A5103278373- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Cancer-related molecular mechanisms research
- RNA Research and Splicing
- Epigenetics and DNA Methylation
- interferon and immune responses
- Chromosomal and Genetic Variations
- Congenital heart defects research
- dental development and anomalies
- Gene expression and cancer classification
- Protein Degradation and Inhibitors
- Genomics and Phylogenetic Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Single-cell and spatial transcriptomics
- Cell Image Analysis Techniques
- Hedgehog Signaling Pathway Studies
- Osteoarthritis Treatment and Mechanisms
University of California, San Francisco
2020
University of Washington
2018-2020
Berlin Institute of Health at Charité - Universitätsmedizin Berlin
2020
Abstract To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis but, due to linkage disequilibrium, the specific variants underlying these associations and mechanisms by which they contribute disease risk yet be pinpointed. Here, we functionally test 1,605 single nucleotide associated with for regulatory activity using a massively parallel reporter assay. We identify six polymorphisms (SNPs) differential between major minor alleles. show that most...
Our understanding of the beads-on-a-string arrangement nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge divide between these approaches, we present single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput method that combines methyltransferase footprinting real-time DNA to natively nondestructively measure nucleosome positions individual...
Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand enhancers primates have typically studied many at low resolution, or single high resolution. Although comparative genomic studies reveal large-scale turnover enhancers, a specific understanding molecular steps which mammalian primate evolve remains elusive.We identified candidate hominoid-specific liver from H3K27ac ChIP-seq data....
Abstract Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Here, we further develop and apply a novel method to assemble test libraries greater than 2000 the same putative enhancers as 192-mers, 354-mers, 678-mers. We achieved yield 95% 354-mers 84% Importantly, observe surprisingly large differences functional activity. This work provides framework experimental design high-throughput assays, suggesting that extended...
ABSTRACT Massively parallel reporter assays (MPRAs) functionally screen thousands of sequences for regulatory activity in parallel. Although MPRAs have been applied to address diverse questions gene regulation, there has no systematic comparison how differences experimental design influence findings. Here, we a library 2,440 sequences, representing candidate liver enhancers and controls, HepG2 cells using nine different approaches (including conventional episomal, STARR-seq, lentiviral MPRA...
Background Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Due to technological limitations, previous efforts understand enhancers primates have typically studied many at low resolution, or single high resolution. Although comparative genomic studies reveal large-scale turnover enhancers, a specific understanding molecular steps which mammalian primate evolve remains elusive. Results We identified candidate...
Abstract To date, genome-wide association studies have implicated at least 35 loci in osteoarthritis, but due to linkage disequilibrium, we yet pinpoint the specific variants that underlie these associations, nor mechanisms by which they contribute disease risk. Here functionally tested 1,605 single nucleotide associated with osteoarthritis for regulatory activity using a massively parallel reporter assay. We identified six polymorphisms (SNPs) differential between major and minor alleles....
ABSTRACT Our understanding of the beads-on-a-string arrangement nucleosomes has been built largely on high-resolution sequence-agnostic imaging methods and sequence-resolved bulk biochemical techniques. To bridge divide between these approaches, we present single-molecule adenine methylated oligonucleosome sequencing assay (SAMOSA). SAMOSA is a high-throughput method that combines methyltransferase footprinting real-time DNA to natively nondestructively measure nucleosome positions...