Intergenic and genic sequence lengths have opposite relationships with respect to gene expression.
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.
Type
Journal articleSubject
ArabidopsisDNA, Intergenic
Epigenesis, Genetic
Gene Expression Profiling
Gene Expression Regulation, Plant
Genetic Variation
Genome, Plant
RNA, Messenger
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https://hdl.handle.net/10161/4506Published Version (Please cite this version)
10.1371/journal.pone.0003670Publication Info
Colinas, Juliette; Schmidler, Scott C; Bohrer, Gil; Iordanov, Borislav; & Benfey,
Philip N (2008). Intergenic and genic sequence lengths have opposite relationships with respect to
gene expression. PLoS One, 3(11). pp. e3670. 10.1371/journal.pone.0003670. Retrieved from https://hdl.handle.net/10161/4506.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Philip N. Benfey
Paul Kramer Distinguished Professor of Biology
This author no longer has a Scholars@Duke profile, so the information shown here reflects
their Duke status at the time this item was deposited.
Scott C. Schmidler
Associate Professor of Statistical Science
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