The rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in <i>Arabidopsis thaliana</i>

Simple item page
dc.contributor.authorAceituno, Felipe F.
dc.contributor.authorMoseyko, Nick
dc.contributor.authorRhee, Seung Y.
dc.contributor.authorGutierrez, Rodrigo A.
dc.date.accessioned2025-01-21T01:04:59Z
dc.date.available2025-01-21T01:04:59Z
dc.date.issued2008
dc.description.abstractBackground: Microarray technology is a widely used approach for monitoring genome-wide gene expression. For Arabidopsis, there are over 1,800 microarray hybridizations representing many different experimental conditions on Affymetrix (TM) ATH1 gene chips alone. This huge amount of data offers a unique opportunity to infer the principles that govern the regulation of gene expression in plants.
dc.description.abstractResults: We used bioinformatics methods to analyze publicly available data obtained using the ATH1 chip from Affymetrix. A total of 1887 ATH1 hybridizations were normalized and filtered to eliminate low-quality hybridizations. We classified and compared control and treatment hybridizations and determined differential gene expression. The largest differences in gene expression were observed when comparing samples obtained from different organs. On average, ten-fold more genes were differentially expressed between organs as compared to any other experimental variable. We defined "gene responsiveness" as the number of comparisons in which a gene changed its expression significantly. We defined genes with the highest and lowest responsiveness levels as hypervariable and housekeeping genes, respectively. Remarkably, housekeeping genes were best distinguished from hypervariable genes by differences in methylation status in their transcribed regions. Moreover, methylation in the transcribed region was inversely correlated (R-2 = 0.8) with gene responsiveness on a genome-wide scale. We provide an example of this negative relationship using genes encoding TCA cycle enzymes, by contrasting their regulatory responsiveness to nitrate and methylation status in their transcribed regions.
dc.description.abstractConclusion: Our results indicate that the Arabidopsis transcriptome is largely established during development and is comparatively stable when faced with external perturbations. We suggest a novel functional role for DNA methylation in the transcribed region as a key determinant capable of restraining the capacity of a gene to respond to internal/external cues. Our findings suggest a prominent role for epigenetic mechanisms in the regulation of gene expression in plants.
dc.fuente.origenWOS
dc.identifier.doi10.1186/1471-2164-9-438
dc.identifier.issn1471-2164
dc.identifier.urihttps://doi.org/10.1186/1471-2164-9-438
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/95771
dc.identifier.wosidWOS:000260172900003
dc.language.isoen
dc.revistaBmc genomics
dc.rightsacceso restringido
dc.subject.ods03 Good Health and Well-being
dc.subject.odspa03 Salud y bienestar
dc.titleThe rules of gene expression in plants: Organ identity and gene body methylation are key factors for regulation of gene expression in <i>Arabidopsis thaliana</i>
dc.typeartículo
dc.volumen9
sipa.indexWOS
sipa.trazabilidadWOS;2025-01-12
Files
Collections
Artículos de revistas