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Biswas U, Deb Mallik T, Pschirer J, Lesche M, Sameith K, Jessberger R. Cohesin SMC1β promotes closed chromatin and controls TERRA expression at spermatocyte telomeres. Life Sci Alliance 2023; 6:e202201798. [PMID: 37160312 PMCID: PMC10172765 DOI: 10.26508/lsa.202201798] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 04/26/2023] [Accepted: 04/26/2023] [Indexed: 05/11/2023] Open
Abstract
Previous data showed that meiotic cohesin SMC1β protects spermatocyte telomeres from damage. The underlying reason, however, remained unknown as the expressions of telomerase and shelterin components were normal in Smc1β -/- spermatocytes. Here. we report that SMC1β restricts expression of the long noncoding RNA TERRA (telomeric repeat containing RNA) in spermatocytes. In somatic cell lines increased TERRA was reported to cause telomere damage through altering telomere chromatin structure. In Smc1β -/- spermatocytes, we observed strongly increased levels of TERRA which accumulate on damaged chromosomal ends, where enhanced R-loop formation was found. This suggested a more open chromatin configuration near telomeres in Smc1β -/- spermatocytes, which was confirmed by ATAC-seq. Telomere-distal regions were not affected by the absence of SMC1β but RNA-seq revealed increased transcriptional activity in telomere-proximal regions. Thus, SMC1β promotes closed chromatin specifically near telomeres and limits TERRA expression in spermatocytes.
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Affiliation(s)
- Uddipta Biswas
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Tanaya Deb Mallik
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Johannes Pschirer
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Matthias Lesche
- Center for Molecular and Cellular Bioengineering, Genome Center Technology Platform, Dresden, Germany
| | - Katrin Sameith
- Center for Molecular and Cellular Bioengineering, Genome Center Technology Platform, Dresden, Germany
| | - Rolf Jessberger
- Institute of Physiological Chemistry, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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Maier AM, Huth K, Alessandrini F, Henkel F, Schnautz B, Arifovic A, Riols F, Haid M, Koegler A, Sameith K, Schmidt-Weber CB, Esser-von-Bieren J, Ohnmacht C. Corrigendum: The aryl hydrocarbon receptor regulates lipid mediator production in alveolar macrophages. Front Immunol 2023; 14:1221064. [PMID: 37342341 PMCID: PMC10277851 DOI: 10.3389/fimmu.2023.1221064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 06/22/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1157373.].
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Affiliation(s)
- Ann-Marie Maier
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Huth
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Francesca Alessandrini
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Fiona Henkel
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Schnautz
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Anela Arifovic
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Fabien Riols
- Metabolomics and Proteomics Core, Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core, Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Anja Koegler
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Katrin Sameith
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Carsten B. Schmidt-Weber
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
- Member of the German Center of Lung Research (DZL), Partner Site Munich, Munich, Germany
| | - Julia Esser-von-Bieren
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Caspar Ohnmacht
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
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3
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Gado M, Heinrich A, Wiedersich D, Sameith K, Dahl A, Alexaki VI, Swarbrick MM, Baschant U, Grafe I, Perakakis N, Bornstein SR, Rauner M, Hofbauer LC, Henneicke H. Activation of beta-adrenergic receptor signaling prevents glucocorticoid-induced obesity and adipose tissue dysfunction in male mice. Am J Physiol Endocrinol Metab 2023. [PMID: 37126848 DOI: 10.1152/ajpendo.00259.2022] [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] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Elevated serum concentrations of glucocorticoids (GCs) result in excessive lipid accumulation in white adipose tissue (WAT) as well as dysfunction of thermogenic brown adipose tissue (BAT) - ultimately leading to the development of obesity and metabolic disease. Here, we hypothesized that activation of the sympathetic nervous system either via cold exposure or use of a selective β3-adrenergic receptor (β3-AR) agonist alleviates the adverse metabolic effects of chronic GC exposure in rodents. To this end, male 10-week-old C57BL/6NRj mice were treated with corticosterone via drinking water or placebo for 4 weeks while being maintained at 29°C (thermoneutrality), 22°C (room temperature) or 13°C (cold temperature); in a follow-up study mice received a selective β3-AR agonist or placebo with and without corticosterone while maintained at room temperature. Body weight and food intake were monitored throughout the study. Histological and molecular analyses were performed on white and brown adipose depots. Cold exposure not only preserved the thermogenic function of brown adipose tissue, but also reversed GC-induced lipid accumulation in white adipose tissue and corrected GC-driven obesity, hyperinsulinemia and hyperglycemia. The metabolic benefits of cold exposure were associated with enhanced sympathetic activity in adipose tissue, thus potentially linking an increase in sympathetic signaling to the observed metabolic benefits. In line with this concept, chronic administration of a selective β3-AR agonist reproduced the beneficial metabolic effects of cold adaption during exposure to exogenous GCs. This preclinical study demonstrates the potential of β3-AR as a therapeutic target in the management and prevention of GC-induced metabolic disease.
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Affiliation(s)
- Manuel Gado
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Medical Faculty, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Annett Heinrich
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
| | - Denise Wiedersich
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
| | - Katrin Sameith
- DRESDEN-concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, c/o Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Vasileia I Alexaki
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
| | - Michael M Swarbrick
- Bone Research Program, ANZAC Research Institute, The University of Sydney, Australia
- Concord Clinical School, The University of Sydney, Australia
| | - Ulrike Baschant
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Ingo Grafe
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Nikolaos Perakakis
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Medical Faculty, Technische Universität Dresden, Dresden, Germany
- German Center for Diabetes Research (DZD e.V.), Neuherberg, Germany
| | - Stefan R Bornstein
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Paul Langerhans Institute Dresden (PLID) of the Helmholtz Center Munich at the University Hospital Carl Gustav Carus and Medical Faculty, Technische Universität Dresden, Dresden, Germany
- Division of Diabetes and Nutritional Sciences, Faculty of Life Sciences and Medicine, King's College London, London, United Kingdom
- Department of Endocrinology and Diabetology, University Hospital Zurich, Switzerland
| | - Martina Rauner
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Lorenz C Hofbauer
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
| | - Holger Henneicke
- Center for Regenerative Therapies Dresden (CRTD), Technische Universität Dresden, Germany
- Department of Medicine III, University Hospital Carl Gustav Carus, Technische Universittät Dresden, Dresden, Germany
- Center for Healthy Aging, University Hospital Carl Gustav Carus, Technische Universität Dresden, Dresden, Germany
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4
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Maier AM, Huth K, Alessandrini F, Schnautz B, Arifovic A, Riols F, Haid M, Koegler A, Sameith K, Schmidt-Weber CB, Esser-von-Bieren J, Ohnmacht C. The aryl hydrocarbon receptor regulates lipid mediator production in alveolar macrophages. Front Immunol 2023; 14:1157373. [PMID: 37081886 PMCID: PMC10110899 DOI: 10.3389/fimmu.2023.1157373] [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] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 03/23/2023] [Indexed: 04/22/2023] Open
Abstract
Allergic inflammation of the airways such as allergic asthma is a major health problem with growing incidence world-wide. One cardinal feature in severe type 2-dominated airway inflammation is the release of lipid mediators of the eicosanoid family that can either promote or dampen allergic inflammation. Macrophages are key producers of prostaglandins and leukotrienes which play diverse roles in allergic airway inflammation and thus require tight control. Using RNA- and ATAC-sequencing, liquid chromatography coupled to mass spectrometry (LC-MS/MS), enzyme immunoassays (EIA), gene expression analysis and in vivo models, we show that the aryl hydrocarbon receptor (AhR) contributes to this control via transcriptional regulation of lipid mediator synthesis enzymes in bone marrow-derived as well as in primary alveolar macrophages. In the absence or inhibition of AhR activity, multiple genes of both the prostaglandin and the leukotriene pathway were downregulated, resulting in lower synthesis of prostanoids, such as prostaglandin E2 (PGE2), and cysteinyl leukotrienes, e.g., Leukotriene C4 (LTC4). These AhR-dependent genes include PTGS1 encoding for the enzyme cyclooxygenase 1 (COX1) and ALOX5 encoding for the arachidonate 5-lipoxygenase (5-LO) both of which major upstream regulators of the prostanoid and leukotriene pathway, respectively. This regulation is independent of the activation stimulus and partially also detectable in unstimulated macrophages suggesting an important role of basal AhR activity for eicosanoid production in steady state macrophages. Lastly, we demonstrate that AhR deficiency in hematopoietic but not epithelial cells aggravates house dust mite induced allergic airway inflammation. These results suggest an essential role for AhR-dependent eicosanoid regulation in macrophages during homeostasis and inflammation.
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Affiliation(s)
- Ann-Marie Maier
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Karsten Huth
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Francesca Alessandrini
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Benjamin Schnautz
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Anela Arifovic
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Fabien Riols
- Metabolomics and Proteomics Core, Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Mark Haid
- Metabolomics and Proteomics Core, Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
| | - Anja Koegler
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Katrin Sameith
- DRESDEN-concept Genome Center, Technology Platform at the Center for Molecular and Cellular Bioengineering (CMCB), Technische Universität Dresden, Dresden, Germany
| | - Carsten B. Schmidt-Weber
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
- Member of the German Center of Lung Research (DZL), Partner Site Munich, Munich, Germany
| | - Julia Esser-von-Bieren
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
- Department of Immunobiology, University of Lausanne, Epalinges, Switzerland
| | - Caspar Ohnmacht
- Center of Allergy and Environment (ZAUM), Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Neuherberg, Germany
- *Correspondence: Caspar Ohnmacht,
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5
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Morcos MNF, Li C, Munz CM, Greco A, Dressel N, Reinhardt S, Sameith K, Dahl A, Becker NB, Roers A, Höfer T, Gerbaulet A. Fate mapping of hematopoietic stem cells reveals two pathways of native thrombopoiesis. Nat Commun 2022; 13:4504. [PMID: 35922411 PMCID: PMC9349191 DOI: 10.1038/s41467-022-31914-z] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 07/11/2022] [Indexed: 11/18/2022] Open
Abstract
Hematopoietic stem cells (HSCs) produce highly diverse cell lineages. Here, we chart native lineage pathways emanating from HSCs and define their physiological regulation by computationally integrating experimental approaches for fate mapping, mitotic tracking, and single-cell RNA sequencing. We find that lineages begin to split when cells leave the tip HSC population, marked by high Sca-1 and CD201 expression. Downstream, HSCs either retain high Sca-1 expression and the ability to generate lymphocytes, or irreversibly reduce Sca-1 level and enter into erythro-myelopoiesis or thrombopoiesis. Thrombopoiesis is the sum of two pathways that make comparable contributions in steady state, a long route via multipotent progenitors and CD48hi megakaryocyte progenitors (MkPs), and a short route from HSCs to developmentally distinct CD48−/lo MkPs. Enhanced thrombopoietin signaling differentially accelerates the short pathway, enabling a rapid response to increasing demand. In sum, we provide a blueprint for mapping physiological differentiation fluxes from HSCs and decipher two functionally distinct pathways of native thrombopoiesis. Hematopoietic stem cells produce diverse cell lineages. Here, the authors apply single-cell RNA-seq, computational integration of non-perturbative approaches for fate-mapping, and mitotic tracking to chart lineage decisions in native hematopoiesis and identify megakaryocyte progenitors that directly link HSCs to megakaryocytes.
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Affiliation(s)
- Mina N F Morcos
- Institute for Immunology, Faculty of Medicine, TU Dresden, 01307, Dresden, Germany
| | - Congxin Li
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany.,Institute for Biomedical Genetics, University of Stuttgart, 70569, Stuttgart, Germany
| | - Clara M Munz
- Institute for Immunology, Faculty of Medicine, TU Dresden, 01307, Dresden, Germany
| | - Alessandro Greco
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany
| | - Nicole Dressel
- Institute for Immunology, Faculty of Medicine, TU Dresden, 01307, Dresden, Germany
| | - Susanne Reinhardt
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Katrin Sameith
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Andreas Dahl
- DRESDEN-concept Genome Center, Center for Molecular and Cellular Bioengineering, TU Dresden, 01307, Dresden, Germany
| | - Nils B Becker
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany
| | - Axel Roers
- Institute for Immunology, Heidelberg University Hospital, 69120, Heidelberg, Germany
| | - Thomas Höfer
- Division of Theoretical Systems Biology, German Cancer Research Center, 69120, Heidelberg, Germany. .,Faculty of Biosciences, Heidelberg University, 69120, Heidelberg, Germany.
| | - Alexander Gerbaulet
- Institute for Immunology, Faculty of Medicine, TU Dresden, 01307, Dresden, Germany.
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6
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Gerbaulet A, Munz C, Li C, Morcos M, Greco A, Dressel N, Reinhardt S, Sameith K, Dahl A, Becker N, Roers A, Höfer T. 3087 – TWO PATHWAYS OF THROMBOPOIESIS IN NATIVE HEMATOPOIESIS. Exp Hematol 2022. [DOI: 10.1016/j.exphem.2022.07.143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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7
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Roscito JG, Sameith K, Kirilenko BM, Hecker N, Winkler S, Dahl A, Rodrigues MT, Hiller M. Convergent and lineage-specific genomic differences in limb regulatory elements in limbless reptile lineages. Cell Rep 2022; 38:110280. [DOI: 10.1016/j.celrep.2021.110280] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 11/24/2021] [Accepted: 12/27/2021] [Indexed: 01/02/2023] Open
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Roscito JG, Sameith K, Pippel M, Francoijs KJ, Winkler S, Dahl A, Papoutsoglou G, Myers G, Hiller M. The genome of the tegu lizard Salvator merianae: combining Illumina, PacBio, and optical mapping data to generate a highly contiguous assembly. Gigascience 2018; 7:5202467. [PMID: 30481296 PMCID: PMC6304105 DOI: 10.1093/gigascience/giy141] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [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: 05/26/2018] [Accepted: 11/13/2018] [Indexed: 01/28/2023] Open
Abstract
Background Reptiles are a species-rich group with great phenotypic and life history diversity but are highly underrepresented among the vertebrate species with sequenced genomes. Results Here, we report a high-quality genome assembly of the tegu lizard, Salvator merianae, the first lacertoid with a sequenced genome. We combined 74X Illumina short-read, 29.8X Pacific Biosciences long-read, and optical mapping data to generate a high-quality assembly with a scaffold N50 value of 55.4 Mb. The contig N50 value of this assembly is 521 Kb, making it the most contiguous reptile assembly so far. We show that the tegu assembly has the highest completeness of coding genes and conserved non-exonic elements (CNEs) compared to other reptiles. Furthermore, the tegu assembly has the highest number of evolutionarily conserved CNE pairs, corroborating a high assembly contiguity in intergenic regions. As in other reptiles, long interspersed nuclear elements comprise the most abundant transposon class. We used transcriptomic data, homology- and de novo gene predictions to annotate 22,413 coding genes, of which 16,995 (76%) likely have human orthologs as inferred by CESAR-derived gene mappings. Finally, we generated a multiple genome alignment comprising 10 squamates and 7 other amniote species and identified conserved regions that are under evolutionary constraint. CNEs cover 38 Mb (1.8%) of the tegu genome, with 3.3 Mb in these elements being squamate specific. In contrast to placental mammal-specific CNEs, very few of these squamate-specific CNEs (<20 Kb) overlap transposons, highlighting a difference in how lineage-specific CNEs originated in these two clades. Conclusions The tegu lizard genome together with the multiple genome alignment and comprehensive conserved element datasets provide a valuable resource for comparative genomic studies of reptiles and other amniotes.
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Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Martin Pippel
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Kees-Jan Francoijs
- BioNano Genomics, Towne Centre Drive Suite, 100, 92121, San Diego, CA, USA
| | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Andreas Dahl
- Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, Fetscherstr. 105, 01307, Dresden, Germany
| | - Georg Papoutsoglou
- BioNano Genomics, Towne Centre Drive Suite, 100, 92121, San Diego, CA, USA
| | - Gene Myers
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307, Dresden, Germany.,Max Planck Institute for the Physics of Complex Systems, Nöthnitzerstr. 38, 01187, Dresden, Germany.,Center for Systems Biology Dresden, Pfotenhauerstr. 108, 01307, Dresden, Germany
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9
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Roscito JG, Sameith K, Parra G, Langer BE, Petzold A, Moebius C, Bickle M, Rodrigues MT, Hiller M. Phenotype loss is associated with widespread divergence of the gene regulatory landscape in evolution. Nat Commun 2018; 9:4737. [PMID: 30413698 PMCID: PMC6226452 DOI: 10.1038/s41467-018-07122-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [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: 01/03/2018] [Accepted: 10/15/2018] [Indexed: 02/07/2023] Open
Abstract
Detecting the genomic changes underlying phenotypic changes between species is a main goal of evolutionary biology and genomics. Evolutionary theory predicts that changes in cis-regulatory elements are important for morphological changes. We combined genome sequencing, functional genomics and genome-wide comparative analyses to investigate regulatory elements in lineages that lost morphological traits. We first show that limb loss in snakes is associated with widespread divergence of limb regulatory elements. We next show that eye degeneration in subterranean mammals is associated with widespread divergence of eye regulatory elements. In both cases, sequence divergence results in an extensive loss of transcription factor binding sites. Importantly, diverged regulatory elements are associated with genes required for normal limb patterning or normal eye development and function, suggesting that regulatory divergence contributed to the loss of these phenotypes. Together, our results show that genome-wide decay of the phenotype-specific cis-regulatory landscape is a hallmark of lost morphological traits. Cis-regulatory elements are important factors for morphological changes. Here, the authors show widespread divergence of limb and eye regulatory elements in limb loss in snakes and eye degeneration in subterranean mammals respectively.
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Affiliation(s)
- Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany.,Instituto de Biociências, Universidade de São Paulo, São Paulo, 05508-090, Brazil
| | - Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Genis Parra
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Bjoern E Langer
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany.,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany.,Center for Systems Biology Dresden, Dresden, 01307, Germany
| | - Andreas Petzold
- Center for Regenerative Therapies TU Dresden, Dresden, 01307, Germany
| | - Claudia Moebius
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | - Marc Bickle
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany
| | | | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, 01307, Germany. .,Max Planck Institute for the Physics of Complex Systems, Dresden, 01187, Germany. .,Center for Systems Biology Dresden, Dresden, 01307, Germany.
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Sameith K, Roscito JG, Hiller M. Iterative error correction of long sequencing reads maximizes accuracy and improves contig assembly. Brief Bioinform 2016; 18:1-8. [PMID: 26868358 PMCID: PMC5221426 DOI: 10.1093/bib/bbw003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 01/02/2016] [Indexed: 11/13/2022] Open
Abstract
Next-generation sequencers such as Illumina can now produce reads up to 300 bp with high throughput, which is attractive for genome assembly. A first step in genome assembly is to computationally correct sequencing errors. However, correcting all errors in these longer reads is challenging. Here, we show that reads with remaining errors after correction often overlap repeats, where short erroneous k-mers occur in other copies of the repeat. We developed an iterative error correction pipeline that runs the previously published String Graph Assembler (SGA) in multiple rounds of k-mer-based correction with an increasing k-mer size, followed by a final round of overlap-based correction. By combining the advantages of small and large k-mers, this approach corrects more errors in repeats and minimizes the total amount of erroneous reads. We show that higher read accuracy increases contig lengths two to three times. We provide SGA-Iteratively Correcting Errors (https://github.com/hillerlab/IterativeErrorCorrection/) that implements iterative error correction by using modules from SGA.
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Affiliation(s)
- Katrin Sameith
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Juliana G Roscito
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
- Max Planck Institute for the Physics of Complex Systems, Dresden, Germany
- Corresponding author. Michael Hiller. Max Planck Institute of Molecular Cell Biology and Genetics & Max Planck Institute for the Physics of Complex Systems, 01307 Dresden, Germany. E-mail:
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11
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Sameith K, Amini S, Groot Koerkamp MJA, van Leenen D, Brok M, Brabers N, Lijnzaad P, van Hooff SR, Benschop JJ, Lenstra TL, Apweiler E, van Wageningen S, Snel B, Holstege FCP, Kemmeren P. A high-resolution gene expression atlas of epistasis between gene-specific transcription factors exposes potential mechanisms for genetic interactions. BMC Biol 2015; 13:112. [PMID: 26700642 PMCID: PMC4690272 DOI: 10.1186/s12915-015-0222-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 12/14/2015] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Genetic interactions, or non-additive effects between genes, play a crucial role in many cellular processes and disease. Which mechanisms underlie these genetic interactions has hardly been characterized. Understanding the molecular basis of genetic interactions is crucial in deciphering pathway organization and understanding the relationship between genotype, phenotype and disease. RESULTS To investigate the nature of genetic interactions between gene-specific transcription factors (GSTFs) in Saccharomyces cerevisiae, we systematically analyzed 72 GSTF pairs by gene expression profiling double and single deletion mutants. These pairs were selected through previously published growth-based genetic interactions as well as through similarity in DNA binding properties. The result is a high-resolution atlas of gene expression-based genetic interactions that provides systems-level insight into GSTF epistasis. The atlas confirms known genetic interactions and exposes new ones. Importantly, the data can be used to investigate mechanisms that underlie individual genetic interactions. Two molecular mechanisms are proposed, "buffering by induced dependency" and "alleviation by derepression". CONCLUSIONS These mechanisms indicate how negative genetic interactions can occur between seemingly unrelated parallel pathways and how positive genetic interactions can indirectly expose parallel rather than same-pathway relationships. The focus on GSTFs is important for understanding the transcription regulatory network of yeast as it uncovers details behind many redundancy relationships, some of which are completely new. In addition, the study provides general insight into the complex nature of epistasis and proposes mechanistic models for genetic interactions, the majority of which do not fall into easily recognizable within- or between-pathway relationships.
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Affiliation(s)
- Katrin Sameith
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Saman Amini
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Marian J A Groot Koerkamp
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Dik van Leenen
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Mariel Brok
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Nathalie Brabers
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Philip Lijnzaad
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Sander R van Hooff
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Joris J Benschop
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Tineke L Lenstra
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Eva Apweiler
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Sake van Wageningen
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Berend Snel
- Theoretical Biology and Bioinformatics, Department of Biology, Utrecht University, Padualaan 8, Utrecht, The Netherlands
| | - Frank C P Holstege
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands
| | - Patrick Kemmeren
- Molecular Cancer Research, University Medical Centre Utrecht, Universiteitsweg 100, Utrecht, The Netherlands.
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Kemmeren P, Sameith K, van de Pasch L, Benschop J, Lenstra T, Margaritis T, O’Duibhir E, Apweiler E, van Wageningen S, Ko C, van Heesch S, Kashani M, Ampatziadis-Michailidis G, Brok M, Brabers N, Miles A, Bouwmeester D, van Hooff S, van Bakel H, Sluiters E, Bakker L, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp M, Holstege F. Large-Scale Genetic Perturbations Reveal Regulatory Networks and an Abundance of Gene-Specific Repressors. Cell 2014; 157:740-52. [DOI: 10.1016/j.cell.2014.02.054] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 12/30/2013] [Accepted: 02/25/2014] [Indexed: 11/17/2022]
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13
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Apweiler E, Sameith K, Margaritis T, Brabers N, van de Pasch L, Bakker LV, van Leenen D, Holstege FC, Kemmeren P. Yeast glucose pathways converge on the transcriptional regulation of trehalose biosynthesis. BMC Genomics 2012; 13:239. [PMID: 22697265 PMCID: PMC3472246 DOI: 10.1186/1471-2164-13-239] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [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: 01/03/2012] [Accepted: 06/14/2012] [Indexed: 01/12/2023] Open
Abstract
Background Cellular glucose availability is crucial for the functioning of most biological processes. Our understanding of the glucose regulatory system has been greatly advanced by studying the model organism Saccharomyces cerevisiae, but many aspects of this system remain elusive. To understand the organisation of the glucose regulatory system, we analysed 91 deletion mutants of the different glucose signalling and metabolic pathways in Saccharomyces cerevisiae using DNA microarrays. Results In general, the mutations do not induce pathway-specific transcriptional responses. Instead, one main transcriptional response is discerned, which varies in direction to mimic either a high or a low glucose response. Detailed analysis uncovers established and new relationships within and between individual pathways and their members. In contrast to signalling components, metabolic components of the glucose regulatory system are transcriptionally more frequently affected. A new network approach is applied that exposes the hierarchical organisation of the glucose regulatory system. Conclusions The tight interconnection between the different pathways of the glucose regulatory system is reflected by the main transcriptional response observed. Tps2 and Tsl1, two enzymes involved in the biosynthesis of the storage carbohydrate trehalose, are predicted to be the most downstream transcriptional components. Epistasis analysis of tps2Δ double mutants supports this prediction. Although based on transcriptional changes only, these results suggest that all changes in perceived glucose levels ultimately lead to a shift in trehalose biosynthesis.
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Affiliation(s)
- Eva Apweiler
- Molecular Cancer Research, University Medical Centre Utrecht, Utrecht, the Netherlands
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14
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van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJA, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LAL, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FCP. Functional overlap and regulatory links shape genetic interactions between signaling pathways. Cell 2011; 143:991-1004. [PMID: 21145464 DOI: 10.1016/j.cell.2010.11.021] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 09/20/2010] [Accepted: 11/09/2010] [Indexed: 01/30/2023]
Abstract
To understand relationships between phosphorylation-based signaling pathways, we analyzed 150 deletion mutants of protein kinases and phosphatases in S. cerevisiae using DNA microarrays. Downstream changes in gene expression were treated as a phenotypic readout. Double mutants with synthetic genetic interactions were included to investigate genetic buffering relationships such as redundancy. Three types of genetic buffering relationships are identified: mixed epistasis, complete redundancy, and quantitative redundancy. In mixed epistasis, the most common buffering relationship, different gene sets respond in different epistatic ways. Mixed epistasis arises from pairs of regulators that have only partial overlap in function and that are coupled by additional regulatory links such as repression of one by the other. Such regulatory modules confer the ability to control different combinations of processes depending on condition or context. These properties likely contribute to the evolutionary maintenance of paralogs and indicate a way in which signaling pathways connect for multiprocess control.
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Sameith K, Antczak P, Marston E, Turan N, Maier D, Stankovic T, Falciani F. Functional modules integrating essential cellular functions are predictive of the response of leukaemia cells to DNA damage. ACTA ACUST UNITED AC 2008; 24:2602-7. [PMID: 18801750 DOI: 10.1093/bioinformatics/btn489] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
MOTIVATION Childhood B-precursor lymphoblastic leukaemia (ALL) is the most common paediatric malignancy. Despite the fact that 80% of ALL patients respond to anti-cancer drugs, the patho-physiology of this disease is still not fully understood. mRNA expression-profiling studies that have been performed have not yet provided novel insights into the mechanisms behind cellular response to DNA damage. More powerful data analysis techniques may be required for identifying novel functional pathways involved in the cellular responses to DNA damage. RESULTS In order to explore the possibility that unforeseen biological processes may be involved in the response to DNA damage, we have developed and applied a novel procedure for the identification of functional modules in ALL cells. We have discovered that the overall activity of functional modules integrating protein degradation and mRNA processing is predictive of response to DNA damage. AVAILABILITY Supplementary material including R code, additional results, experimental datasets, as well as a detailed description of the methodology are available at http://www.bip.bham.ac.uk/vivo/fumo.html. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Katrin Sameith
- School of Biosciences and Institute of Biomedical Research, CRUK Institute for Cancer Studies, University of Birmingham, Birmingham, B152TT, UK
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Ortega F, Sameith K, Turan N, Compton R, Trevino V, Vannucci M, Falciani F. Models and computational strategies linking physiological response to molecular networks from large-scale data. Philos Trans A Math Phys Eng Sci 2008; 366:3067-3089. [PMID: 18559319 DOI: 10.1098/rsta.2008.0085] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
An important area of research in systems biology involves the analysis and integration of genome-wide functional datasets. In this context, a major goal is the identification of a putative molecular network controlling physiological response from experimental data. With very fragmentary mechanistic information, this is a challenging task. A number of methods have been developed, each one with the potential to address an aspect of the problem. Here, we review some of the most widely used methodologies and report new results in support of the usefulness of modularization and other modelling techniques in identifying components of the molecular networks that are predictive of physiological response. We also discuss how system identification in biology could be approached, using a combination of methodologies that aim to reconstruct the relationship between molecular pathways and physiology at different levels of the organizational complexity of the molecular network.
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Affiliation(s)
- Fernando Ortega
- School of Biosciences and IBR, University of Birmingham, Birmingham B15 2TT, UK
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Abstract
Many classes of non-coding RNAs (ncRNAs; including Y RNAs, vault RNAs, RNase P RNAs, and MRP RNAs, as well as a novel class recently discovered in Dictyostelium discoideum) can be characterized by a pattern of short but well-conserved sequence elements that are separated by poorly conserved regions of sometimes highly variable lengths. Local alignment algorithms such as BLAST are therefore ill-suited for the discovery of new homologs of such ncRNAs in genomic sequences. The Fragrep tool instead implements an efficient algorithm for detecting the pattern fragments that occur in a given order. For each pattern fragment, the mismatch tolerance and bounds on the length of the intervening sequences can be specified separately. Furthermore, matches can be ranked by a statistically well-motivated scoring scheme.
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Affiliation(s)
- Axel Mosig
- Department of Combinatorics and Geometry, CAS/MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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