Transcript mapping based on dRNA-seq data

BMC Bioinformatics

Björn Voß²  Matthias Kopf²  Thorsten Bischler¹ 

[1]Julius-Maximilians-University Würzburg, Institute for Molecular Infection Biology, Josef-Schneider-Str. 2/D15, 97080 Würzburg, Germany

[2]Genetics & Experimental Bioinformatics, Institute for Biology 3, Faculty of Biology, Albert-Ludwigs-University Freiburg, Schänzlestr. 1, 79104 Freiburg, Germany

关键词: Dynamic programming;    Transcriptional start site;    Transcriptome;    Transcriptional unit;    Segmentation;    Differential RNA-seq;    RNA-seq;   

Others  :  818632
DOI  :  10.1186/1471-2105-15-122

 received in 2013-10-25, accepted in 2014-04-24,  发布年份 2014

【 摘 要 】

Background

RNA-seq and its variant differential RNA-seq (dRNA-seq) are today routine methods for transcriptome analysis in bacteria. While expression profiling and transcriptional start site prediction are standard tasks today, the problem of identifying transcriptional units in a genome-wide fashion is still not solved for prokaryotic systems.

Results

We present RNASEG, an algorithm for the prediction of transcriptional units based on dRNA-seq data. A key feature of the algorithm is that, based on the data, it distinguishes between transcribed and un-transcribed genomic segments. Furthermore, the program provides many different predictions in a single run, which can be used to infer the significance of transcriptional units in a consensus procedure. We show the performance of our method based on a well-studied dRNA-seq data set for Helicobacter pylori.

Conclusions

With our algorithm it is possible to identify operons and 5’- and 3’-UTRs in an automated fashion. This alleviates the need for labour intensive manual inspection and enables large-scale studies in the area of comparative transcriptomics.

【 授权许可】

   
2014 Bischler et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 1.

Figure 2.

【 参考文献 】

• [1]Wang Z, Gerstein M, Snyder M: RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 2009, 10:57-63.
• [2]Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Sittka SFA, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J: The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010, 464(7286):250-255.
• [3]Huber W, Toedling J, Steinmetz LM: Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 2006, 22(16):1963-1970.
• [4]Nicolas P, Leduc A, Robin S, Rasmussen S, Jarmer H, Bessières P: Transcriptional landscape estimation from tiling array data using a model of signal shift and drift. Bioinformatics 2009, 25(18):2341-2347.
• [5]Roberts A, Pimentel H, Trapnell C, Pachter L: Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics 2011, 27(17):2325-2329.
• [6]Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C, Rinn JL, Lander ES, Regev A: Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol 2010, 28(5):503-510.
• [7]Birol I, Jackman SD, Nielsen CB, Qian JQ, Varhol R, Stazyk G, Morin RD, Zhao Y, Hirst M, Schein JE, Horsman DE, Connors JM, Gascoyne RD, Marra MA, Jones SJM: De novo transcriptome assembly with ABySS. Bioinformatics 2009, 25(21):2872-2877.
• [8]Li R, Yu C, Li Y, Lam T, Yiu S, Kristiansen K, Wang J: SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 2009, 25(15):1966-1967.
• [9]Hoffmann S, Otto C, Kurtz S, Sharma CM, Khaitovich P, Vogel J, Stadler PF, Hackermüller J: Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol 2009, 5(9):e1000502.
• [10]Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream M, Barrell B: Artemis: sequence visualization and annotation. Bioinformatics 2000, 16:944-945.
• [11]Mao F, Dam P, Chou J, Olman V, Xu Y: DOOR: a database for prokaryotic operons. Nucl Acids Res 2009, 37:D459-D463.
• [12]Li W: RNASeqReadSimulator. 2013. [ https://github.com/davidliwei/RNASeqReadSimulator webcite]
• [13]Mitschke J, Georg J, Scholz I, Sharma CM, Dienst D, Bantscheff J, Voß B, Steglich C, Wilde A, Vogel J, Hess WR: An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci U S A 2011, 108(5):2124-2129.
• [14]Landick R: RNA polymerase slides home: pause and termination site recognition. Cell 1997, 88(6):741-744.
• [15]Lesnik EA, Sampath R, Levene HB, Henderson TJ, McNeil JA, Ecker DJ: Prediction of rho-independent transcriptional terminators in Escherichia coli. Nucleic Acids Res 2001, 29(17):3583-3594.
• [16]Vijayan V, Jain IH, O’Shea EK: A high resolution map of a cyanobacterial transcriptome. Genome Biol 2011, 12(5):R47. BioMed Central Full Text
• [17]Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L: Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 2010, 28(5):511-515.
• [18]Trapnell C: Can i use cufflinks with RNA-Seq data from bacteria? 2014. [ http://cufflinks.cbcb.umd.edu/faq.html#bact webcite]
• [19]Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, Hoffmann S, Vogel J, Stadler PF, Bonas U: Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 2012, 40(5):2020-2031.