A5063422669- RNA Research and Splicing
- Genomic variations and chromosomal abnormalities
- RNA regulation and disease
- Autism Spectrum Disorder Research
- Genomics and Rare Diseases
- Genomics and Chromatin Dynamics
- Genetic Associations and Epidemiology
- Essential Oils and Antimicrobial Activity
- Neuroscience and Neuropharmacology Research
- Listeria monocytogenes in Food Safety
- Ion channel regulation and function
- Chromatin Remodeling and Cancer
- RNA and protein synthesis mechanisms
- Genetics and Neurodevelopmental Disorders
- Bioinformatics and Genomic Networks
- Streptococcal Infections and Treatments
- RNA modifications and cancer
- Single-cell and spatial transcriptomics
- Congenital heart defects research
- Neonatal and Maternal Infections
- CRISPR and Genetic Engineering
- Epigenetics and DNA Methylation
- Identification and Quantification in Food
- Pneumonia and Respiratory Infections
- Salmonella and Campylobacter epidemiology
University of California, San Francisco
2018-2024
Public Health Ontario
2016-2018
Public Health Agency of Canada
2018
University of Toronto
2018
Sinai Hospital
2018
INTRODUCTION The DNA of protein-coding genes is transcribed into mRNA, which translated proteins. “coding genome” describes the that contains information to make these proteins and represents ~1.5% human genome. Newly arising de novo mutations (variants observed in a child but not either parent) coding genome contribute numerous childhood developmental disorders, including autism spectrum disorder (ASD). Discovery effects aided by triplet code enables functional impact many be readily...
Gene expression levels vary across developmental stage, cell type, and region in the brain. Genomic variants also contribute to variation expression, some neuropsychiatric disorder loci may exert their effects through this mechanism. To investigate these relationships, we present BrainVar, a unique resource of paired whole-genome bulk tissue RNA sequencing from dorsolateral prefrontal cortex 176 individuals prenatal postnatal development. Here identify common that alter gene (expression...
Many autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). Chromatin immunoprecipitation sequencing (ChIP-seq) was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in developing human mouse cortex. These shared substantial overlap binding sites, especially within open chromatin. The a promoter region, 1–2,000 bp upstream transcription start site, highly predictive brain-expressed genes. This signature...
Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, autism spectrum disorder. The mRNA splicing patterns all four genes vary across development rodent brain, including mutually exclusive copies fifth protein-coding exon detected neonate (5N) adult (5A). A second pair exons is reported only (18N 18A). We aimed to quantify expression individual developing human brain. RNA-seq data from 783 brain samples were...
ABSTRACT Individuals with autism spectrum disorder (ASD) or related neurodevelopmental disorders (NDDs) often carry disruptive mutations in genes that are depleted of functional variation the broader population. We build upon this observation and exome sequencing from 154,842 individuals to explore allelic diversity rare protein-coding contributing risk for ASD NDDs. Using an integrative statistical model, we jointly analyzed protein-truncating variants (PTVs), damaging missense variants,...
Posttranscriptional RNA modifications by adenosine-to-inosine (A-to-I) editing are abundant in the brain, yet elucidating functional sites remains challenging. To bridge this gap, we investigate spatiotemporal and genetically regulated A-to-I across prenatal postnatal stages of human brain development. More than 10,000 spatiotemporally were identified that occur predominately 3′ UTRs introns, as well 37 recode amino acids protein coding regions with precise changes levels Hyper-edited...
Summary Variation in gene expression underlies neurotypical development, while genomic variants contribute to neuropsychiatric disorders. BrainVar is a unique resource of paired whole-genome sequencing and bulk-tissue RNA-sequencing from the human dorsolateral prefrontal cortex 176 individuals across prenatal postnatal providing opportunity assay transcriptomic variation tandem. Leveraging this resource, we identified rare premature stop codons with commensurate reduced allele-specific...
Mobile genetic elements in bacteria, such as plasmids, act important vectors for the transfer of antibiotic resistance, virulence, and metal resistance genes. Here, we report genome sequence a new plasmid pLM-C-273, identified Listeria monocytogenes strain isolated from clinical sample Ontario, Canada.
ABSTRACT Post-transcriptional modifications by RNA editing are essential for neurodevelopment, yet their developmental and regulatory features remain poorly resolved. We constructed a full temporal view of base-specific in the developing human cortex, from early progenitors through fully mature cells found adult brain. Developmental regulation is characterized an increase rates more than 10,000 selective sites, shifting between mid-fetal development infancy, massive expansion hyper-editing...
Abstract Objective Genetic variants in the voltage-gated sodium channels SCN1A, SCN2A, SCN3A, and SCN8A are leading causes of epilepsy, developmental delay, autism spectrum disorder. The mRNA splicing patterns all four genes vary across development rodent brain, including mutually exclusive copies fifth protein-coding exon detected neonate (5N) adult (5A). A second pair exons is reported only (18N 18A). We aimed to quantify expression individual developing human neocortex. Methods RNA-seq...
Abstract Many autism spectrum disorder (ASD)-associated genes act as transcriptional regulators (TRs). ChIP-seq was used to identify the regulatory targets of ARID1B, BCL11A, FOXP1, TBR1, and TCF7L2, ASD-associated TRs in developing human mouse cortex. These shared substantial overlap binding sites, especially within open chromatin. The a promoter region, 1-2,000bp upstream transcription start site, highly predictive brain expressed genes. This signature observed at 96 out 102 In vitro...
Comparative genomic analysis between pathogenic and nonpathogenic Listeria monocytogenes strains provides a good model for studying the virulence of this organism. Here, we report genome sequence L. strain F6540 (sequence type 360) identified specifically in food samples Ontario, Canada, 2010.