The revised nomenclature denotes the largest subunits of Pol IV and Pol V as NRPD1 and NRPE1. of the genome, yet ~90% of the genome is transcribed (Kapranov et al., 2007; Prasanth and Spector, 2007; Willingham et al., 2006). Much of the noncoding RNA (ncRNA) pool corresponds to intergenic sequences or antisense transcripts of unknown function. However, the potential for ncRNAs to epigenetically regulate adjacent genes is increasingly clear (Prasanth and Spector, 2007). Long ncRNAs that regulate adjacent genes include the and RNAs involved in X chromosome inactivation in mammals (Masui and Heard, 2006; Yang and Kuroda, 2007), the H19 and Air ncRNAs involved in imprinting at mouse and human Igf2 and Igf2r loci, respectively (Pauler cAMPS-Rp, triethylammonium salt et al., 2007) and the ncRNAs involved in X-chromosome dosage compensation in flies (Bai Mouse monoclonal to CD53.COC53 monoclonal reacts CD53, a 32-42 kDa molecule, which is expressed on thymocytes, T cells, B cells, NK cells, monocytes and granulocytes, but is not present on red blood cells, platelets and non-hematopoietic cells. CD53 cross-linking promotes activation of human B cells and rat macrophages, as well as signal transduction et al., 2007). The persistence of Xist and roX transcripts at affected loci indicates a role in the assembly of repressive or activating chromatin states, respectively (Bai et al., 2007; Herzing et al., 1997). Likewise, at the Drosophila (transcription (Sanchez-Elsner et al., 2006). In diverse eukaryotes, establishment of DNA methylation and/or repressive heterochromatic histone modifications are ncRNA-directed processes (Buhler et al., 2007; Grewal and Elgin, 2007; Zaratiegui et al., 2007). In plants and fission yeast, small interfering RNAs (siRNAs) of 20C25 nt that are generated from long double-stranded RNA (dsRNA) precursors by dicer endonuclease(s) bind to Argonaute (AGO) proteins and guide chromatin modifications to homologous DNA sequences (Baulcombe, 2006; Brodersen and Voinnet, 2006; Peters and Meister, 2007). Noncoding transcripts in fission yeast serve at least two functions, acting as precursors of siRNAs and as scaffolds to which siRNAs bind in order to recruit the chromatin modifying machinery (Buhler et al., 2007; Buhler et al., 2006; Irvine et al., 2006). AGO-mediated slicing of scaffold transcripts coupled with RNA-dependent RNA polymerase-mediated dsRNA production generates additional siRNAs, thereby perpetuating heterochromatin formation (Irvine et al., 2006; Locke and Martienssen, 2006). RNA-mediated heterochromatin formation requires that an affected region be transcribed (Buhler et al., 2006; Djupedal et al., 2005; Irvine et al., 2006; Kato et al., 2005), presenting an intriguing paradox as to how transcription and transcriptional silencing can occur at the same locus (Grewal and Elgin, 2007). The paradox of transcription-dependent gene silencing in plants might be explained by the existence of two structurally and functionally distinct plant-specific RNA polymerases, RNA Polymerases IVa/Pol IV and Pol IVb/Pol V (Herr et cAMPS-Rp, triethylammonium salt al., 2005; Kanno et al., 2005; Onodera et al., 2005; Pontier et al., 2005). Pol IVa/Pol IV and Pol IVb/Pol V are not essential for viability in Arabidopsis but participate in multiple small RNA-mediated gene silencing pathways (Pikaard et al., 2008). Pol IVa/Pol IV and Pol IVb/Pol V have distinct largest subunits that have been named either NRPD1a and NRPD1b (Herr et al., 2005; cAMPS-Rp, triethylammonium salt Onodera et al., 2005) or RPD1 and RPE1 (Luo and Hall, 2007). The latter terminology has been adopted, in modified form, to allow the naming of Pol IVa/Pol IV subunits using the NRPD (Nuclear RNA Polymerase D) gene symbol and Pol IVb/Pol V subunits using the NRPE (Nuclear RNA Polymerase E) prefix. The transition to the Pol IV and Pol V nomenclature in place of Pol IVa and Pol IVb has been made necessary by the need for a systematic nomenclature defining their numerous subunits (Ream and Pikaard, in preparation) and reflects the fact that the two activities are functionally non-redundant as well as structurally distinct. Therefore, we refer to Pol IVa and Pol IVb as Pol IV and Pol V for the remainder of this paper. cAMPS-Rp, triethylammonium salt The revised nomenclature denotes the largest subunits of Pol IV and Pol V as NRPD1 and NRPE1. Pol IV and Pol V both utilize a second-largest subunit that is encoded by a single gene bearing the synonymous names or or but the catalytic subunits of Pol IV and Pol V have.