Automated Genomewide Annotation of Non-coding RNAs

• Applicant: Professorin Dr. Manja Marz
• Subject Area: Bioinformatics and Theoretical Biology
• Term: from 2010 to 2015
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 184034557

• Final Report Year: 2017

Final Report Abstract

Within the last years more than 1,200 genomes from all domains of life have been sequenced and analyzed to obtain essential insights into the evolution of life and etiology and therapy of diseases. Non-(protein-)coding RNAs (ncRNAs) play a central and regulatory role, which has been broadly recognized since the human ENCODE project as well as several other genome projects. In contrast to protein-coding parts of the DNA, the annotation of ncRNAs is an outstanding challenge owing to the structural selection pressure of its transcripts. During this project an automized genomewide annotation program of ncRNAs has been developed. For each ncRNA class a module with specific biological properties was constructed, which is, on the one hand, executable within an overall program without any a priori knowledge and is, on the other hand, modifiable afterwards for special requirements. The different ncRNA classes, and therewith associated identification problems, as well as the methodological approaches have been described in detail. The very few existing ncRNA identification programs have been integrated to solve the identification problem. A webserver is still planned to facilitate the handling of the program for non-computer scientists. Additionally, we added a plugin for RNA-Seq data and plan to improve the tool also for viral sequences.

Publications

• Animal snoRNAs and scaRNAs with exceptional structures. RNA Biol. 2011 Nov-Dec;8(6):938-46
  Marz M, Gruber AR, Höner Zu Siederdissen C, Amman F, Badelt S, Bartschat S, Bernhart SH, Beyer W, Kehr S, Lorenz R, Tanzer A, Yusuf D, Tafer H, Hofacker IL, Stadler PF
  
• Identification of purple sea urchin telomerase RNA using a next-generation sequencing based approach. RNA. 2013 Jun; 19(6): 852860
  Li Y, Podlevsky JD, Marz M, Qi X, Hoffmann S, Stadler PF, Chen JJL
  
• pRNA: NoRC-associated RNA of rRNA operons. RNA Biol. 2014 Jan 1; 11(1): 39
  Wehner S, Dörrich AK, Ciba P, Wilde A, Marz M
  
• Challenges in RNA virus bioinformatics. Bioinformatics. 2014 Jul 1;30(13):1793-9
  Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf o M, Rattei T, Stadler PF, Töpfer A
  
• Detection of very long antisense transcripts by whole transcriptome RNA-Seq analysis of Listeria monocytogenes by semiconductor sequencing technology. PLoS One. 2014 Oct 6;9(10):e108639
  Wehner S, Mannala GK, Qing X, Madhugiri R, Chakraborty T, Mraheil MA, Hain T, Marz M
  
• Dissemination of 6S RNA among bacteria. RNA Biol. 2014;11(11):1467-78
  Wehner S, Damm K, Hartmann RK, Marz M
  
• Evidence for the existence of two new members of the family Chlamydiaceae and proposal of Chlamydia avium sp. nov. and Chlamydia gallinacea sp. nov. Syst Appl Microbiol. 2014 Mar;37(2):79-88
  Sachse K, Laroucau K, Riege K, Wehner S, Dilcher M, Creasy HH, Weidmann M, Myers G, Vorimore F, Vicari N, Magnino S, Liebler-Tenorio E, Ruettger A, Bavoil PM, Hufert FT, Rossell-Mra R, Marz M
  
• Gene expansion shapes genome architecture in the human pathogen Lichtheimia corymbifera: an evolutionary genomics analysis in the ancient terrestrial mucorales (Mucoromycotina). PLoS Genet. 2014 Aug 14;10(8):e1004496. Erratum in: PLoS Genet. 2016 Dec 5;12 (12 ):e1006491
  Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Samo meth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldn T, Böcker S, Voigt K
  
• Genomewide comparison and novel ncRNAs of Aquificales. BMC Genomics. 2014 Jun 25;15:522
  Lechner M, Nickel AI, Wehner S, Riege K, Wieseke N, Beckmann BM, Hartmann RK, Marz M
  
• Vitamin supplementation by gut symbionts ensures metabolic homeostasis in an insect host. Proc Biol Sci. 2014 Dec 7;281(1796):20141838
  Salem H, Bauer E, Strauss AS, Vogel H, Marz M, Kaltenpoth M
  
• Comprehensive insights in the Mycobacterium avium subsp. paratuberculosis genome using new WGS data of sheep strain JIII-386 from Germany. Genome Biol Evol. 2015 Sep 17 [Epub ahead of print]
  Möbius P, Hölzer M, Felder M, Nordsiek G, Groth M, Köhler H, Reichwald K, Platzer M, Marz M
  
• Conserved RNA secondary structures and long-range interactions in hepatitis C viruses. RNA. 2015 Jul; 21(7): 12191232
  Fricke M, Dünnes N, Zayas M, Bartenschlager R, Niepmann M, Marz M
  
• Defining the transcriptomic landscape of Candida glabrata by RNA-Seq. Nucleic Acids Res. 2015 Feb 18; 43(3): 13921406
  Linde J, Duggan S, Weber M, Horn F, Sieber F, Hellwig D, Riege K, Marz M, Martin R, Guthke R, Kurzai O
  
• Towards a comprehensive picture of alloacceptor tRNA remolding in metazoan mitochondrial genomes. Nucleic Acids Res. 2015 Sep 18;43(16):8044-56
  Sahyoun AH, Hölzer M, Jühling F, Höner zu Siederdissen C, Al-Arab M, Tout K, Marz M, Middendorf M, Stadler PF, Bernt M
  
• Massive Effect on LncRNAs in Human Monocytes During Fungal and Bacterial Infections and in Response to Vitamins A and D. Sci Rep. 2017 Jan 17;7:40598
  Riege K, Hölzer M, Klassert TE, Barth E, Bruer J, Collatz M, Hufsky F, Mostajo N, Stock M, Vogel B, Slevogt H, Marz M
  
• microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3’ untranslated region: function in replication and influence of RNA secondary structure. Cell Mol Life Sci. 2017 Feb;74(4):747-760
  Gerresheim GK, Dünnes N, Nieder-Röhrmann A, Shalamova LA, Fricke M, Hofacker I, Höner Zu Siederdissen C, Marz M, Niepmann M