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

Unneberg P, Claverie JM - PLoS ONE (2007)

Bottom Line: We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal 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.

View Article: PubMed Central - PubMed

Affiliation: Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique (CNRS) UPR-2589, Institut de Biologie Structurale et Microbiologie, Marseille, France. per.unneberg@igs.cnrs-mrs.fr

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.

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Related in: MedlinePlus

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.
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pone-0000254-g002: 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.

Mentions: The 4050 remaining cases (72.3%) represent potential gene–gene interactions. The orientation could be determined for both partners in 3621 chimeras, out of which 2651 consisted of partners that were oriented in the same direction. Figure 2 shows the frequency of chromosome interactions for this subset, where the size of each square is proportional to the number of times a given chromosome–chromosome pair is observed. Plotted above and to the right of the cell frequencies are the gene frequencies for each chromosome. The gene frequencies tell us what to expect if the associations between chromosomes are non-preferential. For instance, since the number of genes is highest on chromosome 1, followed by chromosome 2, one would expect the highest number of observed interactions between these chromosomes; this indeed is the case. The correlation between the observed values and expected values as calculated with gene frequencies is 0.72, confirming the non-preferential nature of the observed associations.


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

Unneberg P, Claverie JM - PLoS ONE (2007)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1804257&req=5

pone-0000254-g002: 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.
Mentions: The 4050 remaining cases (72.3%) represent potential gene–gene interactions. The orientation could be determined for both partners in 3621 chimeras, out of which 2651 consisted of partners that were oriented in the same direction. Figure 2 shows the frequency of chromosome interactions for this subset, where the size of each square is proportional to the number of times a given chromosome–chromosome pair is observed. Plotted above and to the right of the cell frequencies are the gene frequencies for each chromosome. The gene frequencies tell us what to expect if the associations between chromosomes are non-preferential. For instance, since the number of genes is highest on chromosome 1, followed by chromosome 2, one would expect the highest number of observed interactions between these chromosomes; this indeed is the case. The correlation between the observed values and expected values as calculated with gene frequencies is 0.72, confirming the non-preferential nature of the observed associations.

Bottom Line: We have screened public databases for chimeric EST and mRNA sequences with the intent of mapping transcription-induced interchromosomal 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.

View Article: PubMed Central - PubMed

Affiliation: Structural and Genomic Information Laboratory, Centre National de la Recherche Scientifique (CNRS) UPR-2589, Institut de Biologie Structurale et Microbiologie, Marseille, France. per.unneberg@igs.cnrs-mrs.fr

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.

Show MeSH
Related in: MedlinePlus