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Vanden Broeck A, Meese T, Verschelde P, Cox K, Heinze B, Deforce D, De Meester E, Van Nieuwerburgh F. Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar. BMC Biol 2024; 22:30. [PMID: 38317114 PMCID: PMC10845628 DOI: 10.1186/s12915-024-01816-1] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 01/04/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome. RESULTS We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe a biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment. CONCLUSIONS Genome-wide cytosine methylation patterns in symmetrical CG-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in CG-context can be used as biomarkers to infer a common ancestor and thus to investigate the recent environmental history of a specific Lombardy poplar. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.
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Affiliation(s)
- An Vanden Broeck
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium.
| | - Tim Meese
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Pieter Verschelde
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Karen Cox
- Research Institute for Nature and Forest (INBO), Geraardsbergen, Belgium
| | - Berthold Heinze
- Department of Forest Growth, Silviculture and Genetics, Austrian Federal Research Centre for Forests (BFW), Vienna, Austria
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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de Reuver R, Dierick E, Wiernicki B, Staes K, Seys L, De Meester E, Muyldermans T, Botzki A, Lambrecht BN, Van Nieuwerburgh F, Vandenabeele P, Maelfait J. ADAR1 interaction with Z-RNA promotes editing of endogenous double-stranded RNA and prevents MDA5-dependent immune activation. Cell Rep 2021; 36:109500. [PMID: 34380029 DOI: 10.1016/j.celrep.2021.109500] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 05/14/2021] [Accepted: 07/15/2021] [Indexed: 02/06/2023] Open
Abstract
Loss of function of adenosine deaminase acting on double-stranded RNA (dsRNA)-1 (ADAR1) causes the severe autoinflammatory disease Aicardi-Goutières syndrome (AGS). ADAR1 converts adenosines into inosines within dsRNA. This process called A-to-I editing masks self-dsRNA from detection by the antiviral dsRNA sensor MDA5. ADAR1 binds to dsRNA in both the canonical A-form and the poorly defined Z conformation (Z-RNA). Mutations in the Z-RNA-binding Zα domain of ADAR1 are common in patients with AGS. How loss of ADAR1/Z-RNA interaction contributes to disease development is unknown. We demonstrate that abrogated binding of ADAR1 to Z-RNA leads to reduced A-to-I editing of dsRNA structures formed by base pairing of inversely oriented short interspersed nuclear elements. Preventing ADAR1 binding to Z-RNA triggers an MDA5/MAVS-mediated type I interferon response and leads to the development of lethal autoinflammation in mice. This shows that the interaction between ADAR1 and Z-RNA restricts sensing of self-dsRNA and prevents AGS development.
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Affiliation(s)
- Richard de Reuver
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Evelien Dierick
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Bartosz Wiernicki
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Katrien Staes
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Leen Seys
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
| | - Ellen De Meester
- Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium
| | | | | | - Bart N Lambrecht
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Internal Medicine and Pediatrics, Ghent University, 9000 Ghent, Belgium; Department of Pulmonary Medicine, Erasmus University Medical Center Rotterdam, 3015 GJ Rotterdam, the Netherlands
| | - Filip Van Nieuwerburgh
- NXTGNT, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium; Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Peter Vandenabeele
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Jonathan Maelfait
- VIB-UGent Center for Inflammation Research, 9052 Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium.
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Diddens J, Coussement L, Frankl-Vilches C, Majumdar G, Steyaert S, Ter Haar SM, Galle J, De Meester E, De Keulenaer S, Van Criekinge W, Cornil CA, Balthazart J, Van Der Linden A, De Meyer T, Vanden Berghe W. DNA Methylation Regulates Transcription Factor-Specific Neurodevelopmental but Not Sexually Dimorphic Gene Expression Dynamics in Zebra Finch Telencephalon. Front Cell Dev Biol 2021; 9:583555. [PMID: 33816458 PMCID: PMC8017237 DOI: 10.3389/fcell.2021.583555] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 07/15/2020] [Accepted: 02/17/2021] [Indexed: 12/13/2022] Open
Abstract
Song learning in zebra finches (Taeniopygia guttata) is a prototypical example of a complex learned behavior, yet knowledge of the underlying molecular processes is limited. Therefore, we characterized transcriptomic (RNA-sequencing) and epigenomic (RRBS, reduced representation bisulfite sequencing; immunofluorescence) dynamics in matched zebra finch telencephalon samples of both sexes from 1 day post hatching (1 dph) to adulthood, spanning the critical period for song learning (20 and 65 dph). We identified extensive transcriptional neurodevelopmental changes during postnatal telencephalon development. DNA methylation was very low, yet increased over time, particularly in song control nuclei. Only a small fraction of the massive differential expression in the developing zebra finch telencephalon could be explained by differential CpG and CpH DNA methylation. However, a strong association between DNA methylation and age-dependent gene expression was found for various transcription factors (i.e., OTX2, AR, and FOS) involved in neurodevelopment. Incomplete dosage compensation, independent of DNA methylation, was found to be largely responsible for sexually dimorphic gene expression, with dosage compensation increasing throughout life. In conclusion, our results indicate that DNA methylation regulates neurodevelopmental gene expression dynamics through steering transcription factor activity, but does not explain sexually dimorphic gene expression patterns in zebra finch telencephalon.
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Affiliation(s)
- Jolien Diddens
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Louis Coussement
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Carolina Frankl-Vilches
- Department of Behavioral Neurobiology, Max Planck Institute for Ornithology, Seewiesen, Germany
| | - Gaurav Majumdar
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Sandra Steyaert
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Sita M Ter Haar
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jeroen Galle
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Sarah De Keulenaer
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Charlotte A Cornil
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Jacques Balthazart
- Laboratory of Behavioral Neuroendocrinology, GIGA Neuroscience, University of Liège, Liège, Belgium
| | - Annemie Van Der Linden
- Bio-Imaging Lab, Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Tim De Meyer
- Biobix: Laboratory of Bioinformatics and Computational Genomics, Department of Data Analysis and Mathematical Modeling, Ghent University, Ghent, Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Berlamont H, De Witte C, Bauwens E, Min Jou H, Ducatelle R, De Meester E, Gansemans Y, Deforce D, Van Nieuwerburgh F, Haesebrouck F, Smet A. Distinct transcriptome signatures of Helicobacter suis and Helicobacter heilmannii strains upon adherence to human gastric epithelial cells. Vet Res 2020; 51:62. [PMID: 32381076 PMCID: PMC7206758 DOI: 10.1186/s13567-020-00786-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 02/28/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022] Open
Abstract
The porcine Helicobacter suis and canine-feline H. heilmannii are gastric Helicobacter species with zoonotic potential. However, little is known about the pathogenesis of human infections with these Helicobacter species. To gain more insight into the interactions of both zoonotic Helicobacter species with human gastric epithelial cells, we investigated bacterial genes that are differentially expressed in a H. suis and H. heilmannii strain after adhesion to the human gastric epithelial cell line MKN7. In vitro Helicobacter-MKN7 binding assays were performed to obtain bacterial RNA for sequencing analysis. H. suis and H. heilmannii bacteria attached to the gastric epithelial cells (i.e. cases) as well as unbound bacteria (i.e. controls) were isolated, after which prokaryotic RNA was purified and sequenced. Differentially expressed genes were identified using the DESeq2 package and SARTools pipeline in R. A list of 134 (83 up-regulated and 51 down-regulated) and 143 (60 up-regulated and 83 down-regulated) differentially expressed genes (padj ≤ 0.01; fold change ≥ 2) were identified for the adherent H. suis and H. heilmannii strains, respectively. According to BLASTp analyses, only 2 genes were commonly up-regulated and 4 genes commonly down-regulated in both pathogens. Differentially expressed genes of the H. suis and H. heilmannii strains belonged to multiple functional classes, indicating that adhesion of both strains to human gastric epithelial cells evokes pleiotropic adaptive responses. Our results suggest that distinct pathways are involved in human gastric colonization of H. suis and H. heilmannii. Further research is needed to elucidate the clinical significance of these findings.
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Affiliation(s)
- Helena Berlamont
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Chloë De Witte
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Eva Bauwens
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Hannah Min Jou
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Yannick Gansemans
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Freddy Haesebrouck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
| | - Annemieke Smet
- Translational Research in Immunology and Inflammation, Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, Antwerp University, 2610, Antwerp, Belgium.
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Vermeulen LMP, Fraire JC, Raes L, De Meester E, De Keulenaer S, Van Nieuwerburgh F, De Smedt S, Remaut K, Braeckmans K. Photothermally Triggered Endosomal Escape and Its Influence on Transfection Efficiency of Gold-Functionalized JetPEI/pDNA Nanoparticles. Int J Mol Sci 2018; 19:E2400. [PMID: 30110965 PMCID: PMC6121899 DOI: 10.3390/ijms19082400] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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: 08/07/2018] [Accepted: 08/11/2018] [Indexed: 12/22/2022] Open
Abstract
Plasmonic nanoparticles for drug delivery have attracted increasing interest over the last few years. Their localized surface plasmon resonance causes photothermal effects on laser irradiation, which allows for delivering drugs in a spatio-temporally controlled manner. Here, we explore the use of gold nanoparticles (AuNP) as carriers for pDNA in combination with pulsed laser irradiation to induce endosomal escape, which is currently considered to be one of the major bottlenecks in macromolecular drug delivery on the intracellular level. In particular, we evaluate nanocomplexes composed of JetPEI (polyethylenimine)pDNA and 10 nm AuNP, which do not exhibit endosomal escape by themselves. After incubating HeLa cells with these complexes, we evaluated endosomal escape and transfection efficiency using low- and high-energy laser pulses. At low laser energy heat is produced by the nanocomplexes, while, at higher laser energy, explosive vapour nanobubbles (VNB) are formed. We investigated the ability of heat transfer and VNB formation to induce endosomal escape and we examine the integrity of pDNA cargo after inducing both photothermal effects. We conclude that JetPEI/pDNA/AuNP complexes are unable to induce meaningful transfection efficiencies because laser treatment causes either dysfunctionality of the cargo when VNB are formed or forms too small pores in the endosomal membrane to allow pDNA to escape in case of heating. We conclude that laser-induced VNB is the most suitable to induce effective pDNA endosomal escape, but a different nanocomplex structure will be required to keep the pDNA intact.
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Affiliation(s)
- Lotte M P Vermeulen
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Juan C Fraire
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Laurens Raes
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Ellen De Meester
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Sarah De Keulenaer
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Filip Van Nieuwerburgh
- Laboratory of Pharmaceutical Biotechnology, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Stefaan De Smedt
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Katrien Remaut
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
| | - Kevin Braeckmans
- Laboratory of General Biochemistry & Physical Pharmacy, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium.
- IEMN UMR 8520 and Laboratoire de Physique des Lasers, Atomes et Molécules. UMR 8523, Université de Lille, F-59655 Villeneuve d'Ascq CEDEX, France.
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Steyaert S, Diddens J, Galle J, De Meester E, De Keulenaer S, Bakker A, Sohnius-Wilhelmi N, Frankl-Vilches C, Van der Linden A, Van Criekinge W, Berghe WV, De Meyer T. Corrigendum: A genome-wide search for epigenetically regulated genes in zebra finch using MethylCap-seq and RNA-seq. Sci Rep 2016; 6:22472. [PMID: 26984369 PMCID: PMC4794736 DOI: 10.1038/srep22472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Crappé J, Ndah E, Koch A, Steyaert S, Gawron D, De Keulenaer S, De Meester E, De Meyer T, Van Criekinge W, Van Damme P, Menschaert G. PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration. Nucleic Acids Res 2014; 43:e29. [PMID: 25510491 PMCID: PMC4357689 DOI: 10.1093/nar/gku1283] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [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] [Indexed: 12/30/2022] Open
Abstract
An increasing amount of studies integrate mRNA sequencing data into MS-based proteomics to complement the translation product search space. However, several factors, including extensive regulation of mRNA translation and the need for three- or six-frame-translation, impede the use of mRNA-seq data for the construction of a protein sequence search database. With that in mind, we developed the PROTEOFORMER tool that automatically processes data of the recently developed ribosome profiling method (sequencing of ribosome-protected mRNA fragments), resulting in genome-wide visualization of ribosome occupancy. Our tool also includes a translation initiation site calling algorithm allowing the delineation of the open reading frames (ORFs) of all translation products. A complete protein synthesis-based sequence database can thus be compiled for mass spectrometry-based identification. This approach increases the overall protein identification rates with 3% and 11% (improved and new identifications) for human and mouse, respectively, and enables proteome-wide detection of 5′-extended proteoforms, upstream ORF translation and near-cognate translation start sites. The PROTEOFORMER tool is available as a stand-alone pipeline and has been implemented in the galaxy framework for ease of use.
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Affiliation(s)
- Jeroen Crappé
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Elvis Ndah
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Alexander Koch
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Sandra Steyaert
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Daria Gawron
- Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sarah De Keulenaer
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Ellen De Meester
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Tim De Meyer
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Wim Van Criekinge
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Petra Van Damme
- Department of Medical Protein Research, Flemish Institute of Biotechnology, Ghent, Belgium Department of Biochemistry, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Gerben Menschaert
- Lab of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Koch A, Gawron D, Steyaert S, Ndah E, Crappé J, De Keulenaer S, De Meester E, Ma M, Shen B, Gevaert K, Van Criekinge W, Van Damme P, Menschaert G. A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites. Proteomics 2014; 14:2688-98. [PMID: 25156699 DOI: 10.1002/pmic.201400180] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [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: 05/02/2014] [Revised: 07/28/2014] [Accepted: 08/19/2014] [Indexed: 12/24/2022]
Abstract
Next-generation transcriptome sequencing is increasingly integrated with MS to enhance MS-based protein and peptide identification. Recently, a breakthrough in transcriptome analysis was achieved with the development of ribosome profiling (ribo-seq). This technology is based on the deep sequencing of ribosome-protected mRNA fragments, thereby enabling the direct observation of in vivo protein synthesis at the transcript level. In order to explore the impact of a ribo-seq-derived protein sequence search space on MS/MS spectrum identification, we performed a comprehensive proteome study on a human cancer cell line, using both shotgun and N-terminal proteomics, next to ribosome profiling, which was used to delineate (alternative) translational reading frames. By including protein-level evidence of sample-specific genetic variation and alternative translation, this strategy improved the identification score of 69 proteins and identified 22 new proteins in the shotgun experiment. Furthermore, we discovered 18 new alternative translation start sites in the N-terminal proteomics data and observed a correlation between the quantitative measures of ribo-seq and shotgun proteomics with a Pearson correlation coefficient ranging from 0.483 to 0.664. Overall, this study demonstrated the benefits of ribosome profiling for MS-based protein and peptide identification and we believe this approach could develop into a common practice for next-generation proteomics.
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Affiliation(s)
- Alexander Koch
- Laboratory of Bioinformatics and Computational Genomics, Department of Mathematical Modeling, Statistics and Bioinformatics, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
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Coppieters F, De Wilde B, Lefever S, De Meester E, De Rocker N, Van Cauwenbergh C, Pattyn F, Meire F, Leroy BP, Hellemans J, Vandesompele J, De Baere E. In This Issue. Genet Med 2012. [DOI: 10.1038/gim.2012.55] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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