A5070491292- CRISPR and Genetic Engineering
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- RNA regulation and disease
- Advanced biosensing and bioanalysis techniques
- RNA modifications and cancer
- Molecular Biology Techniques and Applications
- RNA Interference and Gene Delivery
- RNA Research and Splicing
- CAR-T cell therapy research
- Cancer-related molecular mechanisms research
- Selenium in Biological Systems
- MicroRNA in disease regulation
- Redox biology and oxidative stress
- Trace Elements in Health
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- FOXO transcription factor regulation
Barcelona Institute for Science and Technology
2017-2022
Centre for Genomic Regulation
2015-2022
Pfizer (United States)
2019-2022
University Hospital of Bern
2021
University of Bern
2021
University College Dublin
2021
Universitat Pompeu Fabra
2010-2017
Hospital del Mar Research Institute
2015-2017
Barcelona Biomedical Research Park
2010
Institut de Biologia Evolutiva
2010
CRISPR genome-editing technology makes it possible to quickly and cheaply delete non-protein-coding regulatory elements. We present a vector system adapted for this purpose called DECKO (Double Excision Knockout), which applies simple two-step cloning generate lentiviral vectors expressing two guide RNAs (gRNAs) simultaneously. The key feature of is its use single 165 bp starting oligonucleotide carrying the variable sequences both gRNAs, making fully scalable from single-locus studies...
CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling individual loci, parallelized loss-of-function screens thousands regulatory elements. However, no solution presented the unique bioinformatic design requirements CRISPR deletion. We here present CRISPETa, a pipeline flexible and scalable paired sgRNA based on an empirical scoring model....
A single nucleotide polymorphism (SNP) in exon 2 of the CD33 gene is associated with reduced susceptibility to late-onset Alzheimer's disease (AD) and causal for elevated mRNA lacking 2. In contrast full-length CD33, transcripts result protein unable suppress activation responses myeloid cells, including microglia. Currently, little known about regulation splicing. Using functional genomics proteomic approaches, we found that SRSF1 PTBP1 act as splicing enhancers increase inclusion mRNA....
CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing role along different processes. In particular, the usage of nuclease active Cas9 coupled single gRNA has proven efficiently impair expression pc-genes by generating deleterious frameshifts. Here, we first demonstrate that targeting same gene simultaneously with two guide RNAs (paired RNAs, pgRNAs) synergistically enhances capacity system knock out pc-genes. We next...
The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedented accuracy, but the high costs full-length mRNA sequencing have posed a limit on accessibility and scalability technology. To address this, we developed 3'Pool-seq: simple, cost-effective, scalable RNA-seq method that focuses 3'-end mRNA. We drew from aspects SMART-seq, Drop-seq, TruSeq implement an easy workflow, optimized parameters such as input RNA concentrations, tagmentation conditions,...
Dynamic redefinition of the 10 UGAs in human and mouse selenoprotein P (Sepp1) mRNAs to specify selenocysteine instead termination involves two 3′ UTR structural elements (SECIS) is regulated by selenium availability. In addition previously known Sepp1 mRNA poly(A) site just SECIS 2, further sites were identified with one resulting 10–25% lacking 2. To address function, mutant mice generated either 1 or 2 deleted first UGA substituted a serine codon. They fed on high selenium-deficient...
In this report we have analyzed the role of antisense transcription in control LEF1 factor expression. A natural transcript (NAT) is transcribed from a promoter present first intron gene and undergoes splicing mesenchymal cells. Although locus silent epithelial cells, neither NAT nor mRNA are expressed, cell lines with an intermediate epithelial-mesenchymal phenotype presenting low expression, synthesized remains unprocessed. Contrarily to spliced NAT, unspliced down-regulates main activity...
Abstract Background The human FOXI1 gene codes for a transcription factor involved in the physiology of inner ear, testis, and kidney. Using three interspecies comparisons, it has been suggested that this may be under human-specific selection. We sought to confirm finding by using an extended set orthologous sequences. Additionally, we explored signals natural selection within humans sequencing 20 Europeans, East Asians Yorubas analysing SNP variation 2 Mb region centered on 39 worldwide...
Abstract Using CRISPR/Cas9, diverse genomic elements may be studied in their endogenous context. Pairs of single guide RNAs (sgRNAs) are used to delete regulatory and small RNA genes, while longer can silenced through promoter deletion. We here present CRISPETa, a bioinformatic pipeline for flexible scalable paired sgRNA design based on an empirical scoring model. Multiple pairs returned each target. Any number targets analyzed parallel, making CRISPETa equally appropriate studies individual...
CRISPR base editors are powerful tools for large-scale mutagenesis studies. This kind of approach can elucidate the mechanism action compounds, a key process in drug discovery. Here, we explore utility an early discovery context focusing on G-protein coupled receptors. A pooled screening framework was set up based modified version CRISPR-X editor system. We determine optimized experimental conditions where sgRNAs delivered by cell transfection or viral infection over extended time periods...
ABSTRACT CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify both protein coding (pc) and non-coding genes playing role along different processes. In particular, the usage of nuclease active Cas9 coupled single gRNA has proven efficiently impair expression pc-genes by generating deleterious frameshifts. Here, we first demonstrate that second targeting same gene synergistically enhances capacity system knock out pc-genes. We next take advantage our paired-guide (pgRNA)...
Abstract Background : CRISPR base editors are powerful tools for large-scale mutagenesis studies. This kind of approach can elucidate the mechanism action compounds, a key process in drug discovery. Here, we explore utility an early discovery context, and focus on G-protein coupled receptors. Results We set up pooled screening framework based modified version CRISPR-X editor system. determine optimized experimental conditions where sgRNAs delivered by cell transfection or viral infection...
Abstract CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein coding (pc) and non-coding genes playing role along different processes. In particular, the usage of nuclease active Cas9 coupled single gRNA has proven efficiently impair expression pc-genes by generating deleterious frameshifts. Here, we first demonstrate that second targeting same gene synergistically enhances capacity system knock out pc-genes. We next design library simultaneously target lncRNAs...