Histone methylation is a dynamic process that participates in a diverse array of cellular processes and has been found to associate with cancer. Recently, several histone demethylases have been identified that catalyze the removal of methylation from histone H3 lysine residues. Through bioinformatic and biochemical analysis, we identified JARID1B as a H3K4 demethylase. Overexpression of JARID1B resulted in loss of tri-, di-, and monomethyl H3K4 but did not affect other histone lysine methylations. In vitro biochemical experiments demonstrated that JARID1B directly catalyzes the demethylation. The enzymatic activity requires the JmjC domain and uses Fe(II) and ␣-ketoglutarate as cofactors. Furthermore, we found that JARID1B is up-regulated in prostate cancer tissues, compared with benign prostate samples. We also demonstrated that JARID1B associates with androgen receptor and regulates its transcriptional activity. Thus, we identified JARID1B as a demethylase capable of removing three methyl groups from histone H3 lysine 4 and up-regulated in prostate cancer. Histone methylation plays an important role in regulating chromatin dynamics and transcription (1). Methylation can occur on either arginine or lysine residues (2). Each lysine can undergo three distinct stages of methylation, having either one (mono), two (di), or three (tri) methyl groups covalently bonded to the amine group of the lysine side chain, and arginine can be mono-or dimethylated (3). Depending on specific residues, methylation can either activate or repress transcription. In general, lysine methylation at H3K9, H3K27, and H4K20 is associated with transcriptional repression, whereas methylation at H3K4, H3K36, and H3K79 is associated with transcriptional activation. However, recent findings have blurred this generality. For example, methylation at H3K9 can result in transcriptional activation, and methylation at H3K36 can repress transcription (4, 5).Methylation had long been considered a stable modification, but recent studies have proved otherwise (6-16). The first histone demethylase identified is LSD1, which can remove di-and monomethylation from H3K4 by using an amine oxidase reaction (8). Subsequently, a JmjC domain-containing protein was identified to possess histone demethylase activity, and the JmjC domain was shown as a demethylase signature motif (9). This class of enzymes catalyzes the removal of methylation by using a hydroxylation reaction and required iron and ␣-ketoglutarate as cofactors. Based on this demethylase signature motif, several proteins were identified to be histone lysine demethylases (6,7,(10)(11)(12)(13)(14)(15)(16).Prostate cancer is the most common nonskin cancer and the second leading cause of cancer in America. Histone methylation has been suggested to be associated with prostate cancer. For example, it was demonstrated that histone methylations and acetylations can be used to predict the risk of prostate cancer recurrence (17). In addition, EZH2, a H3K27 methyltransferase, is shown to be involved in progression...

Histone methylation is an important epigenetic phenomenon that participates in a diverse array of cellular processes and has been found to be associated with cancer. Recent identification of several histone demethylases has proved that histone methylation is a reversible process. Through a candidate approach, we have biochemically identified JMJD3 as an H3K27 demethylase. Transfection of JMJD3 into HeLa cells caused a specific reduction of trimethyl H3K27, but had no effect on di-and monomethyl H3K27, or histone lysine methylations on H3K4 and H3K9. The enzymatic activity requires the JmjC domain and the conserved histidine that has been suggested to be important for a cofactor binding. In vitro biochemical experiments demonstrated that JMJD3 directly catalyzes the demethylation. In addition, we found that JMJD3 is upregulated in prostate cancer, and its expression is higher in metastatic prostate cancer. Thus, we identified JMJD3 as a demethylase capable of removing the trimethyl group from histone H3 lysine 27 and upregulated in prostate cancer.

Histone lysine methylation can be removed by JmjC domain-containing proteins in a sequence-and methylationstate-specific manner. However, how substrate specificity is determined and how the enzymes are regulated were largely unknown. We recently found that ceKDM7A, a PHD-and JmjC domain-containing protein, is a histone demethylase specific for H3K9me2 and H3K27me2, and the PHD finger binding to H3K4me3 guides the demethylation activity in vivo. To provide structural insight into the molecular mechanisms for the enzymatic activity and the function of the PHD finger, we solved six crystal structures of the enzyme in apo form and in complex with single or two peptides containing various combinations of H3K4me3, H3K9me2, and H3K27me2 modifications. The structures indicate that H3K9me2 and H3K27me2 interact with ceKDM7A in a similar fashion, and that the peptide-binding specificity is determined by a network of specific interactions. The geometrical measurement of the structures also revealed that H3K4me3 associated with the PHD finger and H3K9me2 bound to the JmjC domain are from two separate molecules, suggesting a trans-histone peptide-binding mechanism. Thus, our systemic structural studies reveal not only the substrate recognition by the catalytic domain but also more importantly, the molecular mechanism of dual specificity of ceDKM7A for both H3K9me2 and H3K27me2.