Current Understanding of Extrachromosomal Circular DNA In
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The Characterization of a Heat-Activated Retrotransposon ONSEN and the Effect of Zebularine in Adzuki Bean and Title Soybean
The characterization of a heat-activated retrotransposon ONSEN and the effect of zebularine in adzuki bean and Title soybean Author(s) BOONJING, PATWIRA Citation 北海道大学. 博士(生命科学) 甲第14157号 Issue Date 2020-06-30 DOI 10.14943/doctoral.k14157 Doc URL http://hdl.handle.net/2115/82053 Type theses (doctoral) File Information PATWIRA_BOONJING.pdf Instructions for use Hokkaido University Collection of Scholarly and Academic Papers : HUSCAP Thesis for Ph.D. Degree The characterization of a heat-activated retrotransposon ONSEN and the effect of zebularine in adzuki bean and soybean 「アズキとダイズにおける高温活性型レトロトランス ポゾン ONSEN の特徴とゼブラリンの効果について」 by Patwira Boonjing Graduate School of Life Science Hokkaido University June 2020 Thesis for Ph.D. Degree The characterization of a heat-activated retrotransposon ONSEN and the effect of zebularine in adzuki bean and soybean 「アズキとダイズにおける高温活性型レトロトランス ポゾン ONSEN の特徴とゼブラリンの効果について」 by Patwira Boonjing Graduate School of Life Science Hokkaido University June 2020 2 Abstract The Ty1/copia-like retrotransposon ONSEN is conserved among Brassica species, as well as in beans, including adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) and soybean (Glycine max (L.) Merr.), which are the economically important crops in Japan. ONSEN has acquired a heat-responsive element that is recognized by plant-derived heat stress defense factors, resulting in transcribing and producing the full-length extrachromosomal DNA under conditions with elevated temperatures. DNA methylation plays an important role in regulating the activation of transposons in plants. Therefore, chemical inhibition of DNA methyltransferases has been utilized to study the effect of DNA methylation on transposon activation. To understand the effect of DNA methylation on ONSEN activation, Arabidopsis thaliana, adzuki bean, and soybean plants were treated with zebularine, which is known to be an effective chemical demethylation agent. -
Mobile Genetic Elements in Streptococci
Curr. Issues Mol. Biol. (2019) 32: 123-166. DOI: https://dx.doi.org/10.21775/cimb.032.123 Mobile Genetic Elements in Streptococci Miao Lu#, Tao Gong#, Anqi Zhang, Boyu Tang, Jiamin Chen, Zhong Zhang, Yuqing Li*, Xuedong Zhou* State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, PR China. #Miao Lu and Tao Gong contributed equally to this work. *Address correspondence to: [email protected], [email protected] Abstract Streptococci are a group of Gram-positive bacteria belonging to the family Streptococcaceae, which are responsible of multiple diseases. Some of these species can cause invasive infection that may result in life-threatening illness. Moreover, antibiotic-resistant bacteria are considerably increasing, thus imposing a global consideration. One of the main causes of this resistance is the horizontal gene transfer (HGT), associated to gene transfer agents including transposons, integrons, plasmids and bacteriophages. These agents, which are called mobile genetic elements (MGEs), encode proteins able to mediate DNA movements. This review briefly describes MGEs in streptococci, focusing on their structure and properties related to HGT and antibiotic resistance. caister.com/cimb 123 Curr. Issues Mol. Biol. (2019) Vol. 32 Mobile Genetic Elements Lu et al Introduction Streptococci are a group of Gram-positive bacteria widely distributed across human and animals. Unlike the Staphylococcus species, streptococci are catalase negative and are subclassified into the three subspecies alpha, beta and gamma according to the partial, complete or absent hemolysis induced, respectively. The beta hemolytic streptococci species are further classified by the cell wall carbohydrate composition (Lancefield, 1933) and according to human diseases in Lancefield groups A, B, C and G. -
Pnas.201413825SI.Pdf
Supporting Information Impens et al. 10.1073/pnas.1413825111 13 15 13 15 SI Methods beling) (Silantes Gmbh), or C6 N2 L-lysine HCl and C6 N4 L- Plasmids. pSG5-His6-SUMO1 plasmid encodes the N-terminal arginine HCl (heavy labeling) (Silantes Gmbh). L-Lysine HCl was His6-tagged mature Small ubiquitin modifier 1 (SUMO1) isoform added at its normal concentration in DMEM (146 mg/L), but the (kind gift of A. Dejean, Institut Pasteur, Paris). The pSG5-His6- concentration of L-arginine HCl was reduced to 25 mg/L (30% of SUMO1 T95R mutat was derived from this plasmid using PCR the normal concentration in DMEM) to prevent metabolic con- mutagenesis. pSG5-His6-SUMO2 was obtained by inserting the version of arginine to proline (4). Cells were kept for at least six cDNA corresponding to the human mature SUMO2 isoform population doublings to ensure complete incorporation of the la- with an N-terminal His6 tag in the pSG5 vector (Stratagene). beled lysine and arginine. 2 The pSG5-His6-SUMO2 T91R mutant was derived from this For transfections, cells were seeded in 75-cm flasks or in 6- or plasmid by PCR mutagenesis. N-terminally HA-tagged human 24-well plates at a density of 2.7 × 106 cells per flask or 3 × 105 or cDNA of ZBTB20 (Zinc finger and BTB domain containing 0.5 × 105 cells per well, respectively. The next day cells were 20) isoform 2 (UniProt identifier Q9HC78-2), HMBOX1 (Ho- transfected with Lipofectamine LTX reagents (Invitrogen) (20 μg meobox containing protein 1) isoform 1 (HMBOX1A) (UniProt of DNA per flask, 3.5 μg per well in the six-well plates, or 0.75 μg identifier Q6NT76-1), NACC1 (Nucleus accumbens-associated per well in the 24-well plates) for 48 h. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Primate Specific Retrotransposons, Svas, in the Evolution of Networks That Alter Brain Function
Title: Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function. Olga Vasieva1*, Sultan Cetiner1, Abigail Savage2, Gerald G. Schumann3, Vivien J Bubb2, John P Quinn2*, 1 Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, U.K 2 Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK 3 Division of Medical Biotechnology, Paul-Ehrlich-Institut, Langen, D-63225 Germany *. Corresponding author Olga Vasieva: Institute of Integrative Biology, Department of Comparative genomics, University of Liverpool, Liverpool, L69 7ZB, [email protected] ; Tel: (+44) 151 795 4456; FAX:(+44) 151 795 4406 John Quinn: Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool L69 3BX, UK, [email protected]; Tel: (+44) 151 794 5498. Key words: SVA, trans-mobilisation, behaviour, brain, evolution, psychiatric disorders 1 Abstract The hominid-specific non-LTR retrotransposon termed SINE–VNTR–Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about 13.5 Myrs ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid life history were also associated with progressively evolving behavioural features that indicated a potential impact of SVA propagation on a cognitive ability of a modern human. -
World Journal of Advanced Research and Reviews
World Journal of Advanced Research and Reviews, 2020, 08(02), 279–284 World Journal of Advanced Research and Reviews e-ISSN: 2581-9615, Cross Ref DOI: 10.30574/wjarr Journal homepage: https://www.wjarr.com (REVIEW ARTICLE) Fundamentals of extrachromosomal circular DNA in human cells - Genetic activities as regards cancer promotion alongside chromosomal DNA Reinhard H. Dennin * Formerly: Department of Infectious Diseases and Microbiology, University of Lübeck, UKSH, Campus Lübeck, Germany. Publication history: Received on 17 November 2020; revised on 24 November 2020; accepted on 25 November 2020 Article DOI: https://doi.org/10.30574/wjarr.2020.8.2.0442 Abstract In addition to chromosomal DNA (chr-DNA) and mitochondrial DNA, eukaryotic cells contain extrachromosomal DNA (ec-DNA). Analysed extrachromosomal circular DNA (ecc-DNA) accounts for up to 20% of the total cellular DNA. Ecc- DNAs contain coding and non-coding sequences originating from chr-DNA and mobile genetic elements (MGEs). MGEs include sequences such as transposons, which have the potential to move between different and the same DNA molecules, thereby, for example, causing rearrangements and inactivation of genes. Ecc DNAs have aroused interest in diseases such as malignancies and diagnostic procedures relating to this. A database to collect ecc-DNA has been established. Investigations are needed to find possible differences in sequences of chr-DNA after sequencing the whole cellular DNA (WCD), namely: chr-DNA plus ec-/ecc-DNA compared to chr-DNA, which is separated from ec-/ecc-DNA. Standards for sequencing protocols of WCD have to be developed that also reveal the sequences of ecc-DNA; this concerns “single-cell genomics” in particular. -
Genome-Wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells
Journal of Visualized Experiments www.jove.com Video Article Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells Henrik D. Møller1, Rasmus K. Bojsen2, Chris Tachibana3, Lance Parsons4, David Botstein5, Birgitte Regenberg1 1 Department of Biology, University of Copenhagen 2 National Veterinary Institute, Technical University of Denmark 3 Group Health Research Institute 4 Lewis-Sigler Institute for Integrative Genomics, Princeton University 5 Calico Life Sciences LLC Correspondence to: Birgitte Regenberg at [email protected] URL: https://www.jove.com/video/54239 DOI: doi:10.3791/54239 Keywords: Molecular Biology, Issue 110, Circle-Seq, deletion, eccDNA, rDNA, ERC, ECE, microDNA, minichromosomes, small polydispersed circular DNA, spcDNA, double minute, amplification Date Published: 4/4/2016 Citation: Møller, H.D., Bojsen, R.K., Tachibana, C., Parsons, L., Botstein, D., Regenberg, B. Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells. J. Vis. Exp. (110), e54239, doi:10.3791/54239 (2016). Abstract Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. -
Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons
Published OnlineFirst August 12, 2013; DOI: 10.1158/0008-5472.CAN-13-0186 Cancer Tumor and Stem Cell Biology Research Double Minute Chromosomes in Glioblastoma Multiforme Are Revealed by Precise Reconstruction of Oncogenic Amplicons J. Zachary Sanborn1,2,Sofie R. Salama2,3, Mia Grifford2, Cameron W. Brennan4, Tom Mikkelsen6, Suresh Jhanwar5, Sol Katzman2, Lynda Chin7, and David Haussler2,3 Abstract DNA sequencing offers a powerful tool in oncology based on the precise definition of structural rearrange- ments and copy number in tumor genomes. Here, we describe the development of methods to compute copy number and detect structural variants to locally reconstruct highly rearranged regions of the tumor genome with high precision from standard, short-read, paired-end sequencing datasets. We find that circular assemblies are the most parsimonious explanation for a set of highly amplified tumor regions in a subset of glioblastoma multiforme samples sequenced by The Cancer Genome Atlas (TCGA) consortium, revealing evidence for double minute chromosomes in these tumors. Further, we find that some samples harbor multiple circular amplicons and, in some cases, further rearrangements occurred after the initial amplicon-generating event. Fluorescence in situ hybridization analysis offered an initial confirmation of the presence of double minute chromosomes. Gene content in these assemblies helps identify likely driver oncogenes for these amplicons. RNA-seq data available for one double minute chromosome offered additional support for our local tumor genome assemblies, and identified the birth of a novel exon made possible through rearranged sequences present in the double minute chromosomes. Our method was also useful for analysis of a larger set of glioblastoma multiforme tumors for which exome sequencing data are available, finding evidence for oncogenic double minute chromosomes in more than 20% of clinical specimens examined, a frequency consistent with previous estimates. -
The Homeodomain Protein Hmbx-1 Maintains Asymmetric Gene Expression in Adult C
Downloaded from genesdev.cshlp.org on October 1, 2021 - Published by Cold Spring Harbor Laboratory Press The homeodomain protein hmbx-1 maintains asymmetric gene expression in adult C. elegans olfactory neurons Bluma J. Lesch and Cornelia I. Bargmann1 Howard Hughes Medical Institute, Laboratory of Neural Circuits and Behavior, The Rockefeller University, New York, New York 10065, USA Differentiated neurons balance the need to maintain a stable identity with their flexible responses to dynamic environmental inputs. Here we characterize these opposing influences on gene expression in Caenorhabditis elegans olfactory neurons. Using transcriptional reporters that are expressed differentially in two olfactory neurons, AWCON and AWCOFF, we identify mutations that affect the long-term maintenance of appropriate chemoreceptor expression. A newly identified gene from this screen, the conserved transcription factor hmbx-1, stabilizes AWC gene expression in adult animals through dosage-sensitive interactions with its transcriptional targets. The late action of hmbx-1 complements the early role of the transcriptional repressor gene nsy-7: Both repress expression of multiple AWCOFF genes in AWCON neurons, but they act at different developmental stages. Environmental signals are superimposed onto this stable cell identity through at least two different transcriptional pathways that regulate individual chemoreceptor genes: a cGMP pathway regulated by sensory activity, and a daf-7 (TGF-b)/daf-3 (SMAD repressor) pathway regulated by specific components -
Single Cell Multi-Omics Analysis of Chromothriptic Medulloblastoma Highlights Genomic and Transcriptomic Consequences of Genome Instability
bioRxiv preprint doi: https://doi.org/10.1101/2021.06.25.449944; this version posted June 25, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Single cell multi-omics analysis of chromothriptic medulloblastoma highlights genomic and transcriptomic consequences of genome instability R. Gonzalo Parra*1,2, Moritz J Przybilla*1,2,3, Milena Simovic*4,5, Hana Susak*1,2, Manasi Ratnaparkhe4, John KL Wong6, Verena Körber7, Philipp Mallm8, Martin Sill9, Thorsten Kolb4, Rithu Kumar4, Nicola Casiraghi1,2, David R Norali Ghasemi9, Kendra Korinna Maaß9, Kristian W Pajtler9,10, Anna Jauch11, Andrey Korshunov12, Thomas Höfer7, Marc Zapatka6, Stefan M Pfister9,10, Oliver Stegle*#1,2,3, Aurélie Ernst*#4 *These authors contributed equally (author order alphabetically) We suggest to define an explicit order among the first authors at a later stage, to make it as fair as possible also in the line of the revisions. #Corresponding authors 1European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany. 2 Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany 3 Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK 4 Group “Genome Instability in Tumors”, German Cancer Research Center (DKFZ), Heidelberg, Germany 5 Faculty of Biosciences, Heidelberg University 6 Division of Molecular Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany 7 Division of Theoretical Systems Biology, German Cancer Research Center (DKFZ), Heidelberg, Germany 8 Single-cell Open Lab, German Cancer Research Center (DKFZ) and Bioquant, Heidelberg, Germany 9 Hopp Children's Cancer Center (KiTZ), Heidelberg, Germany. -
A Acentric Fragment Linear One Telomere Radiation One Broken End Endonuclease Break-Inducing Mutagen
Chromosome Res https://doi.org/10.1007/s10577-020-09636-z REVIEW Mechanisms driving acentric chromosome transmission Brandt Warecki & William Sullivan Received: 2 June 2020 /Revised: 16 July 2020 /Accepted: 19 July 2020 # Springer Nature B.V. 2020 Abstract The kinetochore-microtubule association is a Keywords Acentric . chromosome fragment . mitosis . core, conserved event that drives chromosome transmis- microtubules . double minutes . genome stability sion during mitosis. Failure to establish this association on even a single chromosome results in aneuploidy Abbreviations leading to cell death or the development of cancer. APC/C Anaphase-promoting complex However, although many chromosomes lacking centro- PtK cells Potorous tridactylus cells meres, termed acentrics, fail to segregate, studies in a UFBs Ultrafine DNA bridges number of systems reveal robust alternative mecha- CHMP4C Charged multivesicular body nisms that can drive segregation and successful pole- protein 4C ward transport of acentrics. In contrast to the canonical ESCRT-III Endosomal sorting complexes mechanism that relies on end-on microtubule attach- required for transport-III ments to kinetochores, mechanisms of acentric trans- mission largely fall into three categories: direct attach- ments to other chromosomes, kinetochore-independent lateral attachments to microtubules, and long-range teth- er-based attachments. Here, we review these “non-ca- Kinetochore-microtubule interactions drive nonical” methods of acentric chromosome transmission. poleward chromosome transmission Just as the discovery and exploration of cell cycle checkpoints provided insight into both the origins of In order to produce genetically identical daughter cells cancer and new therapies, identifying mechanisms and following mitosis, a cell must first duplicate its genome structures specifically involved in acentric segregation and then equally partition genetic material to its daugh- may have a significant impact on basic and applied ter cells through chromatid segregation. -
An All-To-All Approach to the Identification of Sequence-Specific Readers for Epigenetic DNA Modifications on Cytosine
bioRxiv preprint doi: https://doi.org/10.1101/638700; this version posted May 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. An All-to-All Approach to the Identification of Sequence-Specific Readers for Epigenetic DNA Modifications on Cytosine Guang Song1,6, Guohua Wang2,6, Ximei Luo2,3,6, Ying Cheng4, Qifeng Song1, Jun Wan3, Cedric Moore1, Hongjun Song5, Peng Jin4, Jiang Qian3,7,*, Heng Zhu1,7,8,* 1Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA 2School of Computer Science and Technology, Harbin Institute of Technology, Harbin, Heilongjiang 150001, China 3Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA 4Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA 5Department of Neuroscience and Mahoney Institute for Neurosciences, University of Pennsylvania, Philadelphia, PA 19104, USA 6These authors contributed equally 7Senior author 8Lead Contact *Correspondence: [email protected] (H.Z.), [email protected] (J.Q.). 1 bioRxiv preprint doi: https://doi.org/10.1101/638700; this version posted May 16, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. SUMMARY Epigenetic modifications of DNA in mammals play important roles in many biological processes. Identification of readers of these epigenetic marks is a critical step towards understanding the underlying molecular mechanisms. Here, we report the invention and application of an all-to-all approach, dubbed Digital Affinity Profiling via Proximity Ligation (DAPPL), to simultaneously profile human TF-DNA interactions using mixtures of random DNA libraries carrying four different epigenetic modifications (i.e., 5-methylcytosine, 5- hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine).