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Black AJ, Schilder RJ, Kimball SR. Palmitate- and C6 ceramide-induced Tnnt3 pre-mRNA alternative splicing occurs in a PP2A dependent manner. Nutr Metab (Lond) 2018; 15:87. [PMID: 30564278 PMCID: PMC6296074 DOI: 10.1186/s12986-018-0326-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 12/10/2018] [Indexed: 12/24/2022] Open
Abstract
Background In a previous study, we showed that consumption of diets enriched in saturated fatty acids causes changes in alternative splicing of pre-mRNAs encoding a number of proteins in rat skeletal muscle, including the one encoding skeletal muscle Troponin T (Tnnt3). However, whether saturated fatty acids act directly on muscle cells to modulate alternative pre-mRNA splicing was not assessed. Moreover, the signaling pathway through which saturated fatty acids act to promote changes in alternative splicing is unknown. Therefore, the objective of the present study was to characterize the signaling pathway through which saturated fatty acids act to modulate Tnnt3 alternative splicing. Methods The effects of treatment of L6 myotubes with saturated (palmitate), mono- (oleate), or polyunsaturated (linoleate) fatty acids on alternative splicing of pre-mRNA was assessed using Tnnt3 as a marker gene. Results Palmitate treatment caused a two-fold change (p < 0.05) in L6 myotube Tnnt3 alternative splicing whereas treatment with either oleate or linoleate had minimal effects compared to control myotubes. Treatment with a downstream metabolite of palmitate, ceramide, had effects similar to palmitate on Tnnt3 alternative splicing and inhibition of de novo ceramide biosynthesis blocked the palmitate-induced alternative splicing changes. The effects of palmitate and ceramide on Tnnt3 alternative splicing were accompanied by a 40–50% reduction in phosphorylation of Akt on S473. However, inhibition of de novo ceramide biosynthesis did not prevent palmitate-induced Akt dephosphorylation, suggesting that palmitate may act in an Akt-independent manner to modulate Tnnt3 alternative splicing. Instead, pre-treatment with okadaic acid at concentrations that selectively inhibit protein phosphatase 2A (PP2A) blocked both palmitate- and ceramide-induced changes in Tnnt3 alternative splicing, suggesting that palmitate and ceramide act through PP2A to modulate Tnnt3 alternative splicing. Conclusions Overall, the data show that fatty acid saturation level and ceramides are important factors modulating alternative pre-mRNA splicing through activation of PP2A. Electronic supplementary material The online version of this article (10.1186/s12986-018-0326-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Adam J Black
- 1Department of Cellular and Molecular Physiology, Penn State College of Medicine, H166, 500 University Drive, Hershey, PA 17033 USA.,Present Address: Department of Cell Biology and Physiology, 6330 Medical Biomolecular Research Building, 111 Mason Farm Rd, Chapel Hill, NC 27599 USA
| | - Rudolf J Schilder
- 3Department of Entomology and Biology, Penn State University, University Park, PA USA
| | - Scot R Kimball
- 1Department of Cellular and Molecular Physiology, Penn State College of Medicine, H166, 500 University Drive, Hershey, PA 17033 USA
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Evans BA, Smith OL, Pickerill ES, York MK, Buenconsejo KJP, Chambers AE, Bernstein DA. Restriction digest screening facilitates efficient detection of site-directed mutations introduced by CRISPR in C. albicans UME6. PeerJ 2018; 6:e4920. [PMID: 29892505 PMCID: PMC5994162 DOI: 10.7717/peerj.4920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 05/17/2018] [Indexed: 01/14/2023] Open
Abstract
Introduction of point mutations to a gene of interest is a powerful tool when determining protein function. CRISPR-mediated genome editing allows for more efficient transfer of a desired mutation into a wide range of model organisms. Traditionally, PCR amplification and DNA sequencing is used to determine if isolates contain the intended mutation. However, mutation efficiency is highly variable, potentially making sequencing costly and time consuming. To more efficiently screen for correct transformants, we have identified restriction enzymes sites that encode for two identical amino acids or one or two stop codons. We used CRISPR to introduce these restriction sites directly upstream of the Candida albicans UME6 Zn2+-binding domain, a known regulator of C. albicans filamentation. While repair templates coding for different restriction sites were not equally successful at introducing mutations, restriction digest screening enabled us to rapidly identify isolates with the intended mutation in a cost-efficient manner. In addition, mutated isolates have clear defects in filamentation and virulence compared to wild type C. albicans. Our data suggest restriction digestion screening efficiently identifies point mutations introduced by CRISPR and streamlines the process of identifying residues important for a phenotype of interest.
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Affiliation(s)
- Ben A Evans
- Department of Biology, Ball State University, Muncie, IN, United States of America
| | - Olivia L Smith
- Department of Biology, Ball State University, Muncie, IN, United States of America
| | - Ethan S Pickerill
- Department of Biology, Ball State University, Muncie, IN, United States of America
| | - Mary K York
- Department of Biology, Ball State University, Muncie, IN, United States of America
| | - Kristen J P Buenconsejo
- Department of Microbiology and Immunology, Drexel University, Philadelphia, PA, United States of America
| | - Antonio E Chambers
- Department of Biology, Ball State University, Muncie, IN, United States of America
| | - Douglas A Bernstein
- Department of Biology, Ball State University, Muncie, IN, United States of America
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Sharma V, Elghafari A, Hiller M. Coding exon-structure aware realigner (CESAR) utilizes genome alignments for accurate comparative gene annotation. Nucleic Acids Res 2016; 44:e103. [PMID: 27016733 PMCID: PMC4914097 DOI: 10.1093/nar/gkw210] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 03/04/2016] [Accepted: 03/18/2016] [Indexed: 12/03/2022] Open
Abstract
Identifying coding genes is an essential step in genome annotation. Here, we utilize existing whole genome alignments to detect conserved coding exons and then map gene annotations from one genome to many aligned genomes. We show that genome alignments contain thousands of spurious frameshifts and splice site mutations in exons that are truly conserved. To overcome these limitations, we have developed CESAR (Coding Exon-Structure Aware Realigner) that realigns coding exons, while considering reading frame and splice sites of each exon. CESAR effectively avoids spurious frameshifts in conserved genes and detects 91% of shifted splice sites. This results in the identification of thousands of additional conserved exons and 99% of the exons that lack inactivating mutations match real exons. Finally, to demonstrate the potential of using CESAR for comparative gene annotation, we applied it to 188 788 exons of 19 865 human genes to annotate human genes in 99 other vertebrates. These comparative gene annotations are available as a resource (http://bds.mpi-cbg.de/hillerlab/CESAR/). CESAR (https://github.com/hillerlab/CESAR/) can readily be applied to other alignments to accurately annotate coding genes in many other vertebrate and invertebrate genomes.
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Affiliation(s)
- Virag Sharma
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany
| | - Anas Elghafari
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany Technical University, 01069 Dresden, Germany
| | - Michael Hiller
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01307 Dresden, Germany Max Planck Institute for the Physics of Complex Systems, Nöthnitzer Str. 38, 01187 Dresden, Germany
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Turton KB, Annis DS, Rui L, Esnault S, Mosher DF. Ratios of Four STAT3 Splice Variants in Human Eosinophils and Diffuse Large B Cell Lymphoma Cells. PLoS One 2015; 10:e0127243. [PMID: 25984943 PMCID: PMC4436176 DOI: 10.1371/journal.pone.0127243] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Accepted: 04/13/2015] [Indexed: 01/09/2023] Open
Abstract
Signal transducer and activator of transcription 3 (STAT3) is a key mediator of leukocyte differentiation and proliferation. The 3' end of STAT3 transcripts is subject to two alternative splicing events. One results in either full-length STAT3α or in STAT3β, which lacks part of the C-terminal transactivation domain. The other is at a tandem donor (5') splice site and results in the codon for Ser-701 being included (S) or excluded (ΔS). Despite the proximity of Ser-701 to the site of activating phosphorylation at Tyr-705, ΔS/S splicing has barely been studied. Sequencing of cDNA from purified eosinophils revealed the presence of four transcripts (S-α, ΔS-α, S-β, and ΔS-β) rather than the three reported in publically available databases from which ΔS-β is missing. To gain insight into regulation of the two alternative splicing events, we developed a quantitative(q) PCR protocol to compare transcript ratios in eosinophils in which STAT3 is upregulated by cytokines, activated B cell diffuse large B cell Lymphoma (DLBCL) cells in which STAT3 is dysregulated, and in germinal center B cell-like DLBCL cells in which it is not. With the exception of one line of activated B cell DLCBL cells, the four variants were found in roughly the same ratios despite differences in total levels of STAT3 transcripts. S-α was the most abundant, followed by S-β. ΔS-α and ΔS-β together comprised 15.6±4.0 % (mean±SD, n=21) of the total. The percentage of STAT3β variants that were ΔS was 1.5-fold greater than of STAT3α variants that were ΔS. Inspection of Illumina’s “BodyMap” RNA-Seq database revealed that the ΔS variant accounts for 10-26 % of STAT3 transcripts across 16 human tissues, with less variation than three other genes with the identical tandem donor splice site sequence. Thus, it seems likely that all cells contain the S-α, ΔS-α, S-β, and ΔS-β variants of STAT3.
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Affiliation(s)
- Keren B. Turton
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Douglas S. Annis
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
| | - Lixin Rui
- Department of Medicine at University of Wisconsin-Madison, Madison, WI, United States of America
| | - Stephane Esnault
- Department of Medicine at University of Wisconsin-Madison, Madison, WI, United States of America
| | - Deane F. Mosher
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, United States of America
- Department of Medicine at University of Wisconsin-Madison, Madison, WI, United States of America
- * E-mail:
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Wang M, Zhang P, Shu Y, Yuan F, Zhang Y, Zhou Y, Jiang M, Zhu Y, Hu L, Kong X, Zhang Z. Alternative splicing at GYNNGY 5' splice sites: more noise, less regulation. Nucleic Acids Res 2014; 42:13969-80. [PMID: 25428370 PMCID: PMC4267661 DOI: 10.1093/nar/gku1253] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Revised: 10/29/2014] [Accepted: 11/12/2014] [Indexed: 12/28/2022] Open
Abstract
Numerous eukaryotic genes are alternatively spliced. Recently, deep transcriptome sequencing has skyrocketed proportion of alternatively spliced genes; over 95% human multi-exon genes are alternatively spliced. One fundamental question is: are all these alternative splicing (AS) events functional? To look into this issue, we studied the most common form of alternative 5' splice sites-GYNNGYs (Y = C/T), where both GYs can function as splice sites. Global analyses suggest that splicing noise (due to stochasticity of splicing process) can cause AS at GYNNGYs, evidenced by higher AS frequency in non-coding than in coding regions, in non-conserved than in conserved genes and in lowly expressed than in highly expressed genes. However, ∼20% AS GYNNGYs in humans and ∼3% in mice exhibit tissue-dependent regulation. Consistent with being functional, regulated GYNNGYs are more conserved than unregulated ones. And regulated GYNNGYs have distinctive sequence features which may confer regulation. Particularly, each regulated GYNNGY comprises two splice sites more resembling each other than unregulated GYNNGYs, and has more conserved downstream flanking intron. Intriguingly, most regulated GYNNGYs may tune gene expression through coupling with nonsense-mediated mRNA decay, rather than encode different proteins. In summary, AS at GYNNGY 5' splice sites is primarily splicing noise, and secondarily a way of regulation.
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Affiliation(s)
- Meng Wang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Peiwei Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yang Shu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Fei Yuan
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yuchao Zhang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - You Zhou
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Min Jiang
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yufei Zhu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Landian Hu
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xiangyin Kong
- State Key Laboratory of Medical Genomics, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, People's Republic of China Graduate School of the Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhenguo Zhang
- Institute of Molecular Evolutionary Genetics and Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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Alternative splicing of mutually exclusive exons—A review. Biosystems 2013; 114:31-8. [DOI: 10.1016/j.biosystems.2013.07.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 07/03/2013] [Indexed: 12/16/2022]
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Liou SW, Huang YF. An exon/intron disparity framework based on the nucleotide profile of single sequence. ACTA ACUST UNITED AC 2012. [DOI: 10.1007/s13721-012-0007-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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8
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Phosphatidylinositol 4-phosphate 5-kinase Iγ_v6, a new splice variant found in rodents and humans. Biochem Biophys Res Commun 2011; 411:416-20. [PMID: 21756881 PMCID: PMC3176900 DOI: 10.1016/j.bbrc.2011.06.168] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 06/26/2011] [Indexed: 11/23/2022]
Abstract
Phosphatidylinositol 4-phosphate 5-kinase Iγ (PIP5KIγ) is subject to extensive C-terminal splice variation, with four variants, PIP5KIγ_v1, 2, 4 and 5, described in humans Schill and Anderson (2009) [7]. Here firstly, we report a new rodent splice variant, which includes the exon that was previously unique to the rodent neuron-specific PIP5KIγ93 Giudici et al. (2006) [6], but which omits the C-terminal exon of PIP5KIγ93; this new variant shows a wide tissue expression pattern in mouse. Secondly, we show that in humans there is an alternative splicing site 78 nucleotides from the start of exon 16c, such that humans additionally express both PIP5KIγ93 (which we now call PIP5KIγ_v3) specifically in brain and, again expressed more widely, the new variant described here, which we now name PIP5KIγ_v6.
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Sinha R, Lenser T, Jahn N, Gausmann U, Friedel S, Szafranski K, Huse K, Rosenstiel P, Hampe J, Schuster S, Hiller M, Backofen R, Platzer M. TassDB2 - A comprehensive database of subtle alternative splicing events. BMC Bioinformatics 2010; 11:216. [PMID: 20429909 PMCID: PMC2878309 DOI: 10.1186/1471-2105-11-216] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 04/29/2010] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Subtle alternative splicing events involving tandem splice sites separated by a short (2-12 nucleotides) distance are frequent and evolutionarily widespread in eukaryotes, and a major contributor to the complexity of transcriptomes and proteomes. However, these events have been either omitted altogether in databases on alternative splicing, or only the cases of experimentally confirmed alternative splicing have been reported. Thus, a database which covers all confirmed cases of subtle alternative splicing as well as the numerous putative tandem splice sites (which might be confirmed once more transcript data becomes available), and allows to search for tandem splice sites with specific features and download the results, is a valuable resource for targeted experimental studies and large-scale bioinformatics analyses of tandem splice sites. Towards this goal we recently set up TassDB (Tandem Splice Site DataBase, version 1), which stores data about alternative splicing events at tandem splice sites separated by 3 nt in eight species. DESCRIPTION We have substantially revised and extended TassDB. The currently available version 2 contains extensive information about tandem splice sites separated by 2-12 nt for the human and mouse transcriptomes including data on the conservation of the tandem motifs in five vertebrates. TassDB2 offers a user-friendly interface to search for specific genes or for genes containing tandem splice sites with specific features as well as the possibility to download result datasets. For example, users can search for cases of alternative splicing where the proportion of EST/mRNA evidence supporting the minor isoform exceeds a specific threshold, or where the difference in splice site scores is specified by the user. The predicted impact of each event on the protein is also reported, along with information about being a putative target for the nonsense-mediated decay (NMD) pathway. Links are provided to the UCSC genome browser and other external resources. CONCLUSION TassDB2, available via http://www.tassdb.info, provides comprehensive resources for researchers interested in both targeted experimental studies and large-scale bioinformatics analyses of short distance tandem splice sites.
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Affiliation(s)
- Rileen Sinha
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Thorsten Lenser
- Bio Systems Analysis Group, Friedrich Schiller University Jena, Ernst-Abbe-Platz 1-4, D-07743 Jena, Germany
| | - Niels Jahn
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Ulrike Gausmann
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Swetlana Friedel
- Leibniz Institute for Natural Product Research and Infection Biology, Hans-Knöll-Institute, Systems Biology/Bioinformatics, Beutenbergstrasse. 11a, 07745 Jena, Germany
| | - Karol Szafranski
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Klaus Huse
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Jochen Hampe
- Department of General Internal Medicine, University Hospital Schleswig-Holstein, Campus Kiel, Schittenhelmstrasse, 12, 24105 Kiel, Germany
| | - Stefan Schuster
- Department of Bioinformatics, Friedrich Schiller University Jena, Ernst-Abbe-Platz 2, 07743 Jena, Germany
| | - Michael Hiller
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Rolf Backofen
- Bioinformatics group, Albert-Ludwigs-University Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany
- Freiburg Initiative for Systems Biology (FRISYS), University of Freiburg, Schaenzlestrasse 1, 79104 Freiburg, Germany
- Centre for Biological Signalling Studies (bioss), University of Freiburg, Albertstr. 19, 79104 Freiburg, Germany
| | - Matthias Platzer
- Genome Analysis, Leibniz Institute for Age Research - Fritz Lipmann Institute, Beutenbergstr. 11, 07745 Jena, Germany
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