16 Works

Data from: Comparative analysis of 2D and 3D distance measurements to study spatial genome organization

Elizabeth H. Finn, Gianluca Pegoraro, Sigal Shachar & Tom Misteli
The spatial organization of genomes is non-random, cell-type specific, and has been linked to cellular function. The investigation of spatial organization has traditionally relied extensively on fluorescence microscopy. The validity of the imaging methods used to probe spatial genome organization often depends on the accuracy and precision of distance measurements. Imaging-based measurements may either use 2 dimensional datasets or 3D datasets which include the z-axis information in image stacks. Here we compare the suitability of...

Temperature predicts the rate of molecular evolution in Australian Eugongylinae skinks

Jeremias Ivan, Craig Moritz, Sally Potter, Jason Bragg, Rust Turakulov & Xia Hua
Temperature differences over time and space has been hypothesized to cause variation in the rate of molecular evolution of species, but empirical evidence is mixed. To further test this hypothesis, we utilized a large exon-capture sequence data of Australian Eugongylinae skinks, exemplifying a radiation of temperature-sensitive ectotherms spanning a large latitudinal gradient. The association between temperature (and other species traits) and long-term substitution rate was assessed based on 1268 sequenced exons of 44 species pairs...

Data from: Phylogeography and population history of Leopardus guigna, the smallest American felid

Constanza Napolitano, Warren E. Johnson, Jim Sanderson, Stephen J. O'Brien, Rus Hoelzel, Rachel Freer, Nigel Dunstone, Kermit Ritland, Carol E. Ritland, Elie Poulin & A. Rus Hoelzel
The guigna (Leopardus guigna) is the smallest and most-restricted New World cat species, inhabiting only around 160,000 km2 of temperate rain forests in southern South America and is currently threatened by habitat loss, fragmentation and human persecution. We investigated phylogeographic patterns of genetic diversity, demographic history and barriers to gene flow with 116 individuals sampled across the species geographic range by analyzing 1,798 base pairs of the mtDNA (496 bp HVSI region, 720 bp NADH-5...

Data from: Hepatic Aryl hydrocarbon Receptor Nuclear Translocator (ARNT) regulates metabolism in mice

Christopher H. Scott, Kuan-Minn Cha, Jason Ngai, Changtao Jiang, Kim Cheng, Rebecca A. Stokes, Kenneth W.K. Ho, Jacob George, Frank J. Gonzalez, Jenny E. Gunton & Kenneth W. K. Ho
Background & Aims: Aryl hydrocarbon Receptor Nuclear Translocator (ARNT) and its partners hypoxia-inducible factors (HIF)-1α and HIF-2α are candidate factors for the well-known link between the liver, metabolic dysfunction and elevation in circulating lipids and glucose. Methods: Hepatocyte-specific ARNT-null (LARNT), HIF-1α-null (LHIF1α) and HIF-2α-null (LHIF2α) mice were created. Results: LARNT mice had increased fasting glucose, impaired glucose tolerance, increased glucose production, raised post-prandial serum triglycerides (TG) and markedly lower hepatic ATP versus littermate controls. There...

Data from: Live-cell single particle imaging reveals the role of RNA polymerase II in histone H2A.Z eviction

Anand Ranjan, Vu Q. Nguyen, Sheng Liu, Jan Wisniewski, Kim Jee Min, Xiaona Tang, Gaku Mizuguchi, Vivian Jou, Timothy J. Nickels, Brian P. English, Qinsi Zheng, Ed Luk, Timothee Lionnet, Luke D. Lavis, Carl Wu & Ejlal Elalaoui
The H2A.Z histone variant, a genome-wide hallmark of permissive chromatin, is enriched near transcription start sites in all eukaryotes. H2A.Z is deposited by the SWR1 chromatin remodeler and evicted by unclear mechanisms. We tracked H2A.Z in living yeast at single-molecule resolution, and found that H2A.Z eviction is dependent on RNA Polymerase II (Pol II) and the Kin28/Cdk7 kinase, which phosphorylates Serine 5 of heptapeptide repeats on the carboxy-terminal domain of the largest Pol II subunit...

Covid-19 SeroHub

Neal D. Freedman, Liliana Brown, Lori M. Newmann, Jefferson M. Jones, Tina J. Benoit, Francisco Averhoff, Xiangning Bu, Konuralp Bayrak, Anna Lu, Brent Coffey, Latifa Jackson, Stephen J. Chanock & Anthony R. Kerlavag
The COVID-19 Seroprevalence Studies Hub, known as COVID-19 SeroHub, is an online dashboard and data repository intended to help researchers and policymakers monitor studies of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) seroprevalence in the United States. These types of studies use blood tests to identify the proportion of people in the population who possess antibodies to SARS-CoV-2. By abstracting and presenting seroprevalence data in a standard format, COVID-19 SeroHub helps users efficiently review numerous...

GWAS Explorer, an open-source tool to explore, visualize, and access GWAS summary statistics

Machiela J. Mitchell, Wen-Yi Huang, Wendy Wong, Sonja I. Berndt, Joshua Sampson, Jonas De Almeida, Mustapha Abubakar, Jada Hislop, Kai-Ling Chen, Casey Dagnall, Norma Diaz-Mayoral, Mary Ferrell, Michael Furr, Alex Gonzalez, Belynda Hicks, Amy Hutchinson, Kevin Jiang, Kristine Jones, Jia Liu, Erikka Loftfield, Jennifer Loukissas, Jerome Mabie, Shannon Merkle, Eric Miller, Lori Minasian … & Neal Freedman
GWAS explorer provides an interactive resource for genetics researchers as well as other interested individuals to search for, visualize, and download aggregated association results from DCEG genome-wide association analyses (GWAS). Initial results are posted from The Prostate, Lung, Colorectal, Ovarian (PLCO) Cancer Screening Study, a large population-based randomized trial designed and sponsored by the National Cancer Institute (NCI) to determine the effects of screening on cancer-related mortality and secondary endpoints in men and women aged...

Data from: Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus)

Dawn M. Reding, Anne M. Bronikowski, Warren E. Johnson & William R. Clark
The potential for widespread, mobile species to exhibit genetic structure without clear geographic barriers is a topic of growing interest. Yet the patterns and mechanisms of structure – particularly over broad spatial scales – remain largely unexplored for these species. Bobcats occur across North America and possess many characteristics expected to promote gene flow. To test whether historical, topographic, or ecological factors have influenced genetic differentiation in this species, we analyzed 1 KB mtDNA sequence...

Data from: High throughput functional genomics identifies modulators of TCE metabolite genotoxicity and candidate susceptibility genes

Vanessa Y. De La Rosa, Jonathan Asfaha, Michael Fasullo, Alex Loguinov, Peng Li, Lee E. Moore, Nathaniel Rothman, Jun Nakamura, James A. Swenberg, Ghislaine Scelo, Luoping Zhang, Martyn T. Smith & Chris D. Vulpe
Trichloroethylene (TCE), an industrial chemical and environmental contaminant, is a human carcinogen. Reactive metabolites are implicated in renal carcinogenesis associated with TCE exposure, yet the toxicity mechanisms of these metabolites and their contribution to cancer and other adverse effects remain unclear. We employed an integrated functional genomics approach that combined functional profiling studies in yeast and avian DT40 cell models to provide new insights into the specific mechanisms contributing to toxicity associated with TCE metabolites....

Data from: The E3 ubiquitin ligase MARCH1 regulates glucose-tolerance and lipid storage in a sex-specific manner

Candida Bhagwandin, Erin L. Ashbeck, Michael Whalen, Joanna Bandola-Simon, Paul A. Roche, Adam Szajman, Sarah Mai Truong, Betsy C. Wertheim, Yann C. Klimentidis, Satoshi Ishido, Benjamin J. Renquist & Lonnie Lybarger
Type 2 diabetes is typified by insulin-resistance in adipose tissue, skeletal muscle, and liver, leading to chronic hyperglycemia. Additionally, obesity and type 2 diabetes are characterized by chronic low-grade inflammation. Membrane-associated RING-CH-1 (MARCH1) is an E3 ubiquitin ligase best known for suppression of antigen presentation by dendritic and B cells. MARCH1 was recently found to negatively regulate the cell surface levels of the insulin receptor via ubiquitination. This, in turn, impaired insulin sensitivity in mouse...

Data from: The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America

Juan Carlos Marín, Benito A. Gonzalez, Elie Poulin, Ciara S. Casey & Warren E. Johnson
A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold-temperate South American environments, the guanaco (Lama guanicoe), was conducted to detail patterns of molecular genetic structure related with phylogeographic history, barriers to gene flow, to describe and contrast the evolutionary history and patterns of gene flow among populations. Analyses of 514 bp of mtDNA sequence and 14 biparentally-inherited microsatellite markers of 314 individuals from 17 localities...

Data from: Patterns of population structure for inshore bottlenose dolphins along the eastern United States

Vince P. Richards, Thomas W. Greig, Patricia A. Fair, Stephen D. McCulloch, Christine Politz, Ada Natoli, Carlos A. Driscoll, A. Russell Hoelzel, Victor David, Gregory D. Bossart & Jose V. Lopez
Globally distributed, the bottlenose dolphin (Tursiops truncatus) is found in a range of offshore and coastal habitats. Using 15 microsatellite loci and mtDNA control region sequences, we investigated patterns of genetic differentiation among putative populations along the eastern US shoreline (the Indian River Lagoon, Florida, and Charleston Harbor, South Carolina) (microsatellite analyses: n = 125, mtDNA analyses: n = 132). We further utilized the mtDNA to compare these populations with those from the Northwest Atlantic,...

Data from: Anthrax toxin receptor 1 is essential for arteriogenesis in a mouse model of hindlimb ischemia

Nicholas J. Andersen, Elissa A. Boguslawski, Agni S. Naidu, Christopher Szot, Jennifer L. Bromberg-White, Kara Kits, Cynthia Y. Kuk, Laura E. Holton, Bradley St. Croix, Christopher M. Chambers & Nicholas S. Duesbery
Anthrax toxin receptor 1/tumor endothelial marker 8 (Antxr1 or TEM8) is up-regulated in tumor vasculature and serves as a receptor for anthrax toxin, but its physiologic function is unclear. The objective of this study was to evaluate the role of Antxr1 in arteriogenesis. The role of Antxr1 in arteriogenesis was tested by measuring gene expression and immunohistochemistry in a mouse model of hindlimb ischemia using wild-type and ANTXR1-/- mice. Additional tests were performed by measuring...

Data from: Epigenomic study identifies a novel mesenchyme homeobox2-GLI1 transcription axis involved in cancer drug resistance, overall survival and therapy prognosis in lung cancer patients

Leonel Armas-López, Patricia Piña-Sanchez, Oscar Arrieta, Enrique Guzman De Alba, Blanca Ortiz-Quintero, Patricio Santillán-Doherty, David C. Christiani, Joaquín Zúñiga & Federico Ávila-Moreno
Several homeobox-related gene (HOX) transcription factors such as mesenchyme HOX-2 (MEOX2) have previously been associated with cancer drug resistance, malignant progression and/or clinical prognostic responses in lung cancer patients; however, the mechanisms involved in these responses have yet to be elucidated. Here, an epigenomic strategy was implemented to identify novel MEOX2 gene promoter transcription targets and propose a new molecular mechanism underlying lung cancer drug resistance and poor clinical prognosis. Chromatin immunoprecipitation (ChIP) assays derived...

Data from: Recurrent evolution of melanism in South American felids

Alexsandra Schneider, Corneliu Henegar, Kenneth Day, Devin Absher, Constanza Napolitano, Leandro Silveira, Victor A. David, Stephen J. O’Brien, Marilyn Menotti-Raymond, Gregory S. Barsh & Eduardo Eizirik
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of the most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism for melanism but the relative roles played by genetic drift, natural selection, and interspecies hybridization remain uncertain. We identify mutations of Agouti signaling protein (ASIP) or the Melanocortin 1 receptor (MC1R) as independent causes...

The novel ciliogenesis regulator DYRK2 governs Hedgehog signaling during mouse embryogenesis

Saishu Yoshida, Katsuhiko Aoki, Ken Fujiwara, Takashi Nakakura, Akira Kawamura, Kohji Yamada, Masaya Ono, Satomi Yogosawa & Kiyotsugu Yoshida
Mammalian Hedgehog (Hh) signaling plays key roles in embryogenesis and uniquely requires primary cilia. Functional analyses of several ciliogenesis-related genes led to the discovery of the developmental diseases known as ciliopathies. Hence, identification of mammalian factors that regulate ciliogenesis can provide insight into the molecular mechanisms of embryogenesis and ciliopathy. Here, we demonstrate that DYRK2 acts as a novel mammalian ciliogenesis-related protein kinase. Loss of Dyrk2 in mice causes suppression of Hh signaling and results...

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