Abstract
BackgroundFormation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated.ResultsWe mapped nucleosomes along with transcriptional changes after 24-h of Pi starvation in rice (Oryza sativa) by deep sequencing of micrococcal nuclease digested chromatin and ribosome-depleted RNA. We demonstrated that nucleosome patterns at rice genes were affected by both cis- and trans-determinants, including GC content and transcription. Also, categorizing rice genes by nucleosome patterns across the transcription start site (TSS) revealed nucleosome patterns that correlated with distinct functional categories of genes. We further demonstrated that Pi starvation resulted in numerous dynamic nucleosomes, which were enhanced at genes differentially expressed in response to Pi starvation.ConclusionsWe demonstrate that rice nucleosome patterns are suggestive of gene functions, and reveal a link between chromatin remodeling and transcriptional changes in response to deficiency of a major macronutrient. Our findings help to enhance the understanding towards eukaryotic gene regulation at the chromatin level.
Highlights
Formation of nucleosomes along eukaryotic DNA has an impact on transcription
Nucleosome positioning and occupancy of rice genes The goals of this study were to generate a high-resolution map of nucleosome patterns in rice, define the impact of environmental perturbation on these patterns, and establish whether nucleosome dynamics in response to Pi starvation correlate with differential gene expression
Because a recent transcript profiling study in rice demonstrated that major changes in transcript abundance were detected beginning after 24 h of Pi starvation [30], and chromatin remodeling can happen within hours of environmental stress [19], we were interested in observing the changes in the organization of primary chromatin structure and exploring the correlations at this relatively early time point
Summary
Formation of nucleosomes along eukaryotic DNA has an impact on transcription. Major transcriptional changes occur in response to low external phosphate (Pi) in plants, but the involvement of chromatin-level mechanisms in Pi starvation responses have not been investigated. Studies on primary chromatin structure reveal that 146 bp of DNA wrap around a histone octamer consisting of each of two copies of H2A, H2B, H3 and H4 to comprise a nucleosome [1]. The formation of nucleosomes along DNA facilitates DNA compaction, it makes the DNA inaccessible for important cellular processes including DNA replication, recombination, repair and transcription [2,3,4,5]. Phosphorus (P) is an essential nutrient as it is a structural component of nucleic acids and phospholipids, and is involved in the regulation of
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