A5053552465- Seismic Waves and Analysis
- Methane Hydrates and Related Phenomena
- Earthquake Detection and Analysis
- Ionosphere and magnetosphere dynamics
- Genomics and Chromatin Dynamics
- DNA Repair Mechanisms
- Epigenetics and DNA Methylation
- CRISPR and Genetic Engineering
- DNA and Nucleic Acid Chemistry
- Bacterial Genetics and Biotechnology
- Histone Deacetylase Inhibitors Research
- Cancer-related gene regulation
- Digital Games and Media
- RNA modifications and cancer
- Comics and Graphic Narratives
- RNA and protein synthesis mechanisms
- Protein Degradation and Inhibitors
- RNA Interference and Gene Delivery
- HIV Research and Treatment
- Advanced biosensing and bioanalysis techniques
- Cancer Genomics and Diagnostics
- Cinema and Media Studies
- PARP inhibition in cancer therapy
- Autophagy in Disease and Therapy
- Enzyme Structure and Function
University of Kansas Medical Center
2020-2025
The University of Kansas Cancer Center
2020-2024
University of Maryland, College Park
2024
University of Iowa
2017-2021
Polycomb repressive complex 1 (PRC1) is critical for mediating gene expression during development. Five chromobox (CBX) homolog proteins, CBX2, CBX4, CBX6, CBX7, and CBX8, are incorporated into PRC1 complexes, where they mediate targeting to trimethylated lysine 27 of histone H3 (H3K27me3) via the N-terminal chromodomain (ChD). Individual CBX paralogs have been implicated as drug targets in cancer; however, high similarities sequence structure among ChDs provide a major obstacle developing...
Abstract Genomic DNA is continually exposed to endogenous and exogenous factors that promote damage. Eukaryotic genomic packaged into nucleosomes, which present a barrier accessing effectively repairing The mechanisms by repair proteins overcome this damage in the nucleosome protect stability unknown. Here, we determine how base excision (BER) endonuclease AP-endonuclease 1 (APE1) recognizes cleaves nucleosome. Kinetic assays APE1 solvent-exposed AP sites with 3 − 6 orders of magnitude...
<title>Abstract</title> Ligation of DNA single strand breaks is critical for maintaining genome integrity during replication and repair. Ligase III (LIG3α) forms an important complex with X-ray cross complementing protein 1 (XRCC1) break base excision We utilized a real time molecule approach to quantify binding kinetics Halo-tagged LIG3α XRCC1-YFP from nuclear extracts on long substrates containing nicks, nucleosomes or nicks embedded in nucleosomes. displayed higher affinity than XRCC1 the...
Abstract Single-strand breaks (SSBs) are one of the most prevalent forms DNA damage found in chromatinized genome and repaired by single-strand break repair (SSBR) or base excision (BER). polymerase beta (Pol β) is primary enzyme responsible for processing 1-nt gap intermediate chromatin during SSBR BER. To date, mechanism used Pol β to process a context remains poorly understood. Here, we use biochemical assays cryogenic electron microscopy (cryo-EM) determine kinetic structural basis...
Polycomb repressive complex 1 (PRC1) is critical for mediating gene repression during development and adult stem cell maintenance. Five CBX proteins, CBX2,4,6,7,8, form mutually exclusive PRC1 complexes are thought to play a role in the association of with chromatin. Specifically, N-terminal chromodomain (CD) proteins mediate specific targeting methylated histones. For CBX8, however, has demonstrated weak affinity specificity histones vitro, leaving doubt as its CBX8 chromatin association....
Clinical success with poly (ADP-ribose) polymerase inhibitors (PARPi) is impeded by inevitable resistance and associated cytotoxicity. Depletion of Amplified in Liver Cancer 1 (ALC1), a chromatin-remodeling enzyme, can overcome these limitations hypersensitizing BReast CAncer genes 1/2 (BRCA1/2) mutant cells to PARPi. Here, we demonstrate that PARPi hypersensitivity upon ALC1 loss reliant on its role promoting the repair chromatin buried abasic sites. We show enhances ability site processing...
SANT domains are found in a number of chromatin regulators. They contain approximately 50 amino acids and have high similarity to the DNA binding domain Myb related proteins. Though some associate with others been bind unmodified histone tails. There two Enhancer Zeste 2 (EZH2), catalytic subunit Polycomb Repressive Complex (PRC2), unknown function. Here we show that first (SANT1) EZH2 is specificity for H4 N-terminal tail. Using NMR spectroscopy, mutagenesis, molecular modeling structurally...
Abstract 8-oxoguanine (8-oxoG) is a common oxidative DNA lesion that causes G > T substitutions. Determinants of local and regional differences in 8-oxoG-induced mutability across genomes are currently unknown. Here, we show oxidation induces substitutions insertion/deletion (INDEL) mutations human cells cancers. Potassium bromate (KBrO 3 )-induced 8-oxoGs occur with similar sequence preferences as their derived substitutions, indicating the reactivity specific oxidants dictates mutation...
Rapid and accurate bacterial detection methods are needed for clinical diagnostic, water, food testing applications. The wide diversity of nucleases provides a rich source enzymes that could be exploited as signal amplifying biomarkers to enable rapid, selective species. With the exception use micrococcal nuclease activity detect Staphylococcus aureus, rapid pathogens via their activities have not been developed. Here, we identify endonuclease I robust biomarker E. coli develop...
Canonical targeting of Polycomb repressive complex 1 (PRC1) to repress developmental genes is mediated by cell-type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7, and 8). Based on their central role in silencing dysregulation associated with human disease including cancer, CBX are attractive targets for small-molecule chemical probe development. Here, we have used a quantitative target-specific cellular assay discover potent positive allosteric modulator (PAM) CBX8. The PAM...
Significance Translesion synthesis (TLS) DNA polymerases bypass damage that is unable to be accommodated by replicative polymerase active sites. The TLS Rev1 bypasses a variety of damage, including exocyclic guanine adducts and abasic sites using unique protein-template mechanism. Using time-lapse X-ray crystallography, computational analysis, enzyme kinetics, we provide insight into the mechanism used Rev1. Our structural snapshots identify movement primer strand facilitates precatalytic...
Abstract Rev1 is a translesion DNA synthesis (TLS) polymerase involved in the bypass of adducted-guanine bases and abasic sites during replication. During damage bypass, utilizes protein-template mechanism synthesis, where templating base evicted from active site replaced by an arginine side chain that preferentially binds incoming dCTP. Here, we utilize X-ray crystallography molecular dynamics simulations to obtain structural insight into dCTP specificity Rev1. We show R324 forms...
Abstract 8-oxoguanine (8-oxoG) is a common oxidative DNA lesion, which causes G>T substitutions that compose COSMIC single base substitution signature 18 (SBS18) in human cancers. Determinants of local and regional differences 8-oxoG-induced mutability are currently unknown. To uncover factors influencing the topology mutations, we assessed spontaneous KBrO 3 -induced 8-oxoG mutagenesis cell lines. exposure produced SBS18-like spectrum distinct never-before reported INDEL also observed...
Abstract Base excision repair is the main pathway involved in active DNA demethylation. 5-formylctyosine and 5-carboxylcytosine, two oxidized moieties of methylated cytosine, are recognized removed by thymine glycosylase (TDG) to generate an abasic site. Using single molecule fluorescence experiments, we studied TDG presence absence 5-formylctyosine. exhibits multiple modes linear diffusion, including hopping sliding, search a lesion. We probed site variants truncated N-terminus revealing...
Abasic sites are common mutagenic DNA lesions that occur as products of damage, spontaneously arising up to 10,000 times per cell day. To prevent mutagenesis, the repair abasic is initiated by enzyme Apurinic/Apyrimidinic Endonuclease I (APE1). While mechanism used APE1 process well established, how searches for and recognizes amongst a vast excess undamaged remains poorly understood. address this gap in knowledge, we utilized correlative optical tweezers fluorescence microscopy (CTFM)...
Base excision repair is the main pathway involved in active DNA demethylation. 5-formylcytosine and 5-carboxylcytosine, two oxidized moieties of methylated cytosine, are recognized removed by thymine glycosylase (TDG) to generate an abasic site. Using single molecule fluorescence experiments, we study TDG presence absence 5-formylcytosine. exhibits multiple modes linear diffusion, including hopping sliding, search base modifications. site variants truncated N-terminus, reveals these alter...
Abstract Single-strand breaks (SSBs) are one of the most prevalent forms DNA damage found in chromatinized genome and repaired by direct single-strand break repair (SSBR) or base excision (BER). polymerase beta (Pol β) is primary enzyme responsible for processing 1-nt gap intermediate chromatin during SSBR BER. However, mechanism used Pol β to process a context nucleosome remains poorly understood. Here, we use biochemical assays cryogenic electron microscopy (cryo-EM) determine kinetic...
Abstract Proteasomes are formed by chaperone-assisted assembly of core particles (CPs) and regulatory (RPs). The CP chaperone dimer Pba1/Pba2 binds early to proteasome subunits, is thought be replaced Blm10 form Blm10:CP, which promotes ATP-independent degradation disordered proteins. Here, we present evidence distinct parallel pathways for solving five cryo-EM structures including a Blm10:13S pre-assembly intermediate. Our data conflict with the current model sequential activity in single...
By observing one molecule at a time, single-molecule studies can offer detailed insights about biomolecular processes including on rates, off and diffusivity of molecules strands DNA. A recent technological advance (Single-molecule Analysis DNA-binding proteins from Nuclear Extracts, SMADNE) has lowered the barrier to entry for studies, dynamics now be determined directly out nuclear extracts, providing information in an intermediate environment between purified isolation heterogeneity...
ABSTRACT Canonical targeting of Polycomb Repressive Complex 1 (PRC1) to repress developmental genes is mediated by cell type-specific, paralogous chromobox (CBX) proteins (CBX2, 4, 6, 7 and 8). Based on their central role in silencing misregulation associated with human disease including cancer, CBX are attractive targets for small molecule chemical probe development. Here, we have used a quantitative target-specific cellular assay discover potent positive allosteric modulator (PAM) CBX8....