We hypothesize that the opposite effects of REST about PRC1 occupancy at distal versus proximal RE1 elements were due to unique configurations of PRC1 binding at these elements (see Fig. cells, derepressing genes with distal, but not genes with proximal, RE1 elements. In differentiating neurons, knockout reduced PRC1 occupancy and derepressed transcription at distal RE1 elements but improved PRC1 occupancy and repressed transcription at proximal RE1 elements. The opposite effects of REST on PRC1 occupancy at different RE1 elements contributed to the gene-specific control of PRC1 functions during Sera cell differentiation. Intro Epigenetic regulatory factors such as Polycomb group (PcG) proteins are thought to perpetuate genome-wide patterns of transcription when cells RASA4 divide to produce identical child cells. The production G907 of fresh cell types during development requires the displacement of epigenetic regulatory complexes at some genes and the formation of fresh epigenetic complexes at additional genes in the same cell. The genes where G907 existing epigenetic complexes are displaced and the genes where fresh epigenetic complexes are created must be separately specified. Whereas epigenetic mechanisms can maintain transcriptional claims, changes in the transcription of specific genes are likely to require sequence-specific DNA acknowledgement. The association of PcG proteins with individual genes must consequently be controlled by gene- and cell-type-specific mechanisms. Hundreds of genes, many of which encode developmental regulators, are repressed by PcG proteins in mammalian embryonic stem (Sera) cells. Different subsets of these genes are derepressed in different cell lineages and at different phases of development. Conversely, fresh genes are repressed by PcG proteins during differentiation. The mechanisms that determine the opposite changes in the PcG protein associations with different genes during differentiation are mainly unknown. PcG proteins form two classes of Polycomb repressive complexes (PRC1 and PRC2) (28). Earlier studies of the rules G907 of PcG protein occupancy focused on the establishment and maintenance of PRC2 binding (18, 33, 48, 52). The results from those studies do not clarify how PcG protein binding at different genes is definitely regulated in reverse ways in the same cells. Moreover, PRC1 can associate with chromatin in cells lacking PRC2 (31, 42, 46, 51). Mechanisms for the rules of PRC1 binding in the absence of PRC2 are poorly recognized. Each subunit of vertebrate PRC1 is definitely encoded by multiple genes (Cbx, Ring1, Mel18/Bmi1, and Phc family members). Previous studies of the PRC1 association with chromatin have focused on PRC1 binding to DNA/RNA and to histones. Mel18 and reconstituted PRC1 can bind DNA directly (16, 26). PRC1 can wrap about 400 bp of DNA inside a structure expected to exclude nucleosomes and cross-links most efficiently to areas depleted of nucleosomes in cells (34). Cbx7 binding to the ANRIL noncoding RNA was previously proposed to recruit PRC1 to the locus (53). Cbx family proteins can bind H3 trimethylated on K27 (3, 8). Genome-wide H3 K27 trimethylation correlates with PRC1 occupancy in embryonic stem cells and fibroblasts (5, 6, 29). H3 K27 trimethylation is not essential for the PRC1 association with chromatin (31, 42, 46, 51). It is unclear if changes in H3 K27 trimethylation regulate the association of PRC1 proteins with individual genes, since mechanisms for the gene-specific modulation of H3 K27 trimethylation have not been explained. PRC1 subunits copurify with several sequence-specific DNA-binding proteins (13, 38, 45). The respective roles of relationships with DNA, noncoding RNA, histone H3, and DNA-binding proteins in the association of PRC1 proteins with target genes remain incompletely understood. Here, we determine Cbx family protein relationships with REST (NRSF) and REST-associated proteins in Sera cells and in differentiating neurons. REST was originally characterized like a repressor of neuronal genes in nonneuronal cells (10, 47). Subsequent studies have shown that REST regulates neuronal genes during neurogenesis and that it can both activate and repress genes comprising RE1 elements (2, 4,.