Genome-wide Analysis of the H3K4 Histone Demethylase RBP2 Reveals a Transcriptional Program Controlling Differentiation

Abstract

SUMMARY Retinoblastoma protein (pRB) mediates cell-cycle withdrawal and differentiation by interacting with a variety of proteins. RB-Binding Protein 2 (RBP2) has been shown to be a key effector. We sought to determine transcriptional regulation by RBP2 genome-wide by using location analysis and gene expression profiling experiments. We describe that RBP2 shows high correlation with the presence of H3K4me3 and its target genes are separated into two functionally distinct classes: differentiation-independent and differentiation-dependent genes. The former class is enriched by genes that encode mitochondrial proteins, while the latter is represented by cell-cycle genes. We demonstrate the role of RBP2 in mitochondrial biogenesis, which involves regulation of H3K4me3-modified nucleosomes. Analysis of expression changes upon RBP2 depletion depicted genes with a signature of differentiation control, analogous to the changes seen upon reintroduction of pRB. We conclude that, during differentiation, RBP2 exerts inhibitory effects on multiple genes through direct interaction with their promoters.

Coordinated repression of cell cycle genes by KDM5A and E2F4 during differentiation

“…Consistent with this observation, our previous microarray study showed that correlation between recruitment of KDM5A and decreased transcription was characteristic of the whole group of genes specifically bound by KDM5A in the differentiated condition (9). Besides cell cycle genes, during differentiation KDM5A is bound to genes that code for proteins involved in mitochondrial function and to developmental genes, such as the HOX genes (9,11,21). The coexistence of H3K27me3 and H3K4me3 epitomize the epigenetic state of HOX genes and other developmental genes in stem and progenitor cells.…”

“…In quiescent cells, p130/E2F4 is the most prominent pocket protein complex bound to E2F-regulated promoters (3, 6-8). We previously mapped human KDM5A/RBP2 binding regions during differentiation using ChIP-on-chip experiments in diffuse histiocytic lymphoma U937 cells (9). From these two ChIP-on-chip studies, we identified the groups of genes that mapped as condition-specific KDM5A targets (0-h-specific targets, common targets at 0 and 27 h, 27-h-specific targets, common targets at 27 and 96 h, and finally 96-h-specific targets) and DREAM complex targets ( Fig.…”

“…Because of the generally high overlap between KDM5A and E2F4 target genes (Fig. 1C), we asked if conditionspecific KDM5A targets that were predicted by our transcription factor binding analysis to contain E2F binding sites (9) are bound by E2F4 in the same condition. When these regions were subjected to ChIP-qPCR, all regions displayed high E2F4 binding, with p130 bound to most of these KDM5A targets after 96 h of differentiation (Fig.…”

“…Decreased H3K4 methylation has been detected during differentiation at the promoters of MFN2, BRD8/KIF20A, FGF4, OTX2, HOXA1, HOXA5, and HOXA7 genes bound by KDM5A (9,11,14,17). The question of whether the regulation of a cell cycle gene involves removal of H3K4 trimethylation by KDM5A has not been studied.…”

“…Target genes of KDM5A in U937 and expression data of genes in this cell line were obtained from our previous study (9). Genomic location of E2F4 targets was taken from GSE20551 [particularly GSM516408 (5)].…”