RT Journal A1 Hari Sundar G, Vivek A1 Swetha, Chenna A1 Basu, Debjani A1 Pachamuthu, Kannan A1 Raju, Steffi A1 Chakraborty, Tania A1 Mosher, Rebecca A. A1 Shivaprasad, P.V. T1 Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains JF Genome Research JO Genome Research YR 2023 FD May 01 VO 33 IS 5 SP 715 OP 728 DO 10.1101/gr.277353.122 UL http://genome.cshlp.org/content/33/5/715.abstract AB Across eukaryotes, gene regulation is manifested via chromatin states roughly distinguished as heterochromatin and euchromatin. The establishment, maintenance, and modulation of the chromatin states is mediated using several factors including chromatin modifiers. However, factors that avoid the intrusion of silencing signals into protein-coding genes are poorly understood. Here we show that a plant specific paralog of RNA polymerase (Pol) II, named Pol IV, is involved in avoidance of facultative heterochromatic marks in protein-coding genes, in addition to its well-established functions in silencing repeats and transposons. In its absence, H3K27 trimethylation (me3) mark intruded the protein-coding genes, more profoundly in genes embedded with repeats. In a subset of genes, spurious transcriptional activity resulted in small(s) RNA production, leading to post-transcriptional gene silencing. We show that such effects are significantly pronounced in rice, a plant with a larger genome with distributed heterochromatin compared with Arabidopsis. Our results indicate the division of labor among plant-specific polymerases, not just in establishing effective silencing via sRNAs and DNA methylation but also in influencing chromatin boundaries.