A5004810048- RNA and protein synthesis mechanisms
- Bacterial Genetics and Biotechnology
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- RNA modifications and cancer
- Epigenetics and DNA Methylation
- RNA Interference and Gene Delivery
- Escherichia coli research studies
- Data Mining Algorithms and Applications
- Bacteriophages and microbial interactions
- Natural Language Processing Techniques
- Topic Modeling
- DNA and Nucleic Acid Chemistry
- Artificial Intelligence in Law
- Vibrio bacteria research studies
- Legal Education and Practice Innovations
- Advanced biosensing and bioanalysis techniques
- CRISPR and Genetic Engineering
- Law, Economics, and Judicial Systems
- Single-cell and spatial transcriptomics
- Viral gastroenteritis research and epidemiology
- Muscle Physiology and Disorders
- Computational and Text Analysis Methods
- Machine Learning in Healthcare
- Text Readability and Simplification
Harvard University
2008-2025
Boston VA Research Institute
2022-2023
Rutgers, The State University of New Jersey
2009-2018
Ackerman Institute for the Family
2018
Rutgers Sexual and Reproductive Health and Rights
2015
Massachusetts General Hospital
2004-2008
HRL Laboratories (United States)
1991-2002
Intel (United States)
2002
University of California, Los Angeles
1985-1987
Transcription elongation is interrupted by sequences that inhibit nucleotide addition and cause RNA polymerase (RNAP) to pause. Here, use of native elongating transcript sequencing (NET-seq) a variant NET-seq enables analysis mutant RNAP derivatives in merodiploid cells (mNET-seq), we analyze transcriptional pausing genome-wide vivo Escherichia coli. We identify consensus pause-inducing sequence element, G₋₁₀Y₋₁G(+1) (where -1 corresponds the position 3' end). demonstrate sequence-specific...
During eukaryotic transcription elongation, RNA polymerase II (RNAP2) is regulated by a chorus of factors. Here, we identified common binary interaction module consisting TFIIS N-terminal domains (TNDs) and natively unstructured TND-interacting motifs (TIMs). This was conserved among the elongation machinery linked complexes including factor TFIIS, Mediator, super complex, elongin, IWS1, SPT6, PP1-PNUTS phosphatase, H3K36me3 readers, other Using nuclear magnetic resonance, live-cell...
Identifying Abortive Initiation During transcription initiation in vitro, the RNA polymerase enzyme typically engages cycles of synthesis and release short transcripts (“abortive initiation”) before breaking interactions with promoter DNA beginning elongation. Using hybridization methods developed to detect microRNAs, Goldman et al. (p. 927 ) directly detected products abortive bacterial cells vivo. increased when between were strengthened or was prevented. Thus, may help regulate gene expression.
Reactivation of fetal hemoglobin expression by the downregulation BCL11A is a promising treatment for β-hemoglobinopathies. A detailed understanding BCL11A-mediated repression γ-globin gene (HBG1/2) transcription lacking, as studies to date used perturbations shRNA or CRISPR-Cas9 editing. We leveraged dTAG PROTAC degradation platform acutely deplete protein in erythroid cells and examined consequences nascent transcriptomics, proteomics, chromatin accessibility, histone profiling. Among 31...
Despite advances in defining diverse somatic mutations that cause myeloid malignancies, a significant heritable component for these cancers remains largely unexplained. Here, we perform rare variant association studies large population cohort to identify inherited predisposition genes blood cancers. CTR9, which encodes key of the PAF1 transcription elongation complex, is among identified. The risk variants found cases loss function and result ∼10-fold increased odds acquiring malignancy....
Abstract Inactivation of the VHL gene stabilizes HIF2a, which drives clear cell renal carcinoma (ccRCC). The HIF2a inhibitor belzutifan is approved for ccRCC treatment, but de novo and acquired resistance are common. bound to ARNT, transcriptionally activates many genes. We performed CRISPRa screens in HIF2a-dependent lines treated with a analog identify HIF2a-responsive genes that confer cell-autonomous when not downregulated. Sustaining expression target CCND1, encoding Cyclin D1, promoted...
Most phenotype-associated genetic variants map to noncoding regulatory regions of the human genome, but their mechanisms remain elusive in most cases. We developed a highly efficient strategy, Perturb-multiome, simultaneously profile chromatin accessibility and gene expression single cells with CRISPR-mediated perturbation master transcription factors (TFs). examined connection between TFs, accessible regions, across genome throughout hematopoietic differentiation. discovered that within...
Prokaryotic and eukaryotic RNA polymerases can use 2- to ∼4-nt RNAs, “nanoRNAs,” prime transcription initiation in vitro. It has been proposed that nanoRNA-mediated priming of likewise occur under physiological conditions vivo influence start site selection gene expression. However, no direct evidence such regulation presented. Here we demonstrate Escherichia coli nanoRNAs a growth phase-dependent manner, resulting alterations changes We further define sequence element determines, part,...
The Shigella outer membrane protease IcsP removes the actin assembly protein IcsA from bacterial surface, and consequently modulates actin-based motility cell-to-cell spread. Here, we demonstrate that expression is undetectable in mutants lacking either of two transcriptional activators, VirF VirB. In wild-type spp., virB entirely dependent on VirF; therefore, to circumvent this regulatory cascade, independently expressed or VirB strains both activators measured levels transcription icsP...
The primary goal of our effort is the development robust and portable language processing capabilities for information extraction applications. system under evaluation here based on components that have demonstrated strong performance in previous evaluations [Lehnert et al. 1992a]. Having general viability these techniques, we are now concentrating practicality technology by creating trainable to replace hand-coded data manually-engineered software.
Most phenotype-associated genetic variants map to non-coding regulatory regions of the human genome. Moreover, associated with blood cell phenotypes are enriched in active during hematopoiesis. To systematically explore nature these regions, we developed a highly efficient strategy, Perturb-multiome, that makes it possible simultaneously profile both chromatin accessibility and gene expression single cells CRISPR-mediated perturbation range master transcription factors (TFs). This approach...
The σ subunit of bacterial RNA polymerase (RNAP) confers on the enzyme ability to initiate promoter-specific transcription. Although factors are generally classified as initiation factors, can also remain associated with, and modulate behavior of, RNAP during elongation. Here we establish that primary factor in Escherichia coli, σ(70), function an elongation vivo by loading directly onto transcription complex (TEC) trans. We demonstrate σ(70) bind trans TECs emanate from either a...
Shigella flexneri, a gram-negative enteric pathogen, is unusual in that it contains two nonredundant paralogous genes encode the myristoyl transferase MsbB (LpxM) catalyzes final step synthesis of lipid A moiety lipopolysaccharide. MsbB1 encoded on chromosome, and MsbB2 large virulence plasmid present all pathogenic shigellae. We demonstrate activity due to detected limited magnesium medium, but not replete whereas under both conditions. increases overall hexa-acylation Regulation by occurs...
Transcription initiation that involves the use of a 2- to ~4-nt oligoribonucleotide primer, "primer-dependent initiation," (PDI) has been shown be widely prevalent at promoters genes expressed during stationary phase growth in Escherichia coli. However, extent which PDI impacts E. coli physiology, and occurs other bacteria is not known. Here we establish physiological role for as regulatory mechanism modulates biofilm formation. We further demonstrate using high-throughput sequencing RNA 5′...
Abstract Gene regulation is dependent on the production of mRNAs and a repertoire non‐coding RNAs by RNA polymerase II (RNAPII). Precision run‐on sequencing (PRO‐seq) maps position engaged RNAPII complexes at single‐nucleotide resolution can reveal direct targets regulation, locations enhancers, transcription mechanisms that are difficult or impossible to measure analysis total cellular RNA. Briefly, this method first involves permeabilizing cells with mild detergents remove intracellular...
Abstract Androgen receptor (AR)-mediated transcription plays a critical role in development and prostate cancer growth. AR drives gene expression by binding to thousands of cis-regulatory elements (CRE) that loop hundreds target promoters. With multiple CREs interacting with single promoter, it remains unclear how individual bound contribute expression. To characterize the involvement these CREs, we investigate AR-driven epigenetic chromosomal chromatin looping changes generating kinetic...
ABSTRACT The Shigella actin assembly protein IcsA is removed from the bacterial surface by protease IcsP. We show that decreased intracellular spreading of virK ::Tn 10 mutants due in part to significant increases IcsP and IcsP-mediated cleavage expression a critical determinant virulence.