Patterns of Histone H3 Lysine 27 Monomethylation and Erythroid Cell Type-specific Gene Expression

Abstract

Post-translational histone modifications, acting alone or in a context-dependent manner, influence numerous cellular processes via their regulation of gene expression. Monomethylation of histone H3 lysine 27 (K27me1) is a poorly understood histone modification. Some reports describe depletion of K27Me1 at promoters and transcription start sites (TSS), implying its depletion at TSS is necessary for active transcription, while others have associated enrichment of H3K27me1 at TSS with increased levels of mRNA expression. Tissue-and gene-specific patterns of H3K27me1 enrichment and their correlation with gene expression were determined via chromatin immunoprecipitation on chip microarray (ChIP-chip) and human mRNA expression array analyses. Results from erythroid cells were compared with those in neural and muscle cells. H3K27me1 enrichment varied depending on levels of cell-type specific gene expression, with highest enrichment over transcriptionally active genes. Over individual genes, the highest levels of H3K27me1 enrichment were found over the gene bodies of highly expressed genes. In contrast to H3K4me3, which was highly enriched at the TSS of actively transcribing genes, H3K27me1 was selectively depleted at the TSS of actively transcribed genes. There was markedly decreased to no H3K27me1 enrichment in genes with low expression. At some locations, H3K27 monomethylation was also found to be associated with chromatin signatures of gene enhancers.The dynamic state of chromatin is influenced by many factors including nucleosomal configuration (1). Nucleosomes are composed of repetitive histone octamer units wrapped by DNA. Histones are evolutionarily conserved proteins with a characteristic histone fold and flexible NH 2 -terminal tails. Post-translational modifications of histones (2) acting alone or in a context-dependent manner, influence various cellular processes such as transcription, replication, DNA repair, and cell cycle progression by regulating the intrinsic chromatin environment or modifying the binding of non-histone, chromatinmodifying protein complexes (3, 4). Although some histone modifications correlate with specific biologic activities, it is clear that the complexity of histone modifications, and their interactions are just beginning to be revealed (4 -7). Understanding the effect these modifications have on cellular processes will provide important insights into both normal and disease-associated processes (8).Methylation of position-specific lysine residues in NH 2 -terminal histone tails is a critical post translational modification that can be associated with either active or repressed chromatin (9). For example, modifications such as trimethylation of histone H3 lysine 4 and acetylation of histone H3 lysine 9 are generally associated with euchromatin and gene activation (2) while trimethylation of histone H3 lysine 9 is generally associated with hetero-chromatin and gene repression.In addition to the unmodified form, histone H3 K27 exists in three methylation states, monomethylated, dimeth...

A lesson learned from the H3.3K27M mutation found in pediatric glioma

“…For instance, monomethylation of H3 Lys27 is enriched in gene bodies of highly expressed genes. 23 In contrast, di-and tri-methylation of H3 Lys27 is associated with silencing of developmental regulated genes, and the repressive histone mark "H3K27me3" also coats the inactivated X chromosome (Xi) in female mammals. [24][25][26] Furthermore, H3…”

A Role for Monomethylation of Histone H3-K27 in Gene Activity inDrosophila

“…In addition to gene body enrichment, studies on human hematopoietic cells show that K27me1 can also be enriched at enhancers (CUI et al 2009;ERNST and KELLIS 2010;STEINER et al 2011). This is relevant given that a likely impact of the mono-methylating PRC2 used here is to boost K27me1 in regions where PRC2 is normally targeted (i.e.…”

“…Most of these studies detect K27me1 enrichment within gene bodies, suggesting a co-transcriptional role. Enrichment at mammalian gene enhancers and promoters has also been described (CUI et al 2009;ERNST and KELLIS 2010;STEINER et al 2011). In C. elegans, K27me1 is found co-associated with dosage compensation proteins that mediate X-linked gene repression (LIU et al 2011b).…”

Identification of Biologically Relevant Enhancers in Human Erythroid Cells

“…RNA Isolation and Preparation, Microarray Data Acquisition, and Analyses-RNA was prepared from primary human erythroid cells and prepared for microarray analyses as described (44,45) and detailed in the supplemental Methods. Gene expression microarray quality control and data analyses are described in the supplemental Methods.…”

“…Quantitative realtime PCR was performed to confirm expression levels of RNA transcripts with the primers in supplemental Table S1. Realtime PCR data were normalized as described (45). Triplicate analyses were performed for each target (44,46).…”