Biology subjects

Lo, H.-Y. G.

Publications and source records attributed to Lo, H.-Y. G..

3 recordsLinked to original sources

bioRxiv2025

TO BE OR NOT TO BE A PI: ADVICE FOR TRAINEES IN THE BIOMEDICAL/BASIC SCIENCES

When a biomedical or basic science doctoral (PhD) student considers whether or not to become a Principal Investigator (PI), they typically base their decisions on anecdotal data from a limited number of faculty mentors. Alternatively, they may look online for guidance and be met with biased opinions rather than unbiased, comprehensive data. We sought to address this gap by anonymously surveying active faculty at the University of Colorado Anschutz Medical Campus (CU Anschutz) to gain more clarity on the daily life of a PI, the decisions they made as they navigated their career path, and which skills were valuable for securing a faculty position. We also identified important factors in choosing a postdoctoral lab. We found that the majority of PIs would recommend becoming a PI and thought positively of the career path, with most feeling content. But attitudes differed between faculty of different ranks. Further, in addition to scientific vision, hard work, and publications, luck was also deemed as an important factor in becoming and succeeding as a PI. We present our findings so that they may serve as a resource for graduate trainees who are considering a PI/academic research career path. In addition, the information may guide future training plans to optimize achievement of their dream career.

scientific communication and education↗

bioRxiv2024

Quantification of subcellular RNA localization through direct detection of RNA oxidation

Across cell types and organisms, thousands of RNAs display asymmetric subcellular distributions. The study of this process often requires quantifying abundances of specific RNAs at precise subcellular locations. To analyze subcellular transcriptomes, multiple proximity-based techniques have been developed in which RNAs near a localized bait protein are specifically labeled, facilitating their biotinylation and purification. However, these complex methods are often laborious and require expensive enrichment reagents. To streamline the analysis of localized RNA populations, we developed Oxidation-Induced Nucleotide Conversion sequencing (OINC-seq). In OINC-seq, RNAs near a genetically encoded, localized bait protein are specifically oxidized in a photo-controllable manner. These oxidation events are then directly detected and quantified using high-throughput sequencing and our software package, PIGPEN, without the need for biotin-mediated enrichment. We demonstrate that OINC-seq can induce and quantify RNA oxidation with high specificity in a dose- and light-dependent manner. We further show the spatial specificity of OINC-seq by using it to quantify subcellular transcriptomes associated with the cytoplasm, ER, nucleus, and the inner and outer membranes of mitochondria. Finally, using transgenic zebrafish, we demonstrate that OINC-seq allows proximity-mediated RNA labeling in live animals. In sum, OINC-seq together with PIGPEN provide an accessible workflow for the analysis of localized RNAs across different biological systems.

molecular biology↗

bioRxiv2021

Analysis of subcellular transcriptomes by RNA proximity labeling with Halo-seq

Thousands of RNA species display nonuniform distribution within cells. However, quantification of the spatial patterns adopted by individual RNAs remains difficult, in part by a lack of quantitative tools for subcellular transcriptome analysis. In this study, we describe an RNA proximity labeling method that facilitates the quantification of subcellular RNA populations with high spatial specificity. This method, termed Halo-seq, pairs a light-activatable, radical generating small molecule with highly efficient Click chemistry to efficiently label and purify spatially defined RNA samples. We compared Halo-seq with previously reported similar methods and found that Halo-seq displayed a higher efficiency of RNA labeling, indicating that it is well suited to the investigation of small, precisely localized RNA populations. We then used Halo-seq to quantify nuclear, nucleolar, and cytoplasmic transcriptomes, characterize their dynamic nature following perturbation, and identify RNA sequence features associated with their composition. Specifically, we found that RNAs containing AU-rich elements are relatively enriched in the nucleus. This enrichment becomes stronger upon treatment with the nuclear export inhibitor leptomycin B, both expanding the role of HuR in RNA export and generating a comprehensive set of transcripts whose export from the nucleus depends on HuR.

molecular biology↗