Non-coding RNAs and chromatin organization. (A) Protein-coding genes are transcribed in the sense direction in order to produce mRNA. Transcription of ncRNAs can be initiated from genic as well as intergenic regions in both the sense and antisense directions. Often transcription is initiated from nucleosome depleted regions (NDRs) in a bidirectional manner. (B) Typical nucleosomal organization of yeast genes. NDRs are generally found just up- and downstream from coding regions. A highly positioned +1 nucleosome covering the transcription start site (→) directs precise positioning of nearby nucleosomes, but its influence wanes with increasing distance from the TSS. The presence of nucleosomes over coding regions masks the cryptic promoter elements found throughout the genome and thus prevents aberrant transcription initiation. (C) Transcription-dependent distribution of H3 K4 and H3 K36 methylation over gene coding regions. Heatmaps also show high levels of histone acetylation and exchange over promoter-proximal regions which anticorrelate with the distribution of H3 K36 trimethylation.