Stress-Mediated Alterations in Chromatin Architecture Correlate with Down-Regulation of a Gene Encoding 60S rpL32 in Rice

Several ribosomal proteins are down-regulated at the translational, post-transcriptional and transcriptional level in response to abiotic stress, resulting in retardation of growth and productivity in various plants. However, transcriptional mechanisms associated with the stress-mediated down-regulation of such genes have not been well studied. Recently, we reported salt-responsive transcriptional down-regulation of a gene encoding 60S ribosomal protein L32, rpL32_8.1 , in rice. In the present work, chromatin remodeling mechanisms associated with down-regulation of this gene under salt stress have been studied. The data obtained from the sodium bisulfite sequencing of a genomic region containing portions of the promoter and 5′-untranslated region of rpL32_8.1 exclude a role for DNA methylation in this down-regulation event. Fine mapping of the first nucleosome after the transcription start site (TSS) revealed its occupancy over the TSS to a greater extent under salt stress than that observed in a controlled environment, possibly causing a hindrance to transcription initiation during its down-regulation. Using chromatin immunoprecipitation, it was observed that histone modifications that are generally associated with highly active genes were markedly reduced under stress conditions at the 5′ end region of this gene under salt stress. By applying a modified chromatin conformation capture (mCCC) technique, promoter–terminator interaction was detected for this gene under control conditions. The efficiency of this interaction was diminished under salt stress. This work indicates that the stress-responsive transcriptional down-regulation of rpL32_8.1 is accompanied by alterations in nucleosome positioning, histone modification and gene looping, but not DNA methylation.