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ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A - Nucleic Acids Res. (2014)

Bottom Line: Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes.The new database version collects more than 29,000 chimeric transcripts and indicates the expression and tissue specificity for 333 entries confirmed by RNA-seq reads mapping the chimeric junction sites.As a result, the ChiTaRS 2.1 collection of chimeras from eight organisms and human cancer breakpoints extends our understanding of the evolution of chimeric transcripts in eukaryotes as well as their functional role in carcinogenic processes.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

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The most frequent junction motifs of SAS chimeras are incorporate palindromic sequences. (A) Two palindromic motifs found for human SAS chimeras. (B) Motifs of the mouse SAS chimeras. (C) Motifs of the fly SAS chimeras.
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Figure 2: The most frequent junction motifs of SAS chimeras are incorporate palindromic sequences. (A) Two palindromic motifs found for human SAS chimeras. (B) Motifs of the mouse SAS chimeras. (C) Motifs of the fly SAS chimeras.

Mentions: We identified a new class of fusion produced by the conjoining of exons from two different strands of the same open reading frame. We called this new type of chimera ‘SAS’ chimeras. These chimeras produce fusion transcripts incorporating both coding and non-coding exons of the same gene and are typically found in different types of cancers but also in normal cells. Novel SAS chimeras that have been found in any of the eight organisms in ChiTaRS-2.1 can be easily accessed by clicking a check-box (‘Sense-ANTIsense transcripts’) on the ‘Full Collection’ page. More than 6000 of chimeric RNA transcripts in humans that incorporate sense and antisense exons of the same open reading frame have been incorporated into ChiTaRS-2.1 (Table 2). Interestingly, junction sites of SAS chimeras have been found to incorporate palindromic sequences, and might be produced by exon–exon slippage during the transcription process (Figure 2). Thus, the palindromic motifs have been found in more than 60% of junction sites for human (Figure 2A), mouse (Figure 2B) and fly (Figure 2C) chimeras.


ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts.

Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A - Nucleic Acids Res. (2014)

The most frequent junction motifs of SAS chimeras are incorporate palindromic sequences. (A) Two palindromic motifs found for human SAS chimeras. (B) Motifs of the mouse SAS chimeras. (C) Motifs of the fly SAS chimeras.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4383979&req=5

Figure 2: The most frequent junction motifs of SAS chimeras are incorporate palindromic sequences. (A) Two palindromic motifs found for human SAS chimeras. (B) Motifs of the mouse SAS chimeras. (C) Motifs of the fly SAS chimeras.
Mentions: We identified a new class of fusion produced by the conjoining of exons from two different strands of the same open reading frame. We called this new type of chimera ‘SAS’ chimeras. These chimeras produce fusion transcripts incorporating both coding and non-coding exons of the same gene and are typically found in different types of cancers but also in normal cells. Novel SAS chimeras that have been found in any of the eight organisms in ChiTaRS-2.1 can be easily accessed by clicking a check-box (‘Sense-ANTIsense transcripts’) on the ‘Full Collection’ page. More than 6000 of chimeric RNA transcripts in humans that incorporate sense and antisense exons of the same open reading frame have been incorporated into ChiTaRS-2.1 (Table 2). Interestingly, junction sites of SAS chimeras have been found to incorporate palindromic sequences, and might be produced by exon–exon slippage during the transcription process (Figure 2). Thus, the palindromic motifs have been found in more than 60% of junction sites for human (Figure 2A), mouse (Figure 2B) and fly (Figure 2C) chimeras.

Bottom Line: Chimeric RNAs that comprise two or more different transcripts have been identified in many cancers and among the Expressed Sequence Tags (ESTs) isolated from different organisms; they might represent functional proteins and produce different disease phenotypes.The new database version collects more than 29,000 chimeric transcripts and indicates the expression and tissue specificity for 333 entries confirmed by RNA-seq reads mapping the chimeric junction sites.As a result, the ChiTaRS 2.1 collection of chimeras from eight organisms and human cancer breakpoints extends our understanding of the evolution of chimeric transcripts in eukaryotes as well as their functional role in carcinogenic processes.

View Article: PubMed Central - PubMed

Affiliation: Structural Biology and BioComputing Program, Spanish National Cancer Research Centre (CNIO), Madrid 28029, Spain.

Show MeSH
Related in: MedlinePlus