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Plant Cell Reports Jan 2018Active DNA demethylation (enzymatic removal of methylated cytosine) regulates many plant developmental processes. In Arabidopsis, active DNA demethylation entails the... (Review)
Review
Active DNA demethylation (enzymatic removal of methylated cytosine) regulates many plant developmental processes. In Arabidopsis, active DNA demethylation entails the base excision repair pathway initiated by the Repressor of silencing 1/Demeter family of bifunctional DNA glycosylases. In this review, we first present an introduction to the recent advances in our understanding about the mechanisms of active DNA demethylation. We then focus on the role of active DNA demethylation in diverse developmental processes in various plant species, including the regulation of seed development, pollen tube formation, stomatal development, fruit ripening, and nodule development. Finally, we discuss future directions of research in the area of active DNA demethylation.
Topics: DNA Glycosylases; DNA, Plant; Demethylation; Fruit; Gene Expression Regulation, Plant; Genomic Imprinting; Plant Development; Pollen Tube; Seed Storage Proteins; Seeds
PubMed: 29026973
DOI: 10.1007/s00299-017-2215-z -
Communications Biology Dec 2023N-methyladenosine (mA) plays a crucial role in the development and functional homeostasis of the central nervous system. The fat mass and obesity-associated (FTO) gene,...
N-methyladenosine (mA) plays a crucial role in the development and functional homeostasis of the central nervous system. The fat mass and obesity-associated (FTO) gene, which is highly expressed in the hypothalamus, is closely related to female pubertal development. In this study, we found that mA methylation decreased in the hypothalamus gradually with puberty and decreased in female rats with precocious puberty. FTO expression was increased at the same time. Methylated RNA immunoprecipitation sequencing (MeRIP-seq) showed that the mA methylation of PLCβ, a key enzyme of the Ca signalling pathway, was decreased significantly in the hypothalamus in precocious rats. Upregulating FTO increased PLCβ3 expression and activated the Ca signalling pathway, which promoted GnRH expression. Dual-luciferase reporter and MeRIP-qPCR assays confirmed that FTO regulated mA demethylation of PLCβ and promoted PLCβ expression. Upon overexpressing FTO in the hypothalamic arcuate nucleus (ARC) in female rats, we observed advanced puberty onset. Meanwhile, PLCβ and GnRH expression in the hypothalamus increased significantly, and the Ca signalling pathway was activated. Our study demonstrates that FTO enhances GnRH expression, which promotes puberty onset, by regulating mA demethylation of PLCβ3 and activating the Ca signalling pathway.
Topics: Animals; Female; Rats; Demethylation; Gonadotropin-Releasing Hormone; Hypothalamus; Methylation; Signal Transduction
PubMed: 38129517
DOI: 10.1038/s42003-023-05677-2 -
Developmental Cell Oct 2021Epigenetic mechanisms contribute to the regulation of cell differentiation and function. Vascular smooth muscle cells (SMCs) are specialized contractile cells that...
Epigenetic mechanisms contribute to the regulation of cell differentiation and function. Vascular smooth muscle cells (SMCs) are specialized contractile cells that retain phenotypic plasticity even after differentiation. Here, by performing selective demethylation of histone H3 lysine 4 di-methylation (H3K4me2) at SMC-specific genes, we uncovered that H3K4me2 governs SMC lineage identity. Removal of H3K4me2 via selective editing in cultured vascular SMCs and in murine arterial vasculature led to loss of differentiation and reduced contractility due to impaired recruitment of the DNA methylcytosine dioxygenase TET2. H3K4me2 editing altered SMC adaptative capacities during vascular remodeling due to loss of miR-145 expression. Finally, H3K4me2 editing induced a profound alteration of SMC lineage identity by redistributing H3K4me2 toward genes associated with stemness and developmental programs, thus exacerbating plasticity. Our studies identify the H3K4me2-TET2-miR145 axis as a central epigenetic memory mechanism controlling cell identity and function, whose alteration could contribute to various pathophysiological processes.
Topics: Adaptation, Physiological; Animals; Cell Differentiation; Cell Line; Cell Lineage; DNA Methylation; DNA-Binding Proteins; Demethylation; Dioxygenases; Epigenesis, Genetic; Epigenomics; Gene Expression; Gene Expression Regulation; Histones; Homeostasis; Humans; Male; Mice; Mice, Inbred C57BL; Muscle, Smooth, Vascular; Myocytes, Smooth Muscle; Vascular Remodeling
PubMed: 34582749
DOI: 10.1016/j.devcel.2021.09.001 -
Epigenetics & Chromatin Oct 2023Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone...
BACKGROUND
Vitamin C (vitC) enhances the activity of 2-oxoglutarate-dependent dioxygenases, including TET enzymes, which catalyse DNA demethylation, and Jumonji-domain histone demethylases. The epigenetic remodelling promoted by vitC improves the efficiency of induced pluripotent stem cell derivation, and is required to attain a ground-state of pluripotency in embryonic stem cells (ESCs) that closely mimics the inner cell mass of the early blastocyst. However, genome-wide DNA and histone demethylation can lead to upregulation of transposable elements (TEs), and it is not known how vitC addition in culture media affects TE expression in pluripotent stem cells.
RESULTS
Here we show that vitC increases the expression of several TE families, including evolutionarily young LINE-1 (L1) elements, in mouse ESCs. We find that TET activity is dispensable for L1 upregulation, and that instead it occurs largely as a result of H3K9me3 loss mediated by KDM4A/C histone demethylases. Despite increased L1 levels, we did not detect increased somatic insertion rates in vitC-treated cells. Notably, treatment of human ESCs with vitC also increases L1 protein levels, albeit through a distinct, post-transcriptional mechanism.
CONCLUSION
VitC directly modulates the expression of mouse L1s and other TEs through epigenetic mechanisms, with potential for downstream effects related to the multiple emerging roles of L1s in cellular function.
Topics: Humans; Animals; Mice; Ascorbic Acid; Mouse Embryonic Stem Cells; Long Interspersed Nucleotide Elements; DNA Methylation; Histone Demethylases; DNA; Demethylation; Jumonji Domain-Containing Histone Demethylases
PubMed: 37845773
DOI: 10.1186/s13072-023-00514-6 -
JCI Insight Oct 2023Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation,...
Abnormal macrophage polarization is generally present in autoimmune diseases. Overwhelming M1 macrophage activation promotes the continuous progression of inflammation, which is one of the reasons for the development of autoimmune diseases. However, the underlying mechanism is still unclear. Here we explore the function of Regulatory factor X1 (RFX1) in macrophage polarization by constructing colitis and lupus-like mouse models. Both in vivo and in vitro experiments confirmed that RFX1 can promote M1 and inhibit M2 macrophage polarization. Furthermore, we found that RFX1 promoted DNA demethylation of macrophage polarization-related genes by increasing APOBEC3A/Apobec3 expression. We identified a potential RFX1 inhibitor, adenosine diphosphate (ADP), providing a potential strategy for treating autoimmune diseases.
Topics: Animals; Mice; Autoimmune Diseases; DNA Demethylation; Inflammation; Macrophage Activation; Macrophages; Regulatory Factor X1
PubMed: 37733446
DOI: 10.1172/jci.insight.165546 -
The Plant Cell Dec 2017
Topics: Adenosine; Arabidopsis; Demethylation; Methylation; RNA; RNA, Messenger
PubMed: 29203635
DOI: 10.1105/tpc.17.00929 -
Clinical Epigenetics Aug 2023Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this...
BACKGROUND
Promoter hypermethylation of tumour suppressor genes is frequently observed during the malignant transformation of colorectal cancer (CRC). However, whether this epigenetic mechanism is functional in cancer or is a mere consequence of the carcinogenic process remains to be elucidated.
RESULTS
In this work, we performed an integrative multi-omic approach to identify gene candidates with strong correlations between DNA methylation and gene expression in human CRC samples and a set of 8 colon cancer cell lines. As a proof of concept, we combined recent CRISPR-Cas9 epigenome editing tools (dCas9-TET1, dCas9-TET-IM) with a customized arrayed gRNA library to modulate the DNA methylation status of 56 promoters previously linked with strong epigenetic repression in CRC, and we monitored the potential functional consequences of this DNA methylation loss by means of a high-content cell proliferation screen. Overall, the epigenetic modulation of most of these DNA methylated regions had a mild impact on the reactivation of gene expression and on the viability of cancer cells. Interestingly, we found that epigenetic reactivation of RSPO2 in the tumour context was associated with a significant impairment in cell proliferation in p53 cancer cell lines, and further validation with human samples demonstrated that the epigenetic silencing of RSPO2 is a mid-late event in the adenoma to carcinoma sequence.
CONCLUSIONS
These results highlight the potential role of DNA methylation as a driver mechanism of CRC and paves the way for the identification of novel therapeutic windows based on the epigenetic reactivation of certain tumour suppressor genes.
Topics: Humans; DNA Methylation; DNA Demethylation; Epigenesis, Genetic; Carcinogenesis; Colonic Neoplasms; Mixed Function Oxygenases; Proto-Oncogene Proteins
PubMed: 37612734
DOI: 10.1186/s13148-023-01546-1 -
Experimental & Molecular Medicine Dec 2020Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a... (Review)
Review
Lysine-specific histone demethylase 1 (LSD1) represents the first example of an identified nuclear protein with histone demethylase activity. In particular, it plays a special role in the epigenetic regulation of gene expression, as it removes methyl groups from mono- and dimethylated lysine 4 and/or lysine 9 on histone H3 (H3K4me1/2 and H3K9me1/2), behaving as a repressor or activator of gene expression, respectively. Moreover, it has been recently found to demethylate monomethylated and dimethylated lysine 20 in histone H4 and to contribute to the balance of several other methylated lysine residues in histone H3 (i.e., H3K27, H3K36, and H3K79). Furthermore, in recent years, a plethora of nonhistone proteins have been detected as targets of LSD1 activity, suggesting that this demethylase is a fundamental player in the regulation of multiple pathways triggered in several cellular processes, including cancer progression. In this review, we analyze the molecular mechanism by which LSD1 displays its dual effect on gene expression (related to the specific lysine target), placing final emphasis on the use of pharmacological inhibitors of its activity in future clinical studies to fight cancer.
Topics: Alternative Splicing; Animals; Biomarkers, Tumor; Demethylation; Epigenesis, Genetic; Gene Expression Regulation; Histone Demethylases; Histones; Humans; Lysine; Molecular Targeted Therapy; Protein Binding; Protein Processing, Post-Translational; Protein Stability; Receptors, Cytoplasmic and Nuclear; Structure-Activity Relationship
PubMed: 33318631
DOI: 10.1038/s12276-020-00542-2 -
Mutation Research. Reviews in Mutation... 2021APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and... (Review)
Review
APE2 is a rising vital player in the maintenance of genome and epigenome integrity. In the past several years, a series of studies have shown the critical roles and functions of APE2. We seek to provide the first comprehensive review on several aspects of APE2 in genome and epigenome integrity. We first summarize the distinct functional domains or motifs within APE2 including EEP (endonuclease/exonuclease/phosphatase) domain, PIP box and Zf-GRF motifs from eight species (i.e., Homo sapiens, Mus musculus, Xenopus laevis, Ciona intestinalis, Arabidopsis thaliana, Schizosaccharomyces pombe, Saccharomyces cerevisiae, and Trypanosoma cruzi). Then we analyze various APE2 nuclease activities and associated DNA substrates, including AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease activities. We also examine several APE2 interaction proteins, including PCNA, Chk1, APE1, Myh1, and homologous recombination (HR) factors such as Rad51, Rad52, BRCA1, BRCA2, and BARD1. Furthermore, we provide insights into the roles of APE2 in various DNA repair pathways (base excision repair, single-strand break repair, and double-strand break repair), DNA damage response (DDR) pathways (ATR-Chk1 and p53-dependent), immunoglobulin class switch recombination and somatic hypermutation, as well as active DNA demethylation. Lastly, we summarize critical functions of APE2 in growth, development, and diseases. In this review, we provide the first comprehensive perspective which dissects all aspects of the multiple-function protein APE2 in genome and epigenome integrity.
Topics: Animals; Arabidopsis Proteins; DNA Damage; DNA Demethylation; DNA Repair; Endonucleases; Epigenome; Humans; Immunity; Rad51 Recombinase; Saccharomyces cerevisiae
PubMed: 34083046
DOI: 10.1016/j.mrrev.2020.108347 -
Clinical and Translational Medicine Feb 2023Radiation-induced hepatic stellate cell (HSC) activation promotes radiation-induced liver fibrosis (RILF), a complication for hepatocellular carcinoma (HCC)...
BACKGROUND
Radiation-induced hepatic stellate cell (HSC) activation promotes radiation-induced liver fibrosis (RILF), a complication for hepatocellular carcinoma (HCC) radiotherapy. The demethylase alpha-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) decreases N6-methyladenylate methylation (m A) modification of RNA, while its role in regulating RILF pathogenesis and HCC radiosensitivity remains unknown.
METHODS
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) and RNA-sequencing (RNA-seq) were used to screen target genes regulated by ALKBH5. HSC with altered ALKBH5 expression was used to assess irradiation-induced HSC activation and the effect of HSC on recruitment and polarisation of monocytes. Key cytokines in medium from irradiated HSC-educated monocytes were identified by cytokine array detection. The effects of blocking ALKBH5 and key cytokines on RILF and HCC radiosensitivity were also evaluated.
RESULTS
Radiation-induced ALKBH5 expression in HSC mediated m A demethylation of toll-interleukin 1 receptor domain containing adaptor protein (TIRAP) mRNA and activated its downstream NF-κB and JNK/Smad2 pathways to promote HSC activation. Additionally, ALKBH5 regulated CCL5 secretion by irradiated HSC to promote monocyte recruitment and M2 macrophage polarisation. Notably, polarised monocytes secreted CCL20 to up-regulate ALKBH5 expression in HSC, and reduce HCC radiosensitivity by activating ALKBH5/TIRAP axis in HCC cells. ALKBH5 knockdown-combined CCR6 (CCL20 receptor) inhibitor significantly alleviated RILF and improved HCC radiosensitivity in mice. HCC patients with high ALKBH5 and TIRAP expression were prone to radiation-induced liver injury and poor tumour response to radiotherapy.
CONCLUSIONS
Collectively, irradiation up-regulates ALKBH5 in HSC to mediate monocyte recruitment and M2 polarisation and form positive feedback to promote RILF and reduce HCC radiosensitivity. The dual roles of ALKBH5 as a microenvironmental regulator and radiosensitisation target provide new ideas for RILF prevention and radiosensitisation of HCC.
Topics: Animals; Mice; Carcinoma, Hepatocellular; Demethylation; Liver Cirrhosis; Liver Neoplasms; Membrane Glycoproteins; Receptors, Interleukin-1; RNA; RNA, Messenger
PubMed: 36792369
DOI: 10.1002/ctm2.1198