A5012996196- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- Cancer-related molecular mechanisms research
- Computational Drug Discovery Methods
- RNA regulation and disease
- Machine Learning in Materials Science
- Amyotrophic Lateral Sclerosis Research
- Genomics and Phylogenetic Studies
- Genetics and Neurodevelopmental Disorders
- Neurogenetic and Muscular Disorders Research
Stanford University
2017-2025
Howard Hughes Medical Institute
2025
University of California, Berkeley
2025
Harvard University
2014
Emerging studies have linked the ribosome to more selective control of gene regulation. However, an outstanding question is whether heterogeneity at level core ribosomal proteins (RPs) exists and enables ribosomes preferentially translate specific mRNAs genome-wide. Here, we measured absolute abundance RPs in translating profiled transcripts that are enriched or depleted from select subsets within embryonic stem cells. We find RP composition endows with differential selectivity for subpools...
With hundreds of copies rDNA, it is unknown whether they possess sequence variations that form different types ribosomes. Here, we developed an algorithm for long-read variant calling, termed RGA, which revealed in human rDNA loci are predominantly insertion-deletion (indel) variants. We full-length rRNA sequencing (RIBO-RT) and situ (SWITCH-seq), showed translating ribosomes variation rRNA. Over 1,000 variants lowly expressed. However, tens abundant distinct subtypes with structures near...
Abstract Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem differentiation, we identify dozens of changes underlying specification. We observe upregulation RPL10A/uL1-containing in primitive streak followed by progressive decreases mesoderm differentiation. An Rpl10a loss-of-function allele mice...
Abstract Widespread control of gene expression through translation has emerged as a key level spatiotemporal regulation protein expression. A prominent mechanism by which ribosomes can confer is via internal ribosomal entry sites (IRESes), whose functions have however, remained difficult to rigorously characterize. Here we present set technologies in embryos and cells, including IRES-mediated circular RNA (circRNA) reporters, single-molecule messenger (m)RNA isoform imaging, PacBio long-read...
Ribosomal DNA and RNA (rDNA rRNA) sequences are usually discarded from sequencing analyses. But with hundreds of copies rDNA genes it is unknown whether they possess sequence variations that form different types ribosomes affect human physiology disease. Here, we developed an algorithm for variant-calling between paralog (termed RGA) compared found in short- long-read data the 1,000 Genomes Project (1KGP) Genome In A Bottle (GIAB). We additionally a novel protocol full-length rRNA (RIBO-RT)...
Ribosomes have been suggested to directly control gene regulation, however regulatory roles for ribosomal RNA (rRNA) remain largely unexplored. Expansion segments (ESs) consist of a multitude tentacle-like rRNA structures that extend from the core ribosome in eukaryotes. ESs are remarkably variable sequence and size across eukaryotic evolution with unknown function. In characterizing binding element within Homeobox (Hox) 5’ UTR, we unexpectedly identify modular stem-loop this binds single...