High Levels Of H3K4me3 Research Articles

Abstract 5424: Hypoxia Induces the Histone Demethylase Jmjd3 and Epigenetically Reprograms Endothelial Progenitor Cells

Endothelial progenitor cells (EPCs) contribute to vascular repair and postnatal neovascularisation. Cell therapy using EPCs improved neovascularisation and functional recovery after ischemia. However, it has been extensively debated whether EPCs can differentiate into endothelial cells and the mechanisms of EPC differentiation are poorly understood. Endothelial differentiation requires the expression of endothelial marker genes, which are silenced by chromatin dependent repressive mechanisms such as histone H3 lysine 27 trimethylation (H3K27me3) in non-endothelial cells. We observed that induction of hind limb ischemia increased the expression of Jmjd3, which was shown to demethylate H3K27me3 thereby removing repressive histone marks. Therefore, we examined whether EPC might be reprogrammed by hypoxic/ischemic injury through epigenetic pathways. We report here that Jmjd3 was induced when EPCs were exposed to hypoxia for more than 24 hours. Hypoxia additionally stimulated the nuclear translocation of Jmjd3 in EPC as shown by immunostaining (12.0±3.2% in normoxia, 68.5±3.6% in hypoxia, Jmjd3 positive nuclei/whole nuclei). Increased expression and nuclear translocation of Jmjd3 after hypoxic stimulation was associated with a reduction of global H3K27m3. Additionally, chromatin immunoprecipitation showed that the promoter of eNOS and KDR, which is transcriptionally silenced by high levels of H3K27me3 in early EPC under normoxic conditions, is activated by hypoxia. Hypoxia induced a down-regulation of H3K27me3 (0.045±0.017% input in normoxia and 0.024±0.010% input in hypoxia at the eNOS promoter, 0.197±0.067% input in normoxia and 0.126±0.030% input in hypoxia at the KDR promoter) and increased the ratio of active versus repressive chromatin marks at the eNOS and KDR promoter. Consistently, eNOS and KDR mRNA levels in EPC were increased after hypoxia. In summary, these data demonstrate that hypoxia-induced up-regulation and translocation of the histone demethylase Jmjd3 is associated with a reduction of repressive histone marks at the promoter of endothelial genes. These findings indicate that hypoxia may epigenetically modulate endothelial commitment.

Jmjd3 contributes to the control of gene expression in LPS-activated macrophages

Jmjd3, a JmjC family histone demethylase, is induced by the transcription factor NF-kB in response to microbial stimuli. Jmjd3 erases H3K27me3, a histone mark associated with transcriptional repression and involved in lineage determination. However, the specific contribution of Jmjd3 induction and H3K27me3 demethylation to inflammatory gene expression remains unknown. Using chromatin immunoprecipitation-sequencing we found that Jmjd3 is preferentially recruited to transcription start sites characterized by high levels of H3K4me3, a marker of gene activity, and RNA polymerase II (Pol_II). Moreover, 70% of lipopolysaccharide (LPS)-inducible genes were found to be Jmjd3 targets. Although most Jmjd3 target genes were unaffected by its deletion, a few hundred genes, including inducible inflammatory genes, showed moderately impaired Pol_II recruitment and transcription. Importantly, most Jmjd3 target genes were not associated with detectable levels of H3K27me3, and transcriptional effects of Jmjd3 absence in the window of time analysed were uncoupled from measurable effects on this histone mark. These data show that Jmjd3 fine-tunes the transcriptional output of LPS-activated macrophages in an H3K27 demethylation-independent manner.

Dynamic DNA and histone methylation influences the ontogeny of xenobiotic metabolizing genes during postnatal mouse liver maturation

After birth, liver transitions from hematopoiesis to meet new metabolic demands, including xenobiotic (drug) processing. During this maturation, expression of many xenobiotic processing genes increases in distinct patterns. Since the epigenetic code is implicated in regulating gene expression and cellular differentiation during development, we hypothesized that these mechanisms may also be involved in the ontogenic expression of xenobiotic processing genes. In the current study, ChIP‐on‐chip assays representing 14% of the mouse genome were used to define the levels and distributions of DNA methylation (meDNA), histone 3 lysine 4 dimethylation (H3K4me2), and histone 3 lysine 27 trimethylation (H3K27me3) during postnatal liver development. In addition to the epigenetic data, gene expression microarrays defined ontogenic expression patterns. meDNA was not observed in the examined xenobiotic processing genes. Gradual increases in H3K4me2 from prenatal to adult ages were observed in several xenobiotic processing genes (e.g. Cyp3a11 and Cyp2d22). Higher levels of H3K27me3 in prenatal liver coincided with the suppression of gene expression of some xenobiotic processing genes at that age (e.g. Cyp3a16). In conclusion, these data suggest that the epigenetic code is involved in the functional transition of the postnatal liver. This work was supported by National Institute of Health Grant 5P20 RR021940.

Cellular dynamics associated with the genome-wide epigenetic reprogramming in migrating primordial germ cells in mice

We previously reported that primordial germ cells (PGCs) in mice erase genome-wide DNA methylation and histone H3 lysine9 dimethylation (H3K9me2), and instead acquire high levels of tri-methylation of H3K27 (H3K27me3) during their migration, a process that might be crucial for the re-establishment of potential totipotency in the germline. We here explored a cellular dynamics associated with this epigenetic reprogramming. We found that PGCs undergo erasure of H3K9me2 and upregulation of H3K27me3 in a progressive, cell-by-cell manner, presumably depending on their developmental maturation. Before or concomitant with the onset of H3K9 demethylation, PGCs entered the G2 arrest of the cell cycle, which apparently persisted until they acquired high H3K27me3 levels. Interestingly, PGCs exhibited repression of RNA polymerase II-dependent transcription, which began after the onset of H3K9me2 reduction in the G2 phase and tapered off after the acquisition of high-level H3K27me3. The epigenetic reprogramming and transcriptional quiescence were independent from the function of Nanos3. We found that before H3K9 demethylation, PGCs exclusively repress an essential histone methyltransferase, GLP, without specifically upregulating histone demethylases. We suggest the possibility that active repression of an essential enzyme and subsequent unique cellular dynamics ensures successful implementation of genome-wide epigenetic reprogramming in migrating PGCs.

The genomic landscape of histone modifications in human T cells

To understand the molecular basis that supports the dynamic gene expression programs unique to T cells, we investigated the genomic landscape of activating histone modifications, including histone H3 K9/K14 diacetylation (H3K9acK14ac), H3 K4 trimethylation (H3K4me3), and the repressive histone modification H3 K27 trimethylation (H3K27me3) in primary human T cells. We show that H3K9acK14ac and H3K4me3 are associated with active genes required for T cell function and development, whereas H3K27me3 is associated with silent genes that are involved in development in other cell types. Unexpectedly, we find that 3,330 gene promoters are associated with all of these histone modifications. The gene expression levels are correlated with both the absolute and relative levels of the activating H3K4me3 and the repressive H3K27me3 modifications. Our data reveal that rapidly inducible genes are associated with the H3 acetylation and H3K4me3 modifications, suggesting they assume a chromatin structure poised for activation. In addition, we identified a subpopulation of chromatin regions that are associated with high levels of H3K4me3 and H3K27me3 but low levels of H3K9acK14ac. Therefore, these regions have a distinctive chromatin modification pattern and thus may represent a distinct class of chromatin domains.