Tentative mapping of transcription-induced interchromosomal interaction using chimeric EST and mRNA data

Abstract

Recent studies on chromosome conformation show that chromosomes colocalize in the nucleus, bringing together active genes in transcription factories. This spatial proximity of actively transcribing genes could provide a means for RNA interaction at the transcript level. We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal interactions. We suggest that chimeric transcripts may be the result of close encounters of active genes, either as functional products or "noise" in the transcription process, and that they could be used as probes for chromosome interactions. We have found a total of 5,614 chimeric ESTs and 587 chimeric mRNAs that meet our selection criteria. Due to their higher quality, the mRNA findings are of particular interest and we hope that they may serve as food for thought for specialists in diverse areas of molecular biology.

Figure 1. Chimeric mRNA revealing chromsome interaction.

Schematic representation of regions of two chromosomes, represented by red and blue thick lines, with accompanying mRNA transcripts in corresponding colors, represented by wavy lines, transcription factories and RNA polymerases. When chromosomes are not in proximity, mRNAs are less likely to interact (A), whereas proximal chromosomes generate a chimeric mRNA, revealing interchromosomal interaction (B).

Figure 2. Gene interaction plot.

Mosaic plot of gene interactions for 2651 EST chimeras where the direction of the participating partners is the same. The size of each square is proportional to the number of times a fusion event is observed between chromosomes i and j, for i,j∈1,2,…,22,X,Y. The barplots represent known gene densities on each chromosome, according to Ensembl gene counts for all chromosomes.

Figure 3. Chimera distributions by EST library.

Distribution of chimeric observations grouped by dbEST library id. Only libraries with more than 10 observations are shown.

Figure 4. Boxplots of fusion location.

Distribution of fusion location for 5614 EST and 587 mRNA chimeras. The fusion location is represented as a fraction X of sequence length. Fractions Y<0.5 have been transformed to X = 1−Y.