A5069099896- RNA and protein synthesis mechanisms
- Genomics and Chromatin Dynamics
- RNA Research and Splicing
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Bacteriophages and microbial interactions
- Ubiquitin and proteasome pathways
- Protein Degradation and Inhibitors
- Viral gastroenteritis research and epidemiology
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Chromatin Remodeling and Cancer
Cornell University
2014-2022
Society of Health and Physical Educators
2022
University of Washington
2020
Institute for Systems Biology
2019
University of Connecticut
2019
CCCTC-binding factor (CTCF) is a conserved zinc finger transcription implicated in wide range of functions, including genome organization, activation, and elongation. To explore the basis for CTCF functional diversity, we coupled an auxin-induced degron system with precision nuclear run-on. Unexpectedly, oriented motifs gene bodies are associated transcriptional stalling manner independent bound CTCF. Moreover, at different binding sites (CBSs) displays highly variable resistance to...
Abstract Tracking active transcription with the nuclear run-on (NRO) assays has been instrumental in uncovering mechanisms of gene regulation. The coupling NROs high-throughput sequencing facilitated discovery previously unannotated or undetectable RNA classes genome-wide. Precision (PRO-seq) is a variant that maps polymerase sites nucleotide near-nucleotide resolution. One main drawback to this and many other nascent detection methods somewhat intimidating multi-day workflow associated...
ABSTRACT Conventional methods for viral genome sequencing largely use metatranscriptomic approaches or, alternatively, enrich genomes by amplicon with virus-specific PCR or hybridization-based capture. These existing are costly, require extensive sample handling time, and have limited throughput. Here, we describe V-seq, an inexpensive, fast, scalable method that performs targeted multiplexing primers at the cDNA synthesis step. We designed densely tiled reverse transcription (RT) across...
Abstract Gene regulation occurs through trans -acting factors ( e.g. transcription factors) acting on cis -regulatory elements enhancers). Massively parallel reporter assays (MPRAs) functionally survey large numbers of for regulatory potential, but do not identify the that mediate any observed effects. Here we describe MPRA — a assay efficiently combines multiplex CRISPR-mediated perturbation and MPRAs to trans- modulate activity specific enhancers.
Abstract Transcription at most promoters is divergent, initiating closely spaced oppositely oriented core to produce sense transcripts along with often unstable upstream antisense (uasTrx). How transcription regulated and what extent it coordinated largely unknown. Here by combining acute degradation of the multi-functional factor CTCF nascent measurements, we find that specifically suppresses but not hundreds divergent promoters, great majority which bear proximal binding sites. Genome...
Abstract The Drosophila Boundary Element-Associated Factor of 32 kDa (BEAF) binds in promoter regions a few thousand mostly housekeeping genes. BEAF is implicated both chromatin domain boundary activity and function, although molecular mechanisms remain elusive. Here, we show that physically interacts with the polybromo subunit (Pbro) PBAP, SWI/SNF-class remodeling complex. also shows genetic interactions Pbro other PBAP subunits. We examine effect this interaction on gene expression...