In plants, highly expressed genes are the least compact

Ren, Xinfeng; Vorst, Oscar; Fiers, Mark; Stiekema, Willem J.; Nap, Jan-Peter

doi:10.1016/j.tig.2006.08.008

Cited by 158 publications

(157 citation statements)

References 23 publications

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“…14,22,23,[55][56][57][58] This distribution pattern is also in agreement with an anticorrelation of H3K23ac with DNA methylation. 18,59 Surprisingly, we found that H4K16ac and H3K23ac are also enriched across the gene-body of many lowly expressed genes in rice (Fig.…”

Section: Discussionsupporting

confidence: 78%

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

et al. 2015

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Section: Discussionsupporting

confidence: 78%

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

et al. 2015

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“…Several factors can affect gene expression, including gene GC content of the gene (Kudla et al, 2006), intron size (Ren et al, 2006), intron motifs (Rose et al, 2008), methylated transposon distribution (Hollister and Gaut, 2009), and chromosomal rearrangements (Marques-Bonet et al, 2004). Most notable for our study is the negative correlation between transcript level and density of recent transposon insertions that may be methylated (Hollister and Gaut, 2009).…”

Section: Expression Biases Are Correlated With Sequence Divergencementioning

confidence: 79%

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

et al. 2010

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Soybean (Glycine max) has undergone at least two rounds of polyploidization, resulting in a paleopolyploid genome that is a mosaic of homoeologous regions. To determine the structural and functional impact of these duplications, we sequenced two ;1-Mb homoeologous regions of soybean, Gm8 and Gm15, derived from the most recent ;13 million year duplication event and the orthologous region from common bean (Phaseolus vulgaris), Pv5. We observed inversions leading to major structural variation and a bias between the two chromosome segments as Gm15 experienced more gene movement (gene retention rate of 81% in Gm15 versus 91% in Gm8) and a nearly twofold increase in the deletion of long terminal repeat (LTR) retrotransposons via solo LTR formation. Functional analyses of Gm15 and Gm8 revealed decreases in gene expression and synonymous substitution rates for Gm15, for instance, a 38% increase in transcript levels from Gm8 relative to Gm15. Transcriptional divergence of homoeologs was found based on expression patterns among seven tissues and developmental stages. Our results indicate asymmetric evolution between homoeologous regions of soybean as evidenced by structural changes and expression variances of homoeologous genes.

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“…The correlation between expression level and gene size and associated properties such as number and length of introns has been investigated in several studies [28][29][30][31][32][33][34]. Surprisingly, while highly expressed genes were found to be shorter in animals and to harbor fewer and shorter introns [30], they appear least compact and relatively largest in plants [33] and C. elegans [29].…”

Section: Multistimuli Response Genes Are Shorter In Arabidopsismentioning

confidence: 99%

“…Surprisingly, while highly expressed genes were found to be shorter in animals and to harbor fewer and shorter introns [30], they appear least compact and relatively largest in plants [33] and C. elegans [29]. Several evolutionary scenarios such as selection for economy and genomic design have been discussed to explain the observed trends [31,34].…”

Section: Multistimuli Response Genes Are Shorter In Arabidopsismentioning

confidence: 99%

The regulatory code for transcriptional response diversity and its relation to genome structural properties in Arabidopsis thaliana

Walther¹,

Brunnemann²,

Selbig³

2005

PLoS Genet

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Regulation of gene expression via specific cis-regulatory promoter elements has evolved in cellular organisms as a major adaptive mechanism to respond to environmental change. Assuming a simple model of transcriptional regulation, genes that are differentially expressed in response to a large number of different external stimuli should harbor more distinct regulatory elements in their upstream regions than do genes that only respond to few environmental challenges. We tested this hypothesis in Arabidopsis thaliana using the compendium of gene expression profiling data available in AtGenExpress and known cis-element motifs mapped to upstream gene promoter regions and studied the relation of the observed breadth of differential gene expression response with several fundamental genome architectural properties. We observed highly significant positive correlations between the density of ciselements in upstream regions and the number of conditions in which a gene was differentially regulated. The correlation was most pronounced in regions immediately upstream of the transcription start sites. Multistimuli response genes were observed to be associated with significantly longer upstream intergenic regions, retain more paralogs in the Arabidopsis genome, are shorter, have fewer introns, and are more likely to contain TATA-box motifs in their promoters. In abiotic stress time series data, multistimuli response genes were found to be overrepresented among early-responding genes. Genes involved in the regulation of transcription, stress response, and signaling processes were observed to possess the greatest regulatory capacity. Our results suggest that greater gene expression regulatory complexity appears to be encoded by an increased density of cis-regulatory elements and provide further evidence for an evolutionary adaptation of the regulatory code at the genomic layout level. Larger intergenic spaces preceding multistimuli response genes may have evolved to allow greater regulatory gene expression potential.Citation: Walther D, Brunnemann R, Selbig J (2007) The regulatory code for transcriptional response diversity and its relation to genome structural properties in A. thaliana. PLoS Genet 3(2): e11.

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In plants, highly expressed genes are the least compact

Cited by 158 publications

References 23 publications

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns inArabidopsisand rice

Structural and Functional Divergence of a 1-Mb Duplicated Region in the Soybean (Glycine max) Genome and Comparison to an Orthologous Region fromPhaseolus vulgaris

The regulatory code for transcriptional response diversity and its relation to genome structural properties in Arabidopsis thaliana

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