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Urban JM, Bateman JR, Garza KR, Borden J, Jain J, Brown A, Thach BJ, Bliss JE, Gerbi SA. Bradysia (Sciara) coprophila larvae up-regulate DNA repair pathways and down-regulate developmental regulators in response to ionizing radiation. Genetics 2024; 226:iyad208. [PMID: 38066617 PMCID: PMC10917502 DOI: 10.1093/genetics/iyad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
The level of resistance to radiation and the developmental and molecular responses can vary between species, and even between developmental stages of one species. For flies (order: Diptera), prior studies concluded that the fungus gnat Bradysia (Sciara) coprophila (sub-order: Nematocera) is more resistant to irradiation-induced mutations that cause visible phenotypes than the fruit fly Drosophila melanogaster (sub-order: Brachycera). Therefore, we characterized the effects of and level of resistance to ionizing radiation on B. coprophila throughout its life cycle. Our data show that B. coprophila embryos are highly sensitive to even low doses of gamma-irradiation, whereas late-stage larvae can tolerate up to 80 Gy (compared to 40 Gy for D. melanogaster) and still retain their ability to develop to adulthood, though with a developmental delay. To survey the genes involved in the early transcriptional response to irradiation of B. coprophila larvae, we compared larval RNA-seq profiles with and without radiation treatment. The up-regulated genes were enriched for DNA damage response genes, including those involved in DNA repair, cell cycle arrest, and apoptosis, whereas the down-regulated genes were enriched for developmental regulators, consistent with the developmental delay of irradiated larvae. Interestingly, members of the PARP and AGO families were highly up-regulated in the B. coprophila radiation response. We compared the transcriptome responses in B. coprophila to the transcriptome responses in D. melanogaster from 3 previous studies: whereas pathway responses are highly conserved, specific gene responses are less so. Our study lays the groundwork for future work on the radiation responses in Diptera.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD 21218, USA
| | - Jack R Bateman
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Kodie R Garza
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Julia Borden
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Jaison Jain
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Alexia Brown
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Bethany J Thach
- Biology Department, Bowdoin College, Brunswick, ME 04011, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Providence, RI 02912, USA
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Pang LY, DeLuca S, Zhu H, Urban JM, Spradling AC. Chromatin and gene expression changes during female Drosophila germline stem cell development illuminate the biology of highly potent stem cells. eLife 2023; 12:RP90509. [PMID: 37831064 PMCID: PMC10575629 DOI: 10.7554/elife.90509] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2023] Open
Abstract
Highly potent animal stem cells either self renew or launch complex differentiation programs, using mechanisms that are only partly understood. Drosophila female germline stem cells (GSCs) perpetuate without change over evolutionary time and generate cystoblast daughters that develop into nurse cells and oocytes. Cystoblasts initiate differentiation by generating a transient syncytial state, the germline cyst, and by increasing pericentromeric H3K9me3 modification, actions likely to suppress transposable element activity. Relatively open GSC chromatin is further restricted by Polycomb repression of testis or somatic cell-expressed genes briefly active in early female germ cells. Subsequently, Neijre/CBP and Myc help upregulate growth and reprogram GSC metabolism by altering mitochondrial transmembrane transport, gluconeogenesis, and other processes. In all these respects GSC differentiation resembles development of the totipotent zygote. We propose that the totipotent stem cell state was shaped by the need to resist transposon activity over evolutionary timescales.
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Affiliation(s)
- Liang-Yu Pang
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Steven DeLuca
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Haolong Zhu
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - John M Urban
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
| | - Allan C Spradling
- Howard Hughes Medical Institute, Carnegie Institution for ScienceBaltimoreUnited States
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Feyereisen R, Urban JM, Nelson DR. Aliens in the CYPome of the black fungus gnat, Bradysia coprophila. Insect Biochem Mol Biol 2023; 159:103965. [PMID: 37271423 DOI: 10.1016/j.ibmb.2023.103965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 05/21/2023] [Accepted: 05/25/2023] [Indexed: 06/06/2023]
Abstract
The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of "alien" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such "alien" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.
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Affiliation(s)
- René Feyereisen
- Laboratory of Agrozoology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium.
| | - John M Urban
- Carnegie Institution for Science, Department of Embryology, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - David R Nelson
- Department of Microbiology, Immunology and Biochemistry, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
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Baird RB, Urban JM, Mongue AJ, Jaron KS, Hodson CN, Grewoldt M, Martin SH, Ross L. Recent evolution of a maternally-acting sex-determining supergene in a fly with single-sex broods. Mol Biol Evol 2023:msad148. [PMID: 37352554 DOI: 10.1093/molbev/msad148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 05/30/2023] [Accepted: 06/15/2023] [Indexed: 06/25/2023] Open
Abstract
Sex determination is a key developmental process, yet it is remarkably variable across the tree of life. The dipteran family Sciaridae exhibits one of the most unusual sex determination systems in which mothers control offspring sex through selective elimination of paternal X chromosomes. Whereas in some members of the family females produce mixed-sex broods, others such as the dark-winged fungus gnat Bradysia coprophila are monogenic, with females producing single-sex broods. Female-producing females were previously found to be heterozygous for a large X-linked paracentric inversion (X´), which is maternally inherited and absent from male-producing females. Here we assembled and characterized the X´ sequence. As close sequence homology between the X and X´ made identification of the inversion challenging, we developed a k-mer-based approach to bin genomic reads before assembly. We confirmed that the inversion spans most of the X´ chromosome (approximately 55Mb) and encodes around 3500 genes. Analysis of the divergence between the inversion and the homologous region of the X revealed that it originated very recently (<0.5 mya). Surprisingly, we found that the X´ is more complex than previously thought and is likely to have undergone multiple rearrangements that have produced regions of varying ages, resembling a supergene composed of evolutionary strata. We found functional degradation of around 7.3% of genes within the region of recombination suppression, but no evidence of accumulation of repetitive elements. Our findings provide an indication that sex-linked inversions are driving turnover of the strange sex determination system in this family of flies.
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Affiliation(s)
- Robert B Baird
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - John M Urban
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, Baltimore, Maryland 21218. United States of America
| | - Andrew J Mongue
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Kamil S Jaron
- Tree of Life Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Christina N Hodson
- Department of Zoology, University of British Columbia, Vancouver, V6T 1Z4, Canada
| | - Malte Grewoldt
- Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus, Denmark
| | - Simon H Martin
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
| | - Laura Ross
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3JT, UK
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Urban JM, Foulk MS, Bliss JE, Coleman CM, Lu N, Mazloom R, Brown SJ, Spradling AC, Gerbi SA. High contiguity de novo genome assembly and DNA modification analyses for the fungus fly, Sciara coprophila, using single-molecule sequencing. BMC Genomics 2021; 22:643. [PMID: 34488624 PMCID: PMC8419958 DOI: 10.1186/s12864-021-07926-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 08/08/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND The lower Dipteran fungus fly, Sciara coprophila, has many unique biological features that challenge the rule of genome DNA constancy. For example, Sciara undergoes paternal chromosome elimination and maternal X chromosome nondisjunction during spermatogenesis, paternal X elimination during embryogenesis, intrachromosomal DNA amplification of DNA puff loci during larval development, and germline-limited chromosome elimination from all somatic cells. Paternal chromosome elimination in Sciara was the first observation of imprinting, though the mechanism remains a mystery. Here, we present the first draft genome sequence for Sciara coprophila to take a large step forward in addressing these features. RESULTS We assembled the Sciara genome using PacBio, Nanopore, and Illumina sequencing. To find an optimal assembly using these datasets, we generated 44 short-read and 50 long-read assemblies. We ranked assemblies using 27 metrics assessing contiguity, gene content, and dataset concordance. The highest-ranking assemblies were scaffolded using BioNano optical maps. RNA-seq datasets from multiple life stages and both sexes facilitated genome annotation. A set of 66 metrics was used to select the first draft assembly for Sciara. Nearly half of the Sciara genome sequence was anchored into chromosomes, and all scaffolds were classified as X-linked or autosomal by coverage. CONCLUSIONS We determined that X-linked genes in Sciara males undergo dosage compensation. An entire bacterial genome from the Rickettsia genus, a group known to be endosymbionts in insects, was co-assembled with the Sciara genome, opening the possibility that Rickettsia may function in sex determination in Sciara. Finally, the signal level of the PacBio and Nanopore data support the presence of cytosine and adenine modifications in the Sciara genome, consistent with a possible role in imprinting.
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Affiliation(s)
- John M Urban
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA.
| | - Michael S Foulk
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
- Present Address: Department of Biology, Mercyhurst University, Erie, PA, 16546, USA
| | - Jacob E Bliss
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA
| | - C Michelle Coleman
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Nanyan Lu
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Reza Mazloom
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Susan J Brown
- KSU Bioinformatics Center, Kansas State University Division of Biology, Ackert Hall, Manhattan, Kansas, 66502, USA
| | - Allan C Spradling
- Department of Embryology, Carnegie Institution for Science, Howard Hughes Medical Institute Research Laboratories, 3520 San Martin Drive, Baltimore, MD, 21218, USA
| | - Susan A Gerbi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University Division of Biology and Medicine, Sidney Frank Hall for Life Sciences, 185 Meeting Street, Providence, RI, 02912, USA.
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Urban JM, Baranowski M, Surrente A, Wlodarczyk D, Suchocki A, Long G, Wang Y, Klopotowski L, Wang N, Maude DK, Plochocka P. Observation of A Raman mode splitting in few layer black phosphorus encapsulated with hexagonal boron nitride. Nanoscale 2017; 9:19298-19303. [PMID: 29192915 DOI: 10.1039/c7nr05588a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We investigate the impact of encapsulation with hexagonal boron nitride (h-BN) on the Raman spectrum of few layer black phosphorus. The encapsulation results in a significant reduction of the line width of the Raman modes of black phosphorus, due to a reduced phonon scattering rate. We observe a so far elusive peak in the Raman spectra ∼4 cm-1 above the A mode in trilayer and thicker flakes, which had not been observed experimentally. The newly observed mode originates from the strong black phosphorus inter-layer interaction, which induces a hardening of the surface atom vibration with respect to the corresponding modes of the inner layers. The observation of this mode suggests a significant impact of h-BN encapsulation on the properties of black phosphorus and can serve as an indicator of the quality of its surface.
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Affiliation(s)
- J M Urban
- Laboratoire National des Champs Magnétiques Intenses, UPR 3228, CNRS-UGA-UPS-INSA, Grenoble and Toulouse, France.
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Baranowski M, Surrente A, Klopotowski L, Urban JM, Zhang N, Maude DK, Wiwatowski K, Mackowski S, Kung YC, Dumcenco D, Kis A, Plochocka P. Probing the Interlayer Exciton Physics in a MoS 2/MoSe 2/MoS 2 van der Waals Heterostructure. Nano Lett 2017; 17:6360-6365. [PMID: 28895745 DOI: 10.1021/acs.nanolett.7b03184] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Stacking atomic monolayers of semiconducting transition metal dichalcogenides (TMDs) has emerged as an effective way to engineer their properties. In principle, the staggered band alignment of TMD heterostructures should result in the formation of interlayer excitons with long lifetimes and robust valley polarization. However, these features have been observed simultaneously only in MoSe2/WSe2 heterostructures. Here we report on the observation of long-lived interlayer exciton emission in a MoS2/MoSe2/MoS2 trilayer van der Waals heterostructure. The interlayer nature of the observed transition is confirmed by photoluminescence spectroscopy, as well as by analyzing the temporal, excitation power, and temperature dependence of the interlayer emission peak. The observed complex photoluminescence dynamics suggests the presence of quasi-degenerate momentum-direct and momentum-indirect bandgaps. We show that circularly polarized optical pumping results in long-lived valley polarization of interlayer exciton. Intriguingly, the interlayer exciton photoluminescence has helicity opposite to the excitation. Our results show that through a careful choice of the TMDs forming the van der Waals heterostructure it is possible to control the circular polarization of the interlayer exciton emission.
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Affiliation(s)
- M Baranowski
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
- Department of Experimental Physics, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology , Wybrzeze Wyspianskiego 27, 50-370 Wrocaw, Poland
| | - A Surrente
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
| | - L Klopotowski
- Institute of Physics, Polish Academy of Sciences , al. Lotnikow 32/46, 02-668 Warsaw, Poland
| | - J M Urban
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
| | - N Zhang
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
| | - D K Maude
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
| | - K Wiwatowski
- Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University , Grudziadzka 5, 87-100 Torun, Poland
| | - S Mackowski
- Faculty of Physics, Astronomy, and Informatics, Nicolaus Copernicus University , Grudziadzka 5, 87-100 Torun, Poland
| | - Y C Kung
- Electrical Engineering Institute and Institute of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - D Dumcenco
- Electrical Engineering Institute and Institute of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - A Kis
- Electrical Engineering Institute and Institute of Materials Science and Engineering, École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne, Switzerland
| | - P Plochocka
- Laboratoire National des Champs Magnétiques Intenses, CNRS-UGA-UPS-INSA , 143 avenue de Rangueil, 31400 Toulouse, France
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Binder J, Urban JM, Stepniewski R, Strupinski W, Wysmolek A. In situ Raman spectroscopy of the graphene/water interface of a solution-gated field-effect transistor: electron-phonon coupling and spectroelectrochemistry. Nanotechnology 2016; 27:045704. [PMID: 26655462 DOI: 10.1088/0957-4484/27/4/045704] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We present a novel measurement approach which combines the electrical characterization of solution-gated field-effect transistors based on epitaxial bilayer graphene on 4H-SiC (0001) with simultaneous Raman spectroscopy. By changing the gate voltage, we observed Raman signatures related to the resonant electron-phonon coupling. An analysis of these Raman bands enabled the extraction of the geometrical capacitance of the system and an accurate calculation of the Fermi levels for bilayer graphene. An intentional application of higher gate voltages allowed us to trigger electrochemical reactions, which we followed in situ by Raman spectroscopy. The reactions showed a partially reversible character, as indicated by an emergence/disappearance of peaks assigned to C-H and Si-H vibration modes as well as an increase/decrease of the defect-related Raman D band intensity. Our setup provides a highly interesting platform for future spectroelectrochemical research on electrically-induced sorption processes of graphene on the micrometer scale.
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Affiliation(s)
- J Binder
- Faculty of Physics, University of Warsaw, Pasteura 5, 02-093 Warsaw, Poland
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9
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Ip CL, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, Leggett RM, Eccles DA, Zalunin V, Urban JM, Piazza P, Bowden RJ, Paten B, Mwaigwisya S, Batty EM, Simpson JT, Snutch TP, Birney E, Buck D, Goodwin S, Jansen HJ, O'Grady J, Olsen HE. MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Res 2015; 4:1075. [PMID: 26834992 PMCID: PMC4722697 DOI: 10.12688/f1000research.7201.1] [Citation(s) in RCA: 190] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/09/2015] [Indexed: 11/20/2022] Open
Abstract
The advent of a miniaturized DNA sequencing device with a high-throughput contextual sequencing capability embodies the next generation of large scale sequencing tools. The MinION™ Access Programme (MAP) was initiated by Oxford Nanopore Technologies™ in April 2014, giving public access to their USB-attached miniature sequencing device. The MinION Analysis and Reference Consortium (MARC) was formed by a subset of MAP participants, with the aim of evaluating and providing standard protocols and reference data to the community. Envisaged as a multi-phased project, this study provides the global community with the Phase 1 data from MARC, where the reproducibility of the performance of the MinION was evaluated at multiple sites. Five laboratories on two continents generated data using a control strain of Escherichia coli K-12, preparing and sequencing samples according to a revised ONT protocol. Here, we provide the details of the protocol used, along with a preliminary analysis of the characteristics of typical runs including the consistency, rate, volume and quality of data produced. Further analysis of the Phase 1 data presented here, and additional experiments in Phase 2 of E. coli from MARC are already underway to identify ways to improve and enhance MinION performance.
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Affiliation(s)
- Camilla L.C. Ip
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Matthew Loose
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
| | - John R. Tyson
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | | | | | - Miten Jain
- University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - David A. Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Vadim Zalunin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - John M. Urban
- Division of Biology and Medicine, Brown University, Providence, RI, USA
| | - Paolo Piazza
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Rory J. Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Benedict Paten
- University of California, Santa Cruz, Santa Cruz, CA, USA
| | | | - Elizabeth M. Batty
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Jared T. Simpson
- Informatics and Biocomputing, Ontario Institute for Cancer Research, ON, Canada
| | - Terrance P. Snutch
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
| | - Ewan Birney
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - David Buck
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Sara Goodwin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | | | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Hugh E. Olsen
- University of California, Santa Cruz, Santa Cruz, CA, USA
| | - MinION Analysis and Reference Consortium
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- School of Life Sciences, Queens Medical Centre, University of Nottingham, Nottingham, UK
- Michael Smith Laboratories and Djavad Mowafaghian Centre for Brain Health, University of British Columbia, Vancouver, Canada
- Virginia Commonwealth University, Richmond, VA, USA
- University of California, Santa Cruz, Santa Cruz, CA, USA
- The Genome Analysis Centre, Norwich Research Park, Norwich, UK
- Malaghan Institute of Medical Research, Wellington, New Zealand
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Division of Biology and Medicine, Brown University, Providence, RI, USA
- Norwich Medical School, University of East Anglia, Norwich, UK
- Informatics and Biocomputing, Ontario Institute for Cancer Research, ON, Canada
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- ZF-screens B.V., Leiden, Netherlands
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Abstract
Origins of DNA replication (ORIs) occur at defined regions in the genome. Although DNA sequence defines the position of ORIs in budding yeast, the factors for ORI specification remain elusive in metazoa. Several methods have been used recently to map ORIs in metazoan genomes with the hope that features for ORI specification might emerge. These methods are reviewed here with analysis of their advantages and shortcomings. The various factors that may influence ORI selection for initiation of DNA replication are discussed.
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Affiliation(s)
- John M. Urban
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
| | - Michael S. Foulk
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Department of Biology, Mercyhurst University501 East 38th Street, Erie, PA 16546USA
| | - Cinzia Casella
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
- Institute for Molecular Medicine, University of Southern DenmarkJB Winsloews Vej 25, 5000 Odense CDenmark
| | - Susan A. Gerbi
- Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Brown UniversitySidney Frank Hall, 185 Meeting Street, Providence, RI 02912USA
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11
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Foulk MS, Urban JM, Casella C, Gerbi SA. Characterizing and controlling intrinsic biases of lambda exonuclease in nascent strand sequencing reveals phasing between nucleosomes and G-quadruplex motifs around a subset of human replication origins. Genome Res 2015; 25:725-35. [PMID: 25695952 PMCID: PMC4417120 DOI: 10.1101/gr.183848.114] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 02/18/2015] [Indexed: 01/02/2023]
Abstract
Nascent strand sequencing (NS-seq) is used to discover DNA replication origins genome-wide, allowing identification of features for their specification. NS-seq depends on the ability of lambda exonuclease (λ-exo) to efficiently digest parental DNA while leaving RNA-primer protected nascent strands intact. We used genomics and biochemical approaches to determine if λ-exo digests all parental DNA sequences equally. We report that λ-exo does not efficiently digest G-quadruplex (G4) structures in a plasmid. Moreover, λ-exo digestion of nonreplicating genomic DNA (LexoG0) enriches GC-rich DNA and G4 motifs genome-wide. We used LexoG0 data to control for nascent strand–independent λ-exo biases in NS-seq and validated this approach at the rDNA locus. The λ-exo–controlled NS-seq peaks are not GC-rich, and only 35.5% overlap with 6.8% of all G4s, suggesting that G4s are not general determinants for origin specification but may play a role for a subset. Interestingly, we observed a periodic spacing of G4 motifs and nucleosomes around the peak summits, suggesting that G4s may position nucleosomes at this subset of origins. Finally, we demonstrate that use of Na+ instead of K+ in the λ-exo digestion buffer reduced the effect of G4s on λ-exo digestion and discuss ways to increase both the sensitivity and specificity of NS-seq.
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Affiliation(s)
- Michael S Foulk
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - John M Urban
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - Cinzia Casella
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
| | - Susan A Gerbi
- Brown University Division of Biology and Medicine, Department of Molecular Biology, Cell Biology and Biochemistry, Providence, Rhode Island 02912, USA
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Heckman CA, Urban JM, Cayer M, Li Y, Boudreau N, Barnes J, Plummer HK, Hall C, Kozma R, Lim L. Novel p21-activated kinase-dependent protrusions characteristically formed at the edge of transformed cells. Exp Cell Res 2004; 295:432-47. [PMID: 15093742 DOI: 10.1016/j.yexcr.2003.12.020] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2003] [Revised: 12/10/2003] [Indexed: 11/20/2022]
Abstract
During long-term culture, certain lines become neoplastic while accumulating changes in cell shape. Early and late cell populations have characteristic shape phenotypes that have been quantified by computerized assay. Phenotypes are determined from variables describing three-dimensional aspects of the subcellular distribution of mass. The features of cells can be recognized by use of latent factors, which are theoretical variables based on the covariance of the primary variables. Factor #7 represented a cell edge feature different from filopodia. We studied the morphological characteristics and morphogenesis of the feature. Brief exposure of cells from rat tracheal epithelium to phorbol 12-myristate 13-acetate (PMA) enhanced #7 values. The time to reach maximal #7 values was prolonged if PMA was administered with calcium ionophore or lysophosphatidic acid (LPA). Factor #7 was elevated during periods of ruffling suppression and stress fiber reorganization. Cells showing high #7 values were examined by scanning electron microscopy (SEM) and found to exhibit strap-shaped and cupola-shaped projections. Because RhoA regulates stress fiber formation, we sought to perturb #7 features by introducing dominant-acting negative and positive constructs of RhoA, RhoA-N19, and RhoA-V14. Neither affected #7 values. Although overexpression of the kinase inhibitory domain of p21-activated kinase 1 (PAK) had no effect on #7 values, they were affected by overexpression of a domain binding PAK-interacting guanine nucleotide exchange factor (PIX). Because a PAK-PIX complex is implicated in the remodeling of focal complexes (FCs) and recycling of PAK to the cytoplasm, the results implicate a component of FCs in the formation of #7 features. The data suggested that feature formation is driven by activated Cdc42-binding kinase (ACK) and Rac. Moreover, they suggested that the #7 protrusions are neurite-like structures and that their development involves FC regulation.
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Affiliation(s)
- C A Heckman
- Department of Biological Sciences and Center for Microscopy and Microanalysis, Bowling Green State University, Bowling Green, OH 43403, USA.
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