Local Coexpression Domains of Two to Four Genes in the Genome of Arabidopsis

Abstract

Expression of genes in eukaryotic genomes is known to cluster, but cluster size is generally loosely defined and highly variable. We have here taken a very strict definition of cluster as sets of physically adjacent genes that are highly coexpressed and form so-called local coexpression domains. The Arabidopsis (Arabidopsis thaliana) genome was analyzed for the presence of such local coexpression domains to elucidate its functional characteristics. We used expression data sets that cover different experimental conditions, organs, tissues, and cells from the Massively Parallel Signature Sequencing repository and microarray data (Affymetrix) from a detailed root analysis. With these expression data, we identified 689 and 1,481 local coexpression domains, respectively, consisting of two to four genes with a pairwise Pearson's correlation coefficient larger than 0.7. This number is approximately 1-to 5-fold higher than the numbers expected by chance. A small (5%-10%) yet significant fraction of genes in the Arabidopsis genome is therefore organized into local coexpression domains. These local coexpression domains were distributed over the genome. Genes in such local domains were for the major part not categorized in the same functional category (GOslim). Neither tandemly duplicated genes nor shared promoter sequence nor gene distance explained the occurrence of coexpression of genes in such chromosomal domains. This indicates that other parameters in genes or gene positions are important to establish coexpression in local domains of Arabidopsis chromosomes.

Comparative Network Analysis Reveals That Tissue Specificity and Gene Function Are Important Factors Influencing the Mode of Expression Evolution in Arabidopsis and Rice

“…Compared with the expected degree of coexpression (i.e. maximum 10% with the 90th percentile PCC threshold), these genes showed no strong evidence for large-scale coregulation (Ren et al, 2005). Of all orthologous colinear gene pairs, 69% had a conserved ECC.…”

A 3,000-Loci Transcription Map of Chromosome 3B Unravels the Structural and Functional Features of Gene Islands in Hexaploid Wheat

“…This proportion may be even higher if we consider that we only analyzed one-third of the putative 8,000 genes located on chromosome 3B. In particular, the hybridization-based approach cannot detect tandemly duplicated genes that have been shown to be more prone to coexpression than adjacent nontandemly duplicated genes (Williams and Bowles, 2004;Ren et al, 2005;Zhan et al, 2006). We also found a few coexpressed gene clusters that were conserved between wheat and rice or B. distachyon, suggesting that genes maintained their proximity during the evolution and that common regulatory mechanisms are also conserved between plant genomes.…”

“…In the human, mouse (Mus musculus), Arabidopsis, and rice genomes, the percentage of adjacent coexpressed genes ranges from 2% to 10% with two to four genes involved (Ren et al, 2005(Ren et al, , 2007Sémon and Duret, 2006;Zhan et al, 2006). In fruit fly, Spellman and Rubin (2002) found 20% of adjacent genes that were part of large coexpression domains involving 10 to 30 genes.…”

“…Irrespective of genome size or gene space organization, clusters of genes sharing expression profiles were identified in several plants, including Arabidopsis (Ren et al, 2005;Zhan et al, 2006) and rice (Ren et al, 2007). In addition to coexpressed genes, clusters were shown to be significantly enriched in genes sharing the same function or assigned to the same pathway in Arabidopsis, but also in cotton (Gossypium hirsutum), grape, poplar (Populus spp.…”

Detection and Analysis of Functional Specialization in Duplicated Genes

“…nucleosome positions) has a strong effect on gene expression, which suggests that translocated duplicates may show expression divergence by virtue of chromosomal position alone. In addition, Ren et al (2005) found that tandem duplicates that shared expression domains tended to have dissimilar sequence-based functions. Shoja et al (2007) noted that tandem gene duplicates tended to show a relationship between expression divergence and chromosomal distance.…”