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Full-Text Articles in Genetics and Genomics
Mechanism Of Translation Inhibition By Type Ii Gnat Toxin Atat2, Stepan V Ovchinnikov, Dmitry Bikmetov, Alexei Livenskyi, Marina Serebryakova, Brendan Wilcox, Kyle Mangano, Dmitrii I Shiriaev, Ilya A Osterman, Petr V Sergiev, Sergei Borukhov, Nora Vazquez-Laslop, Alexander S Mankin, Konstantin Severinov, Svetlana Dubiley
Mechanism Of Translation Inhibition By Type Ii Gnat Toxin Atat2, Stepan V Ovchinnikov, Dmitry Bikmetov, Alexei Livenskyi, Marina Serebryakova, Brendan Wilcox, Kyle Mangano, Dmitrii I Shiriaev, Ilya A Osterman, Petr V Sergiev, Sergei Borukhov, Nora Vazquez-Laslop, Alexander S Mankin, Konstantin Severinov, Svetlana Dubiley
Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship
Type II toxin-antitoxins systems are widespread in prokaryotic genomes. Typically, they comprise two proteins, a toxin, and an antitoxin, encoded by adjacent genes and forming a complex in which the enzymatic activity of the toxin is inhibited. Under stress conditions, the antitoxin is degraded liberating the active toxin. Though thousands of various toxin-antitoxins pairs have been predicted bioinformatically, only a handful has been thoroughly characterized. Here, we describe the AtaT2 toxin from a toxin-antitoxin system from Escherichia coli O157:H7. We show that AtaT2 is the first GNAT (Gcn5-related N-acetyltransferase) toxin that specifically targets charged glycyl tRNA. In vivo, the AtaT2 …
Model-Based Analysis Of Chromatin Interactions From Dcas9-Based Capture-3c-Seq., Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q Zhang
Model-Based Analysis Of Chromatin Interactions From Dcas9-Based Capture-3c-Seq., Yong Chen, Yunfei Wang, Xin Liu, Jian Xu, Michael Q Zhang
Faculty Scholarship for the College of Science & Mathematics
Deciphering long-range chromatin interactions is critical for understanding temporal and tissue-specific gene expression regulated by cis- and trans-acting factors. By combining the chromosome conformation capture (3C) and biotinylated dCas9 system, we previously established a method CAPTURE-3C-seq to unbiasedly identify high-resolution and locus-specific long-range DNA interactions. Here we present the statistical model and a flexible pipeline, C3S, for analysing CAPTURE-3C-seq or similar experimental data from raw sequencing reads to significantly interacting chromatin loci. C3S provides all steps for data processing, quality control and result illustration. It can automatically define the bin size based on the binding peak of the dCas9-targeted regions. …
Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman
Relative Model Fit Does Not Predict Topological Accuracy In Single-Gene Protein Phylogenetics, Stephanie J. Spielman
Faculty Scholarship for the College of Science & Mathematics
It is regarded as best practice in phylogenetic reconstruction to perform relative model selection to determine an appropriate evolutionary model for the data. This procedure ranks a set of candidate models according to their goodness of fit to the data, commonly using an information theoretic criterion. Users then specify the best-ranking model for inference. Although it is often assumed that better-fitting models translate to increase accuracy, recent studies have shown that the specific model employed may not substantially affect inferences. We examine whether there is a systematic relationship between relative model fit and topological inference accuracy in protein phylogenetics, using …
Multiplexed Capture Of Spatial Configuration And Temporal Dynamics Of Locus-Specific 3d Chromatin By Biotinylated Dcas9., Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A Botten, Hui Cao, Stuart H Orkin, Michael Q Zhang, Jian Xu
Multiplexed Capture Of Spatial Configuration And Temporal Dynamics Of Locus-Specific 3d Chromatin By Biotinylated Dcas9., Xin Liu, Yong Chen, Yuannyu Zhang, Yuxuan Liu, Nan Liu, Giovanni A Botten, Hui Cao, Stuart H Orkin, Michael Q Zhang, Jian Xu
Faculty Scholarship for the College of Science & Mathematics
The spatiotemporal control of 3D genome is fundamental for gene regulation, yet it remains challenging to profile high-resolution chromatin structure at cis-regulatory elements (CREs). Using C-terminally biotinylated dCas9, endogenous biotin ligases, and pooled sgRNAs, we describe the dCas9-based CAPTURE method for multiplexed analysis of locus-specific chromatin interactions. The redesigned system allows for quantitative analysis of the spatial configuration of a few to hundreds of enhancers or promoters in a single experiment, enabling comparisons across CREs within and between gene clusters. Multiplexed analyses of the spatiotemporal configuration of erythroid super-enhancers and promoter-centric interactions reveal organizational principles of genome structure and function.
Geographic Life History Differences Predict Genomic Divergence Better Than Mitochondrial Barcodes Or Phenotype, Daniel P. Duran, Robert A. Laroche, Harlan M. Gough, Rodger A. Gwiazdowski, Charles B. Knisley, David P. Herrmann, Stephen J. Roman, Scott P. Egan
Geographic Life History Differences Predict Genomic Divergence Better Than Mitochondrial Barcodes Or Phenotype, Daniel P. Duran, Robert A. Laroche, Harlan M. Gough, Rodger A. Gwiazdowski, Charles B. Knisley, David P. Herrmann, Stephen J. Roman, Scott P. Egan
School of Earth & Environment Faculty Scholarship
Species diversity can be inferred using multiple data types, however, results based on genetic data can be at odds with patterns of phenotypic variation. Tiger beetles of the Cicindelidia politula (LeConte, 1875) species complex have been taxonomically problematic due to extreme phenotypic variation within and between populations. To better understand the biology and taxonomy of this group, we used mtDNA genealogies and multilocus nuclear analyses of 34,921 SNPs to elucidate its evolutionary history and evaluate the validity of phenotypically circumscribed species and subspecies. Genetic analyses recovered two divergent species that are also ecologically distinct, based on adult life history. These …