How substrate specificity is imposed on a histone demethylase—lessons from KDM2A

Histone lysine methylation and demethylation regulate histone methylation dynamics, which impacts chromatin structure and function. To read and erase the methylated histone residues, lysine demethylases must specifically recognize the histone sequences and methylated sites and discriminate the degree of these methylations. In this issue of Genes & Development, Cheng and colleagues (pp. 1758–1771) determine a crystal structure of histone lysine demethylase KDM2A that specifically targets lower degrees of H3K36 methylation. The results reveal the structural basis for H3K36 substrate specificity and suggest mechanisms of Lys36 demethylation. This KDM2A–H3K36 complex structure, coupled with functional studies, provides needed insight into the process and regulation of histone demethylation.     

A molecular threading mechanism underlies Jumonji lysine demethylase KDM2A regulation of methylated H3K36

The dynamic reversible methylation of lysine residues on histone proteins is central to chromatin biology. Key components are demethylase enzymes, which remove methyl moieties from lysine residues. KDM2A, a member of the Jumonji C domain-containing histone lysine demethylase family, specifically targets lower methylation states of H3K36. Here, structural studies reveal that H3K36 specificity for KDM2A is mediated by the U-shaped threading of the H3K36 peptide through a catalytic groove within KDM2A. The side chain of methylated K36 inserts into the catalytic pocket occupied by Ni²⁺ and cofactor, where it is positioned and oriented for demethylation. Key residues contributing to K36me specificity on histone H3 are G33 and G34 (positioned within a narrow channel), P38 (a turn residue), and Y41 (inserts into its own pocket). Given that KDM2A was found to also bind the H3K36me3 peptide, we postulate that steric constraints could prevent α-ketoglutarate from undergoing an “off-line”-to-“in-line” transition necessary for the demethylation reaction. Furthermore, structure-guided substitutions of residues in the KDM2A catalytic pocket abrogate KDM2A-mediated functions important for suppression of cancer cell phenotypes. Together, our results deduce insights into the molecular basis underlying KDM2A regulation of the biologically important methylated H3K36 mark.     

Genetic variants in the KDM6B gene are associated with neurodevelopmental delays and dysmorphic features

Lysine‐specific demethylase 6B (KDM6B) demethylates trimethylated lysine‐27 on histone H3. The methylation and demethylation of histone proteins affects gene expression during development. Pathogenic alterations in histone lysine methylation and demethylation genes have been associated with multiple neurodevelopmental disorders. We have identified a number of de novo alterations in the KDM6B gene via whole exome sequencing (WES) in a cohort of 12 unrelated patients with developmental delay, intellectual disability, dysmorphic facial features, and other clinical findings. Our findings will allow for further investigation in to the role of the KDM6B gene in human neurodevelopmental disorders.     

组蛋白H3K9甲基修饰酶在2周、4周和6周龄小鼠肝脏中的表达

目的 探讨不同周龄小鼠肝脏组蛋白H3K9甲基转移酶(KMT)和去甲基化酶(KDM)的表达.方法 取2周、4周和6周龄BALB/c雄性小鼠肝脏组织,分别提取总mRNA和蛋白质,应用实时定量反转录-聚合酶链式反应(RT-qPCR)确定几种H3K9甲基转移酶和去甲基化酶的表达差异,使用Western blotting 检测两...     

KDM4A,KDM4B and KDM4C in non-small cell lung cancer

KDM4A, KDM4B and KDM4D are lysine demethylases which demethylate H3 at lysine K9 and K36 sites, additionally KDM4D also the H1.4 linker histone at K26 lysine. Lysine methylation changes can repress or induce gene expression at specific sites thus influencing cellular functions. We analysed the immunohistochemical expression of KDM4A, KDM4B and KDM4D in a clinical material of 188 patients with lung carcinomas. There were 132 (70%) squamous cell carcinomas, 53 (28%) adenocarcinomas and 3 (2%) large cell carcinomas in the study. Additionally, the trimethylated state of chromatin was detected with an antibody to trimethylated H3K9 residue. Nuclear KDM4A and KDM4D were associated with the presence of lymph node metastases in tumors. Cytoplasmic KDM4A was associated with poor survival of the patients (P = 0.015) and with a shorter recurrence free interval (P = 0.028). KDM4A and KDM4D appear to have a significant role in the metastatic spread of lung carcinomas. The findings are also in line with their proposed involvement in mechanisms associated with cell proliferation, apoptosis and DNA repair.     

Ing1 functions in DNA demethylation by directing Gadd45a to H3K4me3

Active DNA demethylation regulates epigenetic gene activation in numerous processes, but how the target site specificity of DNA demethylation is determined and what factors are involved are still poorly understood. Here we show that the tumor suppressor inhibitor of growth protein 1 (Ing1) is required for targeting active DNA demethylation. Ing1 functions by recruiting the regulator of DNA demethylation growth arrest and DNA damage protein 45a (Gadd45a) to histone H3 trimethylated at Lys 4 (H3K4me3). We show that reduced H3K4 methylation impairs recruitment of Gadd45a/Ing1 and gene-specific DNA demethylation. Our results indicate that histone methylation directs DNA demethylation.     

Enhancer-associated H3K4 monomethylation by Trithorax-related,the Drosophila homolog of mammalian Mll3/Mll4

Monomethylation of histone H3 on Lys 4 (H3K4me1) and acetylation of histone H3 on Lys 27 (H3K27ac) are histone modifications that are highly enriched over the body of actively transcribed genes and on enhancers. Although in yeast all H3K4 methylation patterns, including H3K4me1, are implemented by Set1/COMPASS (complex of proteins associated with Set1), there are three classes of COMPASS-like complexes in Drosophila that could carry out H3K4me1 on enhancers: dSet1, Trithorax, and Trithorax-related (Trr). Here, we report that Trr, the Drosophila homolog of the mammalian Mll3/4 COMPASS-like complexes, can function as a major H3K4 monomethyltransferase on enhancers in vivo. Loss of Trr results in a global decrease of H3K4me1 and H3K27ac levels in various tissues. Assays with the cut wing margin enhancer implied a functional role for Trr in enhancer-mediated processes. A genome-wide analysis demonstrated that Trr is required to maintain the H3K4me1 and H3K27ac chromatin signature that resembles the histone modification patterns described for enhancers. Furthermore, studies in the mammalian system suggested a role for the Trr homolog Mll3 in similar processes. Since Trr and mammalian Mll3/4 complexes are distinguished by bearing a unique subunit, the H3K27 demethylase UTX, we propose a model in which the H3K4 monomethyltransferases Trr/Mll3/Mll4 and the H3K27 demethylase UTX cooperate to regulate the transition from inactive/poised to active enhancers.     

组蛋白赖氨酸去甲基化与基因调控

随着组蛋白赖氨酸去甲基化酶的发现,证实组蛋白赖氨酸甲基化是一个可以逆转的组蛋白表遗传修饰。赖氨酸特异性组蛋白去甲基化酶1(lysinespecificdemethylase1,LSD1)是一个FAD依赖性胺氧化酶,它能够特异性脱去单甲基化和二甲基化H3K4和H3K9位点上的甲基基团。JmjC蛋白JHDM1、JHDM2、JMJD23个亚家族都具有组蛋白赖氨酸去甲基化酶活性。目前证实组蛋白甲基化与去甲基化失平衡与肿瘤发生相关。组蛋白赖氨酸去甲基化酶有可能成为一个新的抗肿瘤治疗靶标。     

H3K27me3 demethylase UTX regulates the differentiation of a subset of bipolar cells in the mouse retina

Di‐ and trimethylation of lysine 27 on histone 3 (H3K27me2/3) is a critical gene repression mechanism. We previously showed that down‐regulation of the H3K27 demethylase, Jumonji domain‐containing protein 3 (JMJD3), resulted in a reduced number of protein kinase C (PKC)α‐positive rod ON‐bipolar cells. In this work, we focused on the role of another H3K27 demethylase, ubiquitously transcribed tetratricopeptide repeat X chromosome (UTX), in retinal development. UTX was expressed in the retinal progenitor cells of the embryonic mouse retina and was observed in the inner nuclear layer during late retinal development and in the mature retina. The short hairpin RNA‐mediated knockdown of Utx in a mouse retinal explant led to a reduced number of PKCα‐positive rod ON‐bipolar cells. However, other retinal subtypes were unaffected by this knockdown. Using a retina‐specific knockout of Utx in mice, the in vivo effects of UTX down‐regulation were examined. Again, the number of PKCα‐positive rod ON‐bipolar cells was reduced, and no other apparent phenotypes, including retinal progenitor proliferation, apoptosis or differentiation, were observed. Finally, we examined retina‐specific Utx and Jmjd3 double‐knockout mice and found that although the number of rod ON‐bipolar cells was reduced, no additional effects from the loss of Utx and Jmjd3 were observed. Taken together, our data show that UTX contributes to retinal differentiation in a lineage‐specific manner.     

Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A

Endogenous retroviruses (ERVs) constitute a substantial portion of mammalian genomes, and their retrotransposition activity helped to drive genetic variation, yet their expression is tightly regulated to prevent unchecked amplification. We generated a series of mouse mutants and embryonic stem (ES) cell lines carrying "deletable" and "rescuable" alleles of the lysine-specific demethylase LSD1/KDM1A. In the absence of KDM1A, the murine endogenous retrovirus MuERV-L/MERVL becomes overexpressed and embryonic development arrests at gastrulation. A number of cellular genes normally restricted to the zygotic genome activation (ZGA) period also become up-regulated in Kdm1a mutants. Strikingly, many of these cellular genes are flanked by MERVL sequences or have cryptic LTRs as promoters that are targets of KDM1A repression. Using genome-wide epigenetic profiling of Kdm1a mutant ES cells, we demonstrate that this subset of ZGA genes and MERVL elements displays increased methylation of histone H3K4, increased acetylation of H3K27, and decreased methylation of H3K9. As a consequence, Kdm1a mutant ES cells exhibit an unusual propensity to generate extraembryonic tissues. Our findings suggest that ancient retroviral insertions were used to co-opt regulatory sequences targeted by KDM1A for epigenetic silencing of cell fate genes during early mammalian embryonic development.