Histone methylation regulates chromatin structure, transcription, and epigenetic state of the cell. Histone methylation is dynamically regulated by histone methylases and demethylases such as LSD1 and JHDM1, which mediate demethylation of di- and monomethylated histones. It has been unclear whether demethylases exist that reverse lysine trimethylation. We show the JmjC domain-containing protein JMJD2A reversed trimethylated H3-K9/K36 to di- but not mono- or unmethylated products. Overexpression of JMJD2A but not a catalytically inactive mutant reduced H3-K9/K36 trimethylation levels in cultured cells. In contrast, RNAi depletion of the C. elegans JMJD2A homolog resulted in an increase in general H3-K9Me3 and localized H3-K36Me3 levels on meiotic chromosomes and triggered p53-dependent germline apoptosis. Additionally, other human JMJD2 subfamily members also functioned as trimethylation-specific demethylases, converting H3-K9Me3 to H3-K9Me2 and H3-K9Me1, respectively. Our finding that this family of demethylases generates different methylated states at the same lysine residue provides a mechanism for fine-tuning histone methylation.

Many proteins that respond to DNA damage are recruited to DNA lesions. We used a proteomics approach that coupled isotopic labeling with chromatin fractionation and mass spectrometry to uncover proteins that associate with damaged DNA, many of which are involved in DNA repair or nucleolar function. We show that polycomb group members are recruited by poly(ADP ribose) polymerase (PARP) to DNA lesions following UV laser microirradiation. Loss of polycomb components results in IR sensitivity of mammalian cells and Caenorhabditis elegans. PARP also recruits two components of the repressive nucleosome remodeling and deacetylase (NuRD) complex, chromodomain helicase DNA-binding protein 4 (CHD4) and metastasis associated 1 (MTA1), to DNA lesions. PARP plays a role in removing nascent RNA and elongating RNA polymerase II from sites of DNA damage. We propose that PARP sets up a transient repressive chromatin structure at sites of DNA damage to block transcription and facilitate DNA repair. T he cellular response to DNA damage is initiated by the sensing of structural alterations in DNA that culminates in the activation of phosphoinositide-3-kinase-related protein kinases (PIKKs) that include the ataxia telangiectasia mutated (ATM) and ataxia telangiectasia and Rad3-related (ATR) kinases (1). With the help of mediators, ATM and ATR subsequently signal downstream to activate effector kinases checkpoint 1 (CHK1) and checkpoint 2 (CHK2), leading to transcriptional induction, cell-cycle arrest, DNA repair, senescence, or apoptosis. This DNA damage response induces the sequential recruitment of an extensive network of proteins to the sites of damage. For example, in response to double-strand breaks (DSBs), ATM phosphorylates histone H2AX adjacent to the break to initiate a H2AX-dependent concentration of proteins involved in the DNA damage response, such as mediator of DNA damage checkpoint protein 1 (MDC1), which recruits additional molecules of the ATM kinase. This recruitment effectively initiates a positive feedback loop that promotes the spread of γH2AX-flanking DSBs (2). Phosphorylation of MDC1 by ATM creates a motif that is recognized by the ubiquitin ligase ring finger 8 (RNF8) (3-6) that, with the help of ring finger 168 (RNF168), catalyzes the formation of lysine 63 (K63)-linked polyubiquitin chains that ultimately recruit the breast cancer 1 (BRCA1) A complex containing receptor-associated protein 80 (RAP80), Abraxas, BRCA1, new component of the BRCA1 A complex (NBA1), and BRCA1/BRCA2-containing complex, subunit 3 (BRCC36) (3-10) as well as p53 binding protein 1 (53BP1) and RAD18 homolog (RAD18) (3-8, 11).Several factors, such as Nijmegen breakage syndrome 1 (NBS1), 53BP1, and BRCA1, are recruited to the sites of damage in an H2AX-independent manner (12). However, these interactions appear to be more transient and may play a role as an initial response to DNA damage that is distinct from the extended association of factors via γH2AX. Several additional pathways also have been shown to direct the recruitment of vario...

Since the first histone lysine demethylase KDM1 (LSD1) was discovered in 2004, a great number of histone demethylases have been recognized and shown to play important roles in gene expression, as well as cellular differentiation and animal development. The chemical mechanisms and substrate specificities have already been extensively discussed elsewhere. This review focuses primarily on regulatory mechanisms that modulate demethylase recruitment and activity.

Since the discovery of the first histone lysine demethylase in 2004, two protein families with numerous members have been identified that demethylate various histone lysine residues. Initial studies of the histone lysine demethylases focused on their in vitro enzymatic activity but, more recently, model organisms have been used to examine the roles of these enzymes in vivo. Here, we review recent insights into the roles of the histone lysine demethylases in multiple aspects of development across various species, including in germline maintenance and meiosis, in early embryonic development and differentiation, and in hormone receptor-mediated transcriptional regulation.

The rapid growth and poor vascularization of solid tumors expose cancer cells to hypoxia, which promotes the metastatic phenotype by reducing intercellular adhesion and increasing cell motility and invasiveness. In this study, we found that hypoxia increased free NADH levels in cancer cells, promoting CtBP recruitment to the E-cadherin promoter. This effect was blocked by pyruvate, which prevents the NADH increase. Furthermore, hypoxia repressed Ecadherin gene expression and increased tumor cell migration, effects that were blocked by CtBP knockdown. We propose that CtBP senses levels of free NADH to control expression of cell adhesion genes, thereby promoting tumor cell migration under hypoxic stress.NADH ͉ E-cadherin ͉ metastasis ͉ HIF1␣ ͉ adhesion T he ability of tumors to metastasize is a hallmark of malignancy. A critical event during metastasis is the reduction of adhesion, which facilitates tumor cell invasion into surrounding tissues and vascular channels, ultimately leading to the development of new sites of cancer progression. E-cadherin-mediated cell-cell adhesion is essential for maintaining the homeostasis and architecture of epithelial tissues. Down-regulation of Ecadherin expression occurs concomitantly with dedifferentiation and invasion of epithelial cells during tumorigenesis (1, 2). Consequently, E-cadherin and its associated complex are thought to be key mediators of tumor cell invasion (3).Highly aggressive, rapidly growing tumors are exposed to hypoxia, which occurs as a consequence of high metabolic activity and inadequate blood supply (4). It has been proposed that hypoxia is the initiating event that sets tumors on the road to metastasis (5). We have shown that the transcriptional corepressor CtBP has the unique ability to sense levels of free nuclear NADH and transmit this information to complexes that regulate gene expression (6). Transcription of E-cadherin and several other cell adhesion proteins is known to be repressed by CtBP (7) via ZEB and other factors believed to interact with the E-cadherin promoter (8,9). CtBP binding to these transcriptional repressors is induced by elevations in free NADH (6). We propose that the redox-sensing property of CtBP provides a regulatory switch for E-cadherin expression under hypoxic conditions.In this study, we show that the transcriptional corepressor CtBP has a central role in cancer cell migration in response to hypoxia. Hypoxia increases free NADH levels, which promotes CtBP recruitment to the E-cadherin promoter, repressing Ecadherin gene expression and increasing tumor cell migration. Thus, the pathway we have described links tumor hypoxia to cell migration through NADH regulation of CtBP function.