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Epigenomics Mar 2023
Topics: Humans; DNA Demethylation; 5-Methylcytosine; Embryonic Development; DNA Methylation
PubMed: 37191057
DOI: 10.2217/epi-2023-0104 -
TET Enzymes in the Immune System: From DNA Demethylation to Immunotherapy, Inflammation, and Cancer.Annual Review of Immunology Jun 2024Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine... (Review)
Review
Ten-eleven translocation (TET) proteins are iron-dependent and α-ketoglutarate-dependent dioxygenases that sequentially oxidize the methyl group of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). All three epigenetic modifications are intermediates in DNA demethylation. TET proteins are recruited by transcription factors and by RNA polymerase II to modify 5mC at enhancers and gene bodies, thereby regulating gene expression during development, cell lineage specification, and cell activation. It is not yet clear, however, how the established biochemical activities of TET enzymes in oxidizing 5mC and mediating DNA demethylation relate to the known association of TET deficiency with inflammation, clonal hematopoiesis, and cancer. There are hints that the ability of TET deficiency to promote cell proliferation in a signal-dependent manner may be harnessed for cancer immunotherapy. In this review, we draw upon recent findings in cells of the immune system to illustrate established as well as emerging ideas of how TET proteins influence cellular function.
Topics: Humans; Neoplasms; Animals; Inflammation; Immunotherapy; Dioxygenases; DNA Demethylation; Immune System; Epigenesis, Genetic; Proto-Oncogene Proteins; DNA Methylation; DNA-Binding Proteins; Mixed Function Oxygenases
PubMed: 38360546
DOI: 10.1146/annurev-immunol-080223-044610 -
Advances in Experimental Medicine and... 2022The regulation of the genome relies on the overlying epigenome to instruct, define, and restrict the activities of cellular differentiation and growth integral to...
The regulation of the genome relies on the overlying epigenome to instruct, define, and restrict the activities of cellular differentiation and growth integral to embryonic development, as well as defining the key activities of terminally differentiated cell types. These instructions are positioned as readers, writers, and erasers in their functional roles. Among the sizeable repertoire of epigenetic instructions, DNA methylation is perhaps the best understood process. In mammals, multiple cycles of reprogramming, the addition and removal of DNA methylation coupled with modulation of chromatin post-translational modifications (PMTs), constitute critical phases when the developing embryo must negotiate lineage specification and commitment events which serve to canalise development. During these reprogramming events the DNA methylation instruction is often removed, thereby allowing a change in developmental restriction, resulting in a return to a more plastic and pluripotent state. Thus, in germline reprogramming, DNA demethylation is essential in order to give rise to fully functional gametes which are inherited across generations and poised to restore totipotency. A similar return to a less differentiated state can also be achieved experimentally. DNA methylation constitutes one of the significant barriers to erroneous induced pluripotency, and loss of DNA methylation is a prerequisite for the generation of induced pluripotent stem cells (iPSCs). Taking fully differentiated cells, such as skin fibroblast cells or peripheral blood cells, and turning back the developmental clock by generating iPSCs constituted a technological breakthrough in 2006, offering unprecedented promise in precision regenerative medicine. In this chapter, I will explore mechanistic possibilities for DNA demethylation in the context of natural and experimentally induced epigenetic reprogramming. The balance of the maintenance of DNA methylation as a heritable mark together with its potential for timely removal is essential for lifelong health and may be key in our understanding of aging and the potential to limit or reverse that process.
Topics: Animals; DNA Demethylation; Cellular Reprogramming; DNA Methylation; Embryonic Development; Embryo, Mammalian; Mammals; Epigenesis, Genetic
PubMed: 36350512
DOI: 10.1007/978-3-031-11454-0_9 -
The Enzymes 2023NPAC is a transcriptional co-activator widely associated with the H3K36me3 epigenetic marks present in the gene bodies. NPAC plays a fundamental role in RNA polymerase... (Review)
Review
NPAC is a transcriptional co-activator widely associated with the H3K36me3 epigenetic marks present in the gene bodies. NPAC plays a fundamental role in RNA polymerase progression, and its depletion downregulates gene transcription. In this chapter, we review the current knowledge on the functional and structural features of this multi-domain protein. NPAC (also named GLYR1 or NP60) contains a PWWP motif, a chromatin binder and epigenetic reader that is proposed to weaken the DNA-histone contacts facilitating polymerase passage through the nucleosomes. The C-terminus of NPAC is a catalytically inactive dehydrogenase domain that forms a stable and rigid tetramer acting as an oligomerization module for the formation of co-transcriptional multimeric complexes. The PWWP and dehydrogenase domains are connected by a long, mostly disordered, linker that comprises putative sites for protein and DNA interactions. A short dodecapeptide sequence (residues 214-225) forms the binding site for LSD2, a flavin-dependent lysine-specific histone demethylase. This stretch of residues binds on the surface of LSD2 and facilitates the capture and processing of the H3 tail in the nucleosome context, thus promoting the H3K4me1/2 epigenetic mark removal. LSD2 is associated with other two chromatin modifiers, G9a and NSD3. The LSD2-G9a-NSD3 complex modifies the pattern of the post translational modifications deposited on histones, thus converting the relaxed chromatin into a transcriptionally refractory state after the RNA polymerase passage. NPAC is a scaffolding factor that organizes and coordinates the epigenetic activities required for optimal transcription elongation.
Topics: Nucleosomes; Amino Acid Sequence; Methylation; Histones; Chromatin; Histone Demethylases; Demethylation; DNA; DNA-Directed RNA Polymerases
PubMed: 37748839
DOI: 10.1016/bs.enz.2023.03.003 -
Advances in Experimental Medicine and... 2022Growth arrest and DNA damage 45 (Gadd45) family genes, Gadd45A, Gadd45B, and GADD45 G are implicated as stress sensors that are rapidly induced upon...
Growth arrest and DNA damage 45 (Gadd45) family genes, Gadd45A, Gadd45B, and GADD45 G are implicated as stress sensors that are rapidly induced upon genotoxic/physiological stress. They are involved in regulation of various cellular functions such as DNA repair, senescence, and cell cycle control. Gadd45 family of genes serve as tumor suppressors in response to different stimuli and defects in Gadd45 pathway can give rise to oncogenesis. More recently, Gadd45 has been shown to promote gene activation by demethylation and this function is important for transcriptional regulation and differentiation during development. Gadd45 serves as an adaptor for DNA repair factors to promote removal of 5-methylcytosine from DNA at gene specific loci. Therefore, Gadd45 serves as a powerful link between DNA repair and epigenetic gene regulation.
Topics: Cell Cycle Checkpoints; Cell Cycle Proteins; DNA Damage; DNA Demethylation; DNA Repair
PubMed: 35505162
DOI: 10.1007/978-3-030-94804-7_4 -
Advances in Experimental Medicine and... 2023Epigenetics has major impact on normal development and pathogenesis. Regulation of histone methylation on lysine and arginine residues is a major epigenetic mechanism...
Epigenetics has major impact on normal development and pathogenesis. Regulation of histone methylation on lysine and arginine residues is a major epigenetic mechanism and affects various processes including transcription and DNA repair. Histone lysine methylation is reversible and is added by histone lysine methyltransferases and removed by histone lysine demethylases. As these enzymes are also capable of writing or erasing lysine modifications on non-histone substrates, they were renamed to lysine demethylases (KDMs) in 2007. Since the discovery of the first lysine demethylase LSD1/KDM1A in 2004, eight more subfamilies of lysine demethylases have been identified and further characterized. The joint efforts by academia and industry have led to the development of potent and specific small molecule inhibitors of KDMs for treatment of cancer and several other diseases. Some of these inhibitors have already entered clinical trials since 2013, less than 10 years after the discovery of the first KDM. In this chapter, we briefly summarize the major roles of histone demethylases in normal development and human diseases and the efforts to target these enzymes to treat various diseases.
Topics: Humans; Histones; Lysine; Arginine; DNA Repair; Demethylation; Histone Demethylases
PubMed: 37751133
DOI: 10.1007/978-3-031-38176-8_1 -
BMC Medicine Apr 2023Helicobacter pylori (H. pylori) infection causes aberrant DNA methylation and contributes to the risk of gastric cancer (GC). Guanine nucleotide-binding protein subunit...
BACKGROUND
Helicobacter pylori (H. pylori) infection causes aberrant DNA methylation and contributes to the risk of gastric cancer (GC). Guanine nucleotide-binding protein subunit beta-4 (GNB4) is involved in various tumorigenic processes. We found an aberrant methylation level of GNB4 in H. pylori-induced GC in our previous bioinformatic analysis; however, its expression and underlying molecular mechanisms are poorly understood.
METHODS
The expression, underlying signaling pathways, and clinical significance of GNB4 were analyzed in a local cohort of 107 patients with GC and several public databases. H. pylori infection was induced in in vitro and in vivo models. Methylation-specific PCR, pyrosequencing, and mass spectrometry analysis were used to detect changes in methylation levels. GNB4, TET1, and YAP1 were overexpressed or knocked down in GC cell lines. We performed gain- and loss-of-function experiments, including CCK-8, EdU, colony formation, transwell migration, and invasion assays. Nude mice were injected with genetically manipulated GC cells, and the growth of xenograft tumors and metastases was measured. Real-time quantitative PCR, western blotting, immunofluorescence, immunohistochemistry, chromatin immunoprecipitation, and co-immunoprecipitation experiments were performed to elucidate the underlying molecular mechanisms.
RESULTS
GNB4 expression was significantly upregulated in GC and correlated with aggressive clinical characteristics and poor prognosis. Increased levels of GNB4 were associated with shorter survival times. Infection with H. pylori strains 26695 and SS1 induced GNB4 mRNA and protein expression in GC cell lines and mice. Additionally, silencing of GNB4 blocked the pro-proliferative, metastatic, and invasive ability of H. pylori in GC cells. H. pylori infection remarkably decreased the methylation level of the GNB4 promoter region, particularly at the CpG#5 site (chr3:179451746-179451745). H. pylori infection upregulated TET1 expression via activation of the NF-κB. TET binds to the GNB4 promoter region which undergoes demethylation modification. Functionally, we identified that GNB4 induced oncogenic behaviors of tumors via the Hippo-YAP1 pathway in both in vitro and in vivo models.
CONCLUSIONS
Our findings demonstrate that H. pylori infection activates the NF-κB-TET1-GNB4 demethylation-YAP1 axis, which may be a potential therapeutic target for GC.
Topics: Humans; Mice; Animals; NF-kappa B; Helicobacter pylori; Mice, Nude; Carcinogenesis; Stomach Neoplasms; Demethylation; Cell Line, Tumor; Gene Expression Regulation, Neoplastic; Mixed Function Oxygenases; Proto-Oncogene Proteins; GTP-Binding Protein beta Subunits
PubMed: 37016382
DOI: 10.1186/s12916-023-02842-6 -
European Heart Journal May 2023
Topics: Humans; RNA, Antisense; RNA, Long Noncoding; Ventricular Remodeling; Pericardium; Demethylation; Basic Helix-Loop-Helix Transcription Factors
PubMed: 36928295
DOI: 10.1093/eurheartj/ehad058 -
Cell Death & Disease Jun 2023Tau hyperphosphorylation in hippocampal neurons has an important pathogenetic role in the development of diabetic cognitive dysfunction. N-methyladenosine (mA)...
High glucose induces tau hyperphosphorylation in hippocampal neurons via inhibition of ALKBH5-mediated Dgkh mA demethylation: a potential mechanism for diabetic cognitive dysfunction.
Tau hyperphosphorylation in hippocampal neurons has an important pathogenetic role in the development of diabetic cognitive dysfunction. N-methyladenosine (mA) methylation is the most common modification of eukaryotic mRNA and is involved in regulating diverse biological processes. However, the role of mA alteration in tau hyperphosphorylation of hippocampus neurons has not been reported. We found lower ALKBH5 expression in the hippocampus of diabetic rats and in HN-h cells with high-glucose intervention, accompanied by tau hyperphosphorylation. ALKBH5 overexpression significantly reversed tau hyperphosphorylation in high-glucose-stimulated HN-h cells. Furthermore, we found and confirmed by mA-mRNA epitope transcriptome microarray and transcriptome RNA sequencing coupled with methylated RNA immunoprecipitation that ALKBH5 regulates the mA modification of Dgkh mRNA. High glucose inhibited the demethylation modification of Dgkh by ALKBH5, resulting in decreases in Dgkh mRNA and protein levels. Overexpression of Dgkh reversed tau hyperphosphorylation in HN-h cells after high-glucose stimulation. Overexpression of Dgkh by adenovirus suspension injection into the bilateral hippocampus of diabetic rats significantly ameliorated tau hyperphosphorylation and diabetic cognitive dysfunction. In addition, ALKBH5 targeted Dgkh to activate PKC-α, leading to tau hyperphosphorylation under high-glucose conditions. The results of this study reveal that high glucose suppresses the demethylation modification of Dgkh by ALKBH5, which downregulates Dgkh and leads to tau hyperphosphorylation through activation of PKC-α in hippocampal neurons. These findings may indicate a new mechanism and a novel therapeutic target for diabetic cognitive dysfunction.
Topics: Animals; Rats; Diabetes Mellitus, Experimental; Neurons; RNA, Messenger; Cognitive Dysfunction; Hippocampus; Demethylation; Glucose
PubMed: 37385994
DOI: 10.1038/s41419-023-05909-7 -
Essays in Biochemistry Dec 2019DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of... (Review)
Review
DNA methylation is an essential DNA modification that plays a crucial role in genome regulation during differentiation and development, and is disrupted in a range of disease states. The recent development of CRISPR/catalytically dead CRISPR/Cas9 (dCas9)-based targeted DNA methylation editing tools has enabled new insights into the roles and functional relevance of this modification, including its importance at regulatory regions and the role of aberrant methylation in various diseases. However, while these tools are advancing our ability to understand and manipulate this regulatory layer of the genome, they still possess a variety of limitations in efficacy, implementation, and targeting specificity. Effective targeted DNA methylation editing will continue to advance our fundamental understanding of the role of this modification in different genomic and cellular contexts, and further improvements may enable more accurate disease modeling and possible future treatments. In this review, we discuss strategies, considerations, and future directions for targeted DNA methylation editing.
Topics: Animals; Bacterial Proteins; CRISPR-Associated Protein 9; CRISPR-Cas Systems; DNA; DNA Demethylation; DNA Methylation; Epigenomics; Gene Editing; Humans; Streptococcus pyogenes
PubMed: 31724704
DOI: 10.1042/EBC20190029