A5031822290- Ubiquitin and proteasome pathways
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- Cancer-related gene regulation
- Peptidase Inhibition and Analysis
- Genetics and Neurodevelopmental Disorders
- Genomics and Chromatin Dynamics
- Endoplasmic Reticulum Stress and Disease
- Advanced biosensing and bioanalysis techniques
- Autophagy in Disease and Therapy
- Bacterial Genetics and Biotechnology
- Photoreceptor and optogenetics research
- Enzyme Production and Characterization
- Cancer Research and Treatments
- Biochemical and Molecular Research
- Yersinia bacterium, plague, ectoparasites research
- Glycosylation and Glycoproteins Research
- Cancer, Hypoxia, and Metabolism
- Quantum-Dot Cellular Automata
- RNA Research and Splicing
- Bacillus and Francisella bacterial research
- Fungal and yeast genetics research
- Signaling Pathways in Disease
- Advanced Memory and Neural Computing
Van Andel Institute
2022-2025
Johns Hopkins Medicine
2018-2022
Johns Hopkins University
2018-2022
University of California, Berkeley
2013-2017
QB3
2017
Berkeley College
2014
Whitworth University
2009
The 26S proteasome is responsible for the selective, ATP-dependent degradation of polyubiquitinated cellular proteins. Removal ubiquitin chains from targeted substrates at a prerequisite substrate processing and accomplished by Rpn11, deubiquitinase within ‘lid’ sub-complex. Prior to lid’s incorporation into proteasome, Rpn11 activity inhibited prevent unwarranted deubiquitination Here we present atomic model isolated lid sub-complex, as determined cryo-electron microscopy 3.5 Å resolution,...
Methylation of histone H3K4 is a hallmark actively transcribed genes that depends on mono-ubiquitination H2B (H2B-Ub). methylation in yeast catalyzed by Set1, the methyltransferase subunit COMPASS. We report here cryo-EM structure six-protein core COMPASS subcomplex, which can methylate and be stimulated H2B-Ub, bound to ubiquitinated nucleosome. Our shows spans face nucleosome, recognizing ubiquitin one nucleosome methylating H3 opposing face. As compared isolated complex, Set1 undergoes...
Cellular compartmentalization requires machinery capable of translocating polypeptides across membranes. In many cases, transported proteins must first be unfolded by means the proton motive force and/or ATP hydrolysis. Anthrax toxin, which is composed a channel-forming protein and two substrate proteins, an attractive model system to study translocation-coupled unfolding, because applied driving can externally controlled translocation monitored directly using electrophysiology. By...
The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of H2B. Recent structures the MLL1-WRAD core complex, which comprises MLL1 methyltransferase, W DR5, R bBp5, A sh2L, D PY-30, have revealed variability in docking on nucleosomes. In addition, portions Ash2L structure position DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) mass spectrometry cross-linking...
Mono-ubiquitination of lysine 18 on histone H3 (H3K18ub), catalyzed by UHRF1, is a DNMT1 docking site that facilitates replication-coupled DNA methylation maintenance. Its functions beyond this are unknown. Here, we genomically map simultaneous increases in UHRF1-dependent H3K18ub and SUV39H1/H2-dependent H3K9me3 following inhibition. Mechanistically, transient accumulation hemi-methylated at CpG islands UHRF1 recruitment E3 ligase activity toward H3K18. Notably, enhances SUV39H1/H2...
Abstract Histone H3K9 methylation (H3K9me) by Setdb1 silences retrotransposons (rTE) sequestering them in constitutive heterochromatin. Atf7IP is a binding partner of and responsible for nuclear localization, activation chromatin recruitment. However, structural details the Setdb1/Atf7IP interaction have not been evaluated. We used Alphafold2 predictions biochemical reconstitutions to show that one copy two copies form hetero-trimeric complex vitro cells . also find self-associates, forming...
Abstract De novo cytosine methylation is essential for mammalian development and deposited by DNMT3A DNMT3B. In cells, DNA occurs in the context of chromatin, where nucleosomes are connected linkers. Here, we report Cryo-EM structures DNMT3A2/3B3 bound to di-nucleosomes with different linker lengths. We show that preferentially binds separated short linkers inducing large-scale changes di-nucleosome structure, enabling each DNMT3B3 subunit bind nucleosome. Linker length position cytosines...
The 26S proteasome is the major protease in eukaryotic cells responsible for selective protein degradation to mediate quality control and regulation, yet detailed mechanisms by which proteasomal heterohexameric AAA+ unfoldase drives ATP‐dependent remain poorly understood. Delineating roles of six distinct ATPase subunits substrate processing has been hindered limitations working with endogenous proteasomes due misassembly or lethal defects. We therefore developed a heterologous expression...
Abstract Methylation of histone H3, lysine 79 (H3K79), by Dot1L is a hallmark actively transcribed genes that depends on monoubiquitination H2B at 120 (H2B-Ub), and well-characterized example modification cross-talk conserved from yeast to humans. The mechanism which H2B-Ub stimulates methylate the relatively inaccessible core H3K79 residue unknown. 3.0 Å resolution cryo-EM structure bound ubiquitinated nucleosome reveals contains binding sites for both ubiquitin H4 tail, establish two...
ABSTRACT Methylation of histone H3K4 is a hallmark actively transcribed genes that depends on mono-ubiquitination H2B (H2B-Ub). methylation in yeast catalyzed by Set1, the methyltransferase subunit COMPASS. We report here cryo-EM structure six-protein core COMPASS subcomplex, which can methylate and be stimulated H2B-Ub, bound to ubiquitinated nucleosome. Our shows spans face nucleosome, recognizing ubiquitin one nucleosome methylating H3 opposing face. As compared isolated complex, Set1...
Abstract The human Mixed Lineage Leukemia-1 (MLL1) complex orchestrates methylation of histone H3K4 to promote transcription and is stimulated by monoubiquitination H2B. Recent structures the MLL1-WRAD core complex, which comprises MLL1 methyltransferase, W DR5, R bBp5, A sh2L, D PY-30, have revealed variation in docking on nucleosomes left ambiguous portions Ash2L position DPY30. We used an integrated approach combining cryo-electron microscopy mass spectrometry-crosslinking determine bound...
The eukaryotic 26S proteasome utilizes a complex set of coordinated processing steps for the ATP‐dependent degradation ubiquitin‐tagged substrates. Our cryo‐EM studies reveal important features regulatory particle, including pronounced spiral‐staircase arrangement its heterohexameric ATPase ring, that facilitate substrate engagement and initiation. Substrate induces translocation‐competent conformation, in which de‐ubiquitinating subunit Rpn11 is repositioned to function as gatekeeper at...
The 26S proteasome is a multi‐protein complex responsible for ubiquitin‐mediated protein degradation in eukaryotic cells. Rpn11, the only essential deubiquitinase, removes ubiquitin chains from substrates during degradation, however very little known about regulation and intrinsic cleavage specificity of enzyme. We utilized heterologous expression system lid subcomplex, mutational analyses in‐vitro deubiquitination assays to study activity Rpn11 different assembly intermediates proteasome....