Skip Navigation

This Article
Right arrow Full Text Freely available
Right arrow Print PDF (307K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Romani, A.
Right arrow Articles by Alberti, S.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Romani, A.
Right arrow Articles by Alberti, S.
Related Collections
Right arrow RNA characterisation and manipulation
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Nucleic Acids Research, 2003, Vol. 31, No. 4 e17
© 2003 Oxford University Press

Detection and analysis of spliced chimeric mRNAs in sequence databanks

Antonello Romani, Emanuela Guerra1, Marco Trerotola1 and Saverio Alberti*,1

Department of Experimental Medicine, Section of Molecular Pathology and Immunology, University of Parma, Italy and 1 Laboratory of Experimental Oncology, Department of Cell Biology and Oncology, Institute Mario Negri - Consorzio Mario Negri Sud, 66030 Santa Maria Imbaro (Chieti), Italy

*To whom correspondence should be addressed. Tel: +39 0872 570 293; Fax: +39 0872 570 412; Email: alberti{at}negrisud.it

We have developed a databank screening procedure, the In Silico Trans-splicing Retrieval System (ISTReS), to identify heterologous, spliced mRNAs with potential origin from chromosomal translocations, mRNA trans-splicing and multi-locus transcription. A parsing algorithm to screen cDNA versus genome Blast outputs was implemented. Key filtering criteria were Blast scores of >=300, match lengths of >=95% of the query sequences, junction of the two partners at exon–exon borders and concordant ‘sense/sense’ reading orientation. ISTReS was validated by the successful identification of bona fide chromosomal translocation-derived fusion transcripts in the HGI and RefSeq databanks. The performance of ISTReS was verified against recently identified chimeric antisense transcripts, where it revealed essentially no independent proof of antisense transcription and absence of exon–exon borders at the chimeric join, consistent with an artefactual origin. Analysis of the UNIGENE database revealed 21 742 chimeric sequences overall that correspond to ~1% of the database transcripts. Novel FOP-Rho GAP and methionyl tRNA synthetase-advillin chimeric mRNAs with the canonical features of heterologous-genes spliced-transcripts were identified among 246 chimeras from the RefSeq databank. This suggests a frequency of canonically-spliced chimeras of ~1% of all the hybrid sequences in current databanks. These findings demonstrate the efficiency of ISTReS and the overall feasibility of sequence/structure-based strategies to search for chimeric mRNAs candidate to derive from the splicing of heterologous transcripts.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
P. Kim, S. Yoon, N. Kim, S. Lee, M. Ko, H. Lee, H. Kang, J. Kim, and S. Lee
ChimerDB 2.0--a knowledgebase for fusion genes updated
Nucleic Acids Res., November 11, 2009; (2009) gkp982v1.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
T. T. Torres, M. Dolezal, C. Schlotterer, and B. Ottenwalder
Expression profiling of Drosophila mitochondrial genes via deep mRNA sequencing
Nucleic Acids Res., October 20, 2009; (2009) gkp856v1.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
X. Shao, V. Shepelev, and A. Fedorov
Bioinformatic analysis of exon repetition, exon scrambling and trans-splicing in humans
Bioinformatics, March 15, 2006; 22(6): 692 - 698.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
N. Kim, P. Kim, S. Nam, S. Shin, and S. Lee
ChimerDB--a knowledgebase for fusion sequences
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D21 - D24.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
Y. Hahn, T. K. Bera, K. Gehlhaus, I. R. Kirsch, I. H. Pastan, and B. Lee
Finding fusion genes resulting from chromosome rearrangement by analyzing the expressed sequence databases
PNAS, September 7, 2004; 101(36): 13257 - 13261.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
A. P. GMYL, S. A. KORSHENKO, E. V. BELOUSOV, E. V. KHITRINA, and V. I. AGOL
Nonreplicative homologous RNA recombination: Promiscuous joining of RNA pieces?
RNA, October 1, 2003; 9(10): 1221 - 1231.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.