A5066931743- Bacterial Genetics and Biotechnology
- Genomics and Phylogenetic Studies
- Plant Disease Resistance and Genetics
- Microbial Metabolic Engineering and Bioproduction
- Cancer Genomics and Diagnostics
- Chromatin Remodeling and Cancer
- RNA and protein synthesis mechanisms
- Molecular Biology Techniques and Applications
- Bacteriophages and microbial interactions
- Legume Nitrogen Fixing Symbiosis
- CRISPR and Genetic Engineering
- Ubiquitin and proteasome pathways
- Vibrio bacteria research studies
- Cancer Mechanisms and Therapy
- Cancer-related Molecular Pathways
- Leptospirosis research and findings
- Plant-Microbe Interactions and Immunity
- Epigenetics and DNA Methylation
- Lipid metabolism and biosynthesis
- Single-cell and spatial transcriptomics
- Viral Infections and Vectors
- Diffusion and Search Dynamics
- Colorectal Cancer Treatments and Studies
- Mechanisms of cancer metastasis
- Biosensors and Analytical Detection
Broad Institute
2010-2024
Harvard University
2011-2022
Genomics (United Kingdom)
2021
Massachusetts Institute of Technology
2011-2018
University of Toledo
2007-2011
Whitehead Institute for Biomedical Research
2010
University of Toledo Medical Center
2005-2008
The stochasticity of chromosome organization was investigated by fluorescently labeling genetic loci in live Escherichia coli cells. In spite the common assumption that is well modeled an unstructured polymer, measurements locus distributions reveal E. precisely organized into a nucleoid filament with linear order. Loci body show precision positioning within cell better than 10% length. interlocus distance genomically-proximate 4% measured dependence on genomic singles out intranucleoid...
Significance The “centromere paradox” refers to rapidly evolving and highly diverse centromere DNA sequences even in closely related eukaryotes. However, factors contributing this rapid divergence are largely unknown. Here, we identified large regional, LTR retrotransposon-rich centromeres a group of human fungal pathogens belonging the Cryptococcus species complex. We provide evidence that loss-of-functional RNAi machinery possibly cytosine methylation trigger instability genome by...
Cytosine methylation of DNA is a widespread modification that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG occurs in transposon-rich repeats and requires methyltransferase Dnmt5. We show Dnmt5 displays exquisite maintenance-type specificity vitro vivo utilizes similar cofactors as metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic functional analysis revealed ancestral species lost gene for de novo methylase, DnmtX, between 50–150 mya. examined how has...
We present an automated, high throughput library construction process for 454 technology. Sample handling errors and cross-contamination are minimized via end-to-end barcoding of plasticware, along with molecular DNA constructs. Automation-friendly magnetic bead-based size selection cleanup steps have been devised, eliminating major bottlenecks significant sources error. Using this methodology, one technician can create 96 sequence-ready libraries in 2 days, a dramatic improvement over the...
Abstract PPM1D encodes a serine/threonine phosphatase that regulates numerous pathways including the DNA damage response and p53. Activating mutations amplification of are found across cancer types. GSK2830371 is potent selective allosteric inhibitor PPM1D, but its mechanism binding inhibition catalytic activity unknown. Here we use computational, biochemical functional genetic studies to elucidate molecular basis activity. These data confirm binds an site with high affinity. By further...
Schizosaccharomyces pombe Sre1 is a membrane-bound transcription factor that controls adaptation to hypoxia. Like its mammalian homolog, sterol regulatory element-binding protein (SREBP), activation requires release from the membrane. However, in fission yeast, this occurs through strikingly different mechanism Golgi Dsc E3 ubiquitin ligase complex and proteasome. The mechanistic details of cleavage, including link between proteasome, are not well understood. Here, we present results genetic...
Chromatin remodeling complexes, such as the SWItch/Sucrose Non-Fermentable (SWI/SNF) complex, play key roles in regulating gene expression by modulating nucleosome positioning. The core subunit SMARCB1 is essential for these functions, it anchors complex to acidic patch, enabling effective chromatin remodeling. While biallelic inactivation of a hallmark several aggressive pediatric malignancies, functional implication missense mutations not fully understood. Current diagnostic approaches...
SMARCB1-deficient cancers are aggressive and highly lethal pediatric malignancies. Loss of SMARCB1 protein expression, a subunit within the SWI/SNF chromatin remodeling complex, remains key diagnostic feature these cancers. This can occur through large deletions, balanced translocations, frameshift mutations, or truncating nonsense mutations. Here, we sought to understand effect missense mutations on tumor suppressor function deep mutational scanning (DMS). Specifically, developed introduced...
Borrelia burgdorferi is capable of persistently infecting a variety hosts despite eliciting potent innate and adaptive immune responses. Preliminary studies indicated that IL-10-deficient (IL-10(-/-)) mice exhibit up to 10-fold greater clearance B. from target tissues compared with wild-type mice, establishing IL-10 as the only cytokine currently known have such significant effect on spirochetal clearance. To further delineate these IL-10-mediated effects, kinetic spirochete dissemination...
A widely distributed family of small regulators, called C proteins, controls a subset restriction-modification systems. The proteins studied to date activate transcription their own genes and that downstream endonuclease genes; this arrangement appears delay expression relative the protective methyltransferase when enter new cell. bind conserved sequences boxes. In PvuII system, boxes have been reported extend from -23 +3 start for gene protein, an unexpected starting position bound...
Abstract Background Bacterial genome sequences are being determined rapidly, but few species physiologically well characterized. Predicting regulation from usually involves extrapolation better-studied bacteria, using the hypothesis that a conserved regulator, target gene, and predicted regulator-binding site in promoter imply between two species. However many compared organisms ecologically diverse, limits of have not been tested. In E. coli K- 12 l eucine-responsive r egulatory p rotein...
SUMMARY Cytosine methylation of DNA is a widespread modification that plays numerous critical roles, yet has been lost many times in diverse eukaryotic lineages. In the yeast Cryptococcus neoformans , CG occurs transposon-rich repeats and requires methyltransferase, Dnmt5. We show Dnmt5 displays exquisite maintenance-type specificity vitro vivo utilizes similar cofactors as metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic functional analysis revealed ancestral species gene for...
ABSTRACT The AsnC/Lrp family of regulatory proteins links bacterial and archaeal transcription patterns to metabolism. In Escherichia coli , Lrp regulates approximately 400 genes, over 200 them directly. earlier studies, lrp genes from Vibrio cholerae Proteus mirabilis E. were introduced into the same background yielded overlapping but significantly different regulons. These differences seen despite amino acid sequence identities 92% ( ) 98% Lrp, including complete conservation...
Abstract Pooled variant expression libraries can test the phenotypes of thousands variants a gene in single multiplexed experiment. In library encoding all single-amino-acid substitutions protein, each differs from its reference only at codon-position located anywhere along coding sequence. Consequently, accurately identifying these by sequencing is major technical challenge. A popular but expensive brute-force approach to divide pool into multiple smaller sub-libraries that contains small...
Abstract SMARCB1-deficient cancers are aggressive and highly lethal pediatric malignancies. Loss of SMARCB1 protein expression, a subunit within the SWI/SNF chromatin remodeling complex, remains key diagnostic feature these cancers. This can occur through large deletions, balanced translocations, frameshift mutations, or truncating nonsense mutations. Here, we sought to understand effect missense mutations on tumor suppressor function deep mutational scanning (DMS).Specifically, developed...
Abstract KRAS is the most commonly mutated oncogenes and a major driver of tumor initiation progression. Understanding functional consequences cancer-associated variants may have important clinical implications. For example, mutation status defines those that are likely to respond EGFR-directed therapy in KRAS-mutant metastatic colorectal cancer. A compendium all possible oncogenic alleles would serve as roadmap for future therapeutic strategies directed at itself or downstream signaling...