Biology subjects

Lee, C. T.-Y.

Publications and source records attributed to Lee, C. T.-Y..

3 recordsLinked to original sources

bioRxiv2023

Full-length direct RNA sequencing reveals widespread RNA decay upon cellular stress

Cells react to stress by triggering response pathways, leading to extensive alterations in the transcriptome to restore cellular homeostasis. The role of RNA metabolism in shaping the cellular response to stress is vital, yet the global changes in RNA stability under these conditions remain unclear. In this work, we employ direct RNA sequencing with nanopores, enhanced by 5 end adaptor ligation, to comprehensively interrogate the human transcriptome at single-molecule and nucleotide resolution. By developing a statistical framework to identify robust RNA length variations in nanopore data, we find that cellular stress induces prevalent 5 end RNA decay that is coupled to translation and ribosome occupancy. Unlike typical RNA decay models in normal conditions, we show that stress-induced RNA decay is dependent on XRN1 but does not depend on deadenylation or decapping. We observed that RNAs undergoing decay are predominantly enriched in the stress granule transcriptome while inhibition of stress granule formation via genetic ablation of G3BP1 and G3BP2 rescues RNA length. Our findings reveal RNA decay as a key determinant of RNA metabolism upon cellular stress and dependent on stress-granule formation.

cell biology↗

bioRxiv2021

SamQL: A Structured Query Language and filtering tool for the SAM/BAM file format

The Sequence Alignment/Map Format Specification (SAM) is one of the most widely used file formats in computational biology today and several tools have been developed to process it and use it. It is a flexible file format, used by many bioinformaticians on a daily basis. Despite its flexibility, SAM encoded files can often be difficult to query and understand. As genomic data are rapidly growing, structured and efficient queries on data encoded in SAM/BAM files is becoming critical. Importantly, any new tools should be able to support existing large datasets without requiring any data transformations. Here we introduce SamQL, an SQL-like query language for the SAM format with intuitive syntax that supports complex and efficient queries on top of SAM/BAM files and that can replace commonly used Bash one-liners employed by many bioinformaticians. SamQL is a complete query language that we envision as a step to a structured database engine for genomics. SamQL is written in Go, taking advantage of modern multicore compute systems and is freely available as standalone program and as an open-source library released under an MIT license, https://github.com/maragkakislab/samql/.

bioinformatics↗

bioRxiv2019

Single cell analysis of the effects of developmental lead (Pb) exposure on the hippocampus.

BackgroundLead (Pb) exposure is ubiquitous and has permanent developmental effects on childhood intelligence and behavior and adulthood risk of dementia. The hippocampus is a key brain region involved in learning and memory, and its cellular composition is highly heterogeneous. Pb acts on the hippocampus by altering gene expression, but the cell type-specific responses are unknown. ObjectiveExamine the effects of perinatal Pb treatment on adult hippocampus gene expression, at the level of individual cells, in mice. MethodsIn mice perinatally exposed to control water (n=4) or a human physiologically-relevant level (32 ppm in maternal drinking water) of Pb (n=4), two weeks prior to mating through weaning, we tested for gene expression and cellular differences in the hippocampus at 5-months of age. Analysis was performed using single cell RNA-sequencing of 5,258 cells from the hippocampus by 10x Genomics Chromium to 1) test for gene expression differences averaged across all cells by treatment; 2) compare cell cluster composition by treatment; and 3) test for gene expression and pathway differences within cell clusters by treatment. ResultsGene expression patterns revealed 12 cell clusters in the hippocampus, mapping to major expected cell types (e.g. microglia, astrocytes, neurons, oligodendrocytes). Perinatal Pb treatment was associated with 12.4% more oligodendrocytes (P=4.4x10-21) in adult mice. Across all cells, differential gene expression analysis by Pb treatment revealed cluster marker genes. Within cell clusters, differential gene expression with Pb treatment (q<0.05) was observed in endothelial, microglial, pericyte, and astrocyte cells. Pathways up-regulated with Pb treatment were protein folding in microglia (P=3.4x10-9) and stress response in oligodendrocytes (P=3.2x10-5). ConclusionBulk tissue analysis may be confounded by changes in cell type composition and may obscure effects within vulnerable cell types. This study serves as a biological reference for future single cell studies of toxicant or neuronal complications, to ultimately characterize the molecular basis by which Pb influences cognition and behavior.

pharmacology and toxicology↗