Lysine-specific demethylase 1 inhibitor rescues the osteogenic ability of mesenchymal stem cells under osteoporotic conditions by modulating H3K4 methylation

Bone tissue engineering may be hindered by underlying osteoporosis because of a decreased osteogenic ability of autologous seed cells and an unfavorably changed microenvironment in these patients. Epigenetic regulation plays an important role in the developmental origins of osteoporosis; however, few studies have investigated the potential of epigenetic therapy to improve or rescue the osteogenic ability of bone marrow mesenchymal stem cells(BMMSCs) under osteoporotic conditions. Here, we investigated pargyline, an inhibitor of lysine-specific demethylase 1(LSD1), which mainly catalyzes the demethylation of the di- and mono-methylation of H3K4. We demonstrated that 1.5 mmol·Lpargyline was the optimal concentration for the osteogenic differentiation of human BMMSCs. Pargyline rescued the osteogenic differentiation ability of mouse BMMSCs under osteoporotic conditions by enhancing the dimethylation level of H3K4 at the promoter regions of osteogenesis-related genes. Moreover, pargyline partially rescued or prevented the osteoporotic conditions in aged or ovariectomized mouse models, respectively. By introducing the concept of epigenetic therapy into the field of osteoporosis, this study demonstrated that LSD1 inhibitors could improve the clinical practice of MSC-based bone tissue engineering and proposes their novel use to treat osteoporosis.

Di-and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair

Histone H3 Lys36(H3K36)methylation and its associated modifiers are crucial for DNA double-strand break(DSB)repair,but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is unclear.Here,we unveil the distinct roles of H3K36 dimethylation(H3K36me2)and H3K36 trimethylation(H3K36me3)in DSB repair via non-homologous end joining(NHEJ)or homologous recombination(HR).Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency.y Ku70 and Rfa1 bind H3K36me2-or H3K36me3-modified peptides and chromatin,respectively.Disrupting these interactions impairs y Ku70 and Rfa1 recruitment to damaged H3K36me2-or H3K36me3-rich loci,increasing DNA damage sensitivity and decreasing repair efficiency.Conversely,H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit y Ku70 or Rfa1 under DSB stress.Importantly,human KU70 and RPA1,the homologs of y Ku70 and Rfa1,exclusively associate with H3K36me2 and H3K36me3 in a conserved manner.These findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways,highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.

Structural insights into a novel histone demethylase PHF8

Dynamic regulation of histone methylation/demethylation plays an important role during development. Mutations and truncations in human plant homeodomain （PHD） finger protein 8 （PHF8） are associated with X-linked mental retardation and facial anomalies, such as a long face, broad nasal tip, cleft lip/cleft palate and large hands, yet its molecular function and structural basis remain unclear. Here, we report the crystal structures of the catalytic core of PHF8 with or without α-ketoglutarate （α-KG） at high resolution. Biochemical and structural studies reveal that PHF8 is a novel histone demethylase specific for di- and mono-methylated histone H3 lysine 9 （H3K9me2/1）, but not for H3K9me3. Our analyses also reveal how human PHF8 discriminates between methylation states and achieves sequence specificity for methylated H3K9. The in vitro demethylation assay also showed that the F279S mutant observed in clinical patients possesses no demethylation activity, suggesting that loss of enzymatic activity is crucial for pathogenesis of PHF8 patients. Taken together, these results will shed light on the molecular mechanism underlying PHF8-associated developmental and neurological diseases.

High auxin stimulates callus through SDG8-mediated histone H3K36 methylation in Arabidopsis

Callus induction,which results in fate transition in plant cells,is considered as the first and key step for plant regeneration.This process can be stimulated in different tissues by a callus-inducing medium(CIM),which contains a high concentration of phytohormone auxin.Although a few key regulators for callus induction have been identified,the multiple aspects of the regulatory mechanism driven by high levels of auxin still need further investigation.Here,we find that high auxin induces callus through a H3 K36 histone methylation-dependent mechanism,which requires the methyltransferase SET DOMAIN GROUP 8(SDG8).During callus induction,the increased auxin accumulates SDG8 expression through a TIR1/AFBs-based transcriptional regulation.SDG8 then deposits H3 K36 me3 modifications on the loci of callus-related genes,including a master regulator WOX5 and the cell proliferation-related genes,such as CYCB1.1.This epigenetic regulation in turn is required for the transcriptional activation of these genes during callus formation.These findings suggest that the massive transcriptional reprogramming for cell fate transition by auxin during callus formation requires epigenetic modifications including SDG8-mediated histone H3 K36 methylation.Our results provide insight into the coordination between auxin signaling and epigenetic regulation during fundamental processes in plant development.

Lysine-specific Demethylase 1 Represses THP-1 Monocyte-to-macrophage Differentiation

Objective To investigate the role of lysine-specific demethylase 1 （LSD1） in the process of THP-1 monocyte-to-macrophage differentiation. Methods Quantitative reverse transcription-polymerase chain reaction （qRT-PCR） and Western blotting were performed to analyze the expression of LSD1 and interleukin-6 （IL-6） in THP-1 monocytes and THP-l-derived macrophages. Chromatin immunoprecipitation （ChiP） assay was applied to detect the occupancy of LSD1 and H3K4 methylation at IL-6 promoter during THP-1 monocyte-to-macrophage differentiation. IL-6 mRNA level and H3K4 methylation at IL-6 promoter were analyzed using qRT-PCR and ChiP assay in LSD 1 -knockdown THP- 1 cells treated with 12-O-tetradecanoylphorbol- 13-acetate （TPA） for 0 4, 8, 12, and 24 hours. Fluorescence activated flow cytometry was performed to reveal the percentage of macrophages differentiated from THP- 1 monocytes. Results The expression of LSD1 reduced during THP-1 monocyte-to-macrophage differentiation （P〈0.01）. LSD1 occupancy decreased and H3K4 methylation increased at IL-6 promoter during the differentiation. With knockdown of LSD1, H3K4 methylation at IL-6 promoter was found increased after TPA treatment at different times points （all P〈0.05, except 24 hours）. The percentage of macrophages increased significantly in theTHP-I cells with LSD1 knockdown （P〈0.05）. Conclusions LSD1 is repressed during the monocyte-to-macrophage differentiation of THP-1 cells. Suppression of LSD 1-mediated H3K4 demethylation may be required for THP-1 monocyte-to-macrophage differentiation.

Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation

SETD2 is the only enzyme responsible for transcription-coupled histone H3 lysine 36 trimethylation(H3K36me3).Mutations in SETD2 cause human diseases including cancer and developmental defects.In mice,Setd2 is essential for embryonic vascular remodeling.Given that many epigenetic modifiers have recently been found to possess noncatalytic functions,it is unknown whether the major function(s)of Setd2 is dependent on its catalytic activity or not.Here,we established a site-specific knockin mouse model harboring a cancer patientderived catalytically dead Setd2(Setd2-CD).We found that the essentiality of Setd2 in mouse development is dependent on its methyltransferase activity,as the Setd2 CD/CD and Setd2^(−/−)mice showed similar embryonic lethal phenotypes and largely comparable gene expression patterns.However,compared with Setd2^(−/−),the Setd2 CD/CD mice showed less severe defects in allantois development,and single-cell RNA-seq analysis revealed differentially regulated allantois-specific 5′Hoxa cluster genes in these two models.Collectively,this study clarifies the importance of Setd2 catalytic activity in mouse development and provides a new model for comparative study of previously unrecognized Setd2 functions.

The Intronic cis Element SE1 Recruits trans-Acting Repressor Complexes to Repress the Expression of ELONGATED UPPERMOST INTERNODE1 in Rice

Plant height has a major effect on grain yield in crops such as rice （Oryza sativa）, and the hormone gibberellic acid （GA） regulates many developmental processes that feed into plant height. Rice ELONGATED UPPERMOST INTERNODE1 （Euil） encodes a GA-deactivating enzyme governing elongation of the uppermost internode. The expression of Euil is finely tuned, thereby maintaining homeostasis of endogenous bioactive GA and producing plants of normal plant height. Here, we identified a dominant dwarf mutant, dEuil, caused by the deletion of an RY motif-containing cis-silencing element （SE1） in the intron of Euil. Detailed genetic and molecular analysis of SE1 revealed that this intronic cis element recruits at least one trans-acting repressor complex, containing the B3 repressors OsVAL2 and OsGD1, the SAP18 corepressor, and the histone deacetylase OsHDA710, to negatively regulate the expression of Euil. This com- plex generates closed chromatin at Euil, suppressing Euil expression and modulating GA homeostasis. Loss of SE1 or dysfunction of the complex components impairs histone deacetylation and H3K27me3 methylation of Euil chromatin, thereby increasing Euil transcription and decreasing bioactive GA, producing dwarfism in rice. Together, our results reveal a novel silencing mechanism in which the intronic cis element SE1 negatively regulates Euil expression via repressor complexes that modulate histone deacetylation and/or methylation.

A chromatin modulator sustains self-renewal and enables differentiation of postnatal neural stem and progenitor cells

It remains unknown whether H3K4 methylation,an epigenetic modification associated with gene activation,regulates fate determination of the postnatal neural stem and progenitor cells(NSPCs).By inactivating the Dpy30 subunit of the major H3K4 methyltransferase complexes in specific regions of mouse brain,we demonstrate a crucial role of efficient H3K4 methylation in maintaining both the self-renewal and differentiation capacity of postnatal NSPCs.Dpy30 deficiency disrupts development of hippocampus and especially the dentate gyrus and subventricular zone,the major regions for postnatal NSC activities.Dpy30 is indispensable for sustaining the self-renewal and proliferation of NSPCs in a cell-intrinsic manner and also enables the differentiation of mouse and human neural progenitor cells to neuronal and glial lineages.Dpy30 directly regulates H3K4 methylation and the induction of several genes critical in neurogenesis.These findings link a prominent epigenetic mechanism of gene expression to the fundamental properties of NSPCs and may have implications in neurodevelopmental disorders.

OsASHL1 and OsASHL2,two members of the COMPASS-like complex,control floral transition and plant development in rice

COMPASS or COMPASS-like is a highly conserved polyprotein complex in eukaryotes that is often involved in methylation of histone H3 lysine 4(H3K4).However,the biological function of this complex in rice(Oryza sativa)is unclear.Here,we report the identifiction of their functions in growth and development.The osashl1osashl2 double mutant shows a dwarf and late-flowering phenotype.Lower expression of Ehd1,OsVIL4,and OsMADS51 in the osashl1 osashl2 double mutant background accompanies a delayed vegetative growth phase and photoperiod-sensitive phase compared with that in wild type.Notably,there is less H3K4mono-,di-and tri-methylation genome-wide in the double mutant,in particular less H3K4 tri-methylation at OsVIL4.Consistent with this result,knockout of OsVIL4 gives rise to a late-flowering phenotype similar to that of the osashl1 osashl2 double mutant,suggesting that OsVIL4 is a target of the COMPASS-like complex.In addition,the expression of key genes in brassinosteroid and gibberellic acid metabolism is altered in the osashl1 osashl2 double mutant,suggesting that the COMPASS-like complex regulates plant growth and development by modulating the levels of these two phytohormones.In summary,we demonstrate that OsASHL1 and OsASHL2 are important for floral transition and plant development.

Conservation and divergence of the histone H2B monoubiquitination pathway from yeast to humans and plants

Histone ubiquitination plays a critical role in the regulation of transcription,and histone H2B monoubiquitination(H2Bub1)is mainly associated with transcriptional activation.Recent studies in yeast,humans,and Arabidopsis have revealed the conservation of chromatin modification via H2Bub1 during evolution.Rad6-Bre1 and their homologs are responsible for H2B monoubiquitination in diverse eukaryotic organisms,and the PAF complex is required for H2Bub1 to proceed.H2Bub1 is involved in many developmental processes in yeast,humans,and Arabidopsis,and it activates gene transcription by regulating the H3K4 methylation state.Notably,the level of H3K4 methylation is entirely dependent on H2Bub1 in yeast and humans,whereas the H3K4 methylation level of only a small number of genes in Arabidopsis is dependent on H2Bub1.In this review,we summarize the enzymes involved in H2B monoubiquitination and deubiquitination,and discuss the biologic functions of H2Bub1 in different organisms.In addition,we focus on recent advances in our understanding of the molecular mechanisms that enable H2Bub1 to perform its function.