously described , they are available at public repositories (Jackson Lab stock #23969; MMRRC stock 066789-UCD; and EMMA EM:02125, respectively). Mice were maintained on a C57BL/6J genetic background. The recombinant protein CreERT2 is dependent on tamoxifen (TMX) administration, and its expression is restricted to principal neurons of the forebrain, where CamKIIα is expressed. CaMKIIα–driven, TMX induced Cre recombination results in the elimination of exons 5 and 6 in Kdm1af/f and exons 11 and 12 in Kdm5cf/f . Mice were 2 to 3-month-old at the time of TMX administration., Loss or reduced expression of lysine demethylases (KDMs) is linked to neurodevelopmental disorders and intellectual disability. Given the phenotypic similarities between KDM1A and KDM5C deficient mice, and the convergence of both enzymes in maintaining a repressive state via H3K4 demethylation, we examined their functional interaction using double-inducible, forebrain-specific knockouts (dKDM-ifKOs). These mice showed transcriptional and epigenetic dysregulation beyond the additive effects of individual knockouts, including stronger ectopic expression of non-neuronal genes in hippocampal neurons. Thousands of de novo H3K4me3-enriched regions emerged, indicating synergistic disruption of chromatin regulation. In line with these molecular changes, dKDM-ifKOs displayed more severe behavioral impairments than the single ifKOs, along with altered hippocampal expression of ion channels and increased excitability of CA1 pyramidal neurons. These findings underscore the joint role of ID-linked KDMs in regulating cell-type-specific gene silencing and H3K4 methylation levels to safeguard neuronal identity and responsiveness, as well as cognitive function, Peer reviewed

Kdm5cf/f, and CamKIIα-CreERT2 mouse strains are available at public repositories (MMRRC stock 066789-UCD; and EMMA EM:02125, respectively). Mice were maintained on a C57BL/6J genetic background. The recombinant protein CreERT2 is dependent on tamoxifen (TMX) administration, and its expression is restricted to principal neurons of the forebrain, where CamKIIα is expressed. CaMKIIα–driven, TMX induced Cre recombination results in the elimination of exons 11 and 12 in Kdm5cf/f . Mice were 2 to 3-month-old at the time of TMX administration., Loss or reduced expression of lysine demethylases (KDMs) is linked to neurodevelopmental disorders and intellectual disability. Given the phenotypic similarities between KDM1A and KDM5C deficient mice, and the convergence of both enzymes in maintaining a repressive state via H3K4 demethylation, we examined their functional interaction using double-inducible, forebrain-specific knockouts (dKDM-ifKOs). These mice showed transcriptional and epigenetic dysregulation beyond the additive effects of individual knockouts, including stronger ectopic expression of non-neuronal genes in hippocampal neurons. Thousands of de novo H3K4me3-enriched regions emerged, indicating synergistic disruption of chromatin regulation. In line with these molecular changes, dKDM-ifKOs displayed more severe behavioral impairments than the single ifKOs, along with altered hippocampal expression of ion channels and increased excitability of CA1 pyramidal neurons. These findings underscore the joint role of ID-linked KDMs in regulating cell-type-specific gene silencing and H3K4 methylation levels to safeguard neuronal identity and responsiveness, as well as cognitive function, Peer reviewed

The study included a total of 39 blood samples, comprising 23 from de novo, drug-naïve Parkinson’s disease (PD) patients and 16 from healthy, age- and sex-matched controls. Following quality control assessments, one sample was excluded due to failing labeling control thresholds, resulting in a final dataset of 38 samples. Each patient represented a biological replicate. Peripheral Blood Mononuclear Cells (PBMCs) were isolated, and RNA was extracted and assessed for integrity before transcriptome analysis using the Clariom S Array (Affymetrix). Data preprocessing involved normalization and filtering, leading to a final dataset of 18,091 probes. -- Expression profiling by array, This study investigated gene expression differences in Parkinson’s disease (PD) using blood samples from 23 newly diagnosed, drug-naïve PD patients and 16 healthy controls recruited from two hospitals in Spain. Participants met diagnostic criteria for early-stage PD (Hoehn and Yahr I-II) and had no family history of the disease. Ethical approval and informed consent were obtained. Peripheral Blood Mononuclear Cells (PBMCs) were isolated, frozen, and processed for RNA extraction. RNA integrity was assessed before whole transcriptome analysis using the Clariom S Array (Affymetrix). Data processing was conducted in R using BioConductor packages. Quality control measures led to the exclusion of one sample, and data were normalized using Robust Multi-array Average (RMA). Lowly expressed genes and probes not mapping to known genes were filtered out, resulting in 38 samples with 18,091 probes, Peer reviewed

Peer reviewed

Experiment type: Expression profiling by high throughput sequencing. -- Total RNA was obtained from three biological replicates corresponding to i) parental cell lines (bloodstream S16 or procyclic 449), or ii) cell lines in which DRBD3 was depleted by RNAi (bloodstream and procyclic). In addition, three biological replicates from a bloodstream cell line in which ZC3H41 was depleted by RNAi was included as a control. -- Organism: Trypanosoma brucei brucei, Trypanosomes are unicellular eukaryotes that rely heavily on post-transcriptional mechanisms to control gene expression. DRBD3 is an RNA-binding protein known to play important roles in mRNA processing, stability, transport and translation. It was found to associate with grumpy, a long non-coding RNA (lncRNA) recently characterized in Trypanosoma brucei. Here, we explore the role of DRBD3 in lncRNA metabolism and show that its depletion leads to the upregulation of a specific subset of approximately one hundred lncRNAs in both bloodstream and procyclic forms, likely through the activation of cryptic splice sites. The effect of DRBD3 depletion on lncRNA expression appears to be mostly indirect, and results from reduced levels of the poly(A) polymerase PAP1 following DRBD3 silencing. In addition to its impact on lncRNAs, DRBD3 loss also affects the processing of protein-coding genes, leading to alternative trans-splicing and protein truncation. Furthermore, we demonstrate that DRBD3 regulates the splicing of the newly identified intron in the transcript encoding the RNA-binding protein RBP20, and is important for maintaining the balance between trans- and cis-splicing. Our results position DRBD3 as a high-level regulatory factor that shapes the expression landscape of both coding and non-coding genes in trypanosomes, Peer reviewed

5 Files (2 .txt; 3 .gpzip). License cc-by-4.0 Creative Commons Attribution 4.0 International., Contents of PanOryza pan-genes release v1.0 : 1. The Input fasta and gff folder contains the genomic DNA sequences and the annotation information of the genomes used for running GET_PANGENES pipeline. - Nipponbare_gene_to_transcript_map.txt : tabular details of the pangene identifier and the corresponding gene ids from the 3 Nipponbare annotations (RAPDB, MSU and Gramene). 2. Os4530.POR.1 contains the pangene cluster sequences - genomic(gdna.fna) , cDNA(cDNA.fna), coding sequence(cds.fna), amino acids (cds.faa) and the output files of GET_PANGENES pipeline. - POR.1.clusters_summary : Summarised tabular details of the pangene clusters , gene ids of the rice genome under that cluster, protein length etc. 3. Pan_gene_matrix_transcripts.txt : Pan-gene matrix with re-ordered pangene identifier in 1st column and pan-gene cluster members in subsequent columns. 4. manuscript_data : Workspace files (.RData) to reproduce the manuscript analyses. The codes and other tables are available at GitHub. 5. README.txt, The dataset provides the pan-gene sets release v1.0 for the asian rice developed by the PanOryza consortium., Developed by the PanOryza consortium. Members: 1. University of Liverpool, 2. Estación Experimental de Aula Dei, 3. European Bioinformatics Institute, 4. Oregon State University, 5. International Rice Research Institute, 6. Cold Spring Harbor Laboratory, 7. King Abdullah University of Science and Technology, 8. Huazhong Agricultural University, 9. United States Department of Agriculture, 10. Institute for Systems Biology, 11. University of Arizona, Peer reviewed