A5085943236- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- DNA and Nucleic Acid Chemistry
- Advanced biosensing and bioanalysis techniques
- Bacterial Genetics and Biotechnology
- Diffusion and Search Dynamics
- Protein Degradation and Inhibitors
- RNA Interference and Gene Delivery
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Fungal and yeast genetics research
- Bacteriophages and microbial interactions
- Endoplasmic Reticulum Stress and Disease
- Parkinson's Disease Mechanisms and Treatments
- Ubiquitin and proteasome pathways
- Sperm and Testicular Function
- Reproductive System and Pregnancy
- Chromatin Remodeling and Cancer
- Reproductive Biology and Fertility
- Electron and X-Ray Spectroscopy Techniques
- Plant nutrient uptake and metabolism
- Advanced Proteomics Techniques and Applications
Marine Biological Laboratory
2020-2024
University of Massachusetts Chan Medical School
2021-2024
University of California, San Francisco
2017-2021
Columbia University
2012-2017
Howard Hughes Medical Institute
2014
CRISPR-Cas adaptive immune systems protect bacteria and archaea against foreign genetic elements. In Escherichia coli, Cascade (CRISPR-associated complex for antiviral defense) is an RNA-guided surveillance that binds DNA recruits Cas3, a trans-acting nuclease helicase target degradation. Here, we use single-molecule imaging to visualize Cas3 binding targets. Our analysis reveals two distinct pathways dictated by the presence or absence of protospacer-adjacent motif (PAM). Binding...
In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by proteins can explain these biological observations. Using bulk single-molecule methods, show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These...
The ability of proteins to locate specific targets among a vast excess nonspecific DNA is fundamental theme in biology. Basic principles governing these search mechanisms remain poorly understood, and no study has provided direct visualization single searching for engaging target sites. Here we use the postreplicative mismatch repair MutSα MutLα as model systems understanding diffusion-based searches. Using single-molecule microscopy, directly visualize it searches lesions, lesion-bound...
Matching DNA three bases at a time The exchange of genetic information between strands is vital for accurate repair and effective meiotic cell division. Using single-molecule methods molecular dynamics simulations, Lee et al. show that members the family recombinase enzymes responsible these strand reactions search recognize matching time. A single mismatch abolishes triplet recognition, except meiosis-specific recombinase. This enzyme can stabilize partially mismatched triplet, reflecting...
Methyl readers that repress transcription DNA methylation is a conserved epigenetic mark required for gene silencing in many different organisms. However, how the methyl able to silence genes still largely unknown. Ichino et al. discovered two Arabidopsis proteins named MBD5 and MBD6 are recruited by direct recognition of methylation. These recruit class C J-domain protein SILENZIO chromatin methylated transposons. likely acts through its interaction with heat shock chaperone proteins....
ABSTRACT Archaeal segAB operons are thought to promote chromosome segregation, but their mechanism remains unknown. We employ comparative genomics, structural biology, genetic knockouts, and quantitative cell biology investigate how SegA SegB proteins work together segregate chromosomes in the thermophilic archaeon Sulfolobus acidocaldarius. In vitro , binds a centromeric DNA sequence adjacent operon, vivo forms distinct focus on each segregating chromosome. SegA, ParA-like ATPase,...
ABSTRACT Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it highly tolerant to mutation during selection experiments performed in laboratory. We have proposed that this discrepancy results from difference between fitness under laboratory culture conditions and selective pressures changing environments timescales. Building on our previous work (Mavor et al., 2016), we used deep mutational scanning determine how twelve new chemicals...
Significance Chromosomes are crowded places, and any nucleic acid motor proteins that act on DNA must function within these environments. How environments affect protein behaviors remains largely unexplored. Here, we use single-molecule fluorescence microscopy to visualize the ATP-dependent RecBCD as it travels along molecules bearing long tandem arrays of binding proteins. Our findings show can push through highly while evicting from DNA. This behavior is distinct a previously described...
Genomic DNA is highly compacted in the nucleus of eukaryotic cells as a nucleoprotein assembly called chromatin 1 . The basic unit nucleosome, where ∼146 base pair increments genome are wrapped and around core histone proteins 2,3 Further genomic organization compaction occur through higher order nucleosomes 4 This regulates many nuclear processes, controlled part by post-transtranslational modifications chromatin-binding proteins. Mechanisms that regulate remain unclear 5,6 Here we show...
Abstract Cellular chromatin displays heterogeneous structure and dynamics, properties that control diverse nuclear processes. Models invoke phase separation of conformational ensembles fibers as a mechanism regulating organization in vivo . Here we combine biochemistry molecular dynamics simulations to examine, at single base-pair resolution, how nucleosome spacing controls separation. We show DNA linkers extend from 25 bp 30 bp, examplars 10N+5 10N (integer N) lengths, condensates become...
Protein conformations are shaped by cellular environments, but how environmental changes alter the conformational landscapes of specific proteins in vivo remains largely uncharacterized, part due to challenge probing protein structures living cells. Here, we use deep mutational scanning investigate a toxic conformation α-synuclein, dynamic linked Parkinson's disease, responds perturbations proteostasis. In context course for graduate students UCSF Integrative Program Quantitative Biology,...
In mammals HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, α , β γ display rapid on-off dynamics. Here we investigate whether phase-separation by proteins can explain these biological observations. Using bulk single-molecule methods, show that, within phase-separated -DNA condensates, acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates resistant to large...
Summary Conventional dogma presumes that protamine-mediated DNA compaction in sperm is achieved by passive electrostatics between and the arginine-rich core of protamines. However, phylogenetic analysis reveals several non-arginine residues are conserved within, but not across, species. The functional significance these or post-translational modifications poorly understood. Here, we investigated role K49, a rodent-specific lysine residue mouse protamine 1 (P1) acetylated early spermiogenesis...