Distinct DNase I hypersensitive sites are absent from promoters of transcriptionally incompetent genes in Arabidopsis

Abstract

Specifically accessible chromatin sites, detected as DNase I hypersensitive sites (DNase I HSs), have been found at promoters of most genes in yeast, human as well as in Arabidopsis chromatin. The DNase I HSs are constitutively present at promoters of most genes both at inactive and activated states. On the other hand, appearance and disappearance of DNase I HSs have been observed at several developmentally regulated genes in different tissues of animals. Patterns of appearance and disappearance of DNase I HSs were correlated with transcriptional competency (potential of expression) of the associated genes, suggesting that DNase I HSs are absent from the promoters of transcriptionally incompetent (unexpressed nor inducible) genes. To test this hypothesis in plants, we analyzed DNase I hypersensitivity of several well-characterized genes showing distinct patterns of tissue-specific expression in Arabidopsis leaves, roots and suspension cells. Distinct DNase I HSs were present at transcriptionally competent gene promoters, but absent from incompetent gene promoters. The absence of DNase I HS suggests that nucleosomes are randomly positioned on incompetent promoters, and may contribute to the transcriptional incompetency by blocking the binding of activators in tissues where expression of these genes is unnecessary.