A5066902283- Genomics and Chromatin Dynamics
- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- CRISPR and Genetic Engineering
- DNA and Nucleic Acid Chemistry
- Fungal and yeast genetics research
- Advanced biosensing and bioanalysis techniques
- RNA modifications and cancer
- RNA Interference and Gene Delivery
- Cancer-related gene regulation
- Bacterial Genetics and Biotechnology
- DNA Repair Mechanisms
- Protein Degradation and Inhibitors
- Gene Regulatory Network Analysis
- Pluripotent Stem Cells Research
- Ubiquitin and proteasome pathways
- Gene expression and cancer classification
- Bacteriophages and microbial interactions
- Cancer-related molecular mechanisms research
- Genetic Neurodegenerative Diseases
- Bioinformatics and Genomic Networks
- Epigenetics and DNA Methylation
- Chemical Synthesis and Analysis
- Animal Genetics and Reproduction
- Plant Molecular Biology Research
University of Saskatchewan
2025
St. Jude Children's Research Hospital
2020-2024
Energy Center of Wisconsin
2008-2019
University of Wisconsin–Madison
2010-2019
California Institute of Technology
2000-2007
Kettering University
2002-2005
Memorial Sloan Kettering Cancer Center
1998-2002
Massachusetts Institute of Technology
2001-2002
Whitehead Institute for Biomedical Research
2002
Harvard University
1998-2001
Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA ncRNA in opposite directions. We demonstrate that, adopting a gene-loop conformation, actively transcribed encoding genes restrict divergent transcription of ncRNAs. Because formation depends on protein factor (Ssu72) coassociates with the promoter...
Determining the sequence-recognition properties of DNA-binding proteins and small molecules remains a major challenge. To address this need, we have developed high-throughput approach that provides comprehensive profile binding molecules. The is based on displaying every permutation duplex DNA sequence (up to 10 positional variants) microfabricated array. entire space interrogated simultaneously, affinity molecule for obtained in rapid, unbiased, unsupervised manner. Using platform,...
Three cyclin-dependent kinases, CDK7, -8, and -9, are specifically involved in transcription by RNA polymerase II (Pol II) target the Pol C-terminal domain (CTD). The role of CDK7 CDK8 kinase activity has been unclear, with shown to have variable effects on suggested repress and/or other gene-specific factors. Using a chemical genetics approach, Saccharomyces cerevisiae homologs these Kin28 Srb10, were engineered respond specific inhibitor was used test kinases vivo vitro. In vitro, can both...
How transcription factor dimerization impacts DNA-binding specificity is poorly understood. Guided by protein properties, we examined DNA binding specificities of 270 human bZIP pairs. interactomes 80 heterodimers and 22 homodimers revealed that 72% heterodimer motifs correspond to conjoined half-sites preferred partnering monomers. Remarkably, the remaining are composed variably-spaced (12%) or ‘emergent’ sites (16%) cannot be readily inferred from half-site preferences These were...
Despite the importance of maintaining redox homeostasis for cellular viability, how cells control balance globally is poorly understood. Here we provide new mechanistic insight into between reduced and oxidized electron carriers regulated at level gene expression by mapping regulon response regulator ArcA from Escherichia coli, which responds to quinone/quinol couple via its membrane-bound sensor kinase, ArcB. Our genome-wide analysis reveals that reprograms metabolism under anaerobic...
The control and function of RNA are governed by the specificity binding proteins. Here, we describe a method for global unbiased analysis RNA-protein interactions that uses in vitro selection, high-throughput sequencing, sequence-specificity landscapes. yields affinities vast array RNAs single experiment, including both low- high-affinity sites. It is reproducible accurate. Using this approach,we analyzed members PUF (Pumilio FBF) family eukaryotic mRNA regulators. Our data identify effects...
The release of paused RNA polymerase II into productive elongation is highly regulated, especially at genes that affect human development and disease. To exert control over this rate-limiting step, we designed sequence-specific synthetic transcription factors (Syn-TEFs). These molecules are composed programmable DNA-binding ligands flexibly tethered to a small molecule engages the machinery. By limiting activity targeted loci, Syn-TEFs convert constituent modules from broad-spectrum...
Abstract Stressed cells coordinate a multi‐faceted response spanning many levels of physiology. Yet knowledge the complete stress‐activated regulatory network as well design principles for signal integration remains incomplete. We developed an experimental and computational approach to integrate available protein interaction data with gene fitness contributions, mutant transcriptome profiles, phospho‐proteome changes in responding salt stress, infer salt‐responsive signaling yeast. The...
Eukaryotic transcriptional activators are minimally comprised of a DNA binding domain and separable activation domain; most activator proteins also bear dimerization module. We have replaced these protein modules with synthetic counterparts to create artificial transcription factors. One these, at 4.2 kDa, mediates high levels site-specific in vitro . This molecule contains sequence-specific polyamide place the typical region nonprotein linker usual peptide. Thus our activating region,...
The process of gene transcription requires the recruitment a hypophosphorylated form RNA polymerase II (Pol II) to promoter. TFIIH-associated kinase Cdk7/Kin28 hyperphosphorylates promoter-bound polymerase; this event is thought play crucial role in initiation and promoter clearance. Studies using temperature-sensitive mutants Kin28 have provided most compelling evidence for an essential its activity global mRNA synthesis. In contrast, small molecule inhibitor that specifically inhibits...
The C-terminal domain (CTD) of the largest subunit RNA polymerase II (Pol II) serves an important role in coordinating stage-specific recruitment and release cellular machines during transcription. Dynamic placement removal phosphorylation marks on different residues a repeating heptapeptide (YSPTSPS) CTD underlies engagement relevant machinery. Whereas sequential is well explored, genome-wide phosphatases that remove these poorly understood. In particular, identifying enzyme erases...
Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that hinders ability to decipher gene regulatory networks or engineer act on genomes. Here we compare sequence specificities for different classes proteins and engineered across entire space. These high-content data are visualized interpreted using an interactive “specificity landscape” which simultaneously displays affinity million-plus sequences. Contrary expectation, landscapes reveal synthetic ligands...