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The Plant Cell Dec 2017-methyladenosine (mA) is the most abundant, internal, posttranscriptional modification in mRNA among all higher eukaryotes. In mammals, this modification is reversible...
-methyladenosine (mA) is the most abundant, internal, posttranscriptional modification in mRNA among all higher eukaryotes. In mammals, this modification is reversible and plays broad roles in the regulation of mRNA metabolism and processing. Despite its importance, previous studies on the role and mechanism of mA methylation in have been limited. Here, we report that ALKBH10B is a demethylase that oxidatively reverses mA methylation in mRNA in vitro and in vivo. Depletion of ALKBH10B in the mutant delays flowering and represses vegetative growth. Complementation with wild-type , but not a catalytically inactive mutant (), rescues these effects in mutant plants, suggesting the observed phenotypes are controlled by the catalytic action of We show that -mediated mRNA demethylation affects the stability of target transcripts, thereby influencing floral transition. We identified 1190 mA hypermethylated transcripts in the mutant involved in plant development. The discovery and characterization of the archetypical RNA demethylase in Arabidopsis sheds light on the occurrence and functional role(s) of reversible mRNA methylation in plants and defines the role of mA RNA modification in Arabidopsis floral transition.
Topics: Adenosine; Arabidopsis; Arabidopsis Proteins; Demethylation; Flowers; Gene Expression Regulation, Plant; Genes, Plant; Methylation; Mutation; Oxidoreductases, N-Demethylating; Protein Stability; RNA, Messenger; RNA, Plant; RNA-Binding Proteins; Substrate Specificity; Up-Regulation
PubMed: 29180595
DOI: 10.1105/tpc.16.00912 -
Nature Communications Jun 2023N6-methyladenosine (mA) modification plays important roles in bioprocesses and diseases. AlkB homolog 5 (ALKBH5) is one of two mA demethylases. Here, we reveal that...
N6-methyladenosine (mA) modification plays important roles in bioprocesses and diseases. AlkB homolog 5 (ALKBH5) is one of two mA demethylases. Here, we reveal that ALKBH5 is acetylated at lysine 235 (K235) by lysine acetyltransferase 8 and deacetylated by histone deacetylase 7. K235 acetylation strengthens the mA demethylation activity of ALKBH5 by increasing its recognition of mA on mRNA. RNA-binding protein paraspeckle component 1 (PSCP1) is a regulatory subunit of ALKBH5 and preferentially interacts with K235-acetylated ALKBH5 to recruit and facilitate the recognition of mA mRNA by ALKBH5, thereby promoting mA erasure. Mitogenic signals promote ALKBH5 K235 acetylation. K235 acetylation of ALKBH5 is upregulated in cancers and promotes tumorigenesis. Thus, our findings reveal that the mA demethylation activity of ALKBH5 is orchestrated by its K235 acetylation and regulatory subunit PSPC1 and that K235 acetylation is necessary for the mA demethylase activity and oncogenic roles of ALKBH5.
Topics: Humans; Acetylation; RNA, Messenger; Carcinogenesis; Cell Transformation, Neoplastic; AlkB Homolog 5, RNA Demethylase; Demethylation; RNA-Binding Proteins
PubMed: 37369679
DOI: 10.1038/s41467-023-39414-4 -
Molecular Therapy : the Journal of the... Jul 2022Cancer cells respond to various stressful conditions through the dynamic regulation of RNA m6A modification. Doxorubicin is a widely used chemotherapeutic drug that...
Cancer cells respond to various stressful conditions through the dynamic regulation of RNA m6A modification. Doxorubicin is a widely used chemotherapeutic drug that induces DNA damage. It is interesting to know whether cancer cells regulate the DNA damage response and doxorubicin sensitivity through RNA m6A modification. Here, we found that doxorubicin treatment significantly induced RNA m6A methylation in breast cancer cells in both a dose- and a time-dependent manner. However, protein arginine methyltransferase 5 (PRMT5) inhibited RNA m6A modification under doxorubicin treatment by enhancing the nuclear translocation of the RNA demethylase AlkB homolog 5 (ALKBH5), which was previously believed to be exclusively localized in the nucleus. Then, ALKBH5 removed the m6A methylation of BRCA1 for mRNA stabilization and further enhanced DNA repair competency to decrease doxorubicin efficacy in breast cancer cells. Importantly, we identified the approved drug tadalafil as a novel PRMT5 inhibitor that could decrease RNA m6A methylation and increase doxorubicin sensitivity in breast cancer. The strategy of targeting PRMT5 with tadalafil is a promising approach to promote breast cancer sensitivity to doxorubicin through RNA methylation regulation.
Topics: Breast Neoplasms; Demethylation; Doxorubicin; Female; Humans; Protein-Arginine N-Methyltransferases; RNA; Tadalafil
PubMed: 35278676
DOI: 10.1016/j.ymthe.2022.03.003 -
Proceedings of the National Academy of... Mar 2022RNA modifications regulate a variety of cellular processes including DNA repair.The RNA methyltransferase TRDMT1 generates methyl-5-cytosine (m5C) on messen-ger RNA...
RNA modifications regulate a variety of cellular processes including DNA repair.The RNA methyltransferase TRDMT1 generates methyl-5-cytosine (m5C) on messen-ger RNA (mRNA) at DNA double-strand breaks (DSBs) in transcribed regions, pro-moting transcription-coupled homologous recombination (HR). Here, we identifiedthat Fragile X mental retardation protein (FMRP) promotes transcription-coupled HRvia its interaction with both the m5C writer TRDMT1 and the m5C eraser ten-eleventranslocation protein 1 (TET1). TRDMT1, FMRP, and TET1 function in a temporalorder at the transcriptionally active sites of DSBs. FMRP displays a higher affinity forDNA:RNA hybrids containing m5C-modified RNA than for hybrids without modifica-tion and facilitates demethylation of m5C by TET1 in vitro. Loss of either the chroma-tin- or RNA-binding domain of FMRP compromises demethylation of damage-inducedm5C in cells. Importantly, FMRP is required for R-loop resolving in cells. Due to unre-solved R-loop and m5C preventing completion of DSB repair, FMRP depletion or lowexpression leads to delayed repair of DSBs at transcriptionally active sites and sensitizescancer cells to radiation in a BRCA-independent manner. Together, ourfindings presentan m5C reader, FMRP, which acts as a coordinator between the m5C writer and eraserto promote mRNA-dependent repair and cell survival in cancer.
Topics: Cytosine; Demethylation; Fragile X Mental Retardation Protein; Fragile X Syndrome; Homologous Recombination; Humans; Mixed Function Oxygenases; Proto-Oncogene Proteins; RNA; RNA, Messenger
PubMed: 35290126
DOI: 10.1073/pnas.2116251119 -
Experimental & Molecular Medicine Apr 2017
Topics: Animals; Chromatin; Cytosine; DNA Demethylation; DNA Methylation; Epigenesis, Genetic; Genetic Markers; Histones; Humans; Neoplasms
PubMed: 28450735
DOI: 10.1038/emm.2017.38 -
Theranostics 2023Lymph node (LN) metastasis is common in patients with epithelial ovarian cancer (EOC) and is associated with poor prognosis. Tumor-associated lymphangiogenesis is the...
Lymph node (LN) metastasis is common in patients with epithelial ovarian cancer (EOC) and is associated with poor prognosis. Tumor-associated lymphangiogenesis is the first stage of LN metastasis. Research on lymphangiogenesis and lymph node metastases can help develop new anti-LN-targeted therapies. Aberrant N6-methyladenosine (m6A) modifications have been reported to be linked to LN metastasis in several cancers, however, their role in EOC lymphangiogenesis and LN metastasis remains unclear. m6A levels in EOC tissues with or without LN metastases were evaluated by dot blot analysis. Real-time polymerase chain reaction (PCR) and immunofluorescence were used to examine the expression of m6A-related enzymes. Additionally, and functional studies were performed to discover the importance of the AlkB homolog 5 () gene in EOC lymphatic metastasis. To identify the downstream target genes regulated by ALKBH5, we performed RNA pulldown, RNA-binding protein immunoprecipitation-quantitative PCR, co-immunoprecipitation, m6A-modified RNA immunoprecipitation-quantitative PCR, and luciferase reporter assays. m6A modification was reduced in ovarian cancers with LN metastases. ALKBH5 overexpression increased tumor-associated lymphangiogenesis and LN metastasis both and . ALKBH5 overexpression also reversed the m6A modification in mRNA and suppressed the YTHDF2 protein-mediated m6A-dependent mRNA degradation, which resulted in increased expression of ITGB1 and phosphorylation of the focal adhesion kinase (FAK) and Src proto-oncogene proteins, thereby increasing LN metastasis. Furthermore, hypoxia induced the expression of hypoxia inducible factor 1 subunit alpha, which increased ALKBH5 expression and enhanced LN metastasis in EOC. The ALKBH5/m6A-ITGB1/FAK signalling axis is important in ovarian cancer lymphangiogenesis and LN metastasis. Antibodies that block ITGB1 and FAK kinase-inhibitors are promising anti-metastatic agents.
Topics: Female; Humans; AlkB Homolog 5, RNA Demethylase; Carcinoma, Ovarian Epithelial; Demethylation; Focal Adhesion Protein-Tyrosine Kinases; Lymphangiogenesis; Lymphatic Metastasis; Ovarian Neoplasms; RNA, Messenger
PubMed: 36632222
DOI: 10.7150/thno.77441 -
Cell Death & Disease Oct 2022Cellular senescence is characterized by a tumor-suppressive program as well as a pro-inflammatory secretome. Neutrophils constitute significant compositions of...
Cellular senescence is characterized by a tumor-suppressive program as well as a pro-inflammatory secretome. Neutrophils constitute significant compositions of malignancies and play key roles in tumor development. However, the role of senescent neutrophils in cancer progression is presently unexplored. Here, we demonstrate that neutrophils display enhanced senescence in breast cancer patients receiving chemotherapy. The senescent neutrophils produce increased number of exosomes, which confer drug resistance to tumor cells in vitro and in vivo. Mechanistically, senescent neutrophils-derived exosomal piRNA-17560 enhances the expression of fat mass and obesity-associated protein (FTO) in breast cancer cells. The upregulation of FTO further strengthens ZEB1 transcripts stability and expression by decreasing N6-methyladenosine (m6A) RNA methylation, leading to chemoresistance and epithelial-mesenchymal transition (EMT) of tumor cells. Clinically, the level of exosomal piR-17560 correlates with poor chemotherapy response in patients with breast cancer. In addition, YTHDF2 is essential for the posttranscriptional regulation of ZEB1 by piRNA-17560/FTO signaling. Senescent neutrophils secret exosomal piR-17560 in a STAT3-dependent manner. Altogether, this study suggests that senescent neutrophils-derived exosomal piR-17560 confers chemoresistance to tumor cells and senescent neutrophils may serve as a potential therapeutic target in breast cancer.
Topics: Humans; Female; Epithelial-Mesenchymal Transition; Breast Neoplasms; RNA, Small Interfering; Drug Resistance, Neoplasm; Neutrophils; Demethylation; Alpha-Ketoglutarate-Dependent Dioxygenase FTO
PubMed: 36302751
DOI: 10.1038/s41419-022-05317-3 -
Cell Dec 2004Posttranslational modifications of histone N-terminal tails impact chromatin structure and gene transcription. While the extent of histone acetylation is determined by...
Posttranslational modifications of histone N-terminal tails impact chromatin structure and gene transcription. While the extent of histone acetylation is determined by both acetyltransferases and deacetylases, it has been unclear whether histone methylation is also regulated by enzymes with opposing activities. Here, we provide evidence that LSD1 (KIAA0601), a nuclear homolog of amine oxidases, functions as a histone demethylase and transcriptional corepressor. LSD1 specifically demethylates histone H3 lysine 4, which is linked to active transcription. Lysine demethylation occurs via an oxidation reaction that generates formaldehyde. Importantly, RNAi inhibition of LSD1 causes an increase in H3 lysine 4 methylation and concomitant derepression of target genes, suggesting that LSD1 represses transcription via histone demethylation. The results thus identify a histone demethylase conserved from S. pombe to human and reveal dynamic regulation of histone methylation by both histone methylases and demethylases.
Topics: Conserved Sequence; Formaldehyde; Gene Expression Regulation; HeLa Cells; Histone Demethylases; Histones; Humans; Lysine; Mass Spectrometry; Methylation; Nuclear Proteins; Oxidoreductases, N-Demethylating; RNA Interference; Recombinant Proteins; Repressor Proteins; Schizosaccharomyces pombe Proteins; Substrate Specificity; Transcription, Genetic
PubMed: 15620353
DOI: 10.1016/j.cell.2004.12.012 -
American Journal of Human Genetics Feb 2020Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate...
Germline pathogenic variants in chromatin-modifying enzymes are a common cause of pediatric developmental disorders. These enzymes catalyze reactions that regulate epigenetic inheritance via histone post-translational modifications and DNA methylation. Cytosine methylation (5-methylcytosine [5mC]) of DNA is the quintessential epigenetic mark, yet no human Mendelian disorder of DNA demethylation has yet been delineated. Here, we describe in detail a Mendelian disorder caused by the disruption of DNA demethylation. TET3 is a methylcytosine dioxygenase that initiates DNA demethylation during early zygote formation, embryogenesis, and neuronal differentiation and is intolerant to haploinsufficiency in mice and humans. We identify and characterize 11 cases of human TET3 deficiency in eight families with the common phenotypic features of intellectual disability and/or global developmental delay; hypotonia; autistic traits; movement disorders; growth abnormalities; and facial dysmorphism. Mono-allelic frameshift and nonsense variants in TET3 occur throughout the coding region. Mono-allelic and bi-allelic missense variants localize to conserved residues; all but one such variant occur within the catalytic domain, and most display hypomorphic function in an assay of catalytic activity. TET3 deficiency and other Mendelian disorders of the epigenetic machinery show substantial phenotypic overlap, including features of intellectual disability and abnormal growth, underscoring shared disease mechanisms.
Topics: Adult; Amino Acid Sequence; Autistic Disorder; Child; Child, Preschool; DNA Demethylation; Developmental Disabilities; Dioxygenases; Embryonic Development; Female; Gene Expression Regulation, Developmental; Growth Disorders; Humans; Infant; Male; Middle Aged; Movement Disorders; Pedigree; Protein Conformation; Sequence Homology; Young Adult
PubMed: 31928709
DOI: 10.1016/j.ajhg.2019.12.007 -
European Heart Journal May 2023Epicardium and epicardium-derived cells are critical players in myocardial fibrosis. Mesenchymal stem cell-derived extracellular vesicles (EVs) have been studied for...
AIMS
Epicardium and epicardium-derived cells are critical players in myocardial fibrosis. Mesenchymal stem cell-derived extracellular vesicles (EVs) have been studied for cardiac repair to improve cardiac remodelling, but the actual mechanisms remain elusive. The aim of this study is to investigate the mechanisms of EV therapy for improving cardiac remodelling and develop a promising treatment addressing myocardial fibrosis.
METHODS AND RESULTS
Extracellular vesicles were intrapericardially injected for mice myocardial infarction treatment. RNA-seq, in vitro gain- and loss-of-function experiments, and in vivo studies were performed to identify targets that can be used for myocardial fibrosis treatment. Afterward, a lipid nanoparticle-based long non-coding RNA (lncRNA) therapy was prepared for mouse and porcine models of myocardial infarction treatment. Intrapericardial injection of EVs improved adverse myocardial remodelling in mouse models of myocardial infarction. Mechanistically, Tcf21 was identified as a potential target to improve cardiac remodelling. Loss of Tcf21 function in epicardium-derived cells caused increased myofibroblast differentiation, whereas forced Tcf21 overexpression suppressed transforming growth factor-β signalling and myofibroblast differentiation. LncRNA-Tcf21 antisense RNA inducing demethylation (TARID) that enriched in EVs was identified to up-regulate Tcf21 expression. Formulated lncRNA-TARID-laden lipid nanoparticles up-regulated Tcf21 expression in epicardium-derived cells and improved cardiac function and histology in mouse and porcine models of myocardial infarction.
CONCLUSION
This study identified Tcf21 as a critical target for improving cardiac fibrosis. Up-regulating Tcf21 by using lncRNA-TARID-laden lipid nanoparticles could be a promising way to treat myocardial fibrosis. This study established novel mechanisms underlying EV therapy for improving adverse remodelling and proposed a lncRNA therapy for cardiac fibrosis.
Topics: Mice; Animals; Swine; RNA, Long Noncoding; RNA, Antisense; Ventricular Remodeling; Myocardial Infarction; Fibrosis; Demethylation
PubMed: 36916305
DOI: 10.1093/eurheartj/ehad114