JmjC Domain Research Articles

Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos

Nuclear Matrix (NuMat) is the structural and functional framework of the nucleus. It has been shown that attachment of chromatin to NuMat brings significant regulation of the transcriptional activity of particular genes; however, key components of NuMat involved in this process remain elusive. We have identified Lid (Little imaginal discs) as one of the components of NuMat. It belongs to the TrxG group of proteins involved in activation of important developmental genes. However, unlike other activator proteins of TrxG, Lid is a Jumonji protein involved in H3K4me3 demethylation. Here, we report the association of Lid and its various domains with NuMat which implicates its structural role in chromatin organization and epigenetic basis of cellular memory. We have found that both N and C terminal regions of this protein are capable of associating with NuMat. We have further mapped the association of individual domains and found that, PHD, ARID and JmjC domains can associate with NuMat individually. Moreover, deletion of N-terminal PHD finger does not alter Lid's NuMat association implying that although it is sufficient, yet, it is not necessary for Lid's structural role in NuMat. Based on our findings, we hypothesize that C terminal region of Lid which contains PHD fingers might be responsible for its NuMat association via protein-DNA interactions. However, for the N terminal region harboring both a PHD and an ARID finger, Lid anchors to the NuMat via both protein-protein and protein-DNA interactions. The association of JmjC domain with NuMat is the first report of the association of a demethylase domain with NuMat suggesting that Lid, a demethylase, being part of NuMat might be involved in regulating the chromatin dynamics via its NuMat association.

Phylogenetic and genomic analyses of the ribosomal oxygenases Riox1 (No66) and Riox2 (Mina53) provide new insights into their evolution

BackgroundTranslation of specific mRNAs can be highly regulated in different cells, tissues or under pathological conditions. Ribosome heterogeneity can originate from variable expression or post-translational modifications of ribosomal proteins. The ribosomal oxygenases RIOX1 (NO66) and RIOX2 (MINA53) modify ribosomal proteins by histidine hydroxylation. A similar mechanism is present in prokaryotes. Thus, ribosome hydroxylation may be a well-conserved regulatory mechanism with implications in disease and development. However, little is known about the evolutionary history of Riox1 and Riox2 genes and their encoded proteins across eukaryotic taxa.ResultsIn this study, we have analysed Riox1 and Riox2 orthologous genes from 49 metazoen species and have constructed phylogenomic trees for both genes. Our genomic and phylogenetic analyses revealed that Arthropoda, Annelida, Nematoda and Mollusca lack the Riox2 gene, although in the early phylum Cnidaria both genes, Riox1 and Riox2, are present and expressed. Riox1 is an intronless single-exon-gene in several species, including humans. In contrast to Riox2, Riox1 is ubiquitously present throughout the animal kingdom suggesting that Riox1 is the phylogenetically older gene from which Riox2 has evolved. Both proteins have maintained a unique protein architecture with conservation of active sites within the JmjC domains, a dimerization domain, and a winged-helix domain. In addition, Riox1 proteins possess a unique N-terminal extension domain. Immunofluorescence analyses in Hela cells and in Hydra vulgaris identified a nucleolar localisation signal within the extended N-terminal domain of human RIOX1 and an altered subnuclear localisation for the Hydra Riox2.ConclusionsConserved active site residues and uniform protein domain architecture suggest a consistent enzymatic activity within the Riox orthologs throughout evolution. However, differences in genomic architecture, like single exon genes and alterations in subnuclear localisation, as described for Hydra, point towards adaption mechanisms that may correlate with taxa- or species-specific requirements. The diversification of Riox1/Riox2 gene structures throughout evolution suggest that functional requirements in expression of protein isoforms and/or subcellular localisation of proteins may have evolved by adaptation to lifestyle.

UTX Affects Neural Stem Cell Proliferation and Differentiation through PTEN Signaling.

SummaryNeural stem cell (NSC) proliferation and differentiation in the developing brain is a complex process precisely regulated by intrinsic and extrinsic signals. Although epigenetic modification has been reportedly involved in the regulation of the cerebral cortex, whether UTX, an H3K27me3 demethylase, regulates the development of cerebral cortex during the embryonic period is unclear. In this study, we demonstrate that Utx deficiency by knockdown and conditional knockout increases NSC proliferation and decreases terminal mitosis and neuronal differentiation. Furthermore, we find that impairment of cortical development caused by lack of Utx is less significant in males than in females. In addition, UTX demethylates H3K27me3 at the Pten promoter and promotes Pten expression. P-AKT and P-mTOR levels are increased in the Utx conditional knockout cortices. Finally, Utx or Pten overexpression can rescue the impairment of brain development caused by Utx loss. These findings may provide important clues toward deciphering brain diseases.

Targeting glioma stem-like cell survival and chemoresistance through inhibition of lysine-specific histone demethylase KDM2B.

Glioblastoma (GBM) ranks among the most lethal cancers, with current therapies offering only palliation. Inter‐ and intrapatient heterogeneity is a hallmark of GBM, with epigenetically distinct cancer stem‐like cells (CSCs) at the apex. Targeting GSCs remains a challenging task because of their unique biology, resemblance to normal neural stem/progenitor cells, and resistance to standard cytotoxic therapy. Here, we find that the chromatin regulator, JmjC domain histone H3K36me2/me1 demethylase KDM2B, is highly expressed in glioblastoma surgical specimens compared to normal brain. Targeting KDM2B function genetically or pharmacologically impaired the survival of patient‐derived primary glioblastoma cells through the induction of DNA damage and apoptosis, sensitizing them to chemotherapy. KDM2B loss decreased the GSC pool, which was potentiated by coadministration of chemotherapy. Collectively, our results demonstrate KDM2B is crucial for glioblastoma maintenance, with inhibition causing loss of GSC survival, genomic stability, and chemoresistance.

JmjC domain proteins modulate circadian behaviors and sleep in Drosophila

Jumonji (JmjC) domain proteins are known regulators of gene expression and chromatin organization by way of histone demethylation. Chromatin modification and remodeling provides a means to modulate the activity of large numbers of genes, but the importance of this class of predicted histone-modifying enzymes for different aspects of post-developmental processes remains poorly understood. Here we test the function of all 11 non-lethal members in the regulation of circadian rhythms and sleep. We find loss of every Drosophila JmjC gene affects different aspects of circadian behavior and sleep in a specific manner. Together these findings suggest that the majority of JmjC proteins function as regulators of behavior, rather than controlling essential developmental programs.

Chromatin remodeling: demethylating H3K4me3 of type I IFNs gene by Rbp2 through interacting with Piasy for transcriptional attenuation.

Type I IFNs (IFNIs) are involved in the course of antiviral and antimicrobial activities; however, robust inductions of these can lead to host immunopathology. We have reported that the Pias (protein inhibitor of activated signal transducer and activator of transcription) family member, Piasy, possesses the ability to suppress IFNI transcriptions in mouse embryonic fibroblasts (MEFs), yet the specific molecular mechanism by which it acts remains elusive. Here, we identify that the H3K4me3 levels, one activation mark of genes, in MEFs that were stimulated by poly(I:C) were impaired by Piasy in the IFN-β gene. Piasy bound to the promoter region of the IFN-β gene in MEFs. Meanwhile, retinoblastoma binding protein 2 (Rbp2) was proven to be the only known and novel H3K4me3 demethylase that interacted with Piasy. Overexpression of Rbp2, but not its enzymatically inactive mutant Rbp2H483G/E485Q, retarded the transcription activities of IFNI, whereas small interfering RNA-mediated or short hairpin RNA-mediated knockdown of Rbp2 enhanced IFNI promoter responses. Above all, coexpression of Piasy and Rbp2 led to statistically less IFNI induction than overexpression of either Piasy or Rbp2 alone. Mechanistically, Piasy bound to the Jmjc domain (451-503 aa) of Rbp2 via its PINIT domain (101-218 aa), which is consistent with the domain required for their attenuation of transcription and H3K4me3 levels of IFNI genes. Our study demonstrates that Piasy may prevent exaggerated transcription of IFNI by Rbp2-mediated demethylation of H3K4me3 of IFNI, avoiding excessive immune responses.-Yu, X., Chen, H., Zuo, C., Jin, X., Yin, Y., Wang, H., Jin, M., Ozato, K., Xu, S. Chromatin remodeling: demethylating H3K4me3 of type I IFNs gene by Rbp2 through interacting with Piasy for transcriptional attenuation.

Abstract 12: KMD6A/UTX loss enhances the malignant phenotype of multiple myeloma and sensitizes cells to EZH2 inhibition

Abstract In multiple myeloma (MM), inactivating mutations and deletions encompassing the histone demethylase KDM6A locus are found in up to 10% of newly diagnosed patients and associated with poor prognosis. Future sequencing studies may show an increased incidence of mutation with disease relapse. KMD6A (also named UTX, Ubiquitously transcribed Tetratricopeptide repeat, X chromosome) belongs to a family of Jumonji-C (Jmj-C)-containing demethylases working as a scaffold for a multiprotein complex containing H3K4-specific methyltransferases KMT2D and/or KMT2C (MLL2/3), the histone acetyltransferase CBP/p300, and members of the SWI/SNF chromatin-remodeling complex. In a concerted manner this complex appears to remove the gene repression associated methylation of lysine 27 on histone H3 (H3K27me), a mark placed by EZH2. Hence loss-of-function mutations of KDM6A may affect the function of this complex, which is common in B-cell malignancies. We found that KDM6A act as a tumor suppressor in MM in vivo and in vitro, but how this exactly happens and which genes are affected is incompletely understood. We modeled the loss of KDM6A in MM in vitro, using a pair of cell lines, ARP-1 (KDM6A wild type) and ARD (homozygous KDM6A deletion), derived from the same MM patient. As well, we used CRISPR-Cas9 mediated genome editing to disrupt KDM6A gene in cell lines. We examined gene expression profiles in ARP-1 vs. ARD cells, and vs. ARD cells upon reexpression of KDM6A, in a doxycycline-inducible manner, by whole transcriptome (RNA sequencing). To understand how KDM6A demethylase activity contributes to tumor suppressive role of KDM6A, we abolished the demethylase activity using directed mutagenesis targeting the JmjC domain. Disruptive mutations in functional domain of KDM6A provide a growth advantage in MM cell in vitro. Many genes induced upon KDM6A add-back are found upregulated in KDM6A wild-type ARP-1 cells. Mass spectrometry analysis of these cell lines and the add-back system showed no difference in global H3K27me3 levels, suggesting that the tumor suppressive role of KDM6A does not involve alteration of H3K27 methylation or that the changes in this histone mark following KDM6A loss are loci-specific. Reexpression of JmjC-dead KDM6A and wt KDM6A had similar effect on growth and clonogenicity, suggesting that demethylase activity is dispensable. KDM6A demethylase activity is dispensable for the tumor-suppressive effect of KDM6A in MM. Loss of KDM6A alters the transcriptome of MM cells. We therefore hypothesized that the scaffolding properties of KDM6A may be essential for the tumor-suppressive role of KDM6A. We plan to use CRISPR-Cas9 mediated genome editing to create specific mutations and flag-insertion in KDM6A gene, in both cell lines and mouse model, to further investigate the molecular mechanism of KDM6A activity. Citation Format: Daphne Dupere-Richer, Teresa Ezponda, Christine Will, Eliza Caroline Small, Nobish Varghese, Patel Tej, Xiaoxiao Huang, Zheng Yupeng, Giovanni Tonon, Neil Kelleher, Jonathan Keats, Jonathan D. Licht. KMD6A/UTX loss enhances the malignant phenotype of multiple myeloma and sensitizes cells to EZH2 inhibition [abstract]. In: Proceedings of the Second AACR Conference on Hematologic Malignancies: Translating Discoveries to Novel Therapies; May 6-9, 2017; Boston, MA. Philadelphia (PA): AACR; Clin Cancer Res 2017;23(24_Suppl):Abstract nr 12.

JMJD8 is a novel endoplasmic reticulum protein with a JmjC domain

Jumonji C (JmjC) domain-containing proteins have been shown to regulate cellular processes by hydroxylating or demethylating histone and non-histone targets. JMJD8 belongs to the JmjC domain-only family that was recently shown to be involved in angiogenesis and TNF-induced NF-κB signaling. Here, we employed bioinformatic analysis and immunofluorescence microscopy to examine the physiological properties of JMJD8. We demonstrated that JMJD8 localizes to the lumen of endoplasmic reticulum and that JMJD8 forms dimers or oligomers in vivo. Furthermore, we identified potential JMJD8-interacting proteins that are known to regulate protein complex assembly and protein folding. Taken together, this work demonstrates that JMJD8 is the first JmjC domain-containing protein found in the lumen of the endoplasmic reticulum that may function in protein complex assembly and protein folding.

Two-domain analysis of JmjN-JmjC and PHD-JmjC lysine demethylases: Detecting an inter-domain evolutionary stress.

Residues at different positions of a multiple sequence alignment sometimes evolve together, due to a correlated structural or functional stress at these positions. Co-evolution has thus been evidenced computationally in multiple proteins or protein domains. Here, we wish to study whether an evolutionary stress is exerted on a sequence alignment across protein domains, i.e., on longer sequence separations than within a single protein domain. JmjC-containing lysine demethylases were chosen for analysis, as a follow-up to previous studies; these proteins are important multidomain epigenetic regulators. In these proteins, the JmjC domain is responsible for the demethylase activity, and surrounding domains interact with histones, DNA or partner proteins. This family of enzymes was analyzed at the sequence level, in order to determine whether the sequence of JmjC-domains was affected by the presence of a neighboring JmjN domain or PHD finger in the protein. Multiple positions within JmjC sequences were shown to have their residue distributions significantly altered by the presence of the second domain. Structural considerations confirmed the relevance of the analysis for JmjN-JmjC proteins, while among PHD-JmjC proteins, the length of the linker region could be correlated to the residues observed at the most affected positions. The correlation of domain architecture with residue types at certain positions, as well as that of overall architecture with protein function, is discussed. The present results thus evidence the existence of an across-domain evolutionary stress in JmjC-containing demethylases, and provide further insights into the overall domain architecture of JmjC domain-containing proteins.

Heme promotes transcriptional and demethylase activities of Gis1, a member of the histone demethylase JMJD2/KDM4 family.

The yeast Gis1 protein is a transcriptional regulator belonging to the JMJD2/KDM4 subfamily of demethylases that contain a JmjC domain, which are highly conserved from yeast to humans. They have important functions in histone methylation, cellular signaling and tumorigenesis. Besides serving as a cofactor in many proteins, heme is known to directly regulate the activities of proteins ranging from transcriptional regulators to potassium channels. Here, we report a novel mechanism governing heme regulation of Gis1 transcriptional and histone demethylase activities. We found that two Gis1 modules, the JmjN + JmjC domain and the zinc finger (ZnF), can bind to heme specifically in vitro. In vivo functional analysis showed that the ZnF, not the JmjN + JmjC domain, promotes heme activation of transcriptional activity. Likewise, measurements of the demethylase activity of purified Gis1 proteins showed that full-length Gis1 and the JmjN + JmjC domain both possess demethylase activity. However, heme potentiates the demethylase activity of full-length Gis1, but not that of the JmjN + JmjC domain, which can confer heme activation of transcriptional activity in an unrelated protein. These results demonstrate that Gis1 represents a novel class of multi-functional heme sensing and signaling proteins, and that heme binding to the ZnF stimulates Gis1 demethylase and transcriptional activities.

UTX-guided neural crest function underlies craniofacial features of Kabuki syndrome

Kabuki syndrome, a congenital craniofacial disorder, manifests from mutations in an X-linked histone H3 lysine 27 demethylase (UTX/KDM6A) or a H3 lysine 4 methylase (KMT2D). However, the cellular and molecular etiology of histone-modifying enzymes in craniofacial disorders is unknown. We now establish Kabuki syndrome as a neurocristopathy, whereby the majority of clinical features are modeled in mice carrying neural crest (NC) deletion of UTX, including craniofacial dysmorphism, cardiac defects, and postnatal growth retardation. Female UTX NC knockout (FKO) demonstrates enhanced phenotypic severity over males (MKOs), due to partial redundancy with UTY, a Y-chromosome demethylase-dead homolog. Thus, NC cells may require demethylase-independent UTX activity. Consistently, Kabuki causative point mutations upstream of the JmjC domain do not disrupt UTX demethylation. We have isolated primary NC cells at a phenocritical postmigratory timepoint in both FKO and MKO mice, and genome-wide expression and histone profiling have revealed UTX molecular function in establishing appropriate chromatin structure to regulate crucial NC stem-cell signaling pathways. However, the majority of UTX regulated genes do not experience aberrations in H3K27me3 or H3K4me3, implicating alternative roles for UTX in transcriptional control. These findings are substantiated through demethylase-dead knockin mutation of UTX, which supports appropriate facial development.

Large-scale examination of functional and sequence diversity of 2-oxoglutarate/Fe(II)-dependent oxygenases in Metazoa

BackgroundThe 2-oxoglutarate/Fe(II)-dependent oxygenase (2OG oxygenase) superfamily in Metazoa is responsible for protein modification, nucleic acid repair and/or modification, and fatty acid metabolism. MethodsPhylogenetic analysis, protein sequence similarity network (SSN) and other bioinformatics tools were used to analyze the evolutionary relationship and make functional inferences of Metazoa 2OG oxygenases. ResultsSixty-four 2OG oxygenases have been previously found in Homo sapiens; they catalyze two reactions: hydroxylation and demethylation. Phylogenetic analyses indicated that enzymes with similar domain architecture are always clustered together, and the redox function can be performed by the 2OG oxygenase domain or Jumonji C (JmjC) domain, where the JmjC domain is always fused to other functional domains. We used the SSN to make functional inferences and to conduct distribution analysis of Metazoa 2OG oxygenases. >11,000 putative 2OG oxygenases across Metazoa could be assigned potential functions based on the SSN. The multiple sequence alignments showed that the residues binding iron are most highly conserved in both the 2OG oxygenase domain and JmjC domain. In contrast, the residues binding oxoglutarate are quite different in the two domains: the 2OG oxygenase domain tends to have an Arg/Lys at the C terminus, whereas the JmjC domain, an Asn/Lys residue in the middle region. ConclusionsThe results indicated that gene duplication and vertical gene transfer have played important roles in 2OG oxygenase evolution in Metazoa and clarified the difference between the 2OG oxygenase domain and JmjC domain. General significanceThese findings expand the understanding of the diversity, evolution, and functions of 2OG oxygenases.

JMJ27, an Arabidopsis H3K9 histone demethylase, modulates defense against Pseudomonas syringae and flowering time.

Histone methylation is known to dynamically regulate diverse developmental and physiological processes. Histone methyl marks are written by methyltransferases and erased by demethylases, and result in modification of chromatin structure to repress or activate transcription. However, little is known about how histone methylation may regulate defense mechanisms and flowering time in plants. Here we report characterization of JmjC DOMAIN-CONTAINING PROTEIN 27 (JMJ27), an Arabidopsis JHDM2 (JmjC domain-containing histone demethylase 2) family protein, which modulates defense against pathogens and flowering time. JMJ27 is a nuclear protein containing a zinc-finger motif and a catalytic JmjC domain with conserved Fe(II) and α-ketoglutarate binding sites, and displays H3K9me1/2 demethylase activity both invitro and invivo. JMJ27 is induced in response to virulent Pseudomonas syringae pathogens and is required for resistance against these pathogens. JMJ27 is a negative modulator of WRKY25 (a repressor of defense) and a positive modulator of several pathogenesis-related (PR) proteins. Additionally, loss of JMJ27 function leads to early flowering. JMJ27 negatively modulates the major flowering regulator CONSTANS (CO) and positively modulates FLOWERING LOCUS C (FLC). Taken together, our results indicate that JMJ27 functions as a histone demethylase to modulate both physiological (defense) and developmental (flowering time) processes in Arabidopsis.

Systematic discovery of genetic modulation by Jumonji histone demethylases in Drosophila

Jumonji (JmjC) domain proteins influence gene expression and chromatin organization by way of histone demethylation, which provides a means to regulate the activity of genes across the genome. JmjC proteins have been associated with many human diseases including various cancers, developmental and neurological disorders, however, the shared biology and possible common contribution to organismal development and tissue homeostasis of all JmjC proteins remains unclear. Here, we systematically tested the function of all 13 Drosophila JmjC genes. Generation of molecularly defined null mutants revealed that loss of 8 out of 13 JmjC genes modify position effect variegation (PEV) phenotypes, consistent with their ascribed role in regulating chromatin organization. However, most JmjC genes do not critically regulate development, as 10 members are viable and fertile with no obvious developmental defects. Rather, we find that different JmjC mutants specifically alter the phenotypic outcomes in various sensitized genetic backgrounds. Our data demonstrate that, rather than controlling essential gene expression programs, Drosophila JmjC proteins generally act to “fine-tune” different biological processes.

Epe1 contributes to activation of AMPK by promoting phosphorylation of AMPK alpha subunit, Ssp2

AMP-activated protein kinase (AMPK) is a pivotal cellular energy sensor. It is activated by stresses that cause depletion of energy and initiates adaptive responses by regulating metabolism balance. AMPK forms αβγ heterotrimer. In fission yeast, activation of AMPK mainly depends on the phosphorylation of AMPKα subunit Ssp2 at Thr189 by upstream kinase Ssp1. However, not much is known about the regulation of this process. In this study, we identified Epe1 as a novel positive regulator of AMPK. Epe1, a jmjC-domain-containing protein, is best-known as a negative regulator of heterochromatin spreading. Although the novel role of Epe1 in regulation of AMPK relies on predicted iron- and 2-oxyglutarate-binding residues inside jmjC domain, it seems to be irrelevant to inhibition of heterochromatin spreading. Epe1 is associated with Ssp2 directly and promotes phosphorylation of Ssp2 upon various environmental stresses, including low-glucose, high-sodium, high-pH and oxidative conditions. Similar to Epe1, Jmj1 and Msc1 also contribute to phosphorylation of Ssp2. Deletion of epe1+ impairs downstream events following phosphorylation of Ssp2, including nuclear translocation of Ssp2, sexual differentiation and inhibition of fatty acid synthesis. Our study reveals a novel way in which a jmjC-domain-containing protein regulates adaptive response by directly binding to a principal sensor.

MoJMJ1, Encoding a Histone Demethylase Containing JmjC Domain, Is Required for Pathogenic Development of the Rice Blast Fungus, Magnaporthe oryzae

Histone methylation plays important roles in regulating chromatin dynamics and transcription in eukaryotes. Implication of histone modifications in fungal pathogenesis is, however, beginning to emerge. Here, we report identification and functional analysis of a putative JmjC-domain-containing histone demethylase in Magnaporthe oryzae. Through bioinformatics analysis, we identified seven genes, which encode putative histone demethylases containing JmjC domain. Deletion of one gene, MoJMJ1, belonging to JARID group, resulted in defects in vegetative growth, asexual reproduction, appressorium formation as well as invasive growth in the fungus. Western blot analysis showed that global H3K4me3 level increased in the deletion mutant, compared to wild-type strain, indicating histone demethylase activity of MoJMJ1. Introduction of MoJMJ1 gene into ΔMojmj1 restored defects in pre-penetration developments including appressorium formation, indicating the importance of histone demethylation through MoJMJ1 during infection-specific morphogenesis. However, defects in penetration and invasive growth were not complemented. We discuss such incomplete complementation in detail here. Our work on MoJMJ1 provides insights into H3K4me3-mediated regulation of infection-specific development in the plant pathogenic fungus.

SF-KDM2A binds to ribosomal RNA gene promoter, reduces H4K20me3 level, and elevates ribosomal RNA transcription in breast cancer cells.

Regulation of rRNA transcription is an important factor for control of cell proliferation. We previously found that the JmjC domain-containing demethylase KDM2A reduces H3K36me2 in the rRNA gene promoter and rRNA transcription under starvation, which results in suppression of cell proliferation. The KDM2A gene also produces another protein product, SF-KDM2A, which lacks a JmjC domain and has no demethylase activity. As yet, the function of SF-KDM2A is not clear. Recently, it was reported that KDM2A was frequently amplified and that elevated expression of KDM2A was significantly associated with short survival of breast cancer patients. SF-KDM2A was more abundant than full-length KDM2A in a subset of breast cancers. In the present study, we report that SF-KDM2A localized in nucleoli and bound to the rRNA gene promoter in breast cancer cells. Overexpression of SF-KDM2A stimulated the transcription of rRNA. While the zf-CXXC domain was required for SF-KDM2A binding to the rRNA gene promoter, SF-KDM2A with mutations in the zf-CXXC domain lost the binding to the rRNA gene promoter and did not stimulate rRNA transcription. Knockdown of SF-KDM2A reduced rRNA transcription and cell proliferation. When SF-KDM2A was overexpressed, a transcriptionally repressive mark, H4K20me3, in the rRNA gene promoter was specifically reduced in a zf-CXXC domain-dependent manner, and knockdown of SF-KDM2A increased the H4K20me3 level. Taken together, these results demonstrate that SF-KDM2A binds to the rRNA gene promoter, reduces the H4K20me3 level, and activates rRNA transcription, suggesting that the stimulation of rRNA transcription by SF-KDM2A may contribute to tumorigenesis in breast cancer.

Compounds and methods for inhibiting histone demethylases: a patent evaluation of US20160102096A1

ABSTRACTThe Jumonji C (JmjC) domain containing histone lysine demethylases have a clear role both in the development and in some diseases including inflammation and cancer. The histone lysine demethylases represent an attractive target for the identification of therapeutic agents and the pyridine derivatives are a scaffolds largely investigated for the identification and development of inhibitors of enzymes of the Jumonji family.This commentary is a scientific evaluation of a patent application US20160102096A1 that describes novel pyridine derivatives in which the introduction of specific substituents is used to modulate the selectivity profile of the inhibitors.

Epigenetic gene regulation by histone demethylases: emerging role in oncogenesis and inflammation.

Histone N-terminal tails of nucleosomes are the sites of complex regulation of gene expression through post-translational modifications. Among these modifications, histone methylation had long been associated with permanent gene inactivation until the discovery of Lys-specific demethylase (LSD1), which is responsible for dynamic gene regulation. There are more than 30 members of the Lys demethylase (KDM) family, and with exception of LSD1 and LSD2, all other KDMs possess the Jumonji C (JmjC) domain exhibiting demethylase activity and require unique cofactors, for example, Fe(II) and α-ketoglutarate. These cofactors have been targeted when devising KDM inhibitors, which may yield therapeutic benefit. KDMs and their counterpart Lys methyltransferases (KMTs) regulate multiple biological processes, including oncogenesis and inflammation. KDMs' functional interactions with retinoblastoma (Rb) and E2 factor (E2F) target promoters illustrate their regulatory role in cell cycle progression and oncogenesis. Recent findings also demonstrate the control of inflammation and immune functions by KDMs, such as KDM6B that regulates the pro-inflammatory gene expression and CD4+ T helper (Th) cell lineage determination. This review will highlight the mechanisms by which KDMs and KMTs regulate the target gene expression and how epigenetic mechanisms may be applied to our understanding of oral inflammation.

JMJD8 Regulates Angiogenic Sprouting and Cellular Metabolism by Interacting With Pyruvate Kinase M2 in Endothelial Cells.

Jumonji C (JmjC) domain-containing proteins modify histone and nonhistone proteins thereby controlling cellular functions. However, the role of JmjC proteins in angiogenesis is largely unknown. Here, we characterize the expression of JmjC domain-containing proteins after inducing endothelial differentiation of murine embryonic stem cells and study the function of JmjC domain-only proteins in endothelial cell (EC) functions. We identified a large number of JmjC domain-containing proteins regulated by endothelial differentiation of murine embryonic stem cells. Among the family of JmjC domain-only proteins, Jmjd8 was significantly upregulated on endothelial differentiation. Knockdown of Jmjd8 in ECs significantly decreased in vitro network formation and sprouting in the spheroid assay. JMJD8 is exclusively detectable in the cytoplasm, excluding a function as a histone-modifying enzyme. Mass spectrometry analysis revealed JMJD8-interacting proteins with known functions in cellular metabolism like pyruvate kinase M2. Accordingly, knockdown of pyruvate kinase M2 in human umbilical vein ECs decreased endothelial sprouting in the spheroid assay. Knockdown of JMJD8 caused a reduction of EC metabolism as measured by Seahorse Bioscience extracellular flux analysis. Conversely, overexpression of JMJD8 enhanced cellular oxygen consumption rate of ECs, reflecting an increased mitochondrial respiration. Jmjd8 is upregulated during endothelial differentiation and regulates endothelial sprouting and metabolism by interacting with pyruvate kinase M2.