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Prouteau A, Mottier S, Primot A, Cadieu E, Bachelot L, Botherel N, Cabillic F, Houel A, Cornevin L, Kergal C, Corre S, Abadie J, Hitte C, Gilot D, Lindblad-Toh K, André C, Derrien T, Hedan B. Canine Oral Melanoma Genomic and Transcriptomic Study Defines Two Molecular Subgroups with Different Therapeutical Targets. Cancers (Basel) 2022; 14:cancers14020276. [PMID: 35053440 PMCID: PMC8774001 DOI: 10.3390/cancers14020276] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 11/25/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 02/05/2023] Open
Abstract
Simple Summary In humans, mucosal melanoma (MM) is a rare and aggressive cancer. The canine model is frequently and spontaneously affected by MM, thus facilitating the collection of samples and the study of its genetic bases. Thanks to an integrative genomic and transcriptomic analysis of 32 canine MM samples, we identified two molecular subgroups of MM with a different microenvironment and structural variant (SV) content. We demonstrated that SVs are associated with recurrently amplified regions, and identified new candidate oncogenes (TRPM7, GABPB1, and SPPL2A) for MM. Our findings suggest the existence of two MM molecular subgroups that could benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine. Abstract Mucosal melanoma (MM) is a rare, aggressive clinical cancer. Despite recent advances in genetics and treatment, the prognosis of MM remains poor. Canine MM offers a relevant spontaneous and immunocompetent model to decipher the genetic bases and explore treatments for MM. We performed an integrative genomic and transcriptomic analysis of 32 canine MM samples, which identified two molecular subgroups with a different microenvironment and structural variant (SV) content. The overexpression of genes related to the microenvironment and T-cell response was associated with tumors harboring a lower content of SVs, whereas the overexpression of pigmentation-related pathways and oncogenes, such as TERT, was associated with a high SV burden. Using whole-genome sequencing, we showed that focal amplifications characterized complex chromosomal rearrangements targeting oncogenes, such as MDM2 or CDK4, and a recurrently amplified region on canine chromosome 30. We also demonstrated that the genes TRPM7, GABPB1, and SPPL2A, located in this CFA30 region, play a role in cell proliferation, and thus, may be considered as new candidate oncogenes for human MM. Our findings suggest the existence of two MM molecular subgroups that may benefit from dedicated therapies, such as immune checkpoint inhibitors or targeted therapies, for both human and veterinary medicine.
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Affiliation(s)
- Anais Prouteau
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Stephanie Mottier
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Aline Primot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Edouard Cadieu
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laura Bachelot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Nadine Botherel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Florian Cabillic
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Armel Houel
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Laurence Cornevin
- Laboratoire de Cytogénétique et Biologie Cellulaire, CHU de Rennes, INSERM, INRA, University of Rennes 1, Nutrition Metabolisms and Cancer, 35000 Rennes, France; (F.C.); (L.C.)
| | - Camille Kergal
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Sébastien Corre
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Jérôme Abadie
- Laboniris, Department of Biology, Pathology and Food Sciences, Oniris, 44300 Nantes, France;
| | - Christophe Hitte
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - David Gilot
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA;
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Catherine André
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
| | - Thomas Derrien
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
| | - Benoit Hedan
- IGDR—UMR 6290, CNRS, University of Rennes 1, 35000 Rennes, France; (A.P.); (S.M.); (A.P.); (E.C.); (L.B.); (N.B.); (A.H.); (C.K.); (S.C.); (C.H.); (D.G.); (C.A.)
- Correspondence: (T.D.); (B.H.); Tel.: +33-2-23-23-43-19 (B.H.)
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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Jehl F, Muret K, Bernard M, Boutin M, Lagoutte L, Désert C, Dehais P, Esquerré D, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Pitel F, Zerjal T, Klopp C, Lagarrigue S. Author Correction: An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep 2021; 11:9463. [PMID: 33911173 PMCID: PMC8080728 DOI: 10.1038/s41598-021-89158-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Frédéric Jehl
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - Kévin Muret
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - Maria Bernard
- SIGENAE Platform, INRA, 31326, Castanet-Tolosan, France
| | - Morgane Boutin
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - Laetitia Lagoutte
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | - Colette Désert
- PEGASE UMR 1348, INRA, AGROCAMPUS OUEST, 35590, Saint-Gilles, France
| | | | - Diane Esquerré
- Genotoul, INRA, US 1426 GeT PlaGe, Castanet Tolosan, France
| | - Hervé Acloque
- GenPhySE UMR 1388, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Elisabetta Giuffra
- GABI UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Sarah Djebali
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Sylvain Foissac
- GenPhySE UMR 1388, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | | | - Frédérique Pitel
- GenPhySE UMR 1388, INRA, INPT, ENVT, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Tatiana Zerjal
- GABI UMR 1313, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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Hédan B, Cadieu É, Rimbault M, Vaysse A, Dufaure de Citres C, Devauchelle P, Botherel N, Abadie J, Quignon P, Derrien T, André C. Identification of common predisposing loci to hematopoietic cancers in four dog breeds. PLoS Genet 2021; 17:e1009395. [PMID: 33793571 PMCID: PMC8016107 DOI: 10.1371/journal.pgen.1009395] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [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: 07/28/2020] [Accepted: 02/03/2021] [Indexed: 12/14/2022] Open
Abstract
Histiocytic sarcoma (HS) is a rare but aggressive cancer in both humans and dogs. The spontaneous canine model, which has clinical, epidemiological, and histological similarities with human HS and specific breed predispositions, provides a unique opportunity to unravel the genetic basis of this cancer. In this study, we aimed to identify germline risk factors associated with the development of HS in canine-predisposed breeds. We used a methodology that combined several genome-wide association studies in a multi-breed and multi-cancer approach as well as targeted next-generation sequencing, and imputation We combined several dog breeds (Bernese mountain dogs, Rottweilers, flat-coated retrievers, and golden retrievers), and three hematopoietic cancers (HS, lymphoma, and mast cell tumor). Results showed that we not only refined the previously identified HS risk CDKN2A locus, but also identified new loci on canine chromosomes 2, 5, 14, and 20. Capture and targeted sequencing of specific loci suggested the existence of regulatory variants in non-coding regions and methylation mechanisms linked to risk haplotypes, which lead to strong cancer predisposition in specific dog breeds. We also showed that these canine cancer predisposing loci appeared to be due to the additive effect of several risk haplotypes involved in other hematopoietic cancers such as lymphoma or mast cell tumors as well. This illustrates the pleiotropic nature of these canine cancer loci as observed in human oncology, thereby reinforcing the interest of predisposed dog breeds to study cancer initiation and progression. Because of specific breed structures and artificial selection, pet dogs suffer from numerous genetic diseases, including cancers and represent a unique spontaneous model of human cancers. Here, we focused on histiocytic sarcoma (HS), a rare and highly aggressive cancer in humans. In this study, we have used spontaneous affected and unaffected dogs from three predisposed dog breeds to identify loci involved in HS predisposition. Through genetic analyses, we showed that these canine cancer predispositions are due to the additive effect of several risk haplotypes also involved in the predisposition of other hematopoietic cancers. The corresponding chromosomal regions in humans are involved in the predisposition of several cancers and are also associated with immune traits. This study demonstrates the pleiotropic nature of these canine cancer loci as observed in human oncology, thereby reinforcing the interest of predisposed dog breeds to study mechanisms involved in cancer initiation.
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Affiliation(s)
- Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
- * E-mail:
| | - Édouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | - Maud Rimbault
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | - Amaury Vaysse
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | | | | | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | - Jérôme Abadie
- Oniris, Laboniris—Department of Biology, Pathology and Food Sciences, Nantes, France
| | - Pascale Quignon
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes)–UMR6290, Rennes, France
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5
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Halo JV, Pendleton AL, Shen F, Doucet AJ, Derrien T, Hitte C, Kirby LE, Myers B, Sliwerska E, Emery S, Moran JV, Boyko AR, Kidd JM. Long-read assembly of a Great Dane genome highlights the contribution of GC-rich sequence and mobile elements to canine genomes. Proc Natl Acad Sci U S A 2021; 118:e2016274118. [PMID: 33836575 PMCID: PMC7980453 DOI: 10.1073/pnas.2016274118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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] [Indexed: 11/30/2022] Open
Abstract
Technological advances have allowed improvements in genome reference sequence assemblies. Here, we combined long- and short-read sequence resources to assemble the genome of a female Great Dane dog. This assembly has improved continuity compared to the existing Boxer-derived (CanFam3.1) reference genome. Annotation of the Great Dane assembly identified 22,182 protein-coding gene models and 7,049 long noncoding RNAs, including 49 protein-coding genes not present in the CanFam3.1 reference. The Great Dane assembly spans the majority of sequence gaps in the CanFam3.1 reference and illustrates that 2,151 gaps overlap the transcription start site of a predicted protein-coding gene. Moreover, a subset of the resolved gaps, which have an 80.95% median GC content, localize to transcription start sites and recombination hotspots more often than expected by chance, suggesting the stable canine recombinational landscape has shaped genome architecture. Alignment of the Great Dane and CanFam3.1 assemblies identified 16,834 deletions and 15,621 insertions, as well as 2,665 deletions and 3,493 insertions located on secondary contigs. These structural variants are dominated by retrotransposon insertion/deletion polymorphisms and include 16,221 dimorphic canine short interspersed elements (SINECs) and 1,121 dimorphic long interspersed element-1 sequences (LINE-1_Cfs). Analysis of sequences flanking the 3' end of LINE-1_Cfs (i.e., LINE-1_Cf 3'-transductions) suggests multiple retrotransposition-competent LINE-1_Cfs segregate among dog populations. Consistent with this conclusion, we demonstrate that a canine LINE-1_Cf element with intact open reading frames can retrotranspose its own RNA and that of a SINEC_Cf consensus sequence in cultured human cells, implicating ongoing retrotransposon activity as a driver of canine genetic variation.
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Affiliation(s)
- Julia V Halo
- Department of Biological Sciences, Bowling Green State University, Bowling Green, OH 43403
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Amanda L Pendleton
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Feichen Shen
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Aurélien J Doucet
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Université Côte d'Azur, CNRS, INSERM, Institut de Recherche sur le Cancer et le Vieillissement de Nice, F-06100 Nice, France
| | - Thomas Derrien
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Christophe Hitte
- Université de Rennes 1, CNRS, Institut de Génétique et Développement de Rennes-UMR 6290, F-35000 Rennes, France
| | - Laura E Kirby
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Bridget Myers
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Elzbieta Sliwerska
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - Sarah Emery
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
| | - John V Moran
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Adam R Boyko
- Department of Biomedical Sciences, Cornell University, Ithaca, NY 14850
| | - Jeffrey M Kidd
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109;
- Department Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109
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Prouteau A, Denis JA, De Fornel P, Cadieu E, Derrien T, Kergal C, Botherel N, Ulvé R, Rault M, Bouzidi A, François R, Dorso L, Lespagnol A, Devauchelle P, Abadie J, André C, Hédan B. Circulating tumor DNA is detectable in canine histiocytic sarcoma, oral malignant melanoma, and multicentric lymphoma. Sci Rep 2021; 11:877. [PMID: 33441840 PMCID: PMC7806858 DOI: 10.1038/s41598-020-80332-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 07/09/2020] [Accepted: 12/21/2020] [Indexed: 12/12/2022] Open
Abstract
Circulating tumor DNA (ctDNA) has become an attractive biomarker in human oncology, and its use may be informative in canine cancer. Thus, we used droplet digital PCR or PCR for antigen receptor rearrangement, to explore tumor-specific point mutations, copy number alterations, and chromosomal rearrangements in the plasma of cancer-affected dogs. We detected ctDNA in 21/23 (91.3%) of histiocytic sarcoma (HS), 2/8 (25%) of oral melanoma, and 12/13 (92.3%) of lymphoma cases. The utility of ctDNA in diagnosing HS was explored in 133 dogs, including 49 with HS, and the screening of recurrent PTPN11 mutations in plasma had a specificity of 98.8% and a sensitivity between 42.8 and 77% according to the clinical presentation of HS. Sensitivity was greater in visceral forms and especially related to pulmonary location. Follow-up of four dogs by targeting lymphoma-specific antigen receptor rearrangement in plasma showed that minimal residual disease detection was concordant with clinical evaluation and treatment response. Thus, our study shows that ctDNA is detectable in the plasma of cancer-affected dogs and is a promising biomarker for diagnosis and clinical follow-up. ctDNA detection appears to be useful in comparative oncology research due to growing interest in the study of natural canine tumors and exploration of new therapies.
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Affiliation(s)
- Anaïs Prouteau
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Jérôme Alexandre Denis
- Sorbonne University, Paris, France.,INSERM UMR_S 938, Endocrinology and Oncology Biochemistry Department, APHP Pitié-Salpêtrière Hospital, Paris, France
| | | | - Edouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Camille Kergal
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Ronan Ulvé
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Mélanie Rault
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | | | | | - Laetitia Dorso
- Department of Biology, Pathology and Food Sciences, Oniris, Laboniris, Nantes, France
| | - Alexandra Lespagnol
- Laboratory of Somatic Genetic of Cancers, Hospital of Rennes, Rennes, France
| | | | - Jérôme Abadie
- Department of Biology, Pathology and Food Sciences, Oniris, Laboniris, Nantes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France
| | - Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) UMR6290, 35000, Rennes, France.
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7
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Hédan B, Rault M, Abadie J, Ulvé R, Botherel N, Devauchelle P, Copie-Bergman C, Cadieu E, Parrens M, Alten J, Zalcman EL, Cario G, Damaj G, Mokhtari K, Le Loarer F, Coulomb-Lhermine A, Derrien T, Hitte C, Bachelot L, Breen M, Gilot D, Blay JY, Donadieu J, André C. PTPN11 mutations in canine and human disseminated histiocytic sarcoma. Int J Cancer 2020; 147:1657-1665. [PMID: 32212266 DOI: 10.1002/ijc.32991] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 12/20/2019] [Revised: 02/18/2020] [Accepted: 02/20/2020] [Indexed: 01/20/2023]
Abstract
In humans, histiocytic sarcoma (HS) is an aggressive cancer involving histiocytes. Its rarity and heterogeneity explain that treatment remains a challenge. Sharing high clinical and histopathological similarities with human HS, the canine HS is conversely frequent in specific breeds and thus constitutes a unique spontaneous model for human HS to decipher the genetic bases and to explore therapeutic options. We identified sequence alterations in the MAPK pathway in at least 63.9% (71/111) of HS cases with mutually exclusive BRAF (0.9%; 1/111), KRAS (7.2%; 8/111) and PTPN11 (56.75%; 63/111) mutations concentrated at hotspots common to human cancers. Recurrent PTPN11 mutations are associated to visceral disseminated HS subtype in dogs, the most aggressive clinical presentation. We then identified PTPN11 mutations in 3/19 (15.7%) human HS patients. Thus, we propose PTPN11 mutations as key events for a specific subset of human and canine HS: the visceral disseminated form. Finally, by testing drugs targeting the MAPK pathway in eight canine HS cell lines, we identified a better anti-proliferation activity of MEK inhibitors than PTPN11 inhibitors in canine HS neoplastic cells. In combination, these results illustrate the relevance of naturally affected dogs in deciphering genetic mechanisms and selecting efficient targeted therapies for such rare and aggressive cancers in humans.
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Affiliation(s)
- Benoit Hédan
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Mélanie Rault
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Jérôme Abadie
- Department of Biology, Pathology and Food Sciences, Oniris, Laboniris, Nantes, France
| | - Ronan Ulvé
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Nadine Botherel
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | | | - Christiane Copie-Bergman
- Assistance Publique-Hôpitaux de Paris, Département de Pathologie, Groupe Henri-Mondor Albert-Chenevier, Créteil, France.,INSERM U955, Équipe 9, Faculté de Médecine, Université Paris Est Créteil, Créteil, France
| | - Edouard Cadieu
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Marie Parrens
- Department of Pathology, CHU de Bordeaux, Hôpital du Haut Lévêque, INSERM U1035, Université de Bordeaux, Bordeaux, France
| | - Julia Alten
- Pediatric Oncology/Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Emmanuelle L Zalcman
- Department of Neuropathology, GHU Paris Psychiatrie Neurosciences, Sainte-Anne Hospital, Paris, France
| | - Gunnar Cario
- Pediatric Oncology/Hematology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Gandhi Damaj
- Haemalology Institute, CHU de Caen and Centre François Baclesse, Caen, France
| | - Karima Mokhtari
- Sorbonne University, Inserm, CNRS, Institut du Cerveau et de la Moelle épinière, ICM, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Service de Neuropathologie-Escourolle, Paris, France
| | | | | | - Thomas Derrien
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Christophe Hitte
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Laura Bachelot
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, CVM Research Building, Raleigh, NC, USA
| | - David Gilot
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
| | - Jean Y Blay
- Department of Medical Oncology, Centre Léon Bérard, Lyon, France
| | - Jean Donadieu
- Department of Haematology, APHP, Trousseau Hospital, Paris, France
| | - Catherine André
- Faculty of Medicine, CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, SFR Biosit, Rennes, France
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8
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Foissac S, Djebali S, Munyard K, Vialaneix N, Rau A, Muret K, Esquerré D, Zytnicki M, Derrien T, Bardou P, Blanc F, Cabau C, Crisci E, Dhorne-Pollet S, Drouet F, Faraut T, Gonzalez I, Goubil A, Lacroix-Lamandé S, Laurent F, Marthey S, Marti-Marimon M, Momal-Leisenring R, Mompart F, Quéré P, Robelin D, Cristobal MS, Tosser-Klopp G, Vincent-Naulleau S, Fabre S, der Laan MHPV, Klopp C, Tixier-Boichard M, Acloque H, Lagarrigue S, Giuffra E. Multi-species annotation of transcriptome and chromatin structure in domesticated animals. BMC Biol 2019; 17:108. [PMID: 31884969 PMCID: PMC6936065 DOI: 10.1186/s12915-019-0726-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [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: 10/21/2019] [Accepted: 11/19/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Comparative genomics studies are central in identifying the coding and non-coding elements associated with complex traits, and the functional annotation of genomes is a critical step to decipher the genotype-to-phenotype relationships in livestock animals. As part of the Functional Annotation of Animal Genomes (FAANG) action, the FR-AgENCODE project aimed to create reference functional maps of domesticated animals by profiling the landscape of transcription (RNA-seq), chromatin accessibility (ATAC-seq) and conformation (Hi-C) in species representing ruminants (cattle, goat), monogastrics (pig) and birds (chicken), using three target samples related to metabolism (liver) and immunity (CD4+ and CD8+ T cells). RESULTS RNA-seq assays considerably extended the available catalog of annotated transcripts and identified differentially expressed genes with unknown function, including new syntenic lncRNAs. ATAC-seq highlighted an enrichment for transcription factor binding sites in differentially accessible regions of the chromatin. Comparative analyses revealed a core set of conserved regulatory regions across species. Topologically associating domains (TADs) and epigenetic A/B compartments annotated from Hi-C data were consistent with RNA-seq and ATAC-seq data. Multi-species comparisons showed that conserved TAD boundaries had stronger insulation properties than species-specific ones and that the genomic distribution of orthologous genes in A/B compartments was significantly conserved across species. CONCLUSIONS We report the first multi-species and multi-assay genome annotation results obtained by a FAANG project. Beyond the generation of reference annotations and the confirmation of previous findings on model animals, the integrative analysis of data from multiple assays and species sheds a new light on the multi-scale selective pressure shaping genome organization from birds to mammals. Overall, these results emphasize the value of FAANG for research on domesticated animals and reinforces the importance of future meta-analyses of the reference datasets being generated by this community on different species.
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Affiliation(s)
- Sylvain Foissac
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Sarah Djebali
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Kylie Munyard
- Curtin University, School of Pharmacy & Biomedical Sciences, CHIRI Biosciences, Perth, 24105 Australia
| | - Nathalie Vialaneix
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Andrea Rau
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Kevin Muret
- PEGASE, Agrocampus-Ouest, INRA, Saint-Gilles Cedex, F-35590 France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
- INRA, US1426, GeT-PlaGe, Genotoul, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Matthias Zytnicki
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Fany Blanc
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Cédric Cabau
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Elisa Crisci
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27607 USA
| | - Sophie Dhorne-Pollet
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Ignacio Gonzalez
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Adeline Goubil
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | | | - Sylvain Marthey
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | - Maria Marti-Marimon
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Florence Mompart
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - David Robelin
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Magali San Cristobal
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Christophe Klopp
- MIAT, Université de Toulouse, INRA, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
| | | | - Hervé Acloque
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Chemin de Borde Rouge, Castanet-Tolosan Cedex, F-31326 France
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
| | | | - Elisabetta Giuffra
- GABI, AgroParisTech, INRA, Université Paris Saclay, Jouy-en-Josas, F-78350 France
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9
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Sessegolo C, Cruaud C, Da Silva C, Cologne A, Dubarry M, Derrien T, Lacroix V, Aury JM. Transcriptome profiling of mouse samples using nanopore sequencing of cDNA and RNA molecules. Sci Rep 2019; 9:14908. [PMID: 31624302 PMCID: PMC6797730 DOI: 10.1038/s41598-019-51470-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [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: 03/20/2019] [Accepted: 09/28/2019] [Indexed: 01/27/2023] Open
Abstract
Our vision of DNA transcription and splicing has changed dramatically with the introduction of short-read sequencing. These high-throughput sequencing technologies promised to unravel the complexity of any transcriptome. Generally gene expression levels are well-captured using these technologies, but there are still remaining caveats due to the limited read length and the fact that RNA molecules had to be reverse transcribed before sequencing. Oxford Nanopore Technologies has recently launched a portable sequencer which offers the possibility of sequencing long reads and most importantly RNA molecules. Here we generated a full mouse transcriptome from brain and liver using the Oxford Nanopore device. As a comparison, we sequenced RNA (RNA-Seq) and cDNA (cDNA-Seq) molecules using both long and short reads technologies and tested the TeloPrime preparation kit, dedicated to the enrichment of full-length transcripts. Using spike-in data, we confirmed that expression levels are efficiently captured by cDNA-Seq using short reads. More importantly, Oxford Nanopore RNA-Seq tends to be more efficient, while cDNA-Seq appears to be more biased. We further show that the cDNA library preparation of the Nanopore protocol induces read truncation for transcripts containing internal runs of T’s. This bias is marked for runs of at least 15 T’s, but is already detectable for runs of at least 9 T’s and therefore concerns more than 20% of expressed transcripts in mouse brain and liver. Finally, we outline that bioinformatics challenges remain ahead for quantifying at the transcript level, especially when reads are not full-length. Accurate quantification of repeat-associated genes such as processed pseudogenes also remains difficult, and we show that current mapping protocols which map reads to the genome largely over-estimate their expression, at the expense of their parent gene.
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Affiliation(s)
- Camille Sessegolo
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622, Villeurbanne, France.,EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Corinne Cruaud
- Genoscope, Institut de biologie François-Jacob, Commissariat a l'Energie Atomique (CEA), Université Paris-Saclay, F-91057, Evry, France
| | - Corinne Da Silva
- Genoscope, Institut de biologie François-Jacob, Commissariat a l'Energie Atomique (CEA), Université Paris-Saclay, F-91057, Evry, France
| | - Audric Cologne
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622, Villeurbanne, France.,EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Marion Dubarry
- Genoscope, Institut de biologie François-Jacob, Commissariat a l'Energie Atomique (CEA), Université Paris-Saclay, F-91057, Evry, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Vincent Lacroix
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Évolutive UMR5558, F-69622, Villeurbanne, France.,EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François-Jacob, Commissariat a l'Energie Atomique (CEA), Université Paris-Saclay, F-91057, Evry, France.
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10
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Prouteau A, Chocteau F, de Brito C, Cadieu E, Primot A, Botherel N, Degorce F, Cornevin L, Lagadic MA, Cabillic F, de Fornel-Thibaud P, Devauchelle P, Derrien T, Abadie J, André C, Hédan B. Prognostic value of somatic focal amplifications on chromosome 30 in canine oral melanoma. Vet Comp Oncol 2019; 18:214-223. [PMID: 31461207 DOI: 10.1111/vco.12536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/07/2019] [Revised: 08/02/2019] [Accepted: 08/20/2019] [Indexed: 12/16/2022]
Abstract
Canine oral melanoma is the first malignancy of the oral cavity in dogs and is characterized by a local invasiveness and a high metastatic propensity. A better knowledge of genetic alterations is expected to improve management of this tumour. Copy number alterations are known characteristics of mucosal melanomas both in dogs and humans. The goal of this study was to explore the prognostic value of somatic focal amplifications on chromosomes (Canis Familiaris [CFA]) 10 and 30 in canine oral melanoma. The cohort included 73 dogs with oral melanoma confirmed by histology, removed surgically without adjuvant therapy and with a minimal follow-up of 6 months. Epidemiological, clinical and histological data were collected and quantitative-PCR were performed on formalin-fixed paraffin-embedded (FFPE) samples to identify specific focal amplifications. The 73 dogs included in the study had a median survival time of 220 days. Focal amplifications on CFA 10 and 30 were recurrent (49.3% and 50.7% of cases, respectively) and CFA 30 amplification was significantly associated with the amelanotic phenotype (P = .046) and high mitotic index (MI; P = .0039). CFA 30 amplification was also linked to poor prognosis (P = .0005). Other negative prognostic factors included gingiva location (P = .003), lymphadenomegaly (P = .026), tumour ulceration at diagnosis (P = .003), MI superior to 6 mitoses over 10 fields (P = .001) and amelanotic tumour (P = .029). In multivariate analyses using Cox proportional hazards regression, CFA 30 amplification (Hazard ratio [HR] = 2.08; P = .011), tumour location (HR = 2.20; P = .005) and histological pigmentation (HR = 1.87; P = .036) were significantly associated with shorter survival time. Focal amplification of CFA 30 is linked to an aggressive subset and constitutes a new prognostic factor.
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Affiliation(s)
- Anais Prouteau
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Florian Chocteau
- Oniris, Laboniris - Department of Biology, Pathology and Food Sciences, Nantes, France
| | - Clotilde de Brito
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Edouard Cadieu
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Aline Primot
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Nadine Botherel
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | | | - Laurence Cornevin
- Department of Cytogenetics and Cell Biology, Hospital of Rennes, INSERM, University of Rennes, INRA, Institut NuMeCan (Nutrition, Metabolisms and Cancer), Rennes, France
| | | | - Florian Cabillic
- Department of Cytogenetics and Cell Biology, Hospital of Rennes, INSERM, University of Rennes, INRA, Institut NuMeCan (Nutrition, Metabolisms and Cancer), Rennes, France
| | | | | | - Thomas Derrien
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Jerome Abadie
- Oniris, Laboniris - Department of Biology, Pathology and Food Sciences, Nantes, France
| | - Catherine André
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
| | - Benoît Hédan
- CNRS-University of Rennes 1, UMR6290, Institute of Genetics and Development of Rennes, Faculty of Medicine, Rennes, France
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11
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Hitte C, Le Béguec C, Cadieu E, Wucher V, Primot A, Prouteau A, Botherel N, Hédan B, Lindblad-Toh K, André C, Derrien T. Genome-Wide Analysis of Long Non-Coding RNA Profiles in Canine Oral Melanomas. Genes (Basel) 2019; 10:genes10060477. [PMID: 31234577 PMCID: PMC6628375 DOI: 10.3390/genes10060477] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [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: 04/29/2019] [Revised: 06/17/2019] [Accepted: 06/19/2019] [Indexed: 12/25/2022] Open
Abstract
Mucosal melanomas (MM) are rare aggressive cancers in humans, and one of the most common forms of oral cancers in dogs. Similar biological and histological features are shared between MM in both species, making dogs a powerful model for comparative oncology studies of melanomas. Although exome sequencing recently identified recurrent coding mutations in canine MM, little is known about changes in non-coding gene expression, and more particularly, in canine long non-coding RNAs (lncRNAs), which are commonly dysregulated in human cancers. Here, we sampled a large cohort (n = 52) of canine normal/tumor oral MM from three predisposed breeds (poodles, Labrador retrievers, and golden retrievers), and used deep transcriptome sequencing to identify more than 400 differentially expressed (DE) lncRNAs. We further prioritized candidate lncRNAs by comparative genomic analysis to pinpoint 26 dog–human conserved DE lncRNAs, including SOX21-AS, ZEB2-AS, and CASC15 lncRNAs. Using unsupervised co-expression network analysis with coding genes, we inferred the potential functions of the DE lncRNAs, suggesting associations with cancer-related genes, cell cycle, and carbohydrate metabolism Gene Ontology (GO) terms. Finally, we exploited our multi-breed design to identify DE lncRNAs within breeds. This study provides a unique transcriptomic resource for studying oral melanoma in dogs, and highlights lncRNAs that may potentially be diagnostic or therapeutic targets for human and veterinary medicine.
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Affiliation(s)
- Christophe Hitte
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Céline Le Béguec
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Edouard Cadieu
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Valentin Wucher
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - Aline Primot
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Anaïs Prouteau
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Nadine Botherel
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Benoît Hédan
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 24 Uppsala, Sweden.
| | - Catherine André
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
| | - Thomas Derrien
- University of Rennes, CNRS, IGDR-UMR 6290, F-35000 Rennes, France.
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12
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Hédan B, Cadieu E, Botherel N, Dufaure de Citres C, Letko A, Rimbault M, Drögemüller C, Jagannathan V, Derrien T, Schmutz S, Leeb T, André C. Identification of a Missense Variant in MFSD12 Involved in Dilution of Phaeomelanin Leading to White or Cream Coat Color in Dogs. Genes (Basel) 2019; 10:E386. [PMID: 31117290 PMCID: PMC6562630 DOI: 10.3390/genes10050386] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 04/25/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 11/17/2022] Open
Abstract
White coat color in mammals has been selected several times during the domestication process. Numerous dog breeds are fixed for one form of white coat color that involves darkly pigmented skin. The genetic basis of this color, due to the absence of pigment in the hairs, was suggested to correspond to extreme dilution of the phaeomelanin, by both the expression of only phaeomelanin (locus E) and its extreme dilution (locus I). To go further, we performed genome-wide association studies (GWAS) using a multiple breed approach. The first GWAS, using 34 white dogs and 128 non-white dogs, including White Shepherds, Poodles, Cotons de Tulear and Bichons allowed us to identify two significantly associated loci on the locus E and a novel locus on chromosome 20. A second GWAS using 15 other breeds presenting extreme phaeomelanin dilution confirmed the position of locus I on the chromosome 20 (position 55 Mb pcorrected = 6 × 10-13). Using whole-genome sequencing, we identified a missense variant in the first exon of MFSD12, a gene recently identified to be involved in human, mouse and horse pigmentation. We confirmed the role of this variant in phaeomelanin dilution of numerous canine breeds, and the conserved role of MFSD12 in mammalian pigmentation.
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Affiliation(s)
- Benoit Hédan
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Nadine Botherel
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | | | - Anna Letko
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | - Maud Rimbault
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Cord Drögemüller
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | | | - Thomas Derrien
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
| | - Sheila Schmutz
- Department of Animal and Poultry Science, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada.
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Swizterland.
| | - Catherine André
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes1, 35000 Rennes, France.
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13
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Le Béguec C, Wucher V, Lagoutte L, Cadieu E, Botherel N, Hédan B, De Brito C, Guillory AS, André C, Derrien T, Hitte C. Characterisation and functional predictions of canine long non-coding RNAs. Sci Rep 2018; 8:13444. [PMID: 30194329 PMCID: PMC6128939 DOI: 10.1038/s41598-018-31770-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 04/27/2018] [Accepted: 08/24/2018] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are a family of heterogeneous RNAs that play major roles in multiple biological processes. We recently identified an extended repertoire of more than 10,000 lncRNAs of the domestic dog however, predicting their biological functionality remains challenging. In this study, we have characterised the expression profiles of 10,444 canine lncRNAs in 26 distinct tissue types, representing various anatomical systems. We showed that lncRNA expressions are mainly clustered by tissue type and we highlighted that 44% of canine lncRNAs are expressed in a tissue-specific manner. We further demonstrated that tissue-specificity correlates with specific families of canine transposable elements. In addition, we identified more than 900 conserved dog-human lncRNAs for which we show their overall reproducible expression patterns between dog and human through comparative transcriptomics. Finally, co-expression analyses of lncRNA and neighbouring protein-coding genes identified more than 3,400 canine lncRNAs, suggesting that functional roles of these lncRNAs act as regulatory elements. Altogether, this genomic and transcriptomic integrative study of lncRNAs constitutes a major resource to investigate genotype to phenotype relationships and biomedical research in the dog species.
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Affiliation(s)
- Céline Le Béguec
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Valentin Wucher
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Lætitia Lagoutte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.,UMR PEGASE, Agrocampus Ouest, INRA, 35042, Rennes, France
| | - Edouard Cadieu
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Nadine Botherel
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Benoît Hédan
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Clotilde De Brito
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Anne-Sophie Guillory
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Catherine André
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
| | - Christophe Hitte
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, F-35000, Rennes, France.
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14
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Broeckx BJG, Derrien T, Mottier S, Wucher V, Cadieu E, Hédan B, Le Béguec C, Botherel N, Lindblad-Toh K, Saunders JH, Deforce D, André C, Peelman L, Hitte C. An exome sequencing based approach for genome-wide association studies in the dog. Sci Rep 2017; 7:15680. [PMID: 29142306 PMCID: PMC5688105 DOI: 10.1038/s41598-017-15947-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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: 07/05/2017] [Accepted: 11/04/2017] [Indexed: 12/12/2022] Open
Abstract
Genome-wide association studies (GWAS) are widely used to identify loci associated with phenotypic traits in the domestic dog that has emerged as a model for Mendelian and complex traits. However, a disadvantage of GWAS is that it always requires subsequent fine-mapping or sequencing to pinpoint causal mutations. Here, we performed whole exome sequencing (WES) and canine high-density (cHD) SNP genotyping of 28 dogs from 3 breeds to compare the SNP and linkage disequilibrium characteristics together with the power and mapping precision of exome-guided GWAS (EG-GWAS) versus cHD-based GWAS. Using simulated phenotypes, we showed that EG-GWAS has a higher power than cHD to detect associations within target regions and less power outside target regions, with power being influenced further by sample size and SNP density. We analyzed two real phenotypes (hair length and furnishing), that are fixed in certain breeds to characterize mapping precision of the known causal mutations. EG-GWAS identified the associated exonic and 3'UTR variants within the FGF5 and RSPO2 genes, respectively, with only a few samples per breed. In conclusion, we demonstrated that EG-GWAS can identify loci associated with Mendelian phenotypes both within and across breeds.
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Affiliation(s)
- Bart J G Broeckx
- Laboratory of Animal Genetics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Thomas Derrien
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Stéphanie Mottier
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Valentin Wucher
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Edouard Cadieu
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Benoît Hédan
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Céline Le Béguec
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Nadine Botherel
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Jimmy H Saunders
- Department of Medical Imaging and Orthopedics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Catherine André
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France
| | - Luc Peelman
- Laboratory of Animal Genetics, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-URM6290, Université Rennes1, Rennes, France.
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15
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Ulvé R, Rault M, Bahin M, Lagoutte L, Abadie J, De Brito C, Coindre JM, Botherel N, Rousseau A, Wucher V, Cadieu E, Thieblemont C, Hitte C, Cornevin L, Cabillic F, Bachelot L, Gilot D, Hennuy B, Guillaudeux T, Le Goff A, Derrien T, Hédan B, André C. Discovery of Human-Similar Gene Fusions in Canine Cancers. Cancer Res 2017; 77:5721-5727. [DOI: 10.1158/0008-5472.can-16-2691] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/27/2017] [Accepted: 08/29/2017] [Indexed: 11/16/2022]
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16
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Wucher V, Legeai F, Hédan B, Rizk G, Lagoutte L, Leeb T, Jagannathan V, Cadieu E, David A, Lohi H, Cirera S, Fredholm M, Botherel N, Leegwater PA, Le Béguec C, Fieten H, Johnson J, Alföldi J, André C, Lindblad-Toh K, Hitte C, Derrien T. FEELnc: a tool for long non-coding RNA annotation and its application to the dog transcriptome. Nucleic Acids Res 2017; 45:e57. [PMID: 28053114 PMCID: PMC5416892 DOI: 10.1093/nar/gkw1306] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [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: 09/23/2016] [Revised: 12/13/2016] [Accepted: 12/14/2016] [Indexed: 12/13/2022] Open
Abstract
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames. Benchmarking versus five state-of-the-art tools shows that FEELnc achieves similar or better classification performance on GENCODE and NONCODE data sets. The program also provides specific modules that enable the user to fine-tune classification accuracy, to formalize the annotation of lncRNA classes and to identify lncRNAs even in the absence of a training set of non-coding RNAs. We used FEELnc on a real data set comprising 20 canine RNA-seq samples produced by the European LUPA consortium to substantially expand the canine genome annotation to include 10 374 novel lncRNAs and 58 640 mRNA transcripts. FEELnc moves beyond conventional coding potential classifiers by providing a standardized and complete solution for annotating lncRNAs and is freely available at https://github.com/tderrien/FEELnc.
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Affiliation(s)
- Valentin Wucher
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Fabrice Legeai
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Benoît Hédan
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Guillaume Rizk
- Institut National de Recherche en Informatique et en Automatique, Institut de Recherche en Informatique et Systèmes Aléatoires, Genscale, Campus Beaulieu, Rennes 35042, France
| | - Lætitia Lagoutte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3001, Switzerland
| | - Edouard Cadieu
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Audrey David
- IGEPP, BIPAA, INRA, Campus Beaulieu, Le Rheu 35653, France
| | - Hannes Lohi
- Department of Veterinary Biosciences and Research Programs Unit, Molecular Neurology, University of Helsinki, PO Box 63, Helsinki 00014, Finland
- The Folkhälsan Institute of Genetics, Helsinki 00014, Finland
| | - Susanna Cirera
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Merete Fredholm
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 1870, Denmark
| | - Nadine Botherel
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Peter A.J. Leegwater
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Céline Le Béguec
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Hille Fieten
- Department of Clinical Sciences of Companion Animals, Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584CM, the Netherlands
| | - Jeremy Johnson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jessica Alföldi
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Catherine André
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Kerstin Lindblad-Toh
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 751 23, Sweden
| | - Christophe Hitte
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
| | - Thomas Derrien
- Institut Génétique et Développement de Rennes, CNRS, UMR6290, University Rennes1, Rennes, Cedex 35043, France
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17
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:63. [PMID: 28376841 PMCID: PMC5381131 DOI: 10.1186/s13059-017-1202-6] [Citation(s) in RCA: 2] [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] [Received: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 11/10/2022] Open
Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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18
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Cormier A, Avia K, Sterck L, Derrien T, Wucher V, Andres G, Monsoor M, Godfroy O, Lipinska A, Perrineau MM, Van De Peer Y, Hitte C, Corre E, Coelho SM, Cock JM. Re-annotation, improved large-scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus. New Phytol 2017; 214:219-232. [PMID: 27870061 DOI: 10.1111/nph.14321] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [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: 06/23/2016] [Accepted: 10/08/2016] [Indexed: 05/28/2023]
Abstract
The genome of the filamentous brown alga Ectocarpus was the first to be completely sequenced from within the brown algal group and has served as a key reference genome both for this lineage and for the stramenopiles. We present a complete structural and functional reannotation of the Ectocarpus genome. The large-scale assembly of the Ectocarpus genome was significantly improved and genome-wide gene re-annotation using extensive RNA-seq data improved the structure of 11 108 existing protein-coding genes and added 2030 new loci. A genome-wide analysis of splicing isoforms identified an average of 1.6 transcripts per locus. A large number of previously undescribed noncoding genes were identified and annotated, including 717 loci that produce long noncoding RNAs. Conservation of lncRNAs between Ectocarpus and another brown alga, the kelp Saccharina japonica, suggests that at least a proportion of these loci serve a function. Finally, a large collection of single nucleotide polymorphism-based markers was developed for genetic analyses. These resources are available through an updated and improved genome database. This study significantly improves the utility of the Ectocarpus genome as a high-quality reference for the study of many important aspects of brown algal biology and as a reference for genomic analyses across the stramenopiles.
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Affiliation(s)
- Alexandre Cormier
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Komlan Avia
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Lieven Sterck
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
| | | | | | - Gwendoline Andres
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Misharl Monsoor
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Olivier Godfroy
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnieszka Lipinska
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Marie-Mathilde Perrineau
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yves Van De Peer
- Department of Plant Systems Biology, VIB, B-9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9000, Ghent, Belgium
- Bioinformatics Institute Ghent, Technologiepark 927, 9052, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, 0028, Pretoria, South Africa
| | | | - Erwan Corre
- Abims Platform, CNRS-UPMC, FR2424, Station Biologique de Roscoff, CS 90074, 29688, Roscoff, France
| | - Susana M Coelho
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - J Mark Cock
- Algal Genetics Group, CNRS, UMR 8227, Integrative Biology of Marine Models, Sorbonne Université, UPMC Univ Paris 06, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
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19
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Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DRG, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson ACC, van Oosterhout C, Swarbreck D, Hogenhout SA. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biol 2017; 18:27. [PMID: 28190401 PMCID: PMC5304397 DOI: 10.1186/s13059-016-1145-3] [Citation(s) in RCA: 161] [Impact Index Per Article: 23.0] [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: 07/07/2016] [Accepted: 12/22/2016] [Indexed: 12/04/2022] Open
Abstract
Background The prevailing paradigm of host-parasite evolution is that arms races lead to increasing specialisation via genetic adaptation. Insect herbivores are no exception and the majority have evolved to colonise a small number of closely related host species. Remarkably, the green peach aphid, Myzus persicae, colonises plant species across 40 families and single M. persicae clonal lineages can colonise distantly related plants. This remarkable ability makes M. persicae a highly destructive pest of many important crop species. Results To investigate the exceptional phenotypic plasticity of M. persicae, we sequenced the M. persicae genome and assessed how one clonal lineage responds to host plant species of different families. We show that genetically identical individuals are able to colonise distantly related host species through the differential regulation of genes belonging to aphid-expanded gene families. Multigene clusters collectively upregulate in single aphids within two days upon host switch. Furthermore, we demonstrate the functional significance of this rapid transcriptional change using RNA interference (RNAi)-mediated knock-down of genes belonging to the cathepsin B gene family. Knock-down of cathepsin B genes reduced aphid fitness, but only on the host that induced upregulation of these genes. Conclusions Previous research has focused on the role of genetic adaptation of parasites to their hosts. Here we show that the generalist aphid pest M. persicae is able to colonise diverse host plant species in the absence of genetic specialisation. This is achieved through rapid transcriptional plasticity of genes that have duplicated during aphid evolution. Electronic supplementary material The online version of this article (doi:10.1186/s13059-016-1145-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas C Mathers
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Yazhou Chen
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | | | - Fabrice Legeai
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Sam T Mugford
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,The International Aphid Genomics Consortium, Miami, USA
| | - Patrice Baa-Puyoulet
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France
| | - Anthony Bretaudeau
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France.,IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | | | - Stefano Colella
- The International Aphid Genomics Consortium, Miami, USA.,Univ Lyon, INSA-Lyon, INRA, BF2I, UMR0203, F-69621, Villeurbanne, France.,Present Address: INRA, UMR1342 IRD-CIRAD-INRA-SupAgro-Université de Montpellier, Laboratoire des Symbioses Tropicales et Méditéranéennes, Campus International de Baillarguet, TA-A82/J, F-34398, Montpellier cedex 5, France
| | - Olivier Collin
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Developpement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000, Rennes, France
| | - Honglin Feng
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Toni Gabaldón
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain
| | - Anna Jordan
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Irene Julca
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Graeme J Kettles
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Rothamsted Research, Harpenden, Hertforshire, ALF5 2JQ, UK
| | - Krissana Kowitwanich
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: J. R. Simplot Company, Boise, ID, USA
| | - Dominique Lavenier
- IRISA/INRIA, GenOuest Core Facility, Campus de Beaulieu, Rennes, 35042, France
| | - Paolo Lenzi
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Present address: Alson H. Smith Jr. Agriculture and Extension Center, Virginia Tech, Winchester, 22602, VA, USA
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.,Present address: Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Damian Loska
- The International Aphid Genomics Consortium, Miami, USA.,Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, 08003, Spain.,Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Daniel Mapleson
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Florian Maumus
- The International Aphid Genomics Consortium, Miami, USA.,Unité de Recherche Génomique-Info (URGI), INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Simon Moxon
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Daniel R G Price
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA.,Present address: Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, Midlothian, EH26 0PZ, UK
| | - Akiko Sugio
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Manuella van Munster
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Marilyne Uzest
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR BGPI, CIRAD TA-A54K, Campus International de Baillarguet, 34398, Montpellier Cedex 5, France
| | - Darren Waite
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK
| | - Georg Jander
- The International Aphid Genomics Consortium, Miami, USA.,Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Denis Tagu
- The International Aphid Genomics Consortium, Miami, USA.,INRA, UMR 1349 IGEPP (Institute of Genetics Environment and Plant Protection), Domaine de la Motte, 35653, Le Rheu Cedex, France
| | - Alex C C Wilson
- The International Aphid Genomics Consortium, Miami, USA.,Department of Biology, University of Miami, Coral Gables, FL, 33146, USA
| | - Cock van Oosterhout
- The International Aphid Genomics Consortium, Miami, USA.,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Swarbreck
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UZ, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
| | - Saskia A Hogenhout
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK. .,The International Aphid Genomics Consortium, Miami, USA. .,School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK.
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20
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Muret K, Klopp C, Wucher V, Esquerré D, Legeai F, Lecerf F, Désert C, Boutin M, Jehl F, Acloque H, Giuffra E, Djebali S, Foissac S, Derrien T, Lagarrigue S. Long noncoding RNA repertoire in chicken liver and adipose tissue. Genet Sel Evol 2017; 49:6. [PMID: 28073357 PMCID: PMC5225574 DOI: 10.1186/s12711-016-0275-0] [Citation(s) in RCA: 51] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Accepted: 11/29/2016] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Improving functional annotation of the chicken genome is a key challenge in bridging the gap between genotype and phenotype. Among all transcribed regions, long noncoding RNAs (lncRNAs) are a major component of the transcriptome and its regulation, and whole-transcriptome sequencing (RNA-Seq) has greatly improved their identification and characterization. We performed an extensive profiling of the lncRNA transcriptome in the chicken liver and adipose tissue by RNA-Seq. We focused on these two tissues because of their importance in various economical traits for which energy storage and mobilization play key roles and also because of their high cell homogeneity. To predict lncRNAs, we used a recently developed tool called FEELnc, which also classifies them with respect to their distance and strand orientation to the closest protein-coding genes. Moreover, to confidently identify the genes/transcripts expressed in each tissue (a complex task for weakly expressed molecules such as lncRNAs), we probed a particularly large number of biological replicates (16 per tissue) compared to common multi-tissue studies with a larger set of tissues but less sampling. RESULTS We predicted 2193 lncRNA genes, among which 1670 were robustly expressed across replicates in the liver and/or adipose tissue and which were classified into 1493 intergenic and 177 intragenic lncRNAs located between and within protein-coding genes, respectively. We observed similar structural features between chickens and mammals, with strong synteny conservation but without sequence conservation. As previously reported, we confirm that lncRNAs have a lower and more tissue-specific expression than mRNAs. Finally, we showed that adjacent lncRNA-mRNA genes in divergent orientation have a higher co-expression level when separated by less than 1 kb compared to more distant divergent pairs. Among these, we highlighted for the first time a novel lncRNA candidate involved in lipid metabolism, lnc_DHCR24, which is highly correlated with the DHCR24 gene that encodes a key enzyme of cholesterol biosynthesis. CONCLUSIONS We provide a comprehensive lncRNA repertoire in the chicken liver and adipose tissue, which shows interesting patterns of co-expression between mRNAs and lncRNAs. It contributes to improving the structural and functional annotation of the chicken genome and provides a basis for further studies on energy storage and mobilization traits in the chicken.
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Affiliation(s)
- Kévin Muret
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | | | - Valentin Wucher
- UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France
| | - Diane Esquerré
- Plateforme GENOTOUL, INRA, 31326, Castanet-Tolosan, France.,GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Fabrice Legeai
- UMR IGEPP, INRA, 35042, Rennes, France.,UMR IGEPP, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Frédéric Lecerf
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Colette Désert
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Morgane Boutin
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Frédéric Jehl
- UMR PEGASE, INRA, 35042, Rennes, France.,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France
| | - Hervé Acloque
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Elisabetta Giuffra
- GABI, AgroParisTech, INRA, Université Paris Saclay, 78350, Jouy-en-Josas, France
| | - Sarah Djebali
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Sylvain Foissac
- GenPhySE, INPT, ENVT, INRA, Université de Toulouse, 31326, Castanet-Tolosan, France
| | - Thomas Derrien
- UMR6290 IGDR, CNRS, Université Rennes 1, 35000, Rennes, France.
| | - Sandrine Lagarrigue
- UMR PEGASE, INRA, 35042, Rennes, France. .,UMR PEGASE, AGROCAMPUS OUEST, 35042, Rennes, France.
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21
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Djebali S, Wucher V, Foissac S, Hitte C, Corre E, Derrien T. Erratum to: Bioinformatics Pipeline for Transcriptome Sequencing Analysis. Methods Mol Biol 2017; 1468:E1. [PMID: 27943167 DOI: 10.1007/978-1-4939-4035-6_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Sarah Djebali
- INRA GenPhySE, ch. de Borderouge, Castanet-Tolosan, 31326, France.
| | - Valentin Wucher
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France
| | - Sylvain Foissac
- INRA GenPhySE, ch. de Borderouge, Castanet-Tolosan, 31326, France
| | - Christophe Hitte
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France
| | - Erwan Corre
- CNRS-UPMC, ABiMS Platform, Station Biologique de Roscoff, FR2424, CS 90074, Roscoff, 29688, France
| | - Thomas Derrien
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.
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22
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Abstract
The development of High Throughput Sequencing (HTS) for RNA profiling (RNA-seq) has shed light on the diversity of transcriptomes. While RNA-seq is becoming a de facto standard for monitoring the population of expressed transcripts in a given condition at a specific time, processing the huge amount of data it generates requires dedicated bioinformatics programs. Here, we describe a standard bioinformatics protocol using state-of-the-art tools, the STAR mapper to align reads onto a reference genome, Cufflinks to reconstruct the transcriptome, and RSEM to quantify expression levels of genes and transcripts. We present the workflow using human transcriptome sequencing data from two biological replicates of the K562 cell line produced as part of the ENCODE3 project.
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Affiliation(s)
- Sarah Djebali
- INRA GenPhySE, ch. de Borderouge, Castanet-Tolosan, 31326, France.
| | - Valentin Wucher
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France
| | - Sylvain Foissac
- INRA GenPhySE, ch. de Borderouge, Castanet-Tolosan, 31326, France
| | - Christophe Hitte
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France
| | - Erwan Corre
- CNRS-UPMC, ABiMS Platform, Station Biologique de Roscoff, FR2424, CS 90074, Roscoff, 29688, France
| | - Thomas Derrien
- CNRS UMR6290 Dog Genetic Team, 2 av du Pr. Léon Bernard, Rennes, 35043, France.
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23
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Plassais J, Lagoutte L, Correard S, Paradis M, Guaguère E, Hédan B, Pommier A, Botherel N, Cadiergues MC, Pilorge P, Silversides D, Bizot M, Samuels M, Arnan C, Johnson R, Hitte C, Salbert G, Méreau A, Quignon P, Derrien T, André C. A Point Mutation in a lincRNA Upstream of GDNF Is Associated to a Canine Insensitivity to Pain: A Spontaneous Model for Human Sensory Neuropathies. PLoS Genet 2016; 12:e1006482. [PMID: 28033318 PMCID: PMC5198995 DOI: 10.1371/journal.pgen.1006482] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 05/20/2016] [Accepted: 11/15/2016] [Indexed: 01/06/2023] Open
Abstract
Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1.8 Mb homozygous locus on canine chromosome 4 (adj. p-val = 2.5x10-6). Targeted high-throughput sequencing of this locus in 4 affected and 4 unaffected dogs identified 478 variants. Only one variant perfectly segregated with the expected recessive inheritance in 300 sporting dogs of known clinical status, while it was never present in 900 unaffected dogs from 130 other breeds. This variant, located 90 kb upstream of the GDNF gene, a highly relevant neurotrophic factor candidate gene, lies in a long intergenic non-coding RNAs (lincRNA), GDNF-AS. Using human comparative genomic analysis, we observed that the canine variant maps onto an enhancer element. Quantitative RT-PCR of dorsal root ganglia RNAs of affected dogs showed a significant decrease of both GDNF mRNA and GDNF-AS expression levels (respectively 60% and 80%), as compared to unaffected dogs. We thus performed gel shift assays (EMSA) that reveal that the canine variant significantly alters the binding of regulatory elements. Altogether, these results allowed the identification in dogs of GDNF as a relevant candidate for human HSAN and insensitivity to pain, but also shed light on the regulation of GDNF transcription. Finally, such results allow proposing these sporting dog breeds as natural models for clinical trials with a double benefit for human and veterinary medicine. In this study, we present a canine neuropathy characterized by insensitivity to pain in the feet, sometimes combined with self-mutilation described in four sporting breeds. This particular phenotype has the clinical hallmarks of human Hereditary Sensory Autonomic Neuropathies (HSAN). As we hypothesized that a monogenic recessive disorder was shared between these breeds, we performed a Genome Wide Association Study (GWAS) to search for the genetic causes and found one homozygous chromosomal region in affected dogs. High-throughput sequencing of this region allowed the identification of a point mutation upstream to the GDNF gene and located in the last exon of a long non-coding RNA, GDNF-AS. We confirmed the perfect association of this variant with the disease using more than 900 unaffected dogs that do not present with this mutation. Functional analyses (qRT-PCR, EMSA) confirmed that the mutation alters the binding of regulatory complex, leading to a significant decrease of both GDNF and GDNF-AS mRNA expression levels. This work in canine spontaneous forms of human neuropathies allowed the identification of a novel gene GDNF and its regulation mechanism, not yet described in human HSAN, opening the field of clinical trials to benefit both canine and human medicine.
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Affiliation(s)
- Jocelyn Plassais
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
- * E-mail: (CA); (JP)
| | - Laetitia Lagoutte
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Solenne Correard
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Manon Paradis
- Department of Clinical Sciences, Faculté de Médecine Vétérinaire, University of Montreal, Montreal, Québec, Canada
| | | | - Benoit Hédan
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Alix Pommier
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Nadine Botherel
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | | | | | - David Silversides
- Department of Clinical Sciences, Faculté de Médecine Vétérinaire, University of Montreal, Montreal, Québec, Canada
| | - Maud Bizot
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Mark Samuels
- Department of Biochemistry and Molecular Medicine, CHU Sainte-Justine, University of Montreal, Montreal, Québec, Canada
| | - Carme Arnan
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigations Mèdiques (IMIM), Barcelona, Spain
| | - Rory Johnson
- Centre for Genomic Regulation (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institut Hospital del Mar d’Investigations Mèdiques (IMIM), Barcelona, Spain
| | - Christophe Hitte
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Gilles Salbert
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Agnès Méreau
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Pascale Quignon
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
| | - Catherine André
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Rennes, France
- Université Rennes 1, UEB, Biosit, Faculté de Médecine, Rennes, France
- * E-mail: (CA); (JP)
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24
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Correard S, Plassais J, Lagoutte L, Paradis M, Guaguère E, Quignon P, Derrien T, André C. A spontaneous dog model for a human sensory neuropathy: identification of a mutation in the upstream region of a neurotrophic factor. ACTA ACUST UNITED AC 2016. [DOI: 10.4267/2042/61953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RPMA, Damas J, Davis RVN, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MAM, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JMD, Wragg D, Zhou H. Third Report on Chicken Genes and Chromosomes 2015. Cytogenet Genome Res 2015; 145:78-179. [PMID: 26282327 PMCID: PMC5120589 DOI: 10.1159/000430927] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Affiliation(s)
- Michael Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany
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Legeai F, Derrien T. Identification of long non-coding RNAs in insects genomes. Curr Opin Insect Sci 2015; 7:37-44. [PMID: 32846672 DOI: 10.1016/j.cois.2015.01.003] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2014] [Revised: 01/07/2015] [Accepted: 01/07/2015] [Indexed: 06/11/2023]
Abstract
The development of high throughput sequencing technologies (HTS) has allowed researchers to better assess the complexity and diversity of the transcriptome. Among the many classes of non-coding RNAs (ncRNAs) identified the last decade, long non-coding RNAs (lncRNAs) represent a diverse and numerous repertoire of important ncRNAs, reinforcing the view that they are of central importance to the cell machinery in all branches of life. Although lncRNAs have been involved in essential biological processes such as imprinting, gene regulation or dosage compensation especially in mammals, the repertoire of lncRNAs is poorly characterized for many non-model organisms. In this review, we first focus on what is known about experimentally validated lncRNAs in insects and then review bioinformatic methods to annotate lncRNAs in the genomes of hexapods.
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Affiliation(s)
- Fabrice Legeai
- INRA, UMR1349, Institute of Genetics, Environment and Plant Protection, Domaine de la Motte, BP35327, 35653 Le Rheu cedex, France; IRISA/INRIA GenScale, Campus Beaulieu, 35000 Rennes, France.
| | - Thomas Derrien
- CNRS, UMR 6290, Institut de Génétique et Développement de Rennes, Université de Rennes 1, 2 Avenue du Pr. Léon Bernard, 35000 Rennes, France
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27
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Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res 2013; 22:1760-74. [PMID: 22955987 PMCID: PMC3431492 DOI: 10.1101/gr.135350.111] [Citation(s) in RCA: 3491] [Impact Index Per Article: 317.4] [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] [Indexed: 02/07/2023]
Abstract
The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers.
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Affiliation(s)
- Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Campus, Hinxton, Cambridge CB10 1SA, United Kingdom.
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28
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Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 2013; 22:1775-89. [PMID: 22955988 PMCID: PMC3431493 DOI: 10.1101/gr.132159.111] [Citation(s) in RCA: 3740] [Impact Index Per Article: 340.0] [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: 11/24/2022]
Abstract
The human genome contains many thousands of long noncoding RNAs (lncRNAs). While several studies have demonstrated compelling biological and disease roles for individual examples, analytical and experimental approaches to investigate these genes have been hampered by the lack of comprehensive lncRNA annotation. Here, we present and analyze the most complete human lncRNA annotation to date, produced by the GENCODE consortium within the framework of the ENCODE project and comprising 9277 manually annotated genes producing 14,880 transcripts. Our analyses indicate that lncRNAs are generated through pathways similar to that of protein-coding genes, with similar histone-modification profiles, splicing signals, and exon/intron lengths. In contrast to protein-coding genes, however, lncRNAs display a striking bias toward two-exon transcripts, they are predominantly localized in the chromatin and nucleus, and a fraction appear to be preferentially processed into small RNAs. They are under stronger selective pressure than neutrally evolving sequences—particularly in their promoter regions, which display levels of selection comparable to protein-coding genes. Importantly, about one-third seem to have arisen within the primate lineage. Comprehensive analysis of their expression in multiple human organs and brain regions shows that lncRNAs are generally lower expressed than protein-coding genes, and display more tissue-specific expression patterns, with a large fraction of tissue-specific lncRNAs expressed in the brain. Expression correlation analysis indicates that lncRNAs show particularly striking positive correlation with the expression of antisense coding genes. This GENCODE annotation represents a valuable resource for future studies of lncRNAs.
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Affiliation(s)
- Thomas Derrien
- Bioinformatics and Genomics, Centre for Genomic Regulation and UPF, 08003 Barcelona, Catalonia, Spain
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29
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Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi AM, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature 2012; 489:101-8. [PMID: 22955620 PMCID: PMC3684276 DOI: 10.1038/nature11233] [Citation(s) in RCA: 3720] [Impact Index Per Article: 310.0] [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: 12/10/2011] [Accepted: 05/15/2012] [Indexed: 02/07/2023]
Abstract
Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic subcellular localizations are also poorly understood. Because RNA represents the direct output of the genetic information encoded by genomes and a significant proportion of a cell's regulatory capabilities are focused on its synthesis, processing, transport, modification and translation, the generation of such a catalogue is crucial for understanding genome function. Here we report evidence that three-quarters of the human genome is capable of being transcribed, as well as observations about the range and levels of expression, localization, processing fates, regulatory regions and modifications of almost all currently annotated and thousands of previously unannotated RNAs. These observations, taken together, prompt a redefinition of the concept of a gene.
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Affiliation(s)
- Sarah Djebali
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Carrie A. Davis
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Angelika Merkel
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Alex Dobin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Timo Lassmann
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Ali M. Mortazavi
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Andrea Tanzer
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Julien Lagarde
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Wei Lin
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Felix Schlesinger
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Chenghai Xue
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Georgi K. Marinov
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Jainab Khatun
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Brian A. Williams
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Chris Zaleski
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Joel Rozowsky
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Maik Röder
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Rehab F. Abdelhamid
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Tyler Alioto
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Igor Antoshechkin
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Michael T. Baer
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Nadav S. Bar
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Philippe Batut
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kimberly Bell
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Ian Bell
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Sudipto Chakrabortty
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Xian Chen
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Jacqueline Chrast
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Joao Curado
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas Derrien
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Jorg Drenkow
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Erica Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Jacqueline Dumais
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Radha Duttagupta
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Emilie Falconnet
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Meagan Fastuca
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Kata Fejes-Toth
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Pedro Ferreira
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Sylvain Foissac
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - Melissa J. Fullwood
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Hui Gao
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
| | - David Gonzalez
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Assaf Gordon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Harsha Gunawardena
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Cedric Howald
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Sonali Jha
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Rory Johnson
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Philipp Kapranov
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
- St. Laurent Institute, One Kendall Square, Cambridge, MA
| | - Brandon King
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Colin Kingswood
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Oscar J. Luo
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Eddie Park
- University of California Irvine, Dept of. Developmental and Cell Biology, 2300 Biological Sciences III, Irving, CA USA 92697
| | - Kimberly Persaud
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Jonathan B. Preall
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Paolo Ribeca
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Brian Risk
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Daniel Robyr
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Michael Sammeth
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Lorian Schaffer
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Lei-Hoon See
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Atif Shahab
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Jorgen Skancke
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
- Department of Chemical Engineering, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Ana Maria Suzuki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hazuki Takahashi
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Hagen Tilgner
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Diane Trout
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Nathalie Walters
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Huaien Wang
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - John Wrobel
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
| | - Yanbao Yu
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Xiaoan Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Yoshihide Hayashizaki
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
- Department of Computer Science, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520
| | - Tim Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire United Kingdom CB10 1SA
| | - Alexandre Reymond
- University of Lausanne, Center for Integrative Genomics, Genopode building, Lausanne, Switzerland 1015
| | - Stylianos E. Antonarakis
- University of Geneva Medical School, Department of Genetic Medicine and Development and iGE3 Institute of Genetics and Genomics of Geneva, 1 rue Michel-Servet, Geneva, Switzerland 1015
| | - Gregory Hannon
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
| | - Morgan C. Giddings
- Boise State University, College of Arts & Sciences, 1910 University Dr. Boise, ID USA 83725
- University of North Carolina at Chapel Hill, Department of Biochemistry & Biophysics, 120 Mason Farm Rd., Chapel Hill, NC USA 27599
| | - Yijun Ruan
- Genome Institute of Singapore, Genome Technology and Biology, 60 Biopolis Street, #02-01, Genome, Singapore, Singapore 138672
| | - Barbara Wold
- California Institute of Technology, Division of Biology, 91125. 2 Beckman Institute, Pasadena, CA USA 91125
| | - Piero Carninci
- RIKEN Yokohama Institute, RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa Japan 230-0045
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG) and UPF, Doctor Aiguader, 88 . Barcelona, Catalunya, Spain 08003
| | - Thomas R. Gingeras
- Cold Spring Harbor Laboratory, Functional Genomics, 1 Bungtown Rd. Cold Spring Harbor, NY, USA 11742
- Affymetrix, Inc, 3380 Central Expressway, Santa Clara, CA. USA 95051
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30
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Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res 2012; 22:1698-710. [PMID: 22955982 PMCID: PMC3431487 DOI: 10.1101/gr.134478.111] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [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: 11/07/2011] [Accepted: 05/01/2012] [Indexed: 12/21/2022]
Abstract
Within the ENCODE Consortium, GENCODE aimed to accurately annotate all protein-coding genes, pseudogenes, and noncoding transcribed loci in the human genome through manual curation and computational methods. Annotated transcript structures were assessed, and less well-supported loci were systematically, experimentally validated. Predicted exon-exon junctions were evaluated by RT-PCR amplification followed by highly multiplexed sequencing readout, a method we called RT-PCR-seq. Seventy-nine percent of all assessed junctions are confirmed by this evaluation procedure, demonstrating the high quality of the GENCODE gene set. RT-PCR-seq was also efficient to screen gene models predicted using the Human Body Map (HBM) RNA-seq data. We validated 73% of these predictions, thus confirming 1168 novel genes, mostly noncoding, which will further complement the GENCODE annotation. Our novel experimental validation pipeline is extremely sensitive, far more than unbiased transcriptome profiling through RNA sequencing, which is becoming the norm. For example, exon-exon junctions unique to GENCODE annotated transcripts are five times more likely to be corroborated with our targeted approach than with extensive large human transcriptome profiling. Data sets such as the HBM and ENCODE RNA-seq data fail sampling of low-expressed transcripts. Our RT-PCR-seq targeted approach also has the advantage of identifying novel exons of known genes, as we discovered unannotated exons in ~11% of assessed introns. We thus estimate that at least 18% of known loci have yet-unannotated exons. Our work demonstrates that the cataloging of all of the genic elements encoded in the human genome will necessitate a coordinated effort between unbiased and targeted approaches, like RNA-seq and RT-PCR-seq.
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Affiliation(s)
- Cédric Howald
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Andrea Tanzer
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Jacqueline Chrast
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Felix Kokocinski
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thomas Derrien
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Nathalie Walters
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
| | - Jose M. Gonzalez
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Adam Frankish
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Bronwen L. Aken
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Thibaut Hourlier
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jan-Hinnerk Vogel
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Simon White
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Stephen Searle
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Jennifer Harrow
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Tim J. Hubbard
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Roderic Guigó
- Centre de Regulacio Genomica, Grup de Recerca en Informatica Biomedica, E-08003 Barcelona, Spain
| | - Alexandre Reymond
- Center for Integrative Genomics, University of Lausanne, 1015 Lausanne, Switzerland
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31
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Derrien T, Estellé J, Marco Sola S, Knowles DG, Raineri E, Guigó R, Ribeca P. Fast computation and applications of genome mappability. PLoS One 2012; 7:e30377. [PMID: 22276185 PMCID: PMC3261895 DOI: 10.1371/journal.pone.0030377] [Citation(s) in RCA: 327] [Impact Index Per Article: 27.3] [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] [Received: 01/28/2011] [Accepted: 12/19/2011] [Indexed: 01/17/2023] Open
Abstract
We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of massively parallel sequencing experiments. We investigate the properties of the mappability of eukaryotic DNA/RNA both as a whole and at the level of the gene family, providing for various organisms tracks which allow the mappability information to be visually explored. In addition, we show that mappability varies greatly between species and gene classes. Finally, we suggest several practical applications where mappability can be used to refine the analysis of high-throughput sequencing data (SNP calling, gene expression quantification and paired-end experiments). This work highlights mappability as an important concept which deserves to be taken into full account, in particular when massively parallel sequencing technologies are employed. The GEM mappability program belongs to the GEM (GEnome Multitool) suite of programs, which can be freely downloaded for any use from its website (http://gemlibrary.sourceforge.net).
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Affiliation(s)
- Thomas Derrien
- Institut de Génétique et Développement (IGDR), Université Rennes 1, Rennes, France
- * E-mail: (TD); (PR)
| | - Jordi Estellé
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
| | | | - David G. Knowles
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Roderic Guigó
- Centre for Genomic Regulation (CRG), Universitat Pompeu Fabra, Barcelona, Spain
| | - Paolo Ribeca
- Centro Nacional de Análisis Genómico (CNAG), Barcelona, Spain
- * E-mail: (TD); (PR)
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Abstract
The transcriptome of a cell is represented by a myriad of different RNA molecules with and without protein-coding capacities. In recent years, advances in sequencing technologies have allowed researchers to more fully appreciate the complexity of whole transcriptomes, showing that the vast majority of the genome is transcribed, producing a diverse population of non-protein coding RNAs (ncRNAs). Thus, the biological significance of non-coding RNAs (ncRNAs) have been largely underestimated. Amongst these multiple classes of ncRNAs, the long non-coding RNAs (lncRNAs) are apparently the most numerous and functionally diverse. A small but growing number of lncRNAs have been experimentally studied, and a view is emerging that these are key regulators of epigenetic gene regulation in mammalian cells. LncRNAs have already been implicated in human diseases such as cancer and neurodegeneration, highlighting the importance of this emergent field. In this article, we review the catalogs of annotated lncRNAs and the latest advances in our understanding of lncRNAs.
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Affiliation(s)
- Thomas Derrien
- Bioinformatics and Genomics, Centre for Genomic Regulation, Universitat Pompeu Fabra Barcelona, Spain
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Derrien T, Vaysse A, André C, Hitte C. Annotation of the domestic dog genome sequence: finding the missing genes. Mamm Genome 2011; 23:124-31. [PMID: 22076420 DOI: 10.1007/s00335-011-9372-0] [Citation(s) in RCA: 10] [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] [Received: 09/05/2011] [Accepted: 10/23/2011] [Indexed: 12/20/2022]
Abstract
There are over 350 genetically distinct breeds of domestic dog that present considerable variation in morphology, physiology, and disease susceptibility. The genome sequence of the domestic dog was assembled and released in 2005, providing an estimated 20,000 protein-coding genes that are a great asset to the scientific community that uses the dog system as a genetic biomedical model and for comparative and evolutionary studies. Although the canine gene set had been predicted using a combination of ab initio methods, homology studies, motif analysis, and similarity-based programs, it still requires a deep annotation of noncoding genes, alternative splicing, pseudogenes, regulatory regions, and gain and loss events. Such analyses could benefit from new sequencing technologies (RNA-Seq) to better exploit the advantages of the canine genetic system in tracking disease genes. Here, we review the catalog of canine protein-coding genes and the search for missing genes, and we propose rationales for an accurate identification of noncoding genes though next-generation sequencing.
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Affiliation(s)
- Thomas Derrien
- Institut de Génétique et Développement de Rennes, CNRS-UMR6061, Université de Rennes 1, 2 av Pr. Léon Bernard, 35043 Rennes, France
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Mudge JM, Frankish A, Fernandez-Banet J, Alioto T, Derrien T, Howald C, Reymond A, Guigó R, Hubbard T, Harrow J. The origins, evolution, and functional potential of alternative splicing in vertebrates. Mol Biol Evol 2011; 28:2949-59. [PMID: 21551269 PMCID: PMC3176834 DOI: 10.1093/molbev/msr127] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [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] [Indexed: 12/24/2022] Open
Abstract
Alternative splicing (AS) has the potential to greatly expand the functional repertoire of mammalian transcriptomes. However, few variant transcripts have been characterized functionally, making it difficult to assess the contribution of AS to the generation of phenotypic complexity and to study the evolution of splicing patterns. We have compared the AS of 309 protein-coding genes in the human ENCODE pilot regions against their mouse orthologs in unprecedented detail, utilizing traditional transcriptomic and RNAseq data. The conservation status of every transcript has been investigated, and each functionally categorized as coding (separated into coding sequence [CDS] or nonsense-mediated decay [NMD] linked) or noncoding. In total, 36.7% of human and 19.3% of mouse coding transcripts are species specific, and we observe a 3.6 times excess of human NMD transcripts compared with mouse; in contrast to previous studies, the majority of species-specific AS is unlinked to transposable elements. We observe one conserved CDS variant and one conserved NMD variant per 2.3 and 11.4 genes, respectively. Subsequently, we identify and characterize equivalent AS patterns for 22.9% of these CDS or NMD-linked events in nonmammalian vertebrate genomes, and our data indicate that functional NMD-linked AS is more widespread and ancient than previously thought. Furthermore, although we observe an association between conserved AS and elevated sequence conservation, as previously reported, we emphasize that 30% of conserved AS exons display sequence conservation below the average score for constitutive exons. In conclusion, we demonstrate the value of detailed comparative annotation in generating a comprehensive set of AS transcripts, increasing our understanding of AS evolution in vertebrates. Our data supports a model whereby the acquisition of functional AS has occurred throughout vertebrate evolution and is considered alongside amino acid change as a key mechanism in gene evolution.
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Affiliation(s)
- Jonathan M Mudge
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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Affiliation(s)
- Thomas Derrien
- Institut de génétique et développement de Rennes 1, CNRS UMR6061, 2, avenue du Pr Léon Bernard, Faculté de Médecine, Université de Rennes1, Rennes, France.
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36
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Abstract
The human genome contains thousands of long noncoding RNAs (ncRNAs) transcribed from diverse genomic locations. A large set of long ncRNAs is transcribed independent of protein-coding genes. We have used the GENCODE annotation of the human genome to identify 3019 long ncRNAs expressed in various human cell lines and tissue. This set of long ncRNAs responds to differentiation signals in primary human keratinocytes and is coexpressed with important regulators of keratinocyte development. Depletion of a number of these long ncRNAs leads to the repression of specific genes in their surrounding locus, supportive of an activating function for ncRNAs. Using reporter assays, we confirmed such activating function and show that such transcriptional enhancement is mediated through the long ncRNA transcripts. Our studies show that long ncRNAs exhibit functions similar to classically defined enhancers, through an RNA-dependent mechanism.
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Affiliation(s)
- U A Ørom
- The Wistar Institute, Philadelphia, Pennsylvania 19104, USA
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37
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Ørom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R. Long noncoding RNAs with enhancer-like function in human cells. Cell 2010; 143:46-58. [PMID: 20887892 DOI: 10.1016/j.cell.2010.09.001] [Citation(s) in RCA: 1414] [Impact Index Per Article: 101.0] [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: 04/23/2010] [Revised: 07/01/2010] [Accepted: 08/13/2010] [Indexed: 12/21/2022]
Abstract
While the long noncoding RNAs (ncRNAs) constitute a large portion of the mammalian transcriptome, their biological functions has remained elusive. A few long ncRNAs that have been studied in any detail silence gene expression in processes such as X-inactivation and imprinting. We used a GENCODE annotation of the human genome to characterize over a thousand long ncRNAs that are expressed in multiple cell lines. Unexpectedly, we found an enhancer-like function for a set of these long ncRNAs in human cell lines. Depletion of a number of ncRNAs led to decreased expression of their neighboring protein-coding genes, including the master regulator of hematopoiesis, SCL (also called TAL1), Snai1 and Snai2. Using heterologous transcription assays we demonstrated a requirement for the ncRNAs in activation of gene expression. These results reveal an unanticipated role for a class of long ncRNAs in activation of critical regulators of development and differentiation.
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Searle S, Frankish A, Bignell A, Aken B, Derrien T, Diekhans M, Harte R, Howald C, Kokocinski F, Lin M, Tress M, Van Baren M, Barnes I, Hunt T, Carvalho-Silva D, Davidson C, Donaldson S, Gilbert J, Kay M, Lloyd D, Loveland J, Mudge J, Snow C, Vamathevan J, Wilming L, Brent M, Gerstein M, Guigó R, Kellis M, Reymond A, Zadissa A, Valencia A, Harrow J, Hubbard T. The GENCODE human gene set. Genome Biol 2010. [PMCID: PMC3026266 DOI: 10.1186/gb-2010-11-s1-p36] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Derrien T, Thézé J, Vaysse A, André C, Ostrander EA, Galibert F, Hitte C. Revisiting the missing protein-coding gene catalog of the domestic dog. BMC Genomics 2009; 10:62. [PMID: 19193219 PMCID: PMC2644713 DOI: 10.1186/1471-2164-10-62] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [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] [Received: 08/28/2008] [Accepted: 02/04/2009] [Indexed: 12/19/2022] Open
Abstract
Background Among mammals for which there is a high sequence coverage, the whole genome assembly of the dog is unique in that it predicts a low number of protein-coding genes, ~19,000, compared to the over 20,000 reported for other mammalian species. Of particular interest are the more than 400 of genes annotated in primates and rodent genomes, but missing in dog. Results Using over 14,000 orthologous genes between human, chimpanzee, mouse rat and dog, we built multiple pairwise synteny maps to infer short orthologous intervals that were targeted for characterizing the canine missing genes. Based on gene prediction and a functionality test using the ratio of replacement to silent nucleotide substitution rates (dN/dS), we provide compelling structural and functional evidence for the identification of 232 new protein-coding genes in the canine genome and 69 gene losses, characterized as undetected gene or pseudogenes. Gene loss phyletic pattern analysis using ten species from chicken to human allowed us to characterize 28 canine-specific gene losses that have functional orthologs continuously from chicken or marsupials through human, and 10 genes that arose specifically in the evolutionary lineage leading to rodent and primates. Conclusion This study demonstrates the central role of comparative genomics for refining gene catalogs and exploring the evolutionary history of gene repertoires, particularly as applied for the characterization of species-specific gene gains and losses.
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Affiliation(s)
- Thomas Derrien
- Institut de Génétique et Développement, CNRS UMR6061, Université de Rennes 1, Léon Bernard, Rennes, France.
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Derrien T, André C, Galibert F, Hitte C. Analysis of the unassembled part of the dog genome sequence: chromosomal localization of 115 genes inferred from multispecies comparative genomics. ACTA ACUST UNITED AC 2007; 98:461-7. [PMID: 17573383 DOI: 10.1093/jhered/esm027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [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: 12/16/2022]
Abstract
The identification of dog genes and their accurate localization to chromosomes remain a major challenge in the postgenomics era. The 132 annotated canine genes with human orthologs remaining in the unassembled part (chrUnknown) of the dog sequence assembly (CanFam1) are of limited use for candidate gene approaches or comparative mapping studies. We used a two-step comparative analysis to infer a canine chromosomal interval for localization of the chrUn genes. We first constructed a human-dog synteny map, using 14,456 gene-based comparative anchors. We then mapped the 132 chrUn genes onto the reference (human) synteny map and identified the corresponding, orthologous segment on the canine map, based on conserved gene order. Our results show that 110 chrUn genes could be localized to short intervals on 18 dog chromosomes, whereas 22 genes remained assigned to 2 possible intervals. We extended this comparative analysis to multiple species, using the chimpanzee, mouse, and rat genome sequences. This made it possible to narrow down the intervals concerned and to increase the number of canine chrUn genes with an inferred chromosome location to 115. This study demonstrates that dog chromosomal intervals for chrUn genes can be rapidly inferred, using a reference species, and indicates that comparative strategies based on larger numbers of species may be even more effective.
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Affiliation(s)
- Thomas Derrien
- CNRS UMR6061 Génétique et Développement, Université de Rennes 1, IFR140, 2 Av du Pr Léon Bernard, CS 34317, 35043, Rennes, France
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Abstract
MOTIVATION Genome maps are fundamental to the study of an organism and essential in the process of genome sequencing which in turn provides the ultimate map of the genome. The increased number of genomes being sequenced offers new opportunities for the mapping of closely related organisms. We propose here an algorithmic formalization of a genome comparison approach to marker ordering. RESULTS In order to integrate a comparative mapping approach in the algorithmic process of map construction and selection, we propose to extend the usual statistical model describing the experimental data, here radiation hybrids (RH) data, in a statistical framework that models additionally the evolutionary relationships between a proposed map and a reference map: an existing map of the corresponding orthologous genes or markers in a closely related organism. This has concretely the effect of exploiting, in the process of map selection, the information of marker adjacencies in the related genome when the information provided by the experimental data is not conclusive for the purpose of ordering. In order to compute efficiently the map, we proceed to a reduction of the maximum likelihood estimation to the Traveling Salesman Problem. Experiments on simulated RH datasets as well as on a real RH dataset from the canine RH project show that maps produced using the likelihood defined by the new model are significantly better than maps built using the traditional RH model. AVAILABILITY The comparative mapping approach is available in the last version of de Givry,S. et al. [(2004) Bioinformatics, 21, 1703-1704, www.inra.fr/mia/T/CarthaGene], a free (the LKH part is free for academic use only) mapping software in C++, including LKH (Helsgaun,K. (2000) Eur. J. Oper. Res., 126, 106-130, www.dat.ruc.dk/keld/research/LKH) for maximum likelihood computation.
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Affiliation(s)
- T Faraut
- Laboratoire de génétique cellulaire BP 52627, 31326 Castanet Tolosan, France.
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Abstract
UNLABELLED AutoGRAPH is an interactive web server for automatic multi-species comparative genomics analyses based on personal datasets or pre-inserted public datasets. This program automatically identifies conserved segments (CS) and breakpoint regions, assesses the conservation of marker/gene order between organisms, constructs synteny maps for two to three species and generates high-quality, interactive displays facilitating the identification of chromosomal rearrangements. AutoGRAPH can also be used for the integration and comparison of several types of genomic resources (meiotic maps, radiation hybrid maps and genome sequences) for a single species, making AutoGRAPH a versatile tool for comparative genomics analysis. AVAILABILITY http://genoweb.univ-rennes1.fr/tom_dog/AutoGRAPH/. SUPPLEMENTARY INFORMATION A description of the algorithm and additional information are available at http://genoweb.univ-rennes1.fr/tom_dog/AutoGRAPH/Tutorial.php.
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Affiliation(s)
- Thomas Derrien
- CNRS UMR6061 Génétique et Développement, Université de Rennes1, IFR140, 2 Av du Pr. Léon Bernard, CS 34317, 35043, France
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Hédan B, Corre S, Hitte C, Dréano S, Vilboux T, Derrien T, Denis B, Galibert F, Galibert MD, André C. Coat colour in dogs: identification of the merle locus in the Australian shepherd breed. BMC Vet Res 2006; 2:9. [PMID: 16504149 PMCID: PMC1431520 DOI: 10.1186/1746-6148-2-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [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: 11/11/2005] [Accepted: 02/27/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coat colours in canines have many natural phenotypic variants. Some of the genes and alleles involved also cause genetic developmental defects, which are also observed in humans and mice. We studied the genetic bases of the merle phenotype in dogs to shed light on the pigmentation mechanisms and to identify genes involved in these complex pathways. The merle phenotype includes a lack of eumelanic pigmentation and developmental defects, hearing impairments and microphthalmia. It is similar to that observed in microphthalmia mouse mutants. RESULTS Taking advantage of the dog as a powerful genetic model and using recently available genomic resources, we investigated the segregation of the merle phenotype in a five-generation pedigree, comprising 96 sampled Australian shepherd dogs. Genetic linkage analysis allowed us to identify a locus for the merle phenotype, spanning 5.5 megabases, at the centromeric tip of canine chromosome 10 (CFA10). This locus was supported by a Lod score of 15.65 at a recombination fraction theta = 0. Linkage analysis in three other breeds revealed that the same region is linked to the merle phenotype. This region, which is orthologous to human chromosome 12 (HSA12 q13-q14), belongs to a conserved ordered segment in the human and mouse genome and comprises several genes potentially involved in pigmentation and development. CONCLUSION This study has identified the locus for the merle coat colour in dogs to be at the centromeric end of CFA10. Genetic studies on other breeds segregating the merle phenotype should allow the locus to be defined more accurately with the aim of identifying the gene. This work shows the power of the canine system to search for the genetic bases of mammalian pigmentation and developmental pathways.
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Affiliation(s)
- Benoit Hédan
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Sébastien Corre
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Christophe Hitte
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Stéphane Dréano
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Thierry Vilboux
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Thomas Derrien
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | | | - Francis Galibert
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Marie-Dominique Galibert
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
| | - Catherine André
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, Université de Rennes1, 35043 RENNES Cédex, France
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Hitte C, Madeoy J, Kirkness EF, Priat C, Lorentzen TD, Senger F, Thomas D, Derrien T, Ramirez C, Scott C, Evanno G, Pullar B, Cadieu E, Oza V, Lourgant K, Jaffe DB, Tacher S, Dréano S, Berkova N, André C, Deloukas P, Fraser C, Lindblad-Toh K, Ostrander EA, Galibert F. Facilitating genome navigation: survey sequencing and dense radiation-hybrid gene mapping. Nat Rev Genet 2005; 6:643-8. [PMID: 16012527 DOI: 10.1038/nrg1658] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [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: 11/10/2022]
Abstract
Accurate and comprehensive sequence coverage for large genomes has been restricted to only a few species of specific interest. Lower sequence coverage (survey sequencing) of related species can yield a wealth of information about gene content and putative regulatory elements. But survey sequences lack long-range continuity and provide only a fragmented view of a genome. Here we show the usefulness of combining survey sequencing with dense radiation-hybrid (RH) maps for extracting maximum comparative genome information from model organisms. Based on results from the canine system, we propose that from now on all low-pass sequencing projects should be accompanied by a dense, gene-based RH map-construction effort to extract maximum information from the genome with a marginal extra cost.
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Affiliation(s)
- Christophe Hitte
- CNRS, UMR 6061, Génétique et développement, Faculte de Médecine, Rennes, France
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Hitte C, Derrien T, Andre C, Ostrander EA, Galibert F. CRH_Server: an online comparative and radiation hybrid mapping server for the canine genome. Bioinformatics 2004; 20:3665-7. [DOI: 10.1093/bioinformatics/bth411] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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46
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Guyon R, Kirkness EF, Lorentzen TD, Hitte C, Comstock KE, Quignon P, Derrien T, André C, Fraser CM, Galibert F, Ostrander EA. Building comparative maps using 1.5x sequence coverage: human chromosome 1p and the canine genome. Cold Spring Harb Symp Quant Biol 2003; 68:171-7. [PMID: 15338615 DOI: 10.1101/sqb.2003.68.171] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- R Guyon
- UMR 6061 CNRS, Génétique et Développement, Faculté de Médecine, 35043 Rennes Cedex, France
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