Dr. rer. nat. Bioinformatik

RNA Bioinformatics and High Throughput Analysis Jena
Friedrich Schiller University Jena
Faculty of Mathematics and Computer Science
Leutragraben 1
07743 Jena
Germany

E-Mail: emanuel.barth*
Room: 08S01
Phone: +49-3641-9-46481

*@uni-jena.de

Publications

2019

  • [DOI] P. Sieber, E. Barth, and M. Marz, “The landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues,” bioRxiv, p. 541417, 2019.
    [Bibtex]
    @Article{Sieber:19,
    author = {Patricia Sieber and Emanuel Barth and Manja Marz},
    title = {The landscape of the alternatively spliced transcriptome remains stable during aging across different species and tissues},
    journal = {{bioRxiv}},
    year = {2019},
    pages = {541417},
    doi = {10.1101/541417},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] F. Mock, A. Viehweger, E. Barth, and M. Marz, “Viral host prediction with deep learning,” Biorxiv, 2019.
    [Bibtex]
    @article {Mock:19,
    author = {Mock, Florian and Viehweger, Adrian and Barth, Emanuel and Marz, Manja},
    title = {Viral host prediction with Deep Learning},
    elocation-id = {575571},
    year = {2019},
    doi = {10.1101/575571},
    publisher = {Cold Spring Harbor Laboratory},
    abstract = {Zoonosis, the natural transmission of infections from animal to human, is a far-reaching global problem. The recent outbreaks of Zika virus and Ebola virus are examples of viral zoonosis, which occur more frequently due to globalization. In case of a virus outbreak, it is helpful to know which host organism was the original carrier of the virus. Once the reservoir or intermediate host is known, it can be isolated to prevent further spreading of the viral infection. Recent approaches aim to predict a viral host based on the viral genome, often in combination with the potential host genome and using arbitrary selected features. This methods have a clear limitation in either the amount of different hosts they can predict or the accuracy of the prediction. Here, we present a fast and accurate deep learning approach for viral host prediction, which is based on the viral genome sequence only. To assure a high prediction accuracy we developed an effective selection approach for the training data, to avoid biases due to a highly unbalanced number of known sequences per virus-host combinations. We tested our deep neural network on three different virus species (influenza A virus, rabies lyssavirus, rotavirus A) and reached for each virus species a AUC between 0.94 and 0.98, outperforming previous approaches and allowing highly accurate predictions while only using fractions of the viral genome sequences. We show that deep neural networks are suitable to predict the host of a virus, even with a limited amount of sequences and highly unbalanced available data. The deep neural networks trained for this approach build the core of the virus host predicting tool VIDHOP (VIrus Deep learning HOst Prediction).},
    journal = {bioRxiv}
    }
  • [DOI] D. M. Morales-Prieto, E. Barth, J. M. Murrieta-Coxca, R. R. Favaro, R. N. Gutiérrez-Samudio, W. Chaiwangyen, S. Ospina-Prieto, B. Gruhn, E. Schleußner, M. Marz, and U. R. Markert, “Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines.,” Placenta, vol. 88, p. 20–27, 2019.
    [Bibtex]
    @Article{Morales-Prieto:19,
    author = {Morales-Prieto, Diana M and Barth, Emanuel and Murrieta-Coxca, Jose Martín and Favaro, Rodolfo R and Gutiérrez-Samudio, Ruby N and Chaiwangyen, Wittaya and Ospina-Prieto, Stephanie and Gruhn, Bernd and Schleußner, Ekkehard and Marz, Manja and Markert, Udo R},
    title = {Identification of {miRNAs} and associated pathways regulated by {L}eukemia {I}nhibitory {F}actor in trophoblastic cell lines.},
    journal = {Placenta},
    year = {2019},
    volume = {88},
    pages = {20--27},
    abstract = {Leukemia Inhibitory Factor (LIF) regulates behavior of trophoblast cells and their interaction with immune and endothelial cells. In vitro, trophoblast cell response to LIF may vary depending on the cell model. Reported differences in the miRNA profile of trophoblastic cells may be responsible for these observations. Therefore, miRNA expression was investigated in four trophoblastic cell lines under LIF stimulation followed by in silico analysis of altered miRNAs and their associated pathways. Low density TaqMan miRNA assays were used to quantify levels of 762 mature miRNAs under LIF stimulation in three choriocarcinoma-derived (JEG-3, ACH-3P and AC1-M59) and a trophoblast immortalized (HTR-8/SVneo) cell lines. Expression of selected miRNAs was confirmed in primary trophoblast cells and cell lines by qPCR. Targets and associated pathways of the differentially expressed miRNAs were inferred from the miRTarBase followed by a KEGG Pathway Enrichment Analysis. HTR-8/SVneo and JEG-3 cells were transfected with miR-21-mimics and expression of miR-21 targets was assessed by qPCR. A similar number of miRNAs changed in each tested cell line upon LIF stimulation, however, low coincidence of individual miRNA species was observed and occurred more often among choriocarcinoma-derived cells (complete data set at http://www.ncbi.nlm.nih.gov/geo/ under GEO accession number GSE130489). Altered miRNAs were categorized into pathways involved in human diseases, cellular processes and signal transduction. Six cascades were identified as significantly enriched, including JAK/STAT and TGFB-SMAD. Upregulation of miR-21-3p was validated in all cell lines and primary cells and STAT3 was confirmed as its target. Dissimilar miRNA responses may be involved in differences of LIF effects on trophoblastic cell lines.},
    doi = {10.1016/j.placenta.2019.09.005},
    keywords = {Cell lines; LIF; Placenta; Pregnancy; Trophoblast; miR-21; microRNA},
    pmid = {31586768},
    }
  • [DOI] E. Barth, A. Srivastava, M. Stojiljkovic, C. Frahm, H. Axer, O. W. Witte, and M. Marz, “Conserved aging-related signatures of senescence and inflammation in different tissues and species.,” Aging, vol. 11, 2019.
    [Bibtex]
    @Article{Barth:19,
    author = {Barth, Emanuel and Srivastava, Akash and Stojiljkovic, Milan and Frahm, Christiane and Axer, Hubertus and Witte, Otto W and Marz, Manja},
    title = {Conserved aging-related signatures of senescence and inflammation in different tissues and species.},
    journal = {Aging},
    year = {2019},
    volume = {11},
    abstract = {Increasing evidence indicates that chronic inflammation and senescence are the cause of many severe age-related diseases, with both biological processes highly upregulated during aging. However, until now, it has remained unknown whether specific inflammation- or senescence-related genes exist that are common between different species or tissues. These potential markers of aging could help to identify possible targets for therapeutic interventions of aging-associated afflictions and might also deepen our understanding of the principal mechanisms of aging. With the objective of identifying such signatures of aging and tissue-specific aging markers, we analyzed a multitude of cross-sectional RNA-Seq data from four evolutionarily distinct species (human, mouse and two fish) and four different tissues (blood, brain, liver and skin). In at least three different species and three different tissues, we identified several genes that displayed similar expression patterns that might serve as potential aging markers. Additionally, we show that genes involved in aging-related processes tend to be tighter controlled in long-lived than in average-lived individuals. These observations hint at a general genetic level that affect an individual's life span. Altogether, this descriptive study contributes to a better understanding of common aging signatures as well as tissue-specific aging patterns and supplies the basis for further investigative age-related studies.},
    doi = {10.18632/aging.102345},
    keywords = {RNA-Seq; aging; inflammaging; senescence; transcriptomics},
    pmid = {31606727},
    }

2018

  • [DOI] L. Graf, A. Dick, F. Sendker, E. Barth, M. Marz, O. Daumke, and G. Kochs, “Effects of allelic variations in the human myxovirus resistance protein A on its antiviral activity,” J Biol Chem, vol. 293, p. 3056–3072, 2018.
    [Bibtex]
    @Article{Graf:18,
    author = {Graf, Laura and Dick, Alexej and Sendker, Franziska and Barth, Emanuel and Marz, Manja and Daumke, Oliver and Kochs, Georg},
    title = {Effects of allelic variations in the human myxovirus resistance protein {A} on its antiviral activity},
    journal = {{J Biol Chem}},
    year = {2018},
    volume = {293},
    pages = {3056--3072},
    abstract = {Only a minority of patients infected with seasonal influenza A viruses exhibit a severe or fatal outcome of infection, but the reasons for this inter-individual variability in influenza susceptibility are unclear. To gain further insights into the molecular mechanisms underlying this variability, we investigated naturally occurring allelic variations of the myxovirus resistance 1 ( ) gene coding for the influenza restriction factor MxA. The interferon-induced dynamin-like GTPase consists of an N-terminal GTPase domain, a bundle signaling element, and a C-terminal stalk responsible for oligomerization and viral target recognition. We used online databases to search for variations in the gene. Deploying approaches, we found that non-synonymous variations in the GTPase domain cause the loss of antiviral and enzymatic activities. Furthermore, we showed that these amino acid substitutions disrupt the interface for GTPase domain dimerization required for the stimulation of GTP hydrolysis. Variations in the stalk were neutral or slightly enhanced or abolished MxA antiviral function. Remarkably, two other stalk variants altered MxA's antiviral specificity. Variations causing the loss of antiviral activity were found only in heterozygous carriers. Interestingly, the inactive stalk variants blocked the antiviral activity of WT MxA in a dominant-negative way, suggesting that heterozygotes are phenotypically MxA-negative. In contrast, the GTPase-deficient variants showed no dominant-negative effect, indicating that heterozygous carriers should remain unaffected. Our results demonstrate that naturally occurring mutations in the human gene can influence MxA function, which may explain individual variations in influenza virus susceptibility in the human population.},
    doi = {10.1074/jbc.M117.812784},
    issue = {9},
    keywords = {Mx proteins; allelic variations; antiviral response; dynamin; genetic polymorphism; influenza virus; innate immunity; interferon},
    pmid = {29330299},
    }
  • [DOI] K. Lamkiewicz, E. Barth, M. Marz, and B. Ibrahim, “Identification of potential microRNAs associated with Herpesvirus family based on bioinformatic analysis,” bioRxiv, p. 417782, 2018.
    [Bibtex]
    @Article{Lamkiewicz:18,
    author = {Kevin Lamkiewicz and Emanuel Barth and Manja Marz and Bashar Ibrahim},
    title = {Identification of potential {microRNAs} associated with {H}erpesvirus family based on bioinformatic analysis},
    journal = {{bioRxiv}},
    year = {2018},
    pages = {417782},
    doi = {10.1101/417782},
    publisher = {Cold Spring Harbor Laboratory},
    }
  • [DOI] D. M. Morales-Prieto, E. Barth, R. N. Gutièrrez-Samudio, W. Chaiwangyen, S. Ospina-Prieto, B. Gruhn, E. Schleußner, M. Marz, and U. R. Markert, “Identification of miRNAs and associated pathways regulated by Leukemia Inhibitory Factor in trophoblastic cell lines,” bioRxiv, p. 410381, 2018.
    [Bibtex]
    @Article{Morales-Prieto:18,
    author = {Diana M. Morales-Prieto and Emanuel Barth and Ruby N. Guti{\`{e}}rrez-Samudio and Wittaya Chaiwangyen and Stephanie Ospina-Prieto and Bernd Gruhn and Ekkehard Schleu{\ss}ner and Manja Marz and Udo R. Markert},
    title = {Identification of {miRNAs} and associated pathways regulated by {L}eukemia {I}nhibitory {F}actor in trophoblastic cell lines},
    journal = {{bioRxiv}},
    year = {2018},
    pages = {410381},
    doi = {10.1101/410381},
    publisher = {Cold Spring Harbor Laboratory},
    }

2017

  • [DOI] M. Baumgart, E. Barth, A. Savino, M. Groth, P. Koch, A. Petzold, I. Arisi, M. Platzer, M. Marz, and A. Cellerino, “A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri,” BMC Genomics, vol. 18, p. 693, 2017.
    [Bibtex]
    @Article{Baumgart:17,
    author = {Baumgart, Mario and Barth, Emanuel and Savino, Aurora and Groth, Marco and Koch, Philipp and Petzold, Andreas and Arisi, Ivan and Platzer, Matthias and Marz, Manja and Cellerino, Alessandro},
    title = {A mi{RNA} catalogue and nc{RNA} annotation of the short-living fish {N}othobranchius furzeri},
    journal = {{BMC Genomics}},
    year = {2017},
    volume = {18},
    pages = {693},
    abstract = {The short-lived fish Nothobranchius furzeri is the shortest-lived vertebrate that can be cultured in captivity and was recently established as a model organism for aging research. Small non-coding RNAs, especially miRNAs, are implicated in age dependent control of gene expression. Here, we present a comprehensive catalogue of miRNAs and several other non-coding RNA classes (ncRNAs) for Nothobranchius furzeri. Analyzing multiple small RNA-Seq libraries, we show most of these identified miRNAs are expressed in at least one of seven Nothobranchius species. Additionally, duplication and clustering of N. furzeri miRNAs was analyzed and compared to the four fish species Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Takifugu rubripes. A peculiar characteristic of N. furzeri, as compared to other teleosts, was a duplication of the miR-29 cluster. The completeness of the catalogue we provide is comparable to that of the zebrafish. This catalogue represents a basis to investigate the role of miRNAs in aging and development in this species.},
    doi = {10.1186/s12864-017-3951-8},
    issue = {1},
    keywords = {Aging, genetics; Animals; Cyprinodontiformes, genetics, physiology; Gene Duplication; Gene Library; Longevity, genetics; MicroRNAs, genetics; Molecular Sequence Annotation; RNA, Untranslated, genetics; Fish miRNA evolution; Nothobranchius furzeri; miRNome; ncRNA},
    pmid = {28874118},
    }
  • [DOI] K. Riege, M. Hölzer, T. E. Klassert, E. Barth, J. Bräuer, M. Collatz, F. Hufsky, N. Mostajo, M. Stock, B. Vogel, H. Slevogt, and M. Marz, “Massive effect on lncRNAs in human monocytes during fungal and bacterial infections and in response to vitamins A and D,” Sci Rep, vol. 7, p. 40598, 2017.
    [Bibtex]
    @Article{Riege:17,
    author = {Riege, Konstantin and H\"{o}lzer, Martin and Klassert, Tilman E and Barth, Emanuel and Br\"{a}uer, Julia and Collatz, Maximilian and Hufsky, Franziska and Mostajo, Nelly and Stock, Magdalena and Vogel, Bertram and Slevogt, Hortense and Marz, Manja},
    title = {Massive Effect on Lnc{RNA}s in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins {A} and {D}},
    journal = {{Sci Rep}},
    year = {2017},
    volume = {7},
    pages = {40598},
    abstract = {Mycoses induced by C.albicans or A.fumigatus can cause important host damage either by deficient or exaggerated immune response. Regulation of chemokine and cytokine signaling plays a crucial role for an adequate inflammation, which can be modulated by vitamins A and D. Non-coding RNAs (ncRNAs) as transcription factors or cis-acting antisense RNAs are known to be involved in gene regulation. However, the processes during fungal infections and treatment with vitamins in terms of therapeutic impact are unknown. We show that in monocytes both vitamins regulate ncRNAs involved in amino acid metabolism and immune system processes using comprehensive RNA-Seq analyses. Compared to protein-coding genes, fungi and bacteria induced an expression change in relatively few ncRNAs, but with massive fold changes of up to 4000. We defined the landscape of long-ncRNAs (lncRNAs) in response to pathogens and observed variation in the isoforms composition for several lncRNA following infection and vitamin treatment. Most of the involved antisense RNAs are regulated and positively correlated with their sense protein-coding genes. We investigated lncRNAs with stimulus specific immunomodulatory activity as potential marker genes: LINC00595, SBF2-AS1 (A.fumigatus) and RP11-588G21.2, RP11-394l13.1 (C.albicans) might be detectable in the early phase of infection and serve as therapeutic targets in the future.},
    doi = {10.1038/srep40598},
    keywords = {Bacterial Infections, genetics, microbiology; Gene Expression Regulation, drug effects; Humans; Monocytes, metabolism; Mycoses, genetics, microbiology; RNA, Antisense, genetics; RNA, Long Noncoding, chemistry, genetics; RNA, Messenger, genetics; RNA, Untranslated, genetics; Vitamin A, metabolism, pharmacology; Vitamin D, metabolism, pharmacology},
    pmid = {28094339},
    }
  • [DOI] M. Baumgart, E. Barth, A. Savino, M. Groth, P. Koch, A. Petzold, I. Arisi, M. Platzer, M. Marz, and A. Cellerino, “A miRNA catalogue and ncRNA annotation of the short-living fish Nothobranchius furzeri,” bioRxiv, p. 103697, 2017.
    [Bibtex]
    @Article{Baumgart:17a,
    author = {Mario Baumgart and Emanuel Barth and Aurora Savino and Marco Groth and Philipp Koch and Andreas Petzold and Ivan Arisi and Matthias Platzer and Manja Marz and Alessandro Cellerino},
    title = {A {miRNA} catalogue and {ncRNA} annotation of the short-living fish {N}othobranchius furzeri},
    journal = {{bioRxiv}},
    year = {2017},
    pages = {103697},
    doi = {10.1101/103697},
    publisher = {Cold Spring Harbor Laboratory},
    }

2016

  • [DOI] M. Hölzer, V. Krähling, F. Amman, E. Barth, S. H. Bernhart, V. A. O. Carmelo, M. Collatz, G. Doose, F. Eggenhofer, J. Ewald, J. Fallmann, L. M. Feldhahn, M. Fricke, J. Gebauer, A. J. Gruber, F. Hufsky, H. Indrischek, S. Kanton, J. Linde, N. Mostajo, R. Ochsenreiter, K. Riege, L. Rivarola-Duarte, A. H. Sahyoun, S. J. Saunders, S. E. Seemann, A. Tanzer, B. Vogel, S. Wehner, M. T. Wolfinger, R. Backofen, J. Gorodkin, I. Grosse, I. Hofacker, S. Hoffmann, C. Kaleta, P. F. Stadler, S. Becker, and M. Marz, “Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells,” Sci Rep, vol. 6, p. 34589, 2016.
    [Bibtex]
    @Article{Hoelzer:16,
    author = {H\"{o}lzer, Martin and Kr\"{a}hling, Verena and Amman, Fabian and Barth, Emanuel and Bernhart, Stephan H and Carmelo, Victor A O and Collatz, Maximilian and Doose, Gero and Eggenhofer, Florian and Ewald, Jan and Fallmann, J\"{o}rg and Feldhahn, Lasse M and Fricke, Markus and Gebauer, Juliane and Gruber, Andreas J and Hufsky, Franziska and Indrischek, Henrike and Kanton, Sabina and Linde, J\"{o}rg and Mostajo, Nelly and Ochsenreiter, Roman and Riege, Konstantin and Rivarola-Duarte, Lorena and Sahyoun, Abdullah H and Saunders, Sita J and Seemann, Stefan E and Tanzer, Andrea and Vogel, Bertram and Wehner, Stefanie and Wolfinger, Michael T and Backofen, Rolf and Gorodkin, Jan and Grosse, Ivo and Hofacker, Ivo and Hoffmann, Steve and Kaleta, Christoph and Stadler, Peter F and Becker, Stephan and Marz, Manja},
    title = {Differential transcriptional responses to {E}bola and {M}arburg virus infection in bat and human cells},
    journal = {{Sci Rep}},
    year = {2016},
    volume = {6},
    pages = {34589},
    abstract = {The unprecedented outbreak of Ebola in West Africa resulted in over 28,000 cases and 11,000 deaths, underlining the need for a better understanding of the biology of this highly pathogenic virus to develop specific counter strategies. Two filoviruses, the Ebola and Marburg viruses, result in a severe and often fatal infection in humans. However, bats are natural hosts and survive filovirus infections without obvious symptoms. The molecular basis of this striking difference in the response to filovirus infections is not well understood. We report a systematic overview of differentially expressed genes, activity motifs and pathways in human and bat cells infected with the Ebola and Marburg viruses, and we demonstrate that the replication of filoviruses is more rapid in human cells than in bat cells. We also found that the most strongly regulated genes upon filovirus infection are chemokine ligands and transcription factors. We observed a strong induction of the JAK/STAT pathway, of several genes encoding inhibitors of MAP kinases (DUSP genes) and of PPP1R15A, which is involved in ER stress-induced cell death. We used comparative transcriptomics to provide a data resource that can be used to identify cellular responses that might allow bats to survive filovirus infections.},
    doi = {10.1038/srep34589},
    keywords = {Animals; Cell Line, Tumor; Chiroptera; Ebolavirus, metabolism; Gene Expression Regulation; Hemorrhagic Fever, Ebola, metabolism; Humans; Marburg Virus Disease, metabolism; Marburgvirus, metabolism; Signal Transduction; Transcription, Genetic},
    pmid = {27713552},
    }
  • [DOI] E. Barth, R. Hübler, A. Baniahmad, and M. Marz, “The evolution of COP9 signalosome in unicellular and multicellular organisms,” Genome Biol Evol, vol. 8, p. 1279–1289, 2016.
    [Bibtex]
    @Article{Barth:16,
    author = {Barth, Emanuel and H\"{u}bler, Ron and Baniahmad, Aria and Marz, Manja},
    title = {The Evolution of {COP9} Signalosome in Unicellular and Multicellular Organisms},
    journal = {{Genome Biol Evol}},
    year = {2016},
    volume = {8},
    pages = {1279--1289},
    abstract = {The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible "mini-complexes" or COP9 complexes with independent subunits containing potentially novel and not yet identified functions. },
    doi = {10.1093/gbe/evw073},
    issue = {4},
    keywords = {Alternative Splicing; Animals; COP9 Signalosome Complex; Evolution, Molecular; Exons; Humans; Introns; Multiprotein Complexes, genetics; Peptide Hydrolases, genetics; Phylogeny; Protein Subunits, genetics; animal kingdom; bacteria; comparative informatics for plants; fungi; genomic structure; signalosome subunits CSN},
    pmid = {27044515},
    }

2015

  • L. Graf, F. Sendker, A. Dick, E. Barth, M. Marz, O. Daumke, and G. Kochs, “ID: 187: allelic variations in the interferon-induced human MxA protein affect its antiviral activity against influenza A virus,” Cytokine, vol. 76, iss. 1, p. 98, 2015.
    [Bibtex]
    @Article{Graf:15,
    author = {Graf, Laura and Sendker, Franziska and Dick, Alexej and Barth, Emanuel and Marz, Manja and Daumke, Oliver and Kochs, Georg},
    title = {{ID}: 187: Allelic variations in the interferon-induced human {MxA} protein affect its antiviral activity against influenza {A} virus},
    journal = {Cytokine},
    year = {2015},
    volume = {76},
    number = {1},
    pages = {98},
    publisher = {Elsevier},
    }
Publications in Previous Groups
  • [DOI] M. Gimpel, H. Preis, E. Barth, L. Gramzow, and S. Brantl, “SR1–a small RNA with two remarkably conserved functions,” Nucleic Acids Res, vol. 40, p. 11659–11672, 2012.
    [Bibtex]
    @Article{Gimpel:12,
    author = {Gimpel, Matthias and Preis, Heike and Barth, Emanuel and Gramzow, Lydia and Brantl, Sabine},
    title = {{SR1}--a small {RNA} with two remarkably conserved functions},
    journal = {{Nucleic Acids Res}},
    year = {2012},
    volume = {40},
    pages = {11659--11672},
    abstract = {SR1 is a dual-function sRNA that acts as a base-pairing regulatory RNA on the ahrC mRNA and as a peptide-encoding mRNA on the gapA operon. The SR1-encoded peptide SR1P binds GapA thereby stabilizing gapA mRNA. Under glycolytic conditions, SR1 transcription is repressed by CcpN and CcpA. A computer-based search identified 23 SR1 homologues in Bacillus, Geobacillus, Anoxybacillus and Brevibacillus species. All homologues share a high structural identity with Bacillus subtilis SR1, and the encoded SR1P peptides are highly similar. In the Bacillus cereus group, the sr1p region is present in triplicate or duplicate resulting in longer SR1 species. In all cases, sr1 expression is under control of CcpN, and transcriptional lacZ fusions of nine examined SR1 homologues were sensitive to glucose. Two homologues showed an additional glucose-independent repression by CcpN and an unknown factor. A total of 10 out of 11 tested SR1P homologues complemented a B. subtilis Δsr1 strain in their ability to stabilize gapA mRNA, but only five of them bound GapA tightly. In vitro binding assays with six SR1/ahrC pairs suggest that-despite divergent primary sequences-the base-pairing function is also preserved. In summary, SR1 is an sRNA with two functions that have been conserved over ≈1 billion years.},
    doi = {10.1093/nar/gks895},
    issue = {22},
    keywords = {Bacillus subtilis, genetics; Bacterial Proteins, chemistry, genetics, metabolism; Base Sequence; Carrier Proteins, chemistry, metabolism; Cysteine, physiology; Gene Expression Regulation, Bacterial; Molecular Sequence Data; Nucleic Acid Conformation; Peptides, chemistry; Phylogeny; Promoter Regions, Genetic; RNA Stability; RNA, Bacterial, chemistry, genetics, metabolism; RNA, Messenger, chemistry, metabolism; RNA, Small Untranslated, chemistry, genetics, metabolism; Repressor Proteins, genetics, metabolism; Sequence Homology, Amino Acid; Sequence Homology, Nucleic Acid; Synteny; Trans-Activators, genetics},
    pmid = {23034808},
    }
Conferences
  • 10/2019 17th Herbstseminar der Bioinformatik, Doubice
  • 09/2019 German Conference on Bioinformatics 2019, Heidelberg
  • 02/2018 33th TBI Winterseminar, Bled
  • 10/2017 15th Herbstseminar der Bioinformatik, Doubice
  • 04/2017 1st HACKEN Workshop, Jena
  • 03/2017 1st EVBC Meeting, Jena
  • 02/2017 32th TBI Winterseminar, Bled
  • 05/2017 Central German Meeting on Bioinformatics 2017, Leipzig
  • 10/2016 14th Herbstseminar der Bioinformatik, Doubice
  • 02/2016 31th TBI Winterseminar, Bled
  • 01/2016 ZAJ Symposium, Jena
  • 10/2015 13th Herbstseminar der Bioinformatik, Doubice
  • 08/2015 Central German Meeting on Bioinformatics 2015, Halle
  • 02/2015 30th TBI Winterseminar, Bled
  • 11/2014 ”Fight against Ebola in silico“ Hackathon, Jena
  • 10/2014 12th Herbstseminar der Bioinformatik, Doubice
CV
  • since 02/2019 Post-Doc and Scientific Coordinator at RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena
  • 01/2015 – 01/2019  PhD Student at RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena
    PhD thesis: “Insights into the regulation of aging”
  • 10/2012 – 11/2014 Master of Science in Bioinformatics at Friedrich Schiller University, Jena
    Master thesis: “Comparison of de novo transcriptome assemblers”
  • 10/2009 – 09/2012 Bachelor of Science in Bioinformatics at Friedrich Schiller University, Jena
    Bachelor thesis: “Homology search of small non-coding RNAs in Bacillus subtilis“
Funding