Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression Export

@article{citeulike:3508166, abstract = {Eukaryotic genomes are mostly composed of noncoding DNA whose role is still poorly understood. Studies in several organisms have shown correlations between the length of the intergenic and genic sequences of a gene and the expression of its corresponding mRNA transcript. Some studies have found a positive relationship between intergenic sequence length and expression diversity between tissues, and concluded that genes under greater regulatory control require more regulatory information in their intergenic sequences. Other reports found a negative relationship between expression level and gene length and the interpretation was that there is selection pressure for highly expressed genes to remain small. However, a correlation between gene sequence length and expression diversity, opposite to that observed for intergenic sequences, has also been reported, and to date there is no testable explanation for this observation. To shed light on these varied and sometimes conflicting results, we performed a thorough study of the relationships between sequence length and gene expression using cell-type (tissue) specific microarray data in Arabidopsis thaliana. We measured median gene expression across tissues (expression level), expression variability between tissues (expression pattern uniformity), and expression variability between replicates (expression noise). We found that intergenic (upstream and downstream) and genic (coding and noncoding) sequences have generally opposite relationships with respect to expression, whether it is tissue variability, median, or expression noise. To explain these results we propose a model, in which the lengths of the intergenic and genic sequences have opposite effects on the ability of the transcribed region of the gene to be epigenetically regulated for differential expression. These findings could shed light on the role and influence of noncoding sequences on gene expression.}, author = {Colinas, Juliette and Schmidler, Scott C. and Bohrer, Gil and Iordanov, Borislav and Benfey, Philip N.}, citeulike-article-id = {3508166}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pone.0003670}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18989364}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18989364}, day = {7}, doi = {10.1371/journal.pone.0003670}, journal = {PLoS ONE}, keywords = {exon, expression, length, level, protein, sequence, transcription}, month = {Nov}, number = {11}, pages = {e3670+}, posted-at = {2009-06-18 17:00:16}, priority = {2}, publisher = {Public Library of Science}, title = {Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression}, url = {http://dx.doi.org/10.1371/journal.pone.0003670}, volume = {3}, year = {2008} }

TY - JOUR ID - citeulike:3508166 L3 - citeulike-article-id:3508166 N2 - Eukaryotic genomes are mostly composed of noncoding DNA whose role is still poorly understood. Studies in several organisms have shown correlations between the length of the intergenic and genic sequences of a gene and the expression of its corresponding mRNA transcript. Some studies have found a positive relationship between intergenic sequence length and expression diversity between tissues, and concluded that genes under greater regulatory control require more regulatory information in their intergenic sequences. Other reports found a negative relationship between expression level and gene length and the interpretation was that there is selection pressure for highly expressed genes to remain small. However, a correlation between gene sequence length and expression diversity, opposite to that observed for intergenic sequences, has also been reported, and to date there is no testable explanation for this observation. To shed light on these varied and sometimes conflicting results, we performed a thorough study of the relationships between sequence length and gene expression using cell-type (tissue) specific microarray data in Arabidopsis thaliana. We measured median gene expression across tissues (expression level), expression variability between tissues (expression pattern uniformity), and expression variability between replicates (expression noise). We found that intergenic (upstream and downstream) and genic (coding and noncoding) sequences have generally opposite relationships with respect to expression, whether it is tissue variability, median, or expression noise. To explain these results we propose a model, in which the lengths of the intergenic and genic sequences have opposite effects on the ability of the transcribed region of the gene to be epigenetically regulated for differential expression. These findings could shed light on the role and influence of noncoding sequences on gene expression. IS - 11 JF - PLoS ONE TI - Intergenic and Genic Sequence Lengths Have Opposite Relationships with Respect to Gene Expression PB - Public Library of Science VL - 3 SP - e3670 KW - exon KW - expression KW - length KW - level KW - protein KW - sequence KW - transcription AU - Colinas, Juliette AU - Schmidler, Scott AU - Bohrer, Gil AU - Iordanov, Borislav AU - Benfey, Philip PY - 2008/Nov/07/ UR - http://dx.doi.org/10.1371/journal.pone.0003670 ER -