A5005789196- RNA and protein synthesis mechanisms
- DNA Repair Mechanisms
- Genomics and Chromatin Dynamics
- DNA and Nucleic Acid Chemistry
- RNA modifications and cancer
- CRISPR and Genetic Engineering
- RNA Research and Splicing
- Chromosomal and Genetic Variations
- Genomic variations and chromosomal abnormalities
- Epigenetics and DNA Methylation
- Genetic Neurodegenerative Diseases
- Cancer Genomics and Diagnostics
- Thyroid Disorders and Treatments
- Genomics and Phylogenetic Studies
- PARP inhibition in cancer therapy
- Genetic factors in colorectal cancer
- Genetics and Neurodevelopmental Disorders
- Cancer-related gene regulation
- Bacterial Genetics and Biotechnology
- Advanced biosensing and bioanalysis techniques
- Mitochondrial Function and Pathology
- Enzyme Structure and Function
- RNA regulation and disease
- Cancer-related molecular mechanisms research
- Metabolism and Genetic Disorders
The University of Texas MD Anderson Cancer Center
2011-2024
The University of Texas at Austin
2011-2018
Cardiff University
2015-2016
Frederick National Laboratory for Cancer Research
2012-2015
Texas Research Institute
2012-2015
Leidos (United States)
2015
Science Applications International Corporation (United States)
2010-2013
University of Arkansas – Fort Smith
2013
National Cancer Institute
2011-2012
Texas Medical Center
1997-2009
A method is described to express and purify human DNA (cytosine-5) methyltransferase (human DNMT1) using a protein splicing (intein) fusion partner in baculovirus expression vector. The system produces ∼1 mg of intact recombinant enzyme >95% pure per 1.5 × 109 insect cells. lacks any affinity tag identical the native except for two C-terminal amino acids, proline glycine, that were substituted lysine aspartic acid optimal cleavage from intein tag. Human DNMT1 was used steady-state kinetic...
Genomic rearrangements are a frequent source of instability, but the mechanisms involved poorly understood. A 2.5-kbp poly(purine·pyrimidine) sequence from human PKD1 gene, known to form non-B DNA structures, induced long deletions and other instabilities in plasmids that were mediated by mismatch repair and, some cases, transcription. The breakpoints occurred at predicted structures. Distance measurements also indicated significant proximity alternating purine-pyrimidine...
The non-B DB, available at http://nonb.abcc.ncifcrf.gov, catalogs predicted DNA-forming sequence motifs, including Z-DNA, G-quadruplex, A-phased repeats, inverted mirror direct repeats and their corresponding subsets: cruciforms, triplexes slipped structures, in several genomes. Version 2.0 of the database revises re-implements motif discovery algorithms to better align with accepted definitions thresholds for expands motifs coverage by short tandem adds key visualization tools compare...
Gross chromosomal rearrangements (including translocations, deletions, insertions and duplications) are a hallmark of cancer genomes often create oncogenic fusion genes. An obligate step in the generation such gross is formation DNA double-strand breaks (DSBs). Since genomic distribution rearrangement breakpoints non-random, intrinsic cellular factors may predispose certain regions to breakage. Notably, sequences with potential fold into secondary structures [potential non-B (PONDS); e.g....
Analyses of chromosomal aberrations in human genetic disorders have revealed that inverted repeat sequences (IRs) often co-localize with endogenous instability and breakage hotspots. Approximately 80% all IRs the genome are short (<100 bp), yet mutagenic potential such cruciform-forming has not been characterized. Here, we find enriched at translocation breakpoints cancer stimulate formation DNA double-strand breaks (DSBs) deletions mammalian yeast cells. We provide evidence for...
Lung cancer is the leading cause of cancer‐related deaths worldwide. Recent advances in whole genome transcriptome analysis have enabled identification numerous members a novel class non‐coding RNAs, i.e., long RNAs (lncRNAs), which play important roles wide range biological processes and whose deregulation causes human disease, including cancer. Herein we provide comprehensive survey lncRNAs associated with lung cancer, particular focus on functions that either facilitate or inhibit...
Abstract Poly(ADP-ribose)ylation (PARylation) by PAR polymerase 1 (PARP1) and PARylation removal poly(ADP-ribose) glycohydrolase (PARG) critically regulate DNA damage responses; yet, conflicting reports obscure PARG biology its impact on cancer cell resistance to PARP1 inhibitors. Here, we found that expression is upregulated in many cancers. We employed chemical library screening identify optimize methylxanthine derivatives as selective bioavailable Multiple crystal structures reveal how...
A region of human genomic DNA encompossing the 5′ end thyroglobulin gene has been sequenced and position transcriptional start site determined. The non-translated portion mRNA displays a quasilindromic sequence which could allow this to adopt hairpin structure. first exon encodes 19 amino-acids signal peptide 3 amino acids mature protein. Apart from canonical TATA-Box CAAT-Box homology, promoter contains 209 bp-long poly(purine)-poly (pyrimidine) located between posltions-512 -304 relative...
Naturally occurring poly(purine·pyrimidine) rich regions in the human genome are prone to adopting non-canonical DNA structures such as intramolecular triplexes (i.e., H-DNA). Such structure-forming sequences abundant and can regulate expression of several disease-linked genes. In addition, use triplex-forming oligonucleotides (TFOs) modulate gene structure function has potential an approach targeted therapy. Previously, we found that endogenous H-DNA induce double-strand breaks promote...
Although the capability of DNA to form a variety non-canonical (non-B) structures has long been recognized, overall significance these alternate conformations in biology only recently become accepted en masse . In order provide access genome-wide locations classes predicted structures, we have developed non-B DB, database integrating annotations and analysis DNA-forming sequence motifs. The provides most complete list alternative structure predictions available, including Z-DNA motifs,...
Abstract Sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures in human genome been implicated stimulating genomic instability. Previously, we found a naturally occurring intra-molecular triplex (H-DNA) caused genetic instability mammals largely form of double-strand breaks. Thus, it is interest determine mechanism(s) involved processing H-DNA. Recently, demonstrated DHX9 helicase preferentially unwinds inter-molecular vitro. Herein, used mutation-reporter system...
Abstract RAD51C is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog define separable replication stability roles informed by its three-dimensional structure, assembly, unappreciated polymerization motif. Mapping of cancer...
Abstract Polymerase theta (Polθ) acts in DNA replication and repair, its inhibition is synthetic lethal BRCA1 BRCA2-deficient tumor cells. Novobiocin (NVB) a first-in-class inhibitor of the Polθ ATPase activity, it currently being tested clinical trials as an anti-cancer drug. Here, we investigated molecular mechanism NVB-mediated inhibition. Using hydrogen deuterium exchange-mass spectrometry (HX-MS), biophysical, biochemical, computational cellular assays, found NVB non-competitive ATP...
Abstract TAR DNA-binding protein 43 (TDP43) is increasingly recognized for its involvement in neurodegenerative diseases, particularly amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). TDP43 proteinopathy, characterized by dysregulated nuclear export cytoplasmic aggregation, present most ALS/FTD cases associated with a loss of function genomic instability neurons. Building on prior evidence linking pathology to DNA double-strand breaks (DSBs), this study identifies novel...
Initial velocity determinations were conducted with human DNA (cytosine-5) methyltransferase (DNMT1) on unmethylated and hemimethylated templates in order to assess the mechanism of reaction. data and<i>S</i>-adenosylmethionine (AdoMet) as variable substrates product inhibition studies methylated and<i>S</i>-adenosylhomocysteine (AdoHcy) obtained evaluated double-reciprocal plots. These relationships linear for plasmid DNA, exon-1 from imprinted small nuclear ribonucleoprotein-associated...
Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT), an important therapeutic target in the treatment of AIDS, is effectively inhibited by a class nonnucleoside analog compounds that includes nevirapine (BI-RG-587) and tetrahydroimidazo[4,5,1-jk]-[1,4]benzodiazepin-2(1H)-one -thione. We show both tyrosine residues at positions 181 188 flanking putative catalytic site HIV-1 RT are required for sensitivity enzyme to these compounds. HIV-2 RT, which does not have tyrosines...
Microsatellites are abundant in vertebrate genomes, but their sequence representation and length distributions vary greatly within each family of repeats (e.g., tetranucleotides). Biophysical studies 82 synthetic single-stranded oligonucleotides comprising all tetra- trinucleotide revealed an inverse correlation between the stability folded-back hairpin quadruplex structures for ≥30 bp nine genomes. Alternatively, predicted energies base-stacking interactions correlated directly with longest...