A5088823319- RNA Research and Splicing
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Single-cell and spatial transcriptomics
- Animal Genetics and Reproduction
- RNA modifications and cancer
- 3D Printing in Biomedical Research
- DNA and Nucleic Acid Chemistry
- Cancer-related molecular mechanisms research
- Chromosomal and Genetic Variations
- Genomics and Chromatin Dynamics
- CRISPR and Genetic Engineering
- Circular RNAs in diseases
- Genetics, Aging, and Longevity in Model Organisms
- Cytomegalovirus and herpesvirus research
- Nuclear Receptors and Signaling
- MicroRNA in disease regulation
- Genomics and Phylogenetic Studies
- Renal Transplantation Outcomes and Treatments
- Alzheimer's disease research and treatments
- Neuroinflammation and Neurodegeneration Mechanisms
- Cancer Genomics and Diagnostics
- Microbial Metabolic Engineering and Bioproduction
- Barrier Structure and Function Studies
- Epigenetics and DNA Methylation
Wellcome Sanger Institute
2016-2024
University of Toronto
2022-2023
The Gurdon Institute
2016-2022
University of Cambridge
2016-2022
Wellcome Trust
2017-2022
Pontificia Universidad Católica de Chile
2014-2020
Valparaiso University
1983
Abstract Most methods for single-cell transcriptome sequencing amplify the termini of polyadenylated transcripts, capturing only a small fraction total cellular transcriptome. This precludes detection many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts hinders alternative splicing analysis. We, therefore, developed VASA-seq to detect in single cells, which is enabled by fragmenting tailing all RNA molecules subsequent cell lysis. The method compatible...
Abstract Alternative splicing is central to metazoan gene regulation, but the regulatory mechanisms are incompletely understood. Here, we show that G-quadruplex (G4) motifs enriched ~3-fold near splice junctions. The importance of G4s in RNA emphasised by a higher enrichment for non-template strand. RNA-seq data from mouse and human neurons reveals an at exons were skipped following depolarisation induced potassium chloride. We validate formation stable three candidate sites circular...
Aging is the main risk factor for Alzheimer's disease (AD); being associated with conspicuous changes on microglia activation. Aged exhibit an increased expression of cytokines, exacerbated reactivity to various stimuli, oxidative stress, and reduced phagocytosis β-amyloid (Aβ). Whereas normal inflammation protective, it becomes dysregulated in presence a persistent stimulus, or context inflammatory environment, as observed aging. Thus, neuroinflammation can be self-perpetuating deleterious...
We uncovered the diversity of non-canonical splice sites at human transcriptome using deep profiling. mapped a total 3.7 billion RNA-seq reads and developed set stringent filters to avoid false site detections. identified 184 with dinucleotides U2/U12-like consensus sequences. selected 10 herein events successfully validated 9 them via reverse transcriptase-polymerase chain reaction Sanger sequencing. Analyses indicate that 51% are not annotated in GENCODE. In addition, 28% conserved mouse...
lternative DNA conformations, termed non-B structures, can affect transcription, but the underlying mechanisms and their functional impact have not been systematically characterized. Here, we used computational genomic analyses coupled with massively parallel reporter assays (MPRAs) to show that certain structures a substantial effect on gene expression. Genomic found at promoters harbor an excess of germline variants. Analysis multiple MPRAs, including promoter library specifically designed...
Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify conserved helicase Aquarius/EMB-4 as direct essential link between small pathways transcriptional machinery Caenorhabditis elegans. Aquarius physically interacts with germline HRDE-1. is required initiate small-RNA-induced heritable HRDE-1...
Single traumatic events that elicit an exaggerated stress response can lead to the development of neuropsychiatric conditions. Rodent studies suggested germline RNA as a mediator effects chronic environmental exposures progeny. The acute paternal exposure on and their potential consequences offspring remain be seen. We find administration agonist for stress-sensitive Glucocorticoid receptor, using common corticosteroid dexamethasone, affects payload mature sperm soon 3 hr after exposure. It...
Abstract Background Microexons, exons that are ≤ 30 nucleotides, a highly conserved and dynamically regulated set of cassette exons. They have key roles in nervous system development function, as evidenced by recent results demonstrating the impact microexons on behaviour cognition. However, often overlooked due to difficulty detecting them using standard RNA-seq aligners. Results Here, we present MicroExonator, novel pipeline for reproducible de novo discovery quantification microexons. We...
CoREST (CoREST1, rcor1) transcriptional corepressor together with the histone demethylase LSD1 (KDM1A) and deacetylases HDAC1/2 form LSD1-CoREST-HDAC (LCH) complexes to regulate gene expression. CoREST1 belong a family that also comprises CoREST2 (rcor2) CoREST3 (rcor3). represses expression of neuronal genes during differentiation. However, role paralogs in this process is just starting emerge. Here, we report all CoRESTs partners two models differentiation: Nerve-Growth-Factor...
Abstract Stochastic gene expression leads to inherent variability in outcomes even isogenic single-celled organisms grown the same environment. The Drop-Seq technology facilitates transcriptomic studies of individual mammalian cells, and it has had transformative effects on characterization cell identity function based single-cell transcript counts. However, application this with different size morphology characteristics been challenging. Here we present yeastDrop-Seq, a yeast-optimized...
Abstract Cancer diagnosis using cell-free DNA (cfDNA) has potential to improve treatment and survival but several technical limitations. Here, we show that tumor-associated mutations create neomers, sequences 13-17 nucleotides in length are predominantly absent from genomes of healthy individuals, can accurately detect cancer, including early stages, distinguish subtypes features. Using a neomer-based classifier, twenty-one different tumor-types with higher accuracy than state-of-the-art...
Single-cell RNA-seq (scRNA-seq) is widely used for transcriptome profiling, but most analyses focus on gene-level events, with less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method allow quantitative analysis of cell type-specific splicing events using full-length scRNA-seq data. ScASfind utilizes an efficient data structure store the percent spliced-in value each event. This makes it possible exhaustively search patterns among all...
DNA strand asymmetries can have a major effect on several biological functions, including replication, transcription and factor binding. As such, mutational bias provide information about function. However, versatile tool to explore this does not exist. Here, we present Asymmetron, user-friendly computational that performs statistical analysis visualizations for the evaluation of asymmetries. Asymmetron takes as input features provided with annotation outputs consecutive occurrences single...
Causes of lower induction Hsp70 in neurons during heat shock are still a matter debate. To further inquire into the mechanisms regulating expression neurons, we studied activity Heat Shock Factor 1 (HSF1) and histone posttranslational modifications (PTMs) at hsp70 promoter rat cortical neurons. induced transient efficient translocation HSF1 to neuronal nuclei. However, no binding was detected while it bound hsp25 shock. Histone PTMs analysis showed that harbors levels H3 H4 acetylation...
ABSTRACT In recent years, single-cell transcriptome sequencing has revolutionized biology, allowing for the unbiased characterization of cellular subpopulations. However, most methods amplify termini polyadenylated transcripts capturing only a small fraction total transcriptome. This precludes detection many long non-coding, short non-coding and non-polyadenylated protein-coding transcripts. Additionally, workflows do not sequence full transcript hindering analysis alternative splicing. We...
Abstract Alternative splicing is central to metazoan gene regulation but the regulatory mechanisms involved are only partially understood. Here, we show that G-quadruplex (G4) motifs enriched ~3-fold both upstream and downstream of splice junctions. Analysis in vitro G4-seq data corroborates their formation potential. G4s display highest enrichment at weaker sites, which frequently alternative events. The importance RNA as supposed DNA emphasized by a higher for non-template strand. To...
SUMMARY Small RNAs (sRNAs) play an ancient role in genome defence against transposable elements. In animals, plants and fungi small guide Argonaute proteins to nascent RNA transcripts induce co-transcriptional gene silencing. animals the link between pathways transcriptional machinery remains unclear. Here we show that Caenorhabditis elegans germline HRDE-1 physically interacts with conserved helicase Aquarius/EMB-4. We demonstrate Aquarius/EMB-4 activity is required initiate RNA-induced are...
Abstract Single-cell RNA-seq is widely used for transcriptome profiling, but most analyses have focused on gene-level events, with much less attention devoted to alternative splicing. Here, we present scASfind, a novel computational method allow quantitative analysis of cell type-specific splicing events. scASfind utilizes an efficient data structure store the percent spliced-in value each event. This makes it possible exhaustively search patterns among all differential allowing us identify...
Abstract Microexons, exons that are ≤30 nucleotides, were shown to play key roles in neuronal development, but difficult detect and quantify using standard RNA-Seq alignment tools. Here, we present MicroExonator, a novel pipeline for reproducible de novo discovery quantification of microexons. We processed 289 RNA-seq datasets from eighteen mouse tissues corresponding nine embryonic postnatal stages, providing the most comprehensive survey microexons available mouse. detected 2,984...
Abstract Neurons and immune cells have similar mechanisms for cell to communication. Exists active crosstalk between neurons cells. Neurotransmitters can activate or inhibit cells, cytokines modulate neuronal activity. The transcription factor Nur77 (NR4A1) is highly transiently induced by several stimuli in T-lymphocytes, suggesting that involved the coordination of genetics response both types. By analyzing publicly available databases, we found target genes common nervous systems....