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Implications of chimaeric non-co-linear transcripts

Nature volume 461, pages 206–211 (2009)Cite this article

Abstract

Deep sequencing of 'transcriptomes' — the collection of all RNA transcripts produced at a given time — from worms to humans reveals that some transcripts are composed of sequence segments that are not co-linear, with pieces of sequence coming from distant regions of DNA, even different chromosomes. Some of these 'chimaeric' transcripts are formed by genetic rearrangements, but others arise during post-transcriptional events. The 'trans-splicing' process in lower eukaryotes is well understood, but events in higher eukaryotes are not. The existence of such chimaeric RNAs has far-reaching implications for the potential information content of genomes and the way it is arranged.

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Figure 1: Models of possible organization of the information in DNA and its transfer to RNA.
Figure 2: Characterization of a chimaeric transcript.
Figure 3: Model specialized transcription factory for transcription and the formation of chimaeric RNAs.
Figure 4: Co-linear and non-co-linear combinations of modules of information.

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Acknowledgements

Work in my laboratory is supported by the National Human Genome Research Institute (grants U54 HG004557 and U01 HG004271). I thank P. Kapranov for discussions and long-term collaboration, H. Sussman for helpful discussions and editing of the manuscript, and A. Dobin for help deriving the computational expressions to determine the co-linear and non-co-linear permutations, and for the plot shown in Fig. 4c.

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  1. Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, 11724, New York, USA

    Thomas R. Gingeras

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Competing interests

T.R.G. was an employee of Affymetrix at the same time as some of the studies cited in this Review used its microarray technology.

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Correspondence should be addressed to T.R.G. (gingeras@cshl.edu).

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Gingeras, T. Implications of chimaeric non-co-linear transcripts. Nature 461, 206–211 (2009). https://doi.org/10.1038/nature08452

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