Implications of chimaeric non-co-linear transcripts

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.

Figure 1. Models of possible organization of information contained in DNA and its transfer to RNA

(A) Collinear alignments can be categorized in two forms. Directly collinear in which information (sequence) is transferred in an un-interrupted fashion to RNA as is seen in most bacterial mRNAs and modular alignments in which the information is transferred to RNA in a collinear but interrupted (by introns) fashion. (B) Non-collinear alignments can be categorized in 4 forms. The production of precursor RNAs is shown only for Form 1 but is made in all forms. Form 1 represents the formation of chimeric RNAs from two different loci in a genome at two different genic regions. The precursor RNAs are processed (e.g. by trans-splicing or RNA recombination ) into the chimeric RNA. Form 2 exemplifies the formation of a chimeric RNA from the same gene by rearrangement of exons (see Figure 2 for example). Form 3 illustrates the formation of a chimeric RNA which is made from two precursor RNAs that are transcribed from opposite strands. Form 4 describes the formation of a chimeric RNA that is made from transcripts derived from two alleles of the same gene one of which contains a single nucleotide polymorphism.

Figure 2. Characterization of a chimeric transcript

The example shows a RT-PCR product corresponding to a chimeric transcript derived from SEC14L2 gene where a spliced region corresponding to exons 4, 5 and 6 is inserted downstream of exon 8. A product of 3′ RACE/array reaction is shown, with a primer positioned in exon 6; the nonsequential RT-PCR product is shown aligned to the genome. Note the RACE/array signal upstream from the RACE primer corresponding to exons 4 and 5. A portion of exon 3, which consisted of only 7 bp, is too small to hybridize to the array.

Figure 3. Model of specialized transcription factory in which transcription and formation of chimeric RNAs are carried out

Based on the observation that there are fewer transcription factories in nuclei than the number of transcribed loci and the existence of specialized transcription factories , this model hypothesizes that genes A and B encoded in different regions of the genome are collected in a transcription factory and transcribed into primary transcripts by multiple polymerase II transcriptional complexes (white oval). The primary transcripts are then processed to form mature spliced and chimeric RNAs. In this model most of the primary RNAs are involved in cis-splicing and transported to the cytosol for translation. Consistent with steady state estimates of chimeric RNAs levels, a smaller proportion of the primary RNAs are used to create chimeric RNAs. The model can envision a single or multiple isoforms of chimeric RNAs being made from combinations of primary RNA having been transcribed within the same transcription factory. The occurrences of translocation events involving genomic regions that are transcribed to produce chimeric RNAs raises the interesting possibility that such rearrangements may also be facilitated at these specialized factories.

Figure 4. Collinear and non-collinear combinations of information modules of information

(A) Six possible two-exon combinations derived from a four exon genic region are shown. (B) Five of the possible 350 non-collinear, permuted three-exon transcripts that can be made from two 2 and 3 exon containing transcripts are shown. (C) A semi-log plot comparing the number of transcript isoforms that can be created using 1 to 10 exons considering a non-permuted collinear organization of information (blue) or a permuted non-collinear organization of information (black). The dependence of the total number of mature transcripts on the number of possible exons for the non-collinear permuted case diverges exponentially from the collinear case.