1
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Lång E, Lång A, Blicher P, Rognes T, Dommersnes PG, Bøe SO. Topology-guided polar ordering of collective cell migration. Sci Adv 2024; 10:eadk4825. [PMID: 38630812 PMCID: PMC11023523 DOI: 10.1126/sciadv.adk4825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
The ability of epithelial monolayers to self-organize into a dynamic polarized state, where cells migrate in a uniform direction, is essential for tissue regeneration, development, and tumor progression. However, the mechanisms governing long-range polar ordering of motility direction in biological tissues remain unclear. Here, we investigate the self-organizing behavior of quiescent epithelial monolayers that transit to a dynamic state with long-range polar order upon growth factor exposure. We demonstrate that the heightened self-propelled activity of monolayer cells leads to formation of vortex-antivortex pairs that undergo sequential annihilation, ultimately driving the spread of long-range polar order throughout the system. A computational model, which treats the monolayer as an active elastic solid, accurately replicates this behavior, and weakening of cell-to-cell interactions impedes vortex-antivortex annihilation and polar ordering. Our findings uncover a mechanism in epithelia, where elastic solid material characteristics, activated self-propulsion, and topology-mediated guidance converge to fuel a highly efficient polar self-ordering activity.
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Affiliation(s)
- Emma Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Anna Lång
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Pernille Blicher
- Department of Medical Biochemistry, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Paul Gunnar Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Trondheim, Norway
| | - Stig Ove Bøe
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
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2
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Istvan P, Birkeland E, Avershina E, Kværner AS, Bemanian V, Pardini B, Tarallo S, de Vos WM, Rognes T, Berstad P, Rounge TB. Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study. Nat Commun 2024; 15:1791. [PMID: 38424056 PMCID: PMC10904388 DOI: 10.1038/s41467-024-46033-0] [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: 08/25/2023] [Accepted: 02/08/2024] [Indexed: 03/02/2024] Open
Abstract
Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.
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Affiliation(s)
- Paula Istvan
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Einar Birkeland
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Ekaterina Avershina
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway
| | - Ane S Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Vahid Bemanian
- Pathology Department, Akershus University Hospital, Lørenskog, Norway
| | - Barbara Pardini
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Sonia Tarallo
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
- Italian Institute for Genomic Medicine (IIGM), c/o IRCCS Candiolo, Turin, Italy
| | - Willem M de Vos
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway
| | - Trine B Rounge
- Department of Tumor Biology, Institute of Cancer Research, Oslo University Hospital, Oslo, Norway.
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, Oslo, Norway.
- Department of Research, Cancer Registry of Norway, Norwegian Institute of Public Health, Oslo, Norway.
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3
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Rumbavicius I, Rounge TB, Rognes T. HoCoRT: host contamination removal tool. BMC Bioinformatics 2023; 24:371. [PMID: 37784008 PMCID: PMC10544359 DOI: 10.1186/s12859-023-05492-w] [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: 05/25/2023] [Accepted: 09/21/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods. RESULTS HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to install and use, offering a one-step option for genome indexing. HoCoRT employs a variety of well-known mapping, classification, and alignment methods to classify reads. The user can select the underlying classification method and its parameters, allowing adaptation to different scenarios. Based on our investigation of various methods and parameters using synthetic human gut and oral microbiomes, and on assessment of publicly available data, we provide recommendations for typical datasets with short and long reads. CONCLUSIONS To decontaminate a human gut microbiome with short reads using HoCoRT, we found the optimal combination of speed and accuracy with BioBloom, Bowtie2 in end-to-end mode, and HISAT2. Kraken2 consistently demonstrated the highest speed, albeit with a trade-off in accuracy. The same applies to an oral microbiome, but here Bowtie2 was notably slower than the other tools. For long reads, the detection of human host reads is more difficult. In this case, a combination of Kraken2 and Minimap2 achieved the highest accuracy and detected 59% of human reads. In comparison to the dedicated DeconSeq tool, HoCoRT using Bowtie2 in end-to-end mode proved considerably faster and slightly more accurate. HoCoRT is available as a Bioconda package, and the source code can be accessed at https://github.com/ignasrum/hocort along with the documentation. It is released under the MIT licence and is compatible with Linux and macOS (except for the BioBloom module).
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Affiliation(s)
- Ignas Rumbavicius
- Centre for Bioinformatics, Department of Informatics, University of Oslo, PO Box 1080 Blindern, 0316, Oslo, Norway
| | - Trine B Rounge
- Centre for Bioinformatics, Department of Pharmacy, University of Oslo, PO Box 1068 Blindern, 0316, Oslo, Norway.
- Cancer Registry of Norway, PO Box 5313 Majorstuen, 0304, Oslo, Norway.
| | - Torbjørn Rognes
- Centre for Bioinformatics, Department of Informatics, University of Oslo, PO Box 1080 Blindern, 0316, Oslo, Norway.
- Department of Microbiology, Oslo University Hospital, PO Box 4950 Nydalen, 0424, Oslo, Norway.
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4
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Kalyanasundaram S, Lefol Y, Gundersen S, Rognes T, Alsøe L, Nilsen HL, Hovig E, Sandve GK, Domanska D. hGSuite HyperBrowser: A web-based toolkit for hierarchical metadata-informed analysis of genomic tracks. PLoS One 2023; 18:e0286330. [PMID: 37467208 DOI: 10.1371/journal.pone.0286330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/15/2023] [Indexed: 07/21/2023] Open
Abstract
Many high-throughput sequencing datasets can be represented as objects with coordinates along a reference genome. Currently, biological investigations often involve a large number of such datasets, for example representing different cell types or epigenetic factors. Drawing overall conclusions from a large collection of results for individual datasets may be challenging and time-consuming. Meaningful interpretation often requires the results to be aggregated according to metadata that represents biological characteristics of interest. In this light, we here propose the hierarchical Genomic Suite HyperBrowser (hGSuite), an open-source extension to the GSuite HyperBrowser platform, which aims to provide a means for extracting key results from an aggregated collection of high-throughput DNA sequencing data. The hGSuite utilizes a metadata-informed data cube to calculate various statistics across the multiple dimensions of the datasets. With this work, we show that the hGSuite and its associated data cube methodology offers a quick and accessible way for exploratory analysis of large genomic datasets. The web-based toolkit named hGsuite Hyperbrowser is available at https://hyperbrowser.uio.no/hgsuite under a GPLv3 license.
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Affiliation(s)
- Sumana Kalyanasundaram
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Yohan Lefol
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, University Hospital, Oslo, Norway
| | - Sveinung Gundersen
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Microbiology, University Hospital, Oslo, Norway
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Lene Alsøe
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, University Hospital, Oslo, Norway
| | - Hilde Loge Nilsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Microbiology, University Hospital, Oslo, Norway
| | - Eivind Hovig
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Geir Kjetil Sandve
- Center for Bioinformatics, Department of Informatics, University of Oslo, Oslo, Norway
- Biomedical Informatics, Department of Informatics, University of Oslo, Oslo, Norway
| | - Diana Domanska
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Pathology, University Hospital, Oslo, Norway
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5
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Rossini R, Kumar V, Mathelier A, Rognes T, Paulsen J. MoDLE: high-performance stochastic modeling of DNA loop extrusion interactions. Genome Biol 2022; 23:247. [PMID: 36451166 PMCID: PMC9710047 DOI: 10.1186/s13059-022-02815-7] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/17/2022] [Indexed: 12/03/2022] Open
Abstract
DNA loop extrusion emerges as a key process establishing genome structure and function. We introduce MoDLE, a computational tool for fast, stochastic modeling of molecular contacts from DNA loop extrusion capable of simulating realistic contact patterns genome wide in a few minutes. MoDLE accurately simulates contact maps in concordance with existing molecular dynamics approaches and with Micro-C data and does so orders of magnitude faster than existing approaches. MoDLE runs efficiently on machines ranging from laptops to high performance computing clusters and opens up for exploratory and predictive modeling of 3D genome structure in a wide range of settings.
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Affiliation(s)
- Roberto Rossini
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway
| | - Vipin Kumar
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Anthony Mathelier
- grid.5510.10000 0004 1936 8921Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, 0318 Oslo, Norway
| | - Torbjørn Rognes
- grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway ,grid.55325.340000 0004 0389 8485Department of Microbiology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Jonas Paulsen
- grid.5510.10000 0004 1936 8921Department of Biosciences, University of Oslo, 0316 Oslo, Norway ,grid.5510.10000 0004 1936 8921Centre for Bioinformatics, Department of Informatics, University of Oslo, 0316 Oslo, Norway
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6
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Rognes T, Scheffer L, Greiff V, Sandve GK. CompAIRR: ultra-fast comparison of adaptive immune receptor repertoires by exact and approximate sequence matching. Bioinformatics 2022; 38:4230-4232. [PMID: 35852318 PMCID: PMC9438946 DOI: 10.1093/bioinformatics/btac505] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 12/09/2021] [Revised: 03/20/2022] [Accepted: 07/18/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Adaptive immune receptor (AIR) repertoires (AIRRs) record past immune encounters with exquisite specificity. Therefore, identifying identical or similar AIR sequences across individuals is a key step in AIRR analysis for revealing convergent immune response patterns that may be exploited for diagnostics and therapy. Existing methods for quantifying AIRR overlap scale poorly with increasing dataset numbers and sizes. To address this limitation, we developed CompAIRR, which enables ultra-fast computation of AIRR overlap, based on either exact or approximate sequence matching. RESULTS CompAIRR improves computational speed 1000-fold relative to the state of the art and uses only one-third of the memory: on the same machine, the exact pairwise AIRR overlap of 104 AIRRs with 105 sequences is found in ∼17 min, while the fastest alternative tool requires 10 days. CompAIRR has been integrated with the machine learning ecosystem immuneML to speed up commonly used AIRR-based machine learning applications. AVAILABILITY AND IMPLEMENTATION CompAIRR code and documentation are available at https://github.com/uio-bmi/compairr. Docker images are available at https://hub.docker.com/r/torognes/compairr. The code to replicate the synthetic datasets, scripts for benchmarking and creating figures, and all raw data underlying the figures are available at https://github.com/uio-bmi/compairr-benchmarking. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, 0424 Oslo, Norway
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7
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Eriksson AM, Leikfoss IS, Abrahamsen G, Sundvold V, Isom MM, Keshari PK, Rognes T, Landsverk OJB, Bos SD, Harbo HF, Spurkland A, Berge T. Exploring the role of the multiple sclerosis susceptibility gene CLEC16A in T cells. Scand J Immunol 2021; 94:e13050. [PMID: 34643957 DOI: 10.1111/sji.13050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 06/23/2020] [Revised: 04/20/2021] [Accepted: 04/28/2021] [Indexed: 12/29/2022]
Abstract
C-type lectin-like domain family 16 member A (CLEC16A) is associated with autoimmune disorders, including multiple sclerosis (MS), but its functional relevance is not completely understood. CLEC16A is expressed in several immune cells, where it affects autophagic processes and receptor expression. Recently, we reported that the risk genotype of an MS-associated single nucleotide polymorphism in CLEC16A intron 19 is associated with higher expression of CLEC16A in CD4+ T cells. Here, we show that CLEC16A expression is induced in CD4+ T cells upon T cell activation. By the use of imaging flow cytometry and confocal microscopy, we demonstrate that CLEC16A is located in Rab4a-positive recycling endosomes in Jurkat TAg T cells. CLEC16A knock-down in Jurkat cells resulted in lower cell surface expression of the T cell receptor, however, this did not have a major impact on T cell activation response in vitro in Jurkat nor in human, primary CD4+ T cells.
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Affiliation(s)
- Anna M Eriksson
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ingvild Sørum Leikfoss
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Neuroscience Research Unit, Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway
| | - Greger Abrahamsen
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Vibeke Sundvold
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | | | - Pankaj K Keshari
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | | | - Steffan D Bos
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Hanne F Harbo
- Department of Neurology, Oslo University Hospital, Oslo, Norway.,Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Anne Spurkland
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Tone Berge
- Neuroscience Research Unit, Department of Research, Innovation and Education, Oslo University Hospital, Oslo, Norway.,Department of Mechanical, Electronic and Chemical Engineering, Oslo Metropolitan University, Oslo, Norway
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8
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Kværner AS, Birkeland E, Bucher-Johannessen C, Vinberg E, Nordby JI, Kangas H, Bemanian V, Ellonen P, Botteri E, Natvig E, Rognes T, Hovig E, Lyle R, Ambur OH, de Vos WM, Bultman S, Hjartåker A, Landberg R, Song M, Blix HS, Ursin G, Randel KR, de Lange T, Hoff G, Holme Ø, Berstad P, Rounge TB. The CRCbiome study: a large prospective cohort study examining the role of lifestyle and the gut microbiome in colorectal cancer screening participants. BMC Cancer 2021; 21:930. [PMID: 34407780 PMCID: PMC8371800 DOI: 10.1186/s12885-021-08640-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 12/16/2020] [Accepted: 07/27/2021] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Colorectal cancer (CRC) screening reduces CRC incidence and mortality. However, current screening methods are either hampered by invasiveness or suboptimal performance, limiting their effectiveness as primary screening methods. To aid in the development of a non-invasive screening test with improved sensitivity and specificity, we have initiated a prospective biomarker study (CRCbiome), nested within a large randomized CRC screening trial in Norway. We aim to develop a microbiome-based classification algorithm to identify advanced colorectal lesions in screening participants testing positive for an immunochemical fecal occult blood test (FIT). We will also examine interactions with host factors, diet, lifestyle and prescription drugs. The prospective nature of the study also enables the analysis of changes in the gut microbiome following the removal of precancerous lesions. METHODS The CRCbiome study recruits participants enrolled in the Bowel Cancer Screening in Norway (BCSN) study, a randomized trial initiated in 2012 comparing once-only sigmoidoscopy to repeated biennial FIT, where women and men aged 50-74 years at study entry are invited to participate. Since 2017, participants randomized to FIT screening with a positive test result have been invited to join the CRCbiome study. Self-reported diet, lifestyle and demographic data are collected prior to colonoscopy after the positive FIT-test (baseline). Screening data, including colonoscopy findings are obtained from the BCSN database. Fecal samples for gut microbiome analyses are collected both before and 2 and 12 months after colonoscopy. Samples are analyzed using metagenome sequencing, with taxonomy profiles, and gene and pathway content as primary measures. CRCbiome data will also be linked to national registries to obtain information on prescription histories and cancer relevant outcomes occurring during the 10 year follow-up period. DISCUSSION The CRCbiome study will increase our understanding of how the gut microbiome, in combination with lifestyle and environmental factors, influences the early stages of colorectal carcinogenesis. This knowledge will be crucial to develop microbiome-based screening tools for CRC. By evaluating biomarker performance in a screening setting, using samples from the target population, the generalizability of the findings to future screening cohorts is likely to be high. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT01538550 .
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Affiliation(s)
- Ane Sørlie Kværner
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway
| | - Einar Birkeland
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Cecilie Bucher-Johannessen
- Department of Research, Cancer Registry of Norway, Oslo, Norway
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
| | - Elina Vinberg
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Jan Inge Nordby
- Department of Medical Biochemistry, Oslo University Hospital, Oslo, Norway
| | - Harri Kangas
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Vahid Bemanian
- Department of Multidisciplinary Laboratory Science and Medical Biochemistry, Genetic Unit, Akershus University Hospital, Lørenskog, Norway
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Edoardo Botteri
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway
- Department of Research, Cancer Registry of Norway, Oslo, Norway
| | - Erik Natvig
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, Oslo University Hospital, Oslo, Norway
- Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo, Norway
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Ole Herman Ambur
- Department of Microbiology and Infection Control, Akershus University Hospital, Lørenskog, Norway
- Department of Natural Sciences and Health, Oslo Metropolitan University, Oslo, Norway
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Scott Bultman
- Department of Genetics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | | | - Rikard Landberg
- Department of Biology and Biological Engineering, Division of Food and Nutrition Science, Chalmers University of Technology, Gothenburg, Sweden
| | - Mingyang Song
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Clinical and Translational Epidemiology Unit and Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Hege Salvesen Blix
- Department of Drug Statistics, Norwegian Institute of Public Health, Oslo, Norway
- School of Pharmacy, University of Oslo, Oslo, Norway
| | | | | | - Thomas de Lange
- Medical Department, Sahlgrenska University Hospital-Mölndal, Mölndal, Sweden
- Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Department of Medical Research, Bærum Hospital, Bærum, Norway
| | - Geir Hoff
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway
- Department of Research, Telemark Hospital, Skien, Norway
| | - Øyvind Holme
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway
- Department of Medicine, Sorlandet Hospital Kristiansand, Kristiansand, Norway
- Institute for Health and Society, University of Oslo, Oslo, Norway
| | - Paula Berstad
- Section for Colorectal Cancer Screening, Cancer Registry of Norway, Oslo, Norway.
| | - Trine B Rounge
- Department of Research, Cancer Registry of Norway, Oslo, Norway.
- Department of Informatics, Centre for Bioinformatics, University of Oslo, Oslo, Norway.
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9
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Mahé F, Czech L, Stamatakis A, Quince C, de Vargas C, Dunthorn M, Rognes T. Swarm v3: towards tera-scale amplicon clustering. Bioinformatics 2021; 38:267-269. [PMID: 34244702 PMCID: PMC8696092 DOI: 10.1093/bioinformatics/btab493] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 05/24/2021] [Accepted: 07/01/2021] [Indexed: 02/03/2023] Open
Abstract
MOTIVATION Previously we presented swarm, an open-source amplicon clustering programme that produces fine-scale molecular operational taxonomic units (OTUs) that are free of arbitrary global clustering thresholds. Here, we present swarm v3 to address issues of contemporary datasets that are growing towards tera-byte sizes. RESULTS When compared with previous swarm versions, swarm v3 has modernized C++ source code, reduced memory footprint by up to 50%, optimized CPU-usage and multithreading (more than 7 times faster with default parameters), and it has been extensively tested for its robustness and logic. AVAILABILITY AND IMPLEMENTATION Source code and binaries are available at https://github.com/torognes/swarm. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Lucas Czech
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, USA
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, Heidelberg, Germany,Institute of Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Christopher Quince
- Organisms and Ecosystems, Earlham Institute, Norwich, UK,Gut Microbes and Health, Quadram Institute, Norwich, UK,Warwick Medical School, University of Warwick, Coventry, UK
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, Roscoff, France,Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, Paris, France
| | - Micah Dunthorn
- Natural History Museum, University of Oslo, Oslo, Norway,Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway,Department of Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
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10
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Snipen L, Angell IL, Rognes T, Rudi K. Reduced metagenome sequencing for strain-resolution taxonomic profiles. Microbiome 2021; 9:79. [PMID: 33781324 PMCID: PMC8008692 DOI: 10.1186/s40168-021-01019-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 02/02/2021] [Indexed: 05/05/2023]
Abstract
BACKGROUND Studies of shifts in microbial community composition has many applications. For studies at species or subspecies levels, the 16S amplicon sequencing lacks resolution and is often replaced by full shotgun sequencing. Due to higher costs, this restricts the number of samples sequenced. As an alternative to a full shotgun sequencing we have investigated the use of Reduced Metagenome Sequencing (RMS) to estimate the composition of a microbial community. This involves the use of double-digested restriction-associated DNA sequencing, which means only a smaller fraction of the genomes are sequenced. The read sets obtained by this approach have properties different from both amplicon and shotgun data, and analysis pipelines for both can either not be used at all or not explore the full potential of RMS data. RESULTS We suggest a procedure for analyzing such data, based on fragment clustering and the use of a constrained ordinary least square de-convolution for estimating the relative abundance of all community members. Mock community datasets show the potential to clearly separate strains even when the 16S is 100% identical, and genome-wide differences is < 0.02, indicating RMS has a very high resolution. From a simulation study, we compare RMS to shotgun sequencing and show that we get improved abundance estimates when the community has many very closely related genomes. From a real dataset of infant guts, we show that RMS is capable of detecting a strain diversity gradient for Escherichia coli across time. CONCLUSION We find that RMS is a good alternative to either metabarcoding or shotgun sequencing when it comes to resolving microbial communities at the strain level. Like shotgun metagenomics, it requires a good database of reference genomes and is well suited for studies of the human gut or other communities where many reference genomes exist. A data analysis pipeline is offered, as an R package at https://github.com/larssnip/microRMS . Video abstract.
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Affiliation(s)
- Lars Snipen
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Inga-Leena Angell
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, P.O. Box 1080, Blindern, NO-0316 Oslo, Norway
| | - Knut Rudi
- Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, NO-1432 Ås, Norway
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11
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Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Di Noia JM. The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer 2021; 2:zcaa019. [PMID: 33554121 PMCID: PMC7848951 DOI: 10.1093/narcan/zcaa019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 06/30/2020] [Revised: 08/09/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
In B lymphocytes, the uracil N-glycosylase (UNG) excises genomic uracils made by activation-induced deaminase (AID), thus underpinning antibody gene diversification and oncogenic chromosomal translocations, but also initiating faithful DNA repair. Ung−/− mice develop B-cell lymphoma (BCL). However, since UNG has anti- and pro-oncogenic activities, its tumor suppressor relevance is unclear. Moreover, how the constant DNA damage and repair caused by the AID and UNG interplay affects B-cell fitness and thereby the dynamics of cell populations in vivo is unknown. Here, we show that UNG specifically protects the fitness of germinal center B cells, which express AID, and not of any other B-cell subset, coincident with AID-induced telomere damage activating p53-dependent checkpoints. Consistent with AID expression being detrimental in UNG-deficient B cells, Ung−/− mice develop BCL originating from activated B cells but lose AID expression in the established tumor. Accordingly, we find that UNG is rarely lost in human BCL. The fitness preservation activity of UNG contingent to AID expression was confirmed in a B-cell leukemia model. Hence, UNG, typically considered a tumor suppressor, acquires tumor-enabling activity in cancer cell populations that express AID by protecting cell fitness.
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Affiliation(s)
- Shiva Safavi
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Ariane Larouche
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Kiersten Dionne
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Felix Dingler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Seong-Kwi Kang
- ITR Laboratories Canada, Inc., 19601 Clark Graham Ave, Baie-D'Urfe, QC H9X 3T1, Canada
| | - Yan Liu
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Nathalie Johnson
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, C.P. 6128, Montreal, QC H3C 3J7, Canada
| | - Ramiro E Verdun
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | | | - Francisco Vega
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Hilde Nilsen
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Javier M Di Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
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12
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Safavi S, Larouche A, Zahn A, Patenaude AM, Domanska D, Dionne K, Rognes T, Dingler F, Kang SK, Liu Y, Johnson N, Hébert J, Verdun RE, Rada CA, Vega F, Nilsen H, Noia JMD. Erratum: The uracil-DNA glycosylase UNG protects the fitness of normal and cancer B cells expressing AID. NAR Cancer 2021; 3:zcaa045. [PMID: 34316697 PMCID: PMC8210038 DOI: 10.1093/narcan/zcaa045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Shiva Safavi
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Ariane Larouche
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Astrid Zahn
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Anne-Marie Patenaude
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Kiersten Dionne
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080, Blindern, 0316 Oslo, Norway
| | - Felix Dingler
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Seong-Kwi Kang
- ITR Laboratories Canada, Inc., 19601 Clark Graham Ave, Baie-D'Urfe, QC H9 × 3T1, Canada
| | - Yan Liu
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Nathalie Johnson
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC H4A 3J1, Canada
| | - Josée Hébert
- Department of Medicine, Université de Montréal, C.P. 6128, Montreal, QC H3C 3J7, Canada
| | - Ramiro E Verdun
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | | | - Francisco Vega
- Division of Hematology, Department of Medicine, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL 33136, USA
| | - Hilde Nilsen
- Section for Clinical Molecular Biology, Akershus University Hospital, PO 1000, 1478 Lørenskog, Norway
| | - Javier M D Noia
- Institut de Recherches Cliniques de Montréal, 110 Av des Pins Ouest, Montréal, QC H2W 1R7, Canada
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13
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Khelik K, Sandve GK, Nederbragt AJ, Rognes T. NucBreak: location of structural errors in a genome assembly by using paired-end Illumina reads. BMC Bioinformatics 2020; 21:66. [PMID: 32085722 PMCID: PMC7035700 DOI: 10.1186/s12859-020-3414-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 02/12/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Advances in whole genome sequencing strategies have provided the opportunity for genomic and comparative genomic analysis of a vast variety of organisms. The analysis results are highly dependent on the quality of the genome assemblies used. Assessment of the assembly accuracy may significantly increase the reliability of the analysis results and is therefore of great importance. RESULTS Here, we present a new tool called NucBreak aimed at localizing structural errors in assemblies, including insertions, deletions, duplications, inversions, and different inter- and intra-chromosomal rearrangements. The approach taken by existing alternative tools is based on analysing reads that do not map properly to the assembly, for instance discordantly mapped reads, soft-clipped reads and singletons. NucBreak uses an entirely different and unique method to localise the errors. It is based on analysing the alignments of reads that are properly mapped to an assembly and exploit information about the alternative read alignments. It does not annotate detected errors. We have compared NucBreak with other existing assembly accuracy assessment tools, namely Pilon, REAPR, and FRCbam as well as with several structural variant detection tools, including BreakDancer, Lumpy, and Wham, by using both simulated and real datasets. CONCLUSIONS The benchmarking results have shown that NucBreak in general predicts assembly errors of different types and sizes with relatively high sensitivity and with lower false discovery rate than the other tools. Such a balance between sensitivity and false discovery rate makes NucBreak a good alternative to the existing assembly accuracy assessment tools and SV detection tools. NucBreak is freely available at https://github.com/uio-bmi/NucBreak under the MPL license.
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Affiliation(s)
- Ksenia Khelik
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Geir Kjetil Sandve
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Alexander Johan Nederbragt
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, NO-0316, Oslo, Norway
| | - Torbjørn Rognes
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424, Oslo, Norway.
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14
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Alsøe L, Sarno A, Carracedo S, Domanska D, Dingler F, Lirussi L, SenGupta T, Tekin NB, Jobert L, Alexandrov LB, Galashevskaya A, Rada C, Sandve GK, Rognes T, Krokan HE, Nilsen H. Uracil Accumulation and Mutagenesis Dominated by Cytosine Deamination in CpG Dinucleotides in Mice Lacking UNG and SMUG1. Sci Rep 2017; 7:7199. [PMID: 28775312 PMCID: PMC5543110 DOI: 10.1038/s41598-017-07314-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 06/23/2017] [Indexed: 12/30/2022] Open
Abstract
Both a DNA lesion and an intermediate for antibody maturation, uracil is primarily processed by base excision repair (BER), either initiated by uracil-DNA glycosylase (UNG) or by single-strand selective monofunctional uracil DNA glycosylase (SMUG1). The relative in vivo contributions of each glycosylase remain elusive. To assess the impact of SMUG1 deficiency, we measured uracil and 5-hydroxymethyluracil, another SMUG1 substrate, in Smug1−/− mice. We found that 5-hydroxymethyluracil accumulated in Smug1−/− tissues and correlated with 5-hydroxymethylcytosine levels. The highest increase was found in brain, which contained about 26-fold higher genomic 5-hydroxymethyluracil levels than the wild type. Smug1−/− mice did not accumulate uracil in their genome and Ung−/− mice showed slightly elevated uracil levels. Contrastingly, Ung−/−Smug1−/− mice showed a synergistic increase in uracil levels with up to 25-fold higher uracil levels than wild type. Whole genome sequencing of UNG/SMUG1-deficient tumours revealed that combined UNG and SMUG1 deficiency leads to the accumulation of mutations, primarily C to T transitions within CpG sequences. This unexpected sequence bias suggests that CpG dinucleotides are intrinsically more mutation prone. In conclusion, we showed that SMUG1 efficiently prevent genomic uracil accumulation, even in the presence of UNG, and identified mutational signatures associated with combined UNG and SMUG1 deficiency.
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Affiliation(s)
- Lene Alsøe
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Antonio Sarno
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway.,The Liaison Committee for Education, Research and Innovation in Central Norway, Trondheim, Norway
| | - Sergio Carracedo
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Diana Domanska
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | | | - Lisa Lirussi
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Tanima SenGupta
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Nuriye Basdag Tekin
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway
| | - Laure Jobert
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway.,Akershus University Hospital, Lørenskog, Norway.,LifeTechnologies AS, Ullernschauseen 52, 0379, Oslo, Norway
| | - Ludmil B Alexandrov
- Theoretical Biology and Biophysics (T-6), Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA.,University of New Mexico Comprehensive Cancer Center, Albuquerque, NM, 87102, USA
| | - Anastasia Galashevskaya
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | | | - Geir Kjetil Sandve
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424, Oslo, Norway
| | - Hans E Krokan
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, Ahus Campus, University of Oslo, Oslo, Norway. .,Akershus University Hospital, Lørenskog, Norway.
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15
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Khelik K, Lagesen K, Sandve GK, Rognes T, Nederbragt AJ. NucDiff: in-depth characterization and annotation of differences between two sets of DNA sequences. BMC Bioinformatics 2017; 18:338. [PMID: 28701187 PMCID: PMC5508607 DOI: 10.1186/s12859-017-1748-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 07/04/2017] [Indexed: 12/05/2022] Open
Abstract
Background Comparing sets of sequences is a situation frequently encountered in bioinformatics, examples being comparing an assembly to a reference genome, or two genomes to each other. The purpose of the comparison is usually to find where the two sets differ, e.g. to find where a subsequence is repeated or deleted, or where insertions have been introduced. Such comparisons can be done using whole-genome alignments. Several tools for making such alignments exist, but none of them 1) provides detailed information about the types and locations of all differences between the two sets of sequences, 2) enables visualisation of alignment results at different levels of detail, and 3) carefully takes genomic repeats into consideration. Results We here present NucDiff, a tool aimed at locating and categorizing differences between two sets of closely related DNA sequences. NucDiff is able to deal with very fragmented genomes, repeated sequences, and various local differences and structural rearrangements. NucDiff determines differences by a rigorous analysis of alignment results obtained by the NUCmer, delta-filter and show-snps programs in the MUMmer sequence alignment package. All differences found are categorized according to a carefully defined classification scheme covering all possible differences between two sequences. Information about the differences is made available as GFF3 files, thus enabling visualisation using genome browsers as well as usage of the results as a component in an analysis pipeline. NucDiff was tested with varying parameters for the alignment step and compared with existing alternatives, called QUAST and dnadiff. Conclusions We have developed a whole genome alignment difference classification scheme together with the program NucDiff for finding such differences. The proposed classification scheme is comprehensive and can be used by other tools. NucDiff performs comparably to QUAST and dnadiff but gives much more detailed results that can easily be visualized. NucDiff is freely available on https://github.com/uio-cels/NucDiff under the MPL license. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1748-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ksenia Khelik
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway
| | - Karin Lagesen
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway.,Norwegian Veterinary Institute, PO Box 750 Sentrum, 0106, Oslo, Norway
| | - Geir Kjetil Sandve
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway
| | - Torbjørn Rognes
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway.,Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, 0424, Oslo, Norway
| | - Alexander Johan Nederbragt
- Biomedical Informatics Research Group, Department of Informatics, University of Oslo, PO Box 1080, 0316, Oslo, Norway. .,Centre for Ecological and Evolutionary Synthesis, Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway.
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16
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Abstract
Background VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. Methods When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. Results VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. Discussion VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
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Affiliation(s)
- Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tomáš Flouri
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ben Nichols
- School of Engineering, University of Glasgow , Glasgow , United Kingdom
| | - Christopher Quince
- School of Engineering, University of Glasgow, Glasgow, United Kingdom; Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; UMR LSTM, CIRAD, Montpellier, France
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17
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Namouchi A, Gómez-Muñoz M, Frye SA, Moen LV, Rognes T, Tønjum T, Balasingham SV. The Mycobacterium tuberculosis transcriptional landscape under genotoxic stress. BMC Genomics 2016; 17:791. [PMID: 27724857 PMCID: PMC5057432 DOI: 10.1186/s12864-016-3132-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
Background As an intracellular human pathogen, Mycobacterium tuberculosis (Mtb) is facing multiple stressful stimuli inside the macrophage and the granuloma. Understanding Mtb responses to stress is essential to identify new virulence factors and pathways that play a role in the survival of the tubercle bacillus. The main goal of this study was to map the regulatory networks of differentially expressed (DE) transcripts in Mtb upon various forms of genotoxic stress. We exposed Mtb cells to oxidative (H2O2 or paraquat), nitrosative (DETA/NO), or alkylation (MNNG) stress or mitomycin C, inducing double-strand breaks in the DNA. Total RNA was isolated from treated and untreated cells and subjected to high-throughput deep sequencing. The data generated was analysed to identify DE genes encoding mRNAs, non-coding RNAs (ncRNAs), and the genes potentially targeted by ncRNAs. Results The most significant transcriptomic alteration with more than 700 DE genes was seen under nitrosative stress. In addition to genes that belong to the replication, recombination and repair (3R) group, mainly found under mitomycin C stress, we identified DE genes important for bacterial virulence and survival, such as genes of the type VII secretion system (T7SS) and the proline-glutamic acid/proline-proline-glutamic acid (PE/PPE) family. By predicting the structures of hypothetical proteins (HPs) encoded by DE genes, we found that some of these HPs might be involved in mycobacterial genome maintenance. We also applied a state-of-the-art method to predict potential target genes of the identified ncRNAs and found that some of these could regulate several genes that might be directly involved in the response to genotoxic stress. Conclusions Our study reflects the complexity of the response of Mtb in handling genotoxic stress. In addition to genes involved in genome maintenance, other potential key players, such as the members of the T7SS and PE/PPE gene family, were identified. This plethora of responses is detected not only at the level of DE genes encoding mRNAs but also at the level of ncRNAs and their potential targets. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3132-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Amine Namouchi
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | | | - Stephan A Frye
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway
| | - Line Victoria Moen
- Department of Informatics, University of Oslo, Oslo, Norway.,Current address: Department of Nutrition, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Tone Tønjum
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.,Department of Microbiology, University of Oslo, Oslo, Norway
| | - Seetha V Balasingham
- Department of Microbiology, Oslo University Hospital, Postboks 4950, NO-0424, Oslo, Norway.
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18
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Samarakoon PS, Sorte HS, Stray-Pedersen A, Rødningen OK, Rognes T, Lyle R. cnvScan: a CNV screening and annotation tool to improve the clinical utility of computational CNV prediction from exome sequencing data. BMC Genomics 2016; 17:51. [PMID: 26764020 PMCID: PMC4712464 DOI: 10.1186/s12864-016-2374-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [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: 08/22/2015] [Accepted: 01/06/2016] [Indexed: 12/30/2022] Open
Abstract
Background With advances in next generation sequencing technology and analysis methods, single nucleotide variants (SNVs) and indels can be detected with high sensitivity and specificity in exome sequencing data. Recent studies have demonstrated the ability to detect disease-causing copy number variants (CNVs) in exome sequencing data. However, exonic CNV prediction programs have shown high false positive CNV counts, which is the major limiting factor for the applicability of these programs in clinical studies. Results We have developed a tool (cnvScan) to improve the clinical utility of computational CNV prediction in exome data. cnvScan can accept input from any CNV prediction program. cnvScan consists of two steps: CNV screening and CNV annotation. CNV screening evaluates CNV prediction using quality scores and refines this using an in-house CNV database, which greatly reduces the false positive rate. The annotation step provides functionally and clinically relevant information using multiple source datasets. We assessed the performance of cnvScan on CNV predictions from five different prediction programs using 64 exomes from Primary Immunodeficiency (PIDD) patients, and identified PIDD-causing CNVs in three individuals from two different families. Conclusions In summary, cnvScan reduces the time and effort required to detect disease-causing CNVs by reducing the false positive count and providing annotation. This improves the clinical utility of CNV detection in exome data. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2374-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Hanne Sørmo Sorte
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Asbjørg Stray-Pedersen
- Norwegian National Newborn Screening, Oslo University Hospital, Oslo, Norway. .,Center for Human Immunobiology/Section of Immunology, Allergy, and Rheumatology, Texas Children's Hospital, Houston, TX, USA. .,Baylor-Hopkins Center for Mendelian Genomics of the Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Olaug Kristin Rødningen
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway. .,Department of Microbiology, Oslo University Hospital, Oslo, Norway.
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway.
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19
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Abstract
BACKGROUND VSEARCH is an open source and free of charge multithreaded 64-bit tool for processing and preparing metagenomics, genomics and population genomics nucleotide sequence data. It is designed as an alternative to the widely used USEARCH tool (Edgar, 2010) for which the source code is not publicly available, algorithm details are only rudimentarily described, and only a memory-confined 32-bit version is freely available for academic use. METHODS When searching nucleotide sequences, VSEARCH uses a fast heuristic based on words shared by the query and target sequences in order to quickly identify similar sequences, a similar strategy is probably used in USEARCH. VSEARCH then performs optimal global sequence alignment of the query against potential target sequences, using full dynamic programming instead of the seed-and-extend heuristic used by USEARCH. Pairwise alignments are computed in parallel using vectorisation and multiple threads. RESULTS VSEARCH includes most commands for analysing nucleotide sequences available in USEARCH version 7 and several of those available in USEARCH version 8, including searching (exact or based on global alignment), clustering by similarity (using length pre-sorting, abundance pre-sorting or a user-defined order), chimera detection (reference-based or de novo), dereplication (full length or prefix), pairwise alignment, reverse complementation, sorting, and subsampling. VSEARCH also includes commands for FASTQ file processing, i.e., format detection, filtering, read quality statistics, and merging of paired reads. Furthermore, VSEARCH extends functionality with several new commands and improvements, including shuffling, rereplication, masking of low-complexity sequences with the well-known DUST algorithm, a choice among different similarity definitions, and FASTQ file format conversion. VSEARCH is here shown to be more accurate than USEARCH when performing searching, clustering, chimera detection and subsampling, while on a par with USEARCH for paired-ends read merging. VSEARCH is slower than USEARCH when performing clustering and chimera detection, but significantly faster when performing paired-end reads merging and dereplication. VSEARCH is available at https://github.com/torognes/vsearch under either the BSD 2-clause license or the GNU General Public License version 3.0. DISCUSSION VSEARCH has been shown to be a fast, accurate and full-fledged alternative to USEARCH. A free and open-source versatile tool for sequence analysis is now available to the metagenomics community.
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Affiliation(s)
- Torbjørn Rognes
- Department of Informatics, University of Oslo, Oslo, Norway; Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Tomáš Flouri
- Heidelberg Institute for Theoretical Studies, Heidelberg, Germany; Institute for Theoretical Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Ben Nichols
- School of Engineering, University of Glasgow , Glasgow , United Kingdom
| | - Christopher Quince
- School of Engineering, University of Glasgow, Glasgow, United Kingdom; Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Frédéric Mahé
- Department of Ecology, University of Kaiserslautern, Kaiserslautern, Germany; UMR LSTM, CIRAD, Montpellier, France
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20
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Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm v2: highly-scalable and high-resolution amplicon clustering. PeerJ 2015; 3:e1420. [PMID: 26713226 PMCID: PMC4690345 DOI: 10.7717/peerj.1420] [Citation(s) in RCA: 274] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 10/31/2015] [Indexed: 01/26/2023] Open
Abstract
Previously we presented Swarm v1, a novel and open source amplicon clustering program that produced fine-scale molecular operational taxonomic units (OTUs), free of arbitrary global clustering thresholds and input-order dependency. Swarm v1 worked with an initial phase that used iterative single-linkage with a local clustering threshold (d), followed by a phase that used the internal abundance structures of clusters to break chained OTUs. Here we present Swarm v2, which has two important novel features: (1) a new algorithm for d = 1 that allows the computation time of the program to scale linearly with increasing amounts of data; and (2) the new fastidious option that reduces under-grouping by grafting low abundant OTUs (e.g., singletons and doubletons) onto larger ones. Swarm v2 also directly integrates the clustering and breaking phases, dereplicates sequencing reads with d = 0, outputs OTU representatives in fasta format, and plots individual OTUs as two-dimensional networks.
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Affiliation(s)
- Frédéric Mahé
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
| | - Torbjørn Rognes
- Department of Informatics, University of Oslo , Oslo , Norway ; Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway
| | - Christopher Quince
- Warwick Medical School, University of Warwick , Warwick , United Kingdom
| | - Colomban de Vargas
- UMR 7144, EPEP-Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff, CNRS , Roscoff , France ; UMR7144 Station Biologique de Roscoff, Sorbonne Universités, UPMC Univ Paris 06 , Roscoff , France
| | - Micah Dunthorn
- Department of Ecology, Technische Universität Kaiserslautern , Kaiserslautern , Germany
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21
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Yang M, Lin X, Rowe A, Rognes T, Eide L, Bjørås M. Transcriptome analysis of human OXR1 depleted cells reveals its role in regulating the p53 signaling pathway. Sci Rep 2015; 5:17409. [PMID: 26616534 PMCID: PMC4663793 DOI: 10.1038/srep17409] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [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: 07/28/2015] [Accepted: 10/23/2015] [Indexed: 11/20/2022] Open
Abstract
The oxidation resistance gene 1 (OXR1) is crucial for protecting against oxidative stress; however, its molecular function is unknown. We employed RNA sequencing to examine the role of human OXR1 for genome wide transcription regulation. In total, in non-treated and hydrogen peroxide exposed HeLa cells, OXR1 depletion resulted in down-regulation of 554 genes and up-regulation of 253 genes. These differentially expressed genes include transcription factors (i.e. HIF1A, SP6, E2F8 and TCF3), antioxidant genes (PRDX4, PTGS1 and CYGB) and numerous genes of the p53 signaling pathway involved in cell-cycle arrest (i.e. cyclin D, CDK6 and RPRM) and apoptosis (i.e. CytC and CASP9). We demonstrated that OXR1 depleted cells undergo cell cycle arrest in G2/M phase during oxidative stress and increase protein expression of the apoptosis initiator protease CASP9. In summary, OXR1 may act as a sensor of cellular oxidative stress to regulate the transcriptional networks required to detoxify reactive oxygen species and modulate cell cycle and apoptosis.
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Affiliation(s)
- Mingyi Yang
- Department of Microbiology, Oslo University Hospital and University of Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Norway
| | - Xiaolin Lin
- Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Norway.,Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Breast Oncology, Peking University Cancer Hospital and Institute, Beijing, P.R. China
| | - Alexander Rowe
- Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Norway
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital and University of Oslo, Norway.,Department of Informatics, University of Oslo, Norway
| | - Lars Eide
- Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Norway
| | - Magnar Bjørås
- Department of Microbiology, Oslo University Hospital and University of Oslo, Norway.,Department of Medical Biochemistry, Oslo University Hospital and University of Oslo, Norway.,Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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22
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Ougland R, Rognes T, Klungland A, Larsen E. Non-homologous functions of the AlkB homologs. J Mol Cell Biol 2015; 7:494-504. [PMID: 26003568 DOI: 10.1093/jmcb/mjv029] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [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: 12/10/2014] [Accepted: 02/26/2015] [Indexed: 12/22/2022] Open
Abstract
The DNA repair enzyme AlkB was identified in E. coli more than three decades ago. Since then, nine mammalian homologs, all members of the superfamily of alpha-ketoglutarate and Fe(II)-dependent dioxygenases, have been identified (designated ALKBH1-8 and FTO). While E. coli AlkB serves as a DNA repair enzyme, only two mammalian homologs have been confirmed to repair DNA in vivo. The other mammalian homologs have remarkably diverse substrate specificities and biological functions. Substrates recognized by the different AlkB homologs comprise erroneous methyl- and etheno adducts in DNA, unique wobble uridine modifications in certain tRNAs, methylated adenines in mRNA, and methylated lysines on proteins. The phenotypes of organisms lacking or overexpressing individual AlkB homologs include obesity, severe sensitivity to inflammation, infertility, growth retardation, and multiple malformations. Here we review the present knowledge of the mammalian AlkB homologs and their implications for human disease and development.
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Affiliation(s)
- Rune Ougland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Department of Anesthesiology, Division of Emergencies and Critical Care, Oslo University Hospital, The Norwegian Radium Hospital, 0310 Oslo, Norway
| | - Torbjørn Rognes
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Department of Informatics, University of Oslo, 0316 Oslo, Norway
| | - Arne Klungland
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway Faculty of Medicine, Institute of Basic Medical Sciences, University of Oslo, 0317 Oslo, Norway
| | - Elisabeth Larsen
- Clinic for Diagnostics and Intervention and Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, 0027 Oslo, Norway
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23
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Mahé F, Rognes T, Quince C, de Vargas C, Dunthorn M. Swarm: robust and fast clustering method for amplicon-based studies. PeerJ 2014; 2:e593. [PMID: 25276506 PMCID: PMC4178461 DOI: 10.7717/peerj.593] [Citation(s) in RCA: 472] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Accepted: 09/03/2014] [Indexed: 11/20/2022] Open
Abstract
Popular de novo amplicon clustering methods suffer from two fundamental flaws: arbitrary global clustering thresholds, and input-order dependency induced by centroid selection. Swarm was developed to address these issues by first clustering nearly identical amplicons iteratively using a local threshold, and then by using clusters' internal structure and amplicon abundances to refine its results. This fast, scalable, and input-order independent approach reduces the influence of clustering parameters and produces robust operational taxonomic units.
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Affiliation(s)
- Frédéric Mahé
- CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France ; Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany
| | - Torbjørn Rognes
- Department of Microbiology, Oslo University Hospital, Rikshospitalet , Oslo , Norway ; Department of Informatics, University of Oslo , Oslo , Norway
| | | | - Colomban de Vargas
- CNRS, UMR 7144, EPEP - Évolution des Protistes et des Écosystèmes Pélagiques, Station Biologique de Roscoff , Roscoff , France ; Sorbonne Universités, UPMC Univ Paris 06, UMR 7144, Station Biologique de Roscoff , Roscoff , France
| | - Micah Dunthorn
- Department of Ecology, University of Kaiserslautern , Kaiserslautern , Germany
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24
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Booth JA, Thomassen GOS, Rowe AD, Weel-Sneve R, Lagesen K, Kristiansen KI, Bjørås M, Rognes T, Lindvall JM. Tiling array study of MNNG treated Escherichia coli reveals a widespread transcriptional response. Sci Rep 2013; 3:3053. [PMID: 24157950 PMCID: PMC6505713 DOI: 10.1038/srep03053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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: 07/10/2013] [Accepted: 10/11/2013] [Indexed: 11/25/2022] Open
Abstract
The alkylating agent N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) is known to trigger the adaptive response by inducing the ada-regulon – consisting of three DNA repair enzymes Ada, AlkB, AlkA and the enigmatic AidB. We have applied custom designed tiling arrays to study transcriptional changes in Escherichia coli following a MNNG challenge. Along with the expected upregulation of the adaptive response genes (ada, alkA and alkB), we identified a number of differentially expressed transcripts, both novel and annotated. This indicates a wider regulatory response than previously documented. There were 250 differentially-expressed and 2275 similarly-expressed unannotated transcripts. We found novel upregulation of several stress-induced transcripts, including the SOS inducible genes recN and tisAB, indicating a novel role for these genes in alkylation repair. Furthermore, the ada-regulon A and B boxes were found to be insufficient to explain the regulation of the adaptive response genes after MNNG exposure, suggesting that additional regulatory elements must be involved.
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Affiliation(s)
- James A Booth
- 1] Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [2] Department of Microbiology, University of Oslo, PO Box 4950 Nydalen, NO-0424 Oslo, Norway [3]
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25
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Ougland R, Lando D, Jonson I, Dahl JA, Moen MN, Nordstrand LM, Rognes T, Lee JT, Klungland A, Kouzarides T, Larsen E. ALKBH1 is a histone H2A dioxygenase involved in neural differentiation. Stem Cells 2013; 30:2672-82. [PMID: 22961808 PMCID: PMC3546389 DOI: 10.1002/stem.1228] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [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: 04/11/2012] [Accepted: 08/19/2012] [Indexed: 12/18/2022]
Abstract
AlkB homolog 1 (ALKBH1) is one of nine members of the family of mammalian AlkB homologs. Most Alkbh1(-/-) mice die during embryonic development, and survivors are characterized by defects in tissues originating from the ectodermal lineage. In this study, we show that deletion of Alkbh1 prolonged the expression of pluripotency markers in embryonic stem cells and delayed the induction of genes involved in early differentiation. In vitro differentiation to neural progenitor cells (NPCs) displayed an increased rate of apoptosis in the Alkbh1(-/-) NPCs when compared with wild-type cells. Whole-genome expression analysis and chromatin immunoprecipitation revealed that ALKBH1 regulates both directly and indirectly, a subset of genes required for neural development. Furthermore, our in vitro enzyme activity assays demonstrate that ALKBH1 is a histone dioxygenase that acts specifically on histone H2A. Mass spectrometric analysis demonstrated that histone H2A from Alkbh1(-/-) mice are improperly methylated. Our results suggest that ALKBH1 is involved in neural development by modifying the methylation status of histone H2A.
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Affiliation(s)
- Rune Ougland
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet and University of Oslo, Oslo, Norway
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26
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Backe PH, Simm R, Laerdahl JK, Dalhus B, Fagerlund A, Okstad OA, Rognes T, Alseth I, Kolstø AB, Bjørås M. A new family of proteins related to the HEAT-like repeat DNA glycosylases with affinity for branched DNA structures. J Struct Biol 2013; 183:66-75. [PMID: 23623903 DOI: 10.1016/j.jsb.2013.04.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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: 11/21/2012] [Revised: 04/09/2013] [Accepted: 04/16/2013] [Indexed: 12/27/2022]
Abstract
The recently discovered HEAT-like repeat (HLR) DNA glycosylase superfamily is widely distributed in all domains of life. The present bioinformatics and phylogenetic analysis shows that HLR DNA glycosylase superfamily members in the genus Bacillus form three subfamilies: AlkC, AlkD and AlkF/AlkG. The crystal structure of AlkF shows structural similarity with the DNA glycosylases AlkC and AlkD, however neither AlkF nor AlkG display any DNA glycosylase activity. Instead, both proteins have affinity to branched DNA structures such as three-way and Holliday junctions. A unique β-hairpin in the AlkF/AlkG subfamily is most likely inserted into the DNA major groove, and could be a structural determinant regulating DNA substrate affinity. We conclude that AlkF and AlkG represent a new family of HLR proteins with affinity for branched DNA structures.
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Affiliation(s)
- Paul H Backe
- Department of Microbiology, Oslo University Hospital and University of Oslo, P.O. Box 4950 Nydalen, 0424 Oslo, Norway
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27
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Søberg K, Jahnsen T, Rognes T, Skålhegg BS, Laerdahl JK. Evolutionary paths of the cAMP-dependent protein kinase (PKA) catalytic subunits. PLoS One 2013; 8:e60935. [PMID: 23593352 PMCID: PMC3625193 DOI: 10.1371/journal.pone.0060935] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Accepted: 03/05/2013] [Indexed: 11/19/2022] Open
Abstract
3',5'-cyclic adenosine monophosphate (cAMP) dependent protein kinase or protein kinase A (PKA) has served as a prototype for the large family of protein kinases that are crucially important for signal transduction in eukaryotic cells. The PKA catalytic subunits Cα and Cβ, encoded by the two genes PRKACA and PRKACB, respectively, are among the best understood and characterized human kinases. Here we have studied the evolution of this gene family in chordates, arthropods, mollusks and other animals employing probabilistic methods and show that Cα and Cβ arose by duplication of an ancestral PKA catalytic subunit in a common ancestor of vertebrates. The two genes have subsequently been duplicated in teleost fishes. The evolution of the PRKACG retroposon in simians was also investigated. Although the degree of sequence conservation in the PKA Cα/Cβ kinase family is exceptionally high, a small set of signature residues defining Cα and Cβ subfamilies were identified. These conserved residues might be important for functions that are unique to the Cα or Cβ clades. This study also provides a good example of a seemingly simple phylogenetic problem which, due to a very high degree of sequence conservation and corresponding weak phylogenetic signals, combined with problematic nonphylogenetic signals, is nontrivial for state-of-the-art probabilistic phylogenetic methods.
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Affiliation(s)
- Kristoffer Søberg
- Department of Nutrition, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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28
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Weel-Sneve R, Kristiansen KI, Odsbu I, Dalhus B, Booth J, Rognes T, Skarstad K, Bjørås M. Single transmembrane peptide DinQ modulates membrane-dependent activities. PLoS Genet 2013; 9:e1003260. [PMID: 23408903 PMCID: PMC3567139 DOI: 10.1371/journal.pgen.1003260] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Accepted: 12/05/2012] [Indexed: 11/18/2022] Open
Abstract
The functions of several SOS regulated genes in Escherichia coli are still unknown, including dinQ. In this work we characterize dinQ and two small RNAs, agrA and agrB, with antisense complementarity to dinQ. Northern analysis revealed five dinQ transcripts, but only one transcript (+44) is actively translated. The +44 dinQ transcript translates into a toxic single transmembrane peptide localized in the inner membrane. AgrB regulates dinQ RNA by RNA interference to counteract DinQ toxicity. Thus the dinQ-agr locus shows the classical features of a type I TA system and has many similarities to the tisB-istR locus. DinQ overexpression depolarizes the cell membrane and decreases the intracellular ATP concentration, demonstrating that DinQ can modulate membrane-dependent processes. Augmented DinQ strongly inhibits marker transfer by Hfr conjugation, indicating a role in recombination. Furthermore, DinQ affects transformation of nucleoid morphology in response to UV damage. We hypothesize that DinQ is a transmembrane peptide that modulates membrane-dependent activities such as nucleoid compaction and recombination. Exposure of the bacterium Escherichia coli to DNA damaging agents induces the SOS response, which up-regulates gene functions involved in numerous cellular processes such as DNA repair, cell division, and replication. Most of the SOS regulated genes in E. coli have been characterized, but still there are several genes of unknown function. One of these uncharacterized genes is dinQ. In this work we characterize dinQ and two novel small RNAs, agrA and agrB, that regulate expression of dinQ. The DinQ peptide is localized in the inner membrane as a single transmembrane peptide of 27 amino acids. Small proteins of less than 50 amino acids are important in cellular processes such as regulation, signalling, and antibacterial action. Here we demonstrate that DinQ modulates recombination and transformation of nucleoid morphology in response to UV damage. Our results provide new insights into small hydrophobic peptides that could regulate important DNA metabolic processes dependent on the inner membrane of the cell.
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Affiliation(s)
- Ragnhild Weel-Sneve
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Microbiology, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Knut Ivan Kristiansen
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Microbiology, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- * E-mail: (KIK); (MB)
| | - Ingvild Odsbu
- Department of Cell Biology, Institute for Cancer Research, University of Oslo and Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Bjørn Dalhus
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Biochemistry, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - James Booth
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Microbiology, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Microbiology, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Kirsten Skarstad
- Department of Cell Biology, Institute for Cancer Research, University of Oslo and Oslo University Hospital, Radiumhospitalet, Oslo, Norway
| | - Magnar Bjørås
- Centre for Molecular Biology and Neuroscience (CMBN), University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Microbiology, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Biochemistry, University of Oslo and Oslo University Hospital, Rikshospitalet, Oslo, Norway
- * E-mail: (KIK); (MB)
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29
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Nordstrand LM, Furu K, Paulsen J, Rognes T, Klungland A. Alkbh1 and Tzfp repress a non-repeat piRNA cluster in pachytene spermatocytes. Nucleic Acids Res 2012; 40:10950-63. [PMID: 22965116 PMCID: PMC3505970 DOI: 10.1093/nar/gks839] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [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] [Indexed: 11/14/2022] Open
Abstract
Piwi proteins and Piwi-interacting small RNAs (piRNAs) have known functions in transposon silencing in the male germline of fetal and newborn mice. Both are also present in adult testes; however, their function here remains a mystery. Here, we confirm that most piRNAs in meiotic spermatocytes originate from clusters in non-repeat intergenic regions of DNA. The regulation of these piRNA clusters, including the processing of the precursor transcripts into individual piRNAs, is accomplished through mostly unknown processes. We present a possible regulatory mechanism for one such cluster, named cluster 1082B, located on chromosome 7 in the mouse genome. The 1082B precursor transcript and its 788 unique piRNAs are repressed by the Alkbh1 dioxygenase and the testis-specific transcription repressor Tzfp. We observe a remarkable >1000-fold upregulation of individual piRNAs in pachytene spermatocytes isolated from Alkbh1- and Tzfp-deficient murine testes. Repression of cluster 1082B is further supported by the identification of a 10-bp Tzfp recognition sequence contained within the precursor transcript. Downregulation of LINE1 and IAP transcripts in the Alkbh1- and Tzfp-deficient mice leads us to propose a potential role for the 1082B-encoded piRNAs in transposon control.
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Affiliation(s)
- Line M Nordstrand
- Department of Microbiology, Centre for Molecular Biology and Neuroscience, Oslo University Hospital, Rikshospitalet, PO Box 4950, Nydalen, NO-0424 Oslo, Norway
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30
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Abstract
Background The Smith-Waterman algorithm for local sequence alignment is more sensitive than heuristic methods for database searching, but also more time-consuming. The fastest approach to parallelisation with SIMD technology has previously been described by Farrar in 2007. The aim of this study was to explore whether further speed could be gained by other approaches to parallelisation. Results A faster approach and implementation is described and benchmarked. In the new tool SWIPE, residues from sixteen different database sequences are compared in parallel to one query residue. Using a 375 residue query sequence a speed of 106 billion cell updates per second (GCUPS) was achieved on a dual Intel Xeon X5650 six-core processor system, which is over six times more rapid than software based on Farrar's 'striped' approach. SWIPE was about 2.5 times faster when the programs used only a single thread. For shorter queries, the increase in speed was larger. SWIPE was about twice as fast as BLAST when using the BLOSUM50 score matrix, while BLAST was about twice as fast as SWIPE for the BLOSUM62 matrix. The software is designed for 64 bit Linux on processors with SSSE3. Source code is available from http://dna.uio.no/swipe/ under the GNU Affero General Public License. Conclusions Efficient parallelisation using SIMD on standard hardware makes it possible to run Smith-Waterman database searches more than six times faster than before. The approach described here could significantly widen the potential application of Smith-Waterman searches. Other applications that require optimal local alignment scores could also benefit from improved performance.
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Affiliation(s)
- Torbjørn Rognes
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway.
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Yang M, Aamodt RM, Dalhus B, Balasingham S, Helle I, Andersen P, Tønjum T, Alseth I, Rognes T, Bjørås M. The ada operon of Mycobacterium tuberculosis encodes two DNA methyltransferases for inducible repair of DNA alkylation damage. DNA Repair (Amst) 2011; 10:595-602. [PMID: 21570366 DOI: 10.1016/j.dnarep.2011.03.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Revised: 03/01/2011] [Accepted: 03/15/2011] [Indexed: 11/26/2022]
Abstract
The ada operon of Mycobacterium tuberculosis, which encodes a composite protein of AdaA and AlkA and a separate AdaB/Ogt protein, was characterized. M. tuberculosis treated with N-methyl-N'-nitro-N-nitrosoguanidine induced transcription of the adaA-alkA and adaB genes, suggesting that M. tuberculosis mount an inducible response to methylating agents. Survival assays of the methyltransferase defective Escherichia coli mutant KT233 (ada ogt), showed that expression of the adaB gene rescued the alkylation sensitivity. Further, adaB but not adaA-alkA complemented the hypermutator phenotype of KT233. Purified AdaA-AlkA and AdaB possessed methyltransferase activity. These data suggested that AdaB counteract the cytotoxic and mutagenic effect of O(6)-methylguanine, while AdaA-AlkA most likely transfers methyl groups from innocuous methylphosphotriesters. AdaA-AlkA did not possess alkylbase DNA glycosylase activity nor rescue the alkylation sensitivity of the E. coli mutant BK2118 (tag alkA). We propose that AdaA-AlkA is a positive regulator of the adaptive response in M. tuberculosis. It thus appears that the ada operon of M. tuberculosis suppresses the mutagenic effect of alkylation but not the cytotoxic effect of lesions such as 3-methylpurines. Collectively, these data indicate that M. tuberculosis hypermutator strains with defective adaptive response genes might sustain robustness to cytotoxic alkylation DNA damage and confer a selective advantage contributing to host adaptation.
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Affiliation(s)
- Mingyi Yang
- Department of Microbiology, Oslo University Hospital, Rikshospitalet, PO Box 4950 Nydalen, NO-0424 Oslo, Norway
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Thomassen GOS, Weel-Sneve R, Rowe AD, Booth JA, Lindvall JM, Lagesen K, Kristiansen KI, Bjørås M, Rognes T. Tiling array analysis of UV treated Escherichia coli predicts novel differentially expressed small peptides. PLoS One 2010; 5:e15356. [PMID: 21203457 PMCID: PMC3009722 DOI: 10.1371/journal.pone.0015356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2010] [Accepted: 11/09/2010] [Indexed: 11/19/2022] Open
Abstract
Background Despite comprehensive investigation, the Escherichia coli SOS response system is not yet fully understood. We have applied custom designed whole genome tiling arrays to measure UV invoked transcriptional changes in E. coli. This study provides a more complete insight into the transcriptome and the UV irradiation response of this microorganism. Results We detected a number of novel differentially expressed transcripts in addition to the expected SOS response genes (such as sulA, recN, uvrA, lexA, umuC and umuD) in the UV treated cells. Several of the differentially expressed transcripts might play important roles in regulation of the cellular response to UV damage. We have predicted 23 novel small peptides from our set of detected non-gene transcripts. Further, three of the predicted peptides were cloned into protein expression vectors to test the biological activity. All three constructs expressed the predicted peptides, in which two of them were highly toxic to the cell. Additionally, a remarkably high overlap with previously in-silico predicted non-coding RNAs (ncRNAs) was detected. Generally we detected a far higher transcriptional activity than the annotation suggests, and these findings correspond with previous transcription mappings from E. coli and other organisms. Conclusions Here we demonstrate that the E. coli transcriptome consists of far more transcripts than the present annotation suggests, of which many transcripts seem important to the bacterial stress response. Sequence alignment of promoter regions suggest novel regulatory consensus sequences for some of the upregulated genes. Finally, several of the novel transcripts identified in this study encode putative small peptides, which are biologically active.
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Affiliation(s)
- Gard O. S. Thomassen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Ragnhild Weel-Sneve
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Alexander D. Rowe
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - James A. Booth
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | | | - Karin Lagesen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
| | - Knut I. Kristiansen
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
| | - Magnar Bjørås
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, University of Oslo, Oslo, Norway
- Institute of Clinical Biochemistry, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN) and Department of Microbiology, Rikshospitalet, Oslo University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- * E-mail:
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Nordstrand LM, Svärd J, Larsen E, Nilsen A, Ougland R, Furu K, Lien GF, Rognes T, Namekawa SH, Lee JT, Klungland A. Mice lacking Alkbh1 display sex-ratio distortion and unilateral eye defects. PLoS One 2010; 5:e13827. [PMID: 21072209 PMCID: PMC2972218 DOI: 10.1371/journal.pone.0013827] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Accepted: 10/14/2010] [Indexed: 11/26/2022] Open
Abstract
Background Eschericia coli AlkB is a 2-oxoglutarate- and iron-dependent dioxygenase that reverses alkylated DNA damage by oxidative demethylation. Mouse AlkB homolog 1 (Alkbh1) is one of eight members of the newly discovered family of mammalian dioxygenases. Methods and Findings In the present study we show non-Mendelian inheritance of the Alkbh1 targeted allele in mice. Both Alkbh1−/− and heterozygous Alkbh1+/− offspring are born at a greatly reduced frequency. Additionally, the sex-ratio is considerably skewed against female offspring, with one female born for every three to four males. Most mechanisms that cause segregation distortion, act in the male gametes and affect male fertility. The skewing of the sexes appears to be of paternal origin, and might be set in the pachythene stage of meiosis during spermatogenesis, in which Alkbh1 is upregulated more than 10-fold. In testes, apoptotic spermatids were revealed in 5–10% of the tubules in Alkbh1−/− adults. The deficiency of Alkbh1 also causes misexpression of Bmp2, 4 and 7 at E11.5 during embryonic development. This is consistent with the incompletely penetrant phenotypes observed, particularly recurrent unilateral eye defects and craniofacial malformations. Conclusions Genetic and phenotypic assessment suggests that Alkbh1 mediates gene regulation in spermatogenesis, and that Alkbh1 is essential for normal sex-ratio distribution and embryonic development in mice.
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Affiliation(s)
- Line M. Nordstrand
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Jessica Svärd
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Elisabeth Larsen
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Anja Nilsen
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Rune Ougland
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Kari Furu
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Guro F. Lien
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Satoshi H. Namekawa
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Jeannie T. Lee
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Howard Hughes Medical Institute, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Arne Klungland
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital and University of Oslo, Oslo, Norway
- Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
- * E-mail:
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Abstract
We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it seems that these small regulators have a more important role than has been previously thought. Most microRNAs have been detected by cloning and Northern blotting, but experimental methods are biased towards abundant microRNAs as well as being time-consuming. Computational detection methods must therefore be refined to serve as a faster, better, and more affordable method for microRNA detection. We also present data from a small study investigating the problems of computational miRNA prediction. Our findings suggest that the prediction of microRNA precursor candidates is fairly easy, while excluding false positives as well as exact prediction of the mature microRNA is hard. Finally, we discuss possible improvements to computational microRNA detection.
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Affiliation(s)
- Gard O. S. Thomassen
- Centre for Molecular Biology and Neuroscience (CMBN),
Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, 0027 Oslo, Norway
| | - Øystein Røsok
- Department of Immunology, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Centre, 0310 Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN),
Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, 0027 Oslo, Norway
- Department of Informatics, University of Oslo, PO Box
1080 Blindern, 0316 Oslo, Norway
- *Torbjørn Rognes:
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Fensgård Ø, Kassahun H, Bombik I, Rognes T, Lindvall JM, Nilsen H. A two-tiered compensatory response to loss of DNA repair modulates aging and stress response pathways. Aging (Albany NY) 2010; 2:133-59. [PMID: 20382984 PMCID: PMC2871243 DOI: 10.18632/aging.100127] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Accepted: 03/27/2010] [Indexed: 05/29/2023]
Abstract
Activation of oxidative stress-responses and downregulation of insulin-like signaling (ILS) is seen in Nucleotide Excision Repair (NER) deficient segmental progeroid mice. Evidence suggests that this is a survival response to persistent transcription-blocking DNA damage, although the relevant lesions have not been identified. Here we show that loss of NTH-1, the only Base Excision Repair (BER) enzyme known to initiate repair of oxidative DNA damage inC. elegans, restores normal lifespan of the short-lived NER deficient xpa-1 mutant. Loss of NTH-1 leads to oxidative stress and global expression profile changes that involve upregulation of genes responding to endogenous stress and downregulation of ILS. A similar, but more extensive, transcriptomic shift is observed in the xpa-1 mutant whereas loss of both NTH-1 and XPA-1 elicits a different profile with downregulation of Aurora-B and Polo-like kinase 1 signaling networks as well as DNA repair and DNA damage response genes. The restoration of normal lifespan and absence oxidative stress responses in nth-1;xpa-1 indicate that BER contributes to generate transcription blocking lesions from oxidative DNA damage. Hence, our data strongly suggests that the DNA lesions relevant for aging are repair intermediates resulting from aberrant or attempted processing by BER of lesions normally repaired by NER.
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Affiliation(s)
- Øyvind Fensgård
- University of Oslo, The Biotechnology Centre, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Henok Kassahun
- University of Oslo, The Biotechnology Centre, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Izabela Bombik
- University of Oslo, The Biotechnology Centre, P.O. Box 1125
Blindern, 0317 Oslo, Norway
| | - Torbjørn Rognes
- University of Oslo, Department of Informatics, P.O. Box 1080
Blindern, NO-0316 Oslo, Norway
| | | | - Hilde Nilsen
- University of Oslo, The Biotechnology Centre, P.O. Box 1125
Blindern, 0317 Oslo, Norway
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Nakken S, Rognes T, Hovig E. The disruptive positions in human G-quadruplex motifs are less polymorphic and more conserved than their neutral counterparts. Nucleic Acids Res 2009; 37:5749-56. [PMID: 19617376 PMCID: PMC2761265 DOI: 10.1093/nar/gkp590] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [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] [Indexed: 11/13/2022] Open
Abstract
Specific guanine-rich sequence motifs in the human genome have considerable potential to form four-stranded structures known as G-quadruplexes or G4 DNA. The enrichment of these motifs in key chromosomal regions has suggested a functional role for the G-quadruplex structure in genomic regulation. In this work, we have examined the spectrum of nucleotide substitutions in G4 motifs, and related this spectrum to G4 prevalence. Data collected from the large repository of human SNPs indicates that the core feature of G-quadruplex motifs, 5′-GGG-3′, exhibits specific mutational patterns that preserve the potential for G4 formation. In particular, we find a genome-wide pattern in which sites that disrupt the guanine triplets are more conserved and less polymorphic than their neutral counterparts. This also holds when considering non-CpG sites only. However, the low level of polymorphisms in guanine tracts is not only confined to G4 motifs. A complete mapping of DNA three-mers at guanine polymorphisms indicated that short guanine tracts are the most under-represented sequence context at polymorphic sites. Furthermore, we provide evidence for a strand bias upstream of human genes. Here, a significantly lower rate of G4-disruptive SNPs on the non-template strand supports a higher relative influence of G4 formation on this strand during transcription.
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Affiliation(s)
- Sigve Nakken
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway.
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Thomassen GOS, Rowe AD, Lagesen K, Lindvall JM, Rognes T. Custom design and analysis of high-density oligonucleotide bacterial tiling microarrays. PLoS One 2009; 4:e5943. [PMID: 19536279 PMCID: PMC2691959 DOI: 10.1371/journal.pone.0005943] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 05/18/2009] [Indexed: 11/21/2022] Open
Abstract
Background High-density tiling microarrays are a powerful tool for the characterization of complete genomes. The two major computational challenges associated with custom-made arrays are design and analysis. Firstly, several genome dependent variables, such as the genome's complexity and sequence composition, need to be considered in the design to ensure a high quality microarray. Secondly, since tiling projects today very often exceed the limits of conventional array-experiments, researchers cannot use established computer tools designed for commercial arrays, and instead have to redesign previous methods or create novel tools. Principal Findings Here we describe the multiple aspects involved in the design of tiling arrays for transcriptome analysis and detail the normalisation and analysis procedures for such microarrays. We introduce a novel design method to make two 280,000 feature microarrays covering the entire genome of the bacterial species Escherichia coli and Neisseria meningitidis, respectively, as well as the use of multiple copies of control probe-sets on tiling microarrays. Furthermore, a novel normalisation and background estimation procedure for tiling arrays is presented along with a method for array analysis focused on detection of short transcripts. The design, normalisation and analysis methods have been applied in various experiments and several of the detected novel short transcripts have been biologically confirmed by Northern blot tests. Conclusions Tiling-arrays are becoming increasingly applicable in genomic research, but researchers still lack both the tools for custom design of arrays, as well as the systems and procedures for analysis of the vast amount of data resulting from such experiments. We believe that the methods described herein will be a useful contribution and resource for researchers designing and analysing custom tiling arrays for both bacteria and higher organisms.
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Affiliation(s)
- Gard O. S. Thomassen
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Alexander D. Rowe
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | - Karin Lagesen
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
| | | | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN), Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
- * E-mail:
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Abstract
Pathogenic bacteria continuously encounter multiple forms of stress in their hostile environments, which leads to DNA damage. With the new insight into biology offered by genome sequences, the elucidation of the gene content encoding proteins provides clues toward understanding the microbial lifestyle related to habitat and niche. Campylobacter jejuni, Haemophilus influenzae, Helicobacter pylori, Mycobacterium tuberculosis, the pathogenic Neisseria, Streptococcus pneumoniae, Streptococcus pyogenes and Staphylococcus aureus are major human pathogens causing detrimental morbidity and mortality at a global scale. An algorithm for the clustering of orthologs was established in order to identify whether orthologs of selected genes were present or absent in the genomes of the pathogenic bacteria under study. Based on the known genes for the various functions and their orthologs in selected pathogenic bacteria, an overview of the presence of the different types of genes was created. In this context, we focus on selected processes enabling genome dynamics in these particular pathogens, namely DNA repair, recombination and horizontal gene transfer. An understanding of the precise molecular functions of the enzymes participating in DNA metabolism and their importance in the maintenance of bacterial genome integrity has also, in recent years, indicated a future role for these enzymes as targets for therapeutic intervention.
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Affiliation(s)
- Ole Herman Ambur
- Centre for Molecular Biology and Neuroscience, Institute of Microbiology, University of Oslo, Oslo University Hospital, Norway
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Abstract
Base excision repair (BER) is the primary DNA repair pathway that corrects base lesions that arise due to oxidative, alkylation, deamination, and depurinatiation/depyrimidination damage. BER facilitates the repair of damaged DNA via two general pathways - short-patch and long-patch. The shortpatch BER pathway leads to a repair tract of a single nucleotide. Alternatively, the long-patch BER pathway produces a repair tract of at least two nucleotides. The BER pathway is initiated by one of many DNA glycosylases, which recognize and catalyze the removal of damaged bases. The completion of the BER pathway is accomplished by the coordinated action of at least three additional enzymes. These downstream enzymes carry out strand incision, gap-filling and ligation. The high degree of BER conservation between E. coli and mammals has lead to advances in our understanding of mammalian BER. This review will provide a general overview of the mammalian BER pathway. (Part of a Multi-author Review).
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Affiliation(s)
- A B Robertson
- Centre for Molecular Biology and Neuroscience, Rikshospitalet HF, University of Oslo, Oslo, Norway
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Nakken S, Rødland EA, Rognes T, Hovig E. Large-scale inference of the point mutational spectrum in human segmental duplications. BMC Genomics 2009; 10:43. [PMID: 19161616 PMCID: PMC2640414 DOI: 10.1186/1471-2164-10-43] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [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: 09/02/2008] [Accepted: 01/22/2009] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Recent segmental duplications are relatively large (> or = 1 kb) genomic regions of high sequence identity (> or = 90%). They cover approximately 4-5% of the human genome and play important roles in gene evolution and genomic disease. The DNA sequence differences between copies of a segmental duplication represent the result of various mutational events over time, since any two duplication copies originated from the same ancestral DNA sequence. Based on this fact, we have developed a computational scheme for inference of point mutational events in human segmental duplications, which we collectively term duplication-inferred mutations (DIMs). We have characterized these nucleotide substitutions by comparing them with high-quality SNPs from dbSNP, both in terms of sequence context and frequency of substitution types. RESULTS Overall, DIMs show a lower ratio of transitions relative to transversions than SNPs, although this ratio approaches that of SNPs when considering DIMs within most recent duplications. Our findings indicate that DIMs and SNPs in general are caused by similar mutational mechanisms, with some deviances at the CpG dinucleotide. Furthermore, we discover a large number of reference SNPs that coincide with computationally inferred DIMs. The latter reflects how sequence variation in duplicated sequences can be misinterpreted as ordinary allelic variation. CONCLUSION In summary, we show how DNA sequence analysis of segmental duplications can provide a genome-wide mutational spectrum that mirrors recent genome evolution. The inferred set of nucleotide substitutions represents a valuable complement to SNPs for the analysis of genetic variation and point mutagenesis.
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Affiliation(s)
- Sigve Nakken
- Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316 Oslo, Norway.
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Skotheim RI, Thomassen GOS, Eken M, Lind GE, Micci F, Ribeiro FR, Cerveira N, Teixeira MR, Heim S, Rognes T, Lothe RA. A universal assay for detection of oncogenic fusion transcripts by oligo microarray analysis. Mol Cancer 2009; 8:5. [PMID: 19152679 PMCID: PMC2633275 DOI: 10.1186/1476-4598-8-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Accepted: 01/19/2009] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The ability to detect neoplasia-specific fusion genes is important not only in cancer research, but also increasingly in clinical settings to ensure that correct diagnosis is made and the optimal treatment is chosen. However, the available methodologies to detect such fusions all have their distinct short-comings. RESULTS We describe a novel oligonucleotide microarray strategy whereby one can screen for all known oncogenic fusion transcripts in a single experiment. To accomplish this, we combine measurements of chimeric transcript junctions with exon-wise measurements of individual fusion partners. To demonstrate the usefulness of the approach, we designed a DNA microarray containing 68,861 oligonucleotide probes that includes oligos covering all combinations of chimeric exon-exon junctions from 275 pairs of fusion genes, as well as sets of oligos internal to all the exons of the fusion partners. Using this array, proof of principle was demonstrated by detection of known fusion genes (such as TCF3:PBX1, ETV6:RUNX1, and TMPRSS2:ERG) from all six positive controls consisting of leukemia cell lines and prostate cancer biopsies. CONCLUSION This new method bears promise of an important complement to currently used diagnostic and research tools for the detection of fusion genes in neoplastic diseases.
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Affiliation(s)
- Rolf I Skotheim
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Gard OS Thomassen
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet University Hospital, Oslo, Norway
| | - Marthe Eken
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
| | - Francesca Micci
- Department of Cancer Genetics, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
| | - Franclim R Ribeiro
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Nuno Cerveira
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Manuel R Teixeira
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Genetics, Portuguese Oncology Institute, Porto, Portugal
| | - Sverre Heim
- Department of Cancer Genetics, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Medical Faculty, University of Oslo, Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet University Hospital, Oslo, Norway
- Department of Informatics, University of Oslo, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Cancer Prevention, Institute for Cancer Research, Norwegian Radium Hospital, Rikshospitalet University Hospital, Oslo, Norway
- Centre for Cancer Biomedicine, University of Oslo, Oslo, Norway
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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Røyrvik EC, Ahlquist T, Rognes T, Lothe RA. Slip slidin' away: a duodecennial review of targeted genes in mismatch repair deficient colorectal cancer. Crit Rev Oncog 2008; 13:229-57. [PMID: 18298386 DOI: 10.1615/critrevoncog.v13.i3.20] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Roughly 15% of colorectal tumors are characterized by microsatellite instability (MSI), a deficiency caused by defective DNA mismatch repair, which leads to profuse insertions and deletions in microsatellites. Downstream target genes of this defective repair are those prone to exhibit these insertion/deletion mutations in their coding regions and potentially having functional consequences in, and providing a growth advantage for, the cancer cell. This review presents the last 12 years of research on these MSI target genes, systematizing the mutation details of the more than 160 genes identified to date, and includes their mutation frequencies in colorectal and other MSI (e.g., gastric and endometrial) tumors. Functional aspects of certain targets and the target gene concept itself are also discussed, as is the comparative wealth of potential target genes assessed by scanning the coding sequences of the human genome for mononucleotide repeats--yet to be investigated.
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Affiliation(s)
- Ellen C Røyrvik
- Department of Cancer Prevention, Institute for Cancer Research, Rikshospitalet-Radiumhospitalet Medical Center, Center for Cancer Biomedicine, University of Oslo, Norway
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Cameron J, Holla OL, Laerdahl JK, Kulseth MA, Ranheim T, Rognes T, Berge KE, Leren TP. Characterization of novel mutations in the catalytic domain of the PCSK9 gene. J Intern Med 2008; 263:420-31. [PMID: 18266662 DOI: 10.1111/j.1365-2796.2007.01915.x] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES To expand our understanding of the structure and function of proprotein convertase subtilisin/kexin type 9 (PCSK9) by studying how naturally occurring mutations in PCSK9 disrupt the function of PCSK9. DESIGN Mutations in PCSK9 were identified by sequencing of DNA from subjects with hypo- or hypercholesterolemia. The effect of the identified mutations on the autocatalytic cleavage and secretion of PCSK9, as well as the effect on PCSK9-mediated degradation of the low density lipoprotein receptors, were determined in HepG2 or HEK293 cells transiently transfected with mutant PCSK9-containing plasmids. The findings were collated to the clinical characteristics of the subjects possessing these mutations, and the phenotypic effects were analysed in terms of available structural data for PCSK9. RESULTS Five novel mutations in PCSK9 were identified. Mutation R215H was a gain-of-function mutation which causes hypercholesterolemia. Mutation G236S and N354I were loss-of-function mutations due to failure to exit the endoplasmic reticulum or failure to undergo autocatalytic cleavage, respectively. Mutations A245T and R272Q were most likely normal genetic variants. By comparing the number of patients with gain-of-function mutations in PCSK9 with the number of familial hypercholesterolemia heterozygotes among subjects with hypercholesterolemia, the prevalence of subjects with gain-of-function mutations in PCSK9 in Norway can be estimated to one in 15,000. CONCLUSION This study has provided novel information about the structural requirements for the normal function of PCSK9. However, more studies are needed to determine the mechanisms by which gain-of-function mutations in PCSK9 cause hypercholesterolemia.
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Affiliation(s)
- J Cameron
- Department of Medical Genetics, Medical Genetics Laboratory, Rigshospitalet-Radiumhospitalet Medical Centre, Oslo, Norway
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Abstract
The publication of a complete genome sequence is usually accompanied by annotations of its genes. In contrast to protein coding genes, genes for ribosomal RNA (rRNA) are often poorly or inconsistently annotated. This makes comparative studies based on rRNA genes difficult. We have therefore created computational predictors for the major rRNA species from all kingdoms of life and compiled them into a program called RNAmmer. The program uses hidden Markov models trained on data from the 5S ribosomal RNA database and the European ribosomal RNA database project. A pre-screening step makes the method fast with little loss of sensitivity, enabling the analysis of a complete bacterial genome in less than a minute. Results from running RNAmmer on a large set of genomes indicate that the location of rRNAs can be predicted with a very high level of accuracy. Novel, unannotated rRNAs are also predicted in many genomes. The software as well as the genome analysis results are available at the CBS web server.
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Affiliation(s)
- Karin Lagesen
- Centre for Molecular Biology and Neuroscience and Institute of Medical Microbiology, University of Oslo, NO-0027 Oslo, Norway.
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Dalhus B, Helle IH, Backe PH, Alseth I, Rognes T, Bjørås M, Laerdahl JK. Structural insight into repair of alkylated DNA by a new superfamily of DNA glycosylases comprising HEAT-like repeats. Nucleic Acids Res 2007; 35:2451-9. [PMID: 17395642 PMCID: PMC1874660 DOI: 10.1093/nar/gkm039] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of DNA glycosylases with an alpha–alpha superhelix fold comprising six HEAT-like repeats. The structure reveals a wide, positively charged groove, including a putative base recognition pocket. This groove appears to be suitable for the accommodation of double-stranded DNA with a flipped-out alkylated base. Site-specific mutagenesis within the recognition pocket identified several residues essential for enzyme activity. The results suggest that the aromatic side chain of a tryptophan residue recognizes electron-deficient alkylated bases through stacking interactions, while an interacting aspartate–arginine pair is essential for removal of the damaged base. A structural model of AlkD bound to DNA with a flipped-out purine moiety gives insight into the catalytic machinery for this new class of DNA glycosylases.
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Affiliation(s)
- Bjørn Dalhus
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Ina Høydal Helle
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Paul H. Backe
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Ingrun Alseth
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Magnar Bjørås
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
| | - Jon K. Laerdahl
- Centre for Molecular Biology and Neuroscience (CMBN) and Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, N-0027 Oslo, Norway, Institute of Clinical Biochemistry, University of Oslo, N-0027 Oslo, Norway and Department of Informatics, University of Oslo, PO Box 1080 Blindern, N-0316 Oslo, Norway
- *To whom correspondence should be addressed. +47 22844784+47 22844782
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Nakken S, Alseth I, Rognes T. Computational prediction of the effects of non-synonymous single nucleotide polymorphisms in human DNA repair genes. Neuroscience 2006; 145:1273-9. [PMID: 17055652 DOI: 10.1016/j.neuroscience.2006.09.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2006] [Revised: 09/08/2006] [Accepted: 09/12/2006] [Indexed: 10/24/2022]
Abstract
Non-synonymous single nucleotide polymorphisms (nsSNPs) represent common genetic variation that alters encoded amino acids in proteins. All nsSNPs may potentially affect the structure or function of expressed proteins and could therefore have an impact on complex diseases. In an effort to evaluate the phenotypic effect of all known nsSNPs in human DNA repair genes, we have characterized each polymorphism in terms of different functional properties. The properties are computed based on amino acid characteristics (e.g. residue volume change); position-specific phylogenetic information from multiple sequence alignments and from prediction programs such as SIFT (Sorting Intolerant From Tolerant) and PolyPhen (Polymorphism Phenotyping). We provide a comprehensive, updated list of all validated nsSNPs from dbSNP (public database of human single nucleotide polymorphisms at National Center for Biotechnology Information, USA) located in human DNA repair genes. The list includes repair enzymes, genes associated with response to DNA damage as well as genes implicated with genetic instability or sensitivity to DNA damaging agents. Out of a total of 152 genes involved in DNA repair, 95 had validated nsSNPs in them. The fraction of nsSNPs that had high probability of being functionally significant was predicted to be 29.6% and 30.9%, by SIFT and PolyPhen respectively. The resulting list of annotated nsSNPs is available online (http://dna.uio.no/repairSNP), and is an ongoing project that will continue assessing the function of coding SNPs in human DNA repair genes.
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Affiliation(s)
- S Nakken
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Rikshospitalet-Radiumhospitalet Medical Centre, NO-0027 Oslo, Norway
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Alseth I, Rognes T, Lindbäck T, Solberg I, Robertsen K, Kristiansen KI, Mainieri D, Lillehagen L, Kolstø AB, Bjørås M. A new protein superfamily includes two novel 3-methyladenine DNA glycosylases from Bacillus cereus, AlkC and AlkD. Mol Microbiol 2006; 59:1602-9. [PMID: 16468998 PMCID: PMC1413580 DOI: 10.1111/j.1365-2958.2006.05044.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Soil bacteria are heavily exposed to environmental methylating agents such as methylchloride and may have special requirements for repair of alkylation damage on DNA. We have used functional complementation of an Escherichia coli tag alkA mutant to screen for 3-methyladenine DNA glycosylase genes in genomic libraries of the soil bacterium Bacillus cereus. Three genes were recovered: alkC, alkD and alkE. The amino acid sequence of AlkE is homologous to the E. coli AlkA sequence. AlkC and AlkD represent novel proteins without sequence similarity to any protein of known function. However, iterative and indirect sequence similarity searches revealed that AlkC and AlkD are distant homologues of each other within a new protein superfamily that is ubiquitous in the prokaryotic kingdom. Homologues of AlkC and AlkD were also identified in the amoebas Entamoeba histolytica and Dictyostelium discoideum, but no other eukaryotic counterparts of the superfamily were found. The alkC and alkD genes were expressed in E. coli and the proteins were purified to homogeneity. Both proteins were found to be specific for removal of N-alkylated bases, and showed no activity on oxidized or deaminated base lesions in DNA. B. cereus AlkC and AlkD thus define novel families of alkylbase DNA glycosylases within a new protein superfamily.
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Affiliation(s)
- Ingrun Alseth
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
| | - Torbjørn Rognes
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
- Department of Informatics, University of OsloPO Box 1080 Blindern, N-0316 Oslo, Norway.
| | - Toril Lindbäck
- Department of Food Safety and Infection BiologyNorwegian School of Veterinary Science, N-0033 Oslo, Norway
- Biotechnology Centre of Oslo and Department of Pharmaceutical Biosciences, University of OsloPO Box 1125 Blindern, N-0317 Oslo, Norway
| | - Inger Solberg
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
| | - Kristin Robertsen
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
| | - Knut Ivan Kristiansen
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
| | - Davide Mainieri
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
| | - Lucy Lillehagen
- Biotechnology Centre of Oslo and Department of Pharmaceutical Biosciences, University of OsloPO Box 1125 Blindern, N-0317 Oslo, Norway
| | - Anne-Brit Kolstø
- Biotechnology Centre of Oslo and Department of Pharmaceutical Biosciences, University of OsloPO Box 1125 Blindern, N-0317 Oslo, Norway
| | - Magnar Bjørås
- Department of Molecular Biology, Institute of Medical Microbiology and Centre of Molecular Biology and Neuroscience, University of OsloRikshospitalet-Radiumhospitalet HF, N-0027 Oslo, Norway
- *For correspondence. E-mail ; Tel. (+47) 23074061; Fax (+47) 23074060
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Sæbø PE, Andersen SM, Myrseth J, Laerdahl JK, Rognes T. PARALIGN: rapid and sensitive sequence similarity searches powered by parallel computing technology. Nucleic Acids Res 2005; 33:W535-9. [PMID: 15980529 PMCID: PMC1160184 DOI: 10.1093/nar/gki423] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith-Waterman and ParAlign. The ParAlign algorithm is similar to Smith-Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known as multimedia technology that is available in modern processors, but rarely used by other bioinformatics software, has been exploited to achieve the high speed. The software is also designed to run efficiently on computer clusters using the message-passing interface standard. A public search service powered by a large computer cluster has been set-up and is freely available at www.paralign.org, where the major public databases can be searched. The software can also be downloaded free of charge for academic use.
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Affiliation(s)
- Per Eystein Sæbø
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo and Rikshospitalet-Radiumhospitalet HFNO-0027 Oslo, Norway
| | | | - Jon Myrseth
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo and Rikshospitalet-Radiumhospitalet HFNO-0027 Oslo, Norway
| | - Jon K. Laerdahl
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo and Rikshospitalet-Radiumhospitalet HFNO-0027 Oslo, Norway
| | - Torbjørn Rognes
- Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, University of Oslo and Rikshospitalet-Radiumhospitalet HFNO-0027 Oslo, Norway
- Sencel Bioinformatics ASMotzfeldts gate 16, NO-0187 Oslo, Norway
- Department of Informatics, University of OsloPO Box 1080, NO-0316, Oslo, Norway
- To whom correspondence should be addressed. Tel: +47 22844787; Fax: +47 22844782;
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Saetrom P, Sneve R, Kristiansen KI, Snøve O, Grünfeld T, Rognes T, Seeberg E. Predicting non-coding RNA genes in Escherichia coli with boosted genetic programming. Nucleic Acids Res 2005; 33:3263-70. [PMID: 15942029 PMCID: PMC1143698 DOI: 10.1093/nar/gki644] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Several methods exist for predicting non-coding RNA (ncRNA) genes in Escherichia coli (E.coli). In addition to about sixty known ncRNA genes excluding tRNAs and rRNAs, various methods have predicted more than thousand ncRNA genes, but only 95 of these candidates were confirmed by more than one study. Here, we introduce a new method that uses automatic discovery of sequence patterns to predict ncRNA genes. The method predicts 135 novel candidates. In addition, the method predicts 152 genes that overlap with predictions in the literature. We test sixteen predictions experimentally, and show that twelve of these are actual ncRNA transcripts. Six of the twelve verified candidates were novel predictions. The relatively high confirmation rate indicates that many of the untested novel predictions are also ncRNAs, and we therefore speculate that E.coli contains more ncRNA genes than previously estimated.
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Affiliation(s)
- Pål Saetrom
- Interagon AS, Medisinsk teknisk senter NO-7489 Trondheim, Norway.
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50
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Davidsen T, Rødland EA, Lagesen K, Seeberg E, Rognes T, Tønjum T. Biased distribution of DNA uptake sequences towards genome maintenance genes. Nucleic Acids Res 2004; 32:1050-8. [PMID: 14960717 PMCID: PMC373393 DOI: 10.1093/nar/gkh255] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Repeated sequence signatures are characteristic features of all genomic DNA. We have made a rigorous search for repeat genomic sequences in the human pathogens Neisseria meningitidis, Neisseria gonorrhoeae and Haemophilus influenzae and found that by far the most frequent 9-10mers residing within coding regions are the DNA uptake sequences (DUS) required for natural genetic transformation. More importantly, we found a significantly higher density of DUS within genes involved in DNA repair, recombination, restriction-modification and replication than in any other annotated gene group in these organisms. Pasteurella multocida also displayed high frequencies of a putative DUS identical to that previously identified in H.influenzae and with a skewed distribution towards genome maintenance genes, indicating that this bacterium might be transformation competent under certain conditions. These results imply that the high frequency of DUS in genome maintenance genes is conserved among phylogenetically divergent species and thus are of significant biological importance. Increased DUS density is expected to enhance DNA uptake and the over-representation of DUS in genome maintenance genes might reflect facilitated recovery of genome preserving functions. For example, transient and beneficial increase in genome instability can be allowed during pathogenesis simply through loss of antimutator genes, since these DUS-containing sequences will be preferentially recovered. Furthermore, uptake of such genes could provide a mechanism for facilitated recovery from DNA damage after genotoxic stress.
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Affiliation(s)
- Tonje Davidsen
- Centre for Molecular Biology and Neuroscience and Institute of Microbiology, University of Oslo, Rikshospitalet, N-0027 Oslo, Norway
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