Abstract
Identifying interspecies changes in gene regulation, one of the two primary sources of phenotypic variation, is challenging on a genome-wide scale. The use of paired time-course data on cold-responsive gene expression in maize (Zea mays) and sorghum (Sorghum bicolor) allowed us to identify differentially regulated orthologs. While the majority of cold-responsive transcriptional regulation of conserved gene pairs is species specific, the initial transcriptional responses to cold appear to be more conserved than later responses. In maize, the promoters of genes with conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters, a proxy for open chromatin. Genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions. Genes involved in lipid metabolism, known to be involved in cold acclimation, tended to show consistent regulation in both species. Genes with species-specific cold responses did not cluster in particular pathways nor were they enriched in particular functional categories. We propose that cold-responsive transcriptional regulation in individual species may not be a reliable marker for function, while a core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold-responsive regulation across the grass tribe Andropogoneae.
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Claims 8
Claim · model-written summary
Most conserved gene pairs have species-specific cold-responsive regulation.
Zea maysOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the majority of cold-responsive transcriptional regulation of conserved gene pairs is species specific”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
Initial cold transcriptional responses are more conserved than later responses.
SorghumOrganisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“the initial transcriptional responses to cold appear to be more conserved than later responses”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
In maize, genes with conserved cold responses have more promoter hypersensitive sites.
- Gene
- genes with conserved transcriptional responses to colde0
- Outcome
- micrococcal nuclease hypersensitive sitese0
- Direction
- moree0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“In maize, the promoters of genes with conserved transcriptional responses to cold tend to contain more micrococcal nuclease hypersensitive sites in their promoters”
Claim · model-written summary
Genes with conserved regulation have lower nonsynonymous to synonymous substitution ratios.
- Gene
- Genes with conserved patterns of transcriptional regulatione0
- Outcome
- ratios of nonsynonymous to synonymous substitutionse0
- Direction
- lowere0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genes with conserved patterns of transcriptional regulation between the two species show lower ratios of nonsynonymous to synonymous substitutions”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
Lipid metabolism genes tended to have consistent regulation in both species.
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genes involved in lipid metabolism, known to be involved in cold acclimation, tended to show consistent regulation in both species”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
Species-specific cold response genes did not cluster in pathways or functional categories.
- Gene
- Genes with species-specific cold responsese0
- Outcome
- cluster in particular pathways nor were they enriched in particular functional categoriese0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Genes with species-specific cold responses did not cluster in particular pathways nor were they enriched in particular functional categories”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
The authors propose that species-specific cold transcriptional responses may be unreliable functional markers.
- Outcome
- may not be a reliable marker for functione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“cold-responsive transcriptional regulation in individual species may not be a reliable marker for function”
t0“Sorghum and the Subgenomes of Maize”
Claim · model-written summary
A conserved core of cold-response genes is proposed to be under functional constraint across Andropogoneae.
- Gene
- a core set of genes involved in perceiving and responding to cold stresse0
- Outcome
- functionally constrained cold-responsive regulatione0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“a core set of genes involved in perceiving and responding to cold stress are subject to functionally constrained cold-responsive regulation across the grass tribe Andropogoneae”
t0“Sorghum and the Subgenomes of Maize”