1
|
Abebe JS, Alwie Y, Fuhrmann E, Leins J, Mai J, Verstraten R, Schreiner S, Wilson AC, Depledge DP. Nanopore Guided Annotation of Transcriptome Architectures. bioRxiv 2024:2024.04.02.587744. [PMID: 38617228 PMCID: PMC11014626 DOI: 10.1101/2024.04.02.587744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
High-resolution annotations of transcriptomes from all domains of life are essential for many sequencing-based RNA analyses, including Nanopore direct RNA sequencing (DRS), which would otherwise be hindered by misalignments and other analysis artefacts. DRS allows the capture and full-length sequencing of native RNAs, without recoding or amplification bias, and resulting data may be interrogated to define the identity and location of chemically modified ribonucleotides, as well as the length of poly(A) tails on individual RNA molecules. Existing software solutions for generating high-resolution transcriptome annotations are poorly suited to small gene dense organisms such as viruses due to the challenge of identifying distinct transcript isoforms where alternative splicing and overlapping RNAs are prevalent. To resolve this, we identified key characteristics of DRS datasets and developed a novel approach to transcriptome. We demonstrate, using a combination of synthetic and original datasets, that our novel approach yields a high level of precision and recall when reconstructing both gene sparse and gene dense transcriptomes from DRS datasets. We further apply this approach to generate a new high resolution transcriptome annotation of the neglected pathogen human adenovirus type F 41 for which we identify 77 distinct transcripts encoding at least 23 different proteins.
Collapse
Affiliation(s)
- Jonathan S. Abebe
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Yasmine Alwie
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Erik Fuhrmann
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Jonas Leins
- Institute of Virology, Hannover Medical School, Hannover, Germany
| | - Julia Mai
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
| | - Ruth Verstraten
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
| | - Sabrina Schreiner
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Institute of Virology, University Medical Center, Albert-Ludwigs-University Freiburg, Freiburg, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| | - Angus C. Wilson
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Daniel P. Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY, USA
- Institute of Virology, Hannover Medical School, Hannover, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Hannover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany
| |
Collapse
|
2
|
Adams DJ, Barlas B, McIntyre RE, Salguero I, van der Weyden L, Barros A, Vicente JR, Karimpour N, Haider A, Ranzani M, Turner G, Thompson NA, Harle V, Olvera-León R, Robles-Espinoza CD, Speak AO, Geisler N, Weninger WJ, Geyer SH, Hewinson J, Karp NA, Fu B, Yang F, Kozik Z, Choudhary J, Yu L, van Ruiten MS, Rowland BD, Lelliott CJ, Del Castillo Velasco-Herrera M, Verstraten R, Bruckner L, Henssen AG, Rooimans MA, de Lange J, Mohun TJ, Arends MJ, Kentistou KA, Coelho PA, Zhao Y, Zecchini H, Perry JRB, Jackson SP, Balmus G. Genetic determinants of micronucleus formation in vivo. Nature 2024; 627:130-136. [PMID: 38355793 PMCID: PMC10917660 DOI: 10.1038/s41586-023-07009-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/21/2023] [Indexed: 02/16/2024]
Abstract
Genomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR-Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.
Collapse
Affiliation(s)
- D J Adams
- Wellcome Sanger Institute, Cambridge, UK.
| | - B Barlas
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | | | - I Salguero
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - A Barros
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - J R Vicente
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - N Karimpour
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - A Haider
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - M Ranzani
- Wellcome Sanger Institute, Cambridge, UK
| | - G Turner
- Wellcome Sanger Institute, Cambridge, UK
| | | | - V Harle
- Wellcome Sanger Institute, Cambridge, UK
| | | | - C D Robles-Espinoza
- Wellcome Sanger Institute, Cambridge, UK
- Laboratorio Internacional de Investigación Sobre el Genoma Humano, Universidad Nacional Autónoma de México, Santiago de Querétaro, México
| | - A O Speak
- Wellcome Sanger Institute, Cambridge, UK
| | - N Geisler
- Wellcome Sanger Institute, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - W J Weninger
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - S H Geyer
- Division of Anatomy, MIC, Medical University of Vienna, Wien, Austria
| | - J Hewinson
- Wellcome Sanger Institute, Cambridge, UK
| | - N A Karp
- Wellcome Sanger Institute, Cambridge, UK
| | - B Fu
- Wellcome Sanger Institute, Cambridge, UK
| | - F Yang
- Wellcome Sanger Institute, Cambridge, UK
| | - Z Kozik
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - J Choudhary
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - L Yu
- Functional Proteomics Group, Chester Beatty Laboratories, The Institute of Cancer Research, London, UK
| | - M S van Ruiten
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - B D Rowland
- Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - L Bruckner
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
| | - A G Henssen
- Experimental and Clinical Research Center (ECRC) of the MDC and Charité Berlin, Berlin, Germany
- Max-Delbrück-Centrum für Molekulare Medizin, Berlin, Germany
- Department of Pediatric Oncology and Hematology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - M A Rooimans
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - J de Lange
- Department of Human Genetics, Section of Oncogenetics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Cancer Center Amsterdam, Cancer Biology and Immunology, Amsterdam, The Netherlands
| | - T J Mohun
- Division of Developmental Biology, MRC, National Institute for Medical Research, London, UK
| | - M J Arends
- Division of Pathology, Cancer Research UK Scotland Centre, Institute of Genetics & Cancer The University of Edinburgh, Edinburgh, UK
| | - K A Kentistou
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - P A Coelho
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Y Zhao
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - H Zecchini
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - J R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - S P Jackson
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
- Cancer Research UK Cambridge Institute, Cambridge, UK
| | - G Balmus
- Wellcome Sanger Institute, Cambridge, UK.
- UK Dementia Research Institute at the University of Cambridge, University of Cambridge, Cambridge, UK.
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
- Department of Molecular Neuroscience, Transylvanian Institute of Neuroscience, Cluj-Napoca, Romania.
| |
Collapse
|
3
|
Anbunathan H, Verstraten R, Singh AD, Harbour JW, Bowcock AM. Integrative Copy Number Analysis of Uveal Melanoma Reveals Novel Candidate Genes Involved in Tumorigenesis Including a Tumor Suppressor Role for PHF10/BAF45a. Clin Cancer Res 2019; 25:5156-5166. [PMID: 31227497 DOI: 10.1158/1078-0432.ccr-18-3052] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 04/23/2019] [Accepted: 06/17/2019] [Indexed: 12/18/2022]
Abstract
PURPOSE Uveal melanoma is a primary malignancy of the eye with oncogenic mutations in GNAQ, GNA11, or CYSLTR2, and additional mutations in BAP1 (usually associated with LOH of Chr 3), SF3B1, or EIF1AX. There are other characteristic chromosomal alterations, but their significance is not clear. EXPERIMENTAL DESIGN To investigate genes driving chromosomal alterations, we integrated copy number, transcriptome, and mutation data from three cohorts and followed up key findings. RESULTS We observed significant enrichment of transcripts on chromosomes 1p, 3, 6, 8, and 16q and identified seven shared focal copy number alterations (FCNAs) on Chr 1p36, 2q37, 3, 6q25, 6q27, and 8q24. Integrated analyses revealed clusters of genes in focal copy number regions whose expression was associated with metastasis and worse overall survival. This included genes from Chr 1p36, 3p21, and 8q24.3. At Chr 6q27, we identified two tumors with homozygous deletion of PHF10/BAF45a and one with a frameshift mutation with concomitant loss of the wild-type allele. Downregulation of PHF10 in uveal melanoma cell lines and tumors altered a number of biological pathways including development and adhesion. These findings provide support for a role for PHF10 as a novel tumor suppressor at Chr 6q27. CONCLUSIONS Integration of copy number, transcriptome, and mutation data revealed novel candidate genes playing a role in uveal melanoma pathogenesis and a potential tumor suppressor role for PHF10.
Collapse
Affiliation(s)
- Hima Anbunathan
- National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Ruth Verstraten
- National Heart and Lung Institute, Imperial College, London, United Kingdom.,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Arun D Singh
- Department of Ophthalmic Oncology, Cole Eye Institute, Cleveland Clinic, Cleveland, Ohio
| | - J William Harbour
- Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, Florida
| | - Anne M Bowcock
- National Heart and Lung Institute, Imperial College, London, United Kingdom. .,Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York.,Departments of Dermatology and Genetics & Genome Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| |
Collapse
|
4
|
McIntyre RE, Nicod J, Robles-Espinoza CD, Maciejowski J, Cai N, Hill J, Verstraten R, Iyer V, Rust AG, Balmus G, Mott R, Flint J, Adams DJ. A Genome-Wide Association Study for Regulators of Micronucleus Formation in Mice. G3 (Bethesda) 2016; 6:2343-54. [PMID: 27233670 PMCID: PMC4978889 DOI: 10.1534/g3.116.030767] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/24/2016] [Indexed: 12/29/2022]
Abstract
In mammals the regulation of genomic instability plays a key role in tumor suppression and also controls genome plasticity, which is important for recombination during the processes of immunity and meiosis. Most studies to identify regulators of genomic instability have been performed in cells in culture or in systems that report on gross rearrangements of the genome, yet subtle differences in the level of genomic instability can contribute to whole organism phenotypes such as tumor predisposition. Here we performed a genome-wide association study in a population of 1379 outbred Crl:CFW(SW)-US_P08 mice to dissect the genetic landscape of micronucleus formation, a biomarker of chromosomal breaks, whole chromosome loss, and extranuclear DNA. Variation in micronucleus levels is a complex trait with a genome-wide heritability of 53.1%. We identify seven loci influencing micronucleus formation (false discovery rate <5%), and define candidate genes at each locus. Intriguingly at several loci we find evidence for sexual dimorphism in micronucleus formation, with a locus on chromosome 11 being specific to males.
Collapse
Affiliation(s)
- Rebecca E McIntyre
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Jérôme Nicod
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Carla Daniela Robles-Espinoza
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Boulevard Juriquilla 3001, Santiago de Querétaro 76230, Mexico
| | - John Maciejowski
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, New York 10065
| | - Na Cai
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - Jennifer Hill
- Microbial Pathogenesis, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Ruth Verstraten
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Vivek Iyer
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Alistair G Rust
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK Tumour Profiling Unit, The Institute of Cancer Research, London SW3 6JB, UK
| | - Gabriel Balmus
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK The Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, CB2 1QN, UK
| | - Richard Mott
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK UCL Genetics Institute, University College London, WC1E 6BT, UK
| | - Jonathan Flint
- Wellcome Trust Centre for Human Genetics, Oxford OX3 7BN, UK
| | - David J Adams
- Experimental Cancer Genetics, The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| |
Collapse
|
5
|
Brosch M, Saunders GI, Frankish A, Collins MO, Yu L, Wright J, Verstraten R, Adams DJ, Harrow J, Choudhary JS, Hubbard T. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res 2011; 21:756-67. [PMID: 21460061 DOI: 10.1101/gr.114272.110] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recent advances in proteomic mass spectrometry (MS) offer the chance to marry high-throughput peptide sequencing to transcript models, allowing the validation, refinement, and identification of new protein-coding loci. We present a novel pipeline that integrates highly sensitive and statistically robust peptide spectrum matching with genome-wide protein-coding predictions to perform large-scale gene validation and discovery in the mouse genome for the first time. In searching an excess of 10 million spectra, we have been able to validate 32%, 17%, and 7% of all protein-coding genes, exons, and splice boundaries, respectively. Moreover, we present strong evidence for the identification of multiple alternatively spliced translations from 53 genes and have uncovered 10 entirely novel protein-coding genes, which are not covered in any mouse annotation data sources. One such novel protein-coding gene is a fusion protein that spans the Ins2 and Igf2 loci to produce a transcript encoding the insulin II and the insulin-like growth factor 2-derived peptides. We also report nine processed pseudogenes that have unique peptide hits, demonstrating, for the first time, that they are not just transcribed but are translated and are therefore resurrected into new coding loci. This work not only highlights an important utility for MS data in genome annotation but also provides unique insights into the gene structure and propagation in the mouse genome. All these data have been subsequently used to improve the publicly available mouse annotation available in both the Vega and Ensembl genome browsers (http://vega.sanger.ac.uk).
Collapse
Affiliation(s)
- Markus Brosch
- The Wellcome Trust Sanger Institute, The Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, United Kingdom
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|