A5075476653- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- Advanced biosensing and bioanalysis techniques
- RNA Interference and Gene Delivery
- RNA Research and Splicing
- Force Microscopy Techniques and Applications
- Advanced Fluorescence Microscopy Techniques
- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- DNA and Nucleic Acid Chemistry
- Epigenetics and DNA Methylation
- Protein Degradation and Inhibitors
- DNA Repair Mechanisms
- Photosynthetic Processes and Mechanisms
- Cellular Mechanics and Interactions
- Histone Deacetylase Inhibitors Research
- Bacterial Genetics and Biotechnology
- Protein Structure and Dynamics
- Microbial Metabolites in Food Biotechnology
- Kruppel-like factors research
- Chromatin Remodeling and Cancer
- Hemoglobin structure and function
- Ubiquitin and proteasome pathways
- Chemical Reactions and Isotopes
- Microtubule and mitosis dynamics
Johns Hopkins University
2013-2025
Pontificia Universidad Católica de Chile
2009
Howard Hughes Medical Institute
2009
Princeton University
1999-2002
Chd1- and ISWI-type chromatin remodelers can sense extranucleosomal DNA preferentially shift nucleosomes toward longer stretches of available DNA. The DNA-binding domains these are believed to be responsible for sensing needed robust sliding, but it is unclear how contribute directional movement nucleosomes. Here, we show that the domain Chd1 not essential nucleosome sliding critical centering mononucleosomes on short fragments. Remarkably, was achieved by replacing native with foreign...
ABSTRACT Nucleosome repositioning is essential for establishing nucleosome-depleted regions (NDRs) to initiate transcription. This process has been extensively studied using structural, biochemical, and single-molecule approaches, which require homogenously positioned nucleosomes. often achieved the Widom 601 sequence, a highly efficient nucleosome positioning element (NPE) selected its unusually strong binding H3-H4 histone tetramer. Due artificial nature of 601, native NPEs are needed...
Torsional stress in linear biopolymers such as DNA and chromatin has important consequences for nanoscale biological processes. We have developed a new method to directly measure torque on single molecules. Using cylindrical magnet, we manipulate novel probe consisting of nanorod with 0.1 μm ferromagnetic segment coupled magnetic bead. achieve controlled introduction turns into the molecule precise measurement extension function number at low pulling force. show molecules demonstrate first...
As superfamily 2 (SF2)-type translocases, chromatin remodelers are expected to use an inchworm-type mechanism walk along DNA. Yet how they move DNA around the histone core has not been clear. Here we show that a remodeler ATPase motor can shift large segments of by changing twist and length nucleosomal at superhelix location (SHL2). Using canonical variant 601 nucleosomes, find Saccharomyces cerevisiae Chd1 decreased SHL2 in nucleotide-free ADP-bound states, increased with transition state...
Chromatin remodelers can either organize or disrupt nucleosomal arrays, yet the mechanisms specifying these opposing actions are not clear. Here, we show that outcome of nucleosome sliding by Chd1 changes dramatically depending on how chromatin remodeler is targeted to nucleosomes. Using a Chd1–streptavidin fusion remodeler, found targeting via biotinylated DNA resulted in directional towards recruitment site, whereas histones produced distribution positions. Remarkably, shifted nucleosomes...
The histone acetyltransferase (HAT) enzymes p300 and CBP are closely related paralogs that serve as transcriptional coactivators have been found to be dysregulated in cancer other diseases. p300/CBP is a multidomain protein possesses highly conserved bromodomain has shown bind acetylated Lys residues both proteins various small molecules, including I-CBP112 CBP30. Here we show the ligand can stimulate nucleosome acetylation up 3-fold while CBP30 does not. Activation of by not observed with...
Actin-depolymerizing factor (ADF) and cofilin define a family of actin-binding proteins essential for the rapid turnover filamentous actin in vivo. Here we present 2.0 Å crystal structure Arabidopsis thaliana ADF1 (AtADF1), first plant from ADF/cofilin (AC) family. Superposition four AC isoform structures permits an accurate sequence alignment that differs previously reported data location vertebrate-specific inserts reveals contiguous, surface opposite putative surface. Extending...
Abstract Nucleosomes are substrates for a broad range of factors, including those involved in transcription or chromosome maintenance/reorganization and enzymes that covalently modify histones. Given the heterogeneous nature nucleosomes vivo (i.e., varying histone composition, post‐translational modifications, DNA sequence register), understanding specificity activities chromatin‐interacting factors has required vitro studies using well‐defined nucleosome substrates. Here, we provide...
Following DNA replication, the newly reassembled chromatin is disorganized and must mature to its steady state maintain both genome epigenome integrity. However, regulatory mechanisms governing this critical process remain poorly understood. Here, we show that histone H3K56 acetylation (H3K56ac), a mark on newly-synthesized H3, facilitates remodeling of nucleosomes in nascent chromatin, removal at subsequent G2/M phase cell cycle marks completion maturation. In vitro, H3K56ac enhances...
Sex-specific penetrance in autosomal dominant Mendelian conditions is largely understudied. The neurodevelopmental disorder Pilarowski-Bjornsson syndrome (PILBOS) was initially described females. Here, we describe the clinical and genetic characteristics of largest PILBOS cohort to date, showing that both sexes can exhibit features, although males are overrepresented. A mouse model carrying a human-derived Chd1 missense variant ( R 616 Q /+ ) displays female-restricted phenotypes, including...
Chromatin remodelers are essential for establishing and maintaining the placement of nucleosomes along genomic DNA. Yet how chromatin recognize respond to distinct environments surrounding is poorly understood. Here, we use Lac repressor as a tool probe DNA-bound factor influences action Chd1 remodeler. We show that preferentially shifts away from repressor, demonstrating defines barrier nucleosome positioning. Rather than an absolute block in sliding, effect was achieved by altered rates...
Chromatin remodelers are ATP (adenosine triphosphate)-powered motors that reposition nucleosomes throughout eukaryotic chromosomes. Remodelers possess autoinhibitory elements control the direction of nucleosome sliding, but underlying mechanisms inhibition have been unclear. Here, we show yeast Chd1 remodeler block sliding by preventing initiation twist defects. We two elements-the chromodomains and bridge-reinforce each other to when DNA-binding domain is not bound entry-side DNA. Our data...
The redox potential of cytochromes sets the energy yield possible in metabolism and is also a key determinant rate at which reactions proceed. Here, heme protein, cytochrome b562, used to study vitro evolution within library variants containing same structural archetype, four-helix bundle. Multisite variations active site b562 were introduced. A random mutations place R98 R106 was created, potentials statistical sampling this measured. This procedure carried out for both low- high-potential...
ATP‐dependent chromatin remodeling complexes play a central role in the assembly, disassembly, and repositioning of nucleosomes. While reaction is driven by conserved ATPase motor, it not known how this motor regulated auxiliary domains. We have solved crystal structure Chd1 chromodomains coupled to which suggests that negatively regulate motor. In crystal, acidic helical linker between contacts DNA‐binding surface on blocking DNA access Naked poor substrate for ATPase, we find disruption...
Chromatin remodelers are ATP‐dependent enzymes required for the active reorganization of nucleosomes. Accompanying conserved ATPase is a broad diversity auxiliary domains that define different remodeler subfamilies, and presumably help guide outcome remodeling reactions. We discovered double chromodomain unit Chd1 regulates activation motor by blocking access to DNA. Disruption chromo‐ATPase interface results in loss specificity nucleosomes over naked DNA, allowing robust DNA‐dependent...