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JOURNAL ARTICLE
Shoji Tajima, Isao Suetake, Kohei Takeshita, Atsushi Nakagawa, Hironobu Kimura, Jikui Song
In mammals, three major DNA methyltransferases, Dnmt1, Dnmt3a, and Dnmt3b, have been identified. Dnmt3a and Dnmt3b are responsible for establishing DNA methylation patterns produced through their de novo-type DNA methylation activity in implantation stage embryos and during germ cell differentiation. Dnmt3-like (Dnmt3l), which is a member of the Dnmt3 family but does not possess DNA methylation activity, was reported to be indispensable for global methylation in germ cells. Once the DNA methylation patterns are established, maintenance-type DNA methyltransferase Dnmt1 faithfully propagates them to the next generation via replication...
2022: Advances in Experimental Medicine and Biology
#22
JOURNAL ARTICLE
Richard H van Jaarsveld, Jack Reilly, Marie-Claire Cornips, Michael A Hadders, Emanuele Agolini, Priyanka Ahimaz, Kwame Anyane-Yeboa, Severine Audebert Bellanger, Ellen van Binsbergen, Marie-Jose van den Boogaard, Elise Brischoux-Boucher, Raymond C Caylor, Andrea Ciolfi, Ton A J van Essen, Paolo Fontana, Saskia Hopman, Maria Iascone, Margaret M Javier, Erik-Jan Kamsteeg, Jennifer Kerkhof, Jun Kido, Hyung-Goo Kim, Tjitske Kleefstra, Fortunato Lonardo, Abbe Lai, Dorit Lev, Michael A Levy, M E Suzanne Lewis, Angie Lichty, Marcel M A M Mannens, Naomichi Matsumoto, Idit Maya, Haley McConkey, Andre Megarbane, Vincent Michaud, Evelina Miele, Marcello Niceta, Antonio Novelli, Roberta Onesimo, Rolph Pfundt, Bernt Popp, Eloise Prijoles, Raissa Relator, Sylvia Redon, Dmitrijs Rots, Karen Rouault, Ken Saida, Jolanda Schieving, Marco Tartaglia, Romano Tenconi, Kevin Uguen, Nienke Verbeek, Christopher A Walsh, Keren Yosovich, Christopher J Yuskaitis, Giuseppe Zampino, Bekim Sadikovic, Mariëlle Alders, Renske Oegema
PURPOSE: Pathogenic variants in genes involved in the epigenetic machinery are an emerging cause of neurodevelopment disorders (NDDs). Lysine-demethylase 2B (KDM2B) encodes an epigenetic regulator and mouse models suggest an important role during development. We set out to determine whether KDM2B variants are associated with NDD. METHODS: Through international collaborations, we collected data on individuals with heterozygous KDM2B variants. We applied methylation arrays on peripheral blood DNA samples to determine a KDM2B associated epigenetic signature...
November 1, 2022: Genetics in Medicine: Official Journal of the American College of Medical Genetics
#23
JOURNAL ARTICLE
Dogus Murat Altintas, Simona Gallo, Cristina Basilico, Marina Cerqua, Alessio Bocedi, Annapia Vitacolonna, Orsola Botti, Elena Casanova, Ilaria Rancati, Chiara Milanese, Sara Notari, Giorgia Gambardella, Giorgio Ricci, Pier Giorgio Mastroberardino, Carla Boccaccio, Tiziana Crepaldi, Paolo Maria Comoglio
The tyrosine kinase receptor encoded by the MET oncogene has been extensively studied. Surprisingly, one extracellular domain, PSI, evolutionary conserved between plexins, semaphorins, and integrins, has no established function. The MET PSI sequence contains two CXXC motifs, usually found in protein disulfide isomerases (PDI). Using a scrambled oxidized RNAse enzymatic activity assay in vitro, we show, for the first time, that the MET extracellular domain displays disulfide isomerase activity, abolished by PSI domain antibodies...
October 17, 2022: International Journal of Molecular Sciences
#24
JOURNAL ARTICLE
Jian-Hong Xu, Faiza Irshad, Yan Yan, Chao Li
For crop seed production, the development of anthers and male fertility are the main agronomic traits and key biological processes for flowering plants. Active DNA demethylation regulates many plant developmental processes and is ensured by 5-meC DNA glycosylase enzymes. To find out the role of OsROS1a , OsROS1a gene editing mutants were generated using the CRISPR/Cas9 system. The osros1a mutants had shrink spikelets, smaller anthers and pollen grains, and were not stained by iodine staining showing a significant reduction in total soluble sugar and starch contents as compared to wildtype (WT), which caused complete male sterility...
September 26, 2022: International Journal of Molecular Sciences
#25
JOURNAL ARTICLE
Marek Łuczkowski, Michał Padjasek, Józef Tran, Lars Hemmingsen, Olga Kerber, Jelena Habjanič, Eva Freisinger, Artur Krezel
In nature, thiolate-based systems are the primary targets of divalent mercury (HgII) toxicity. The formation of Hg(Cys)x cores in catalytic and structural protein centers mediates mercury's toxic effects and ultimately leads to cellular damage. Multiple studies have revealed distinct HgII-thiolate coordination preferences, among which the linear HgII complexes are the most commonly observed in solution at physiological pH. Trigonal or tetrahedral geometries are formed at basic pH or in tight intraprotein Cys-rich metal sites...
October 12, 2022: Chemistry: a European Journal
#26
JOURNAL ARTICLE
Tyler D R Vance, Patrick Yip, Elisabet Jiménez, Sheng Li, Diana Gawol, James Byrnes, Isabel Usón, Ahmed Ziyyat, Jeffrey E Lee
SPACA6 is a sperm-expressed surface protein that is critical for gamete fusion during mammalian sexual reproduction. Despite this fundamental role, little is known about how SPACA6 specifically functions. We elucidated the crystal structure of the SPACA6 ectodomain at 2.2-Å resolution, revealing a two-domain protein containing a four-helix bundle and Ig-like β-sandwich connected via a quasi-flexible linker. This structure is reminiscent of IZUMO1, another gamete fusion-associated protein, making SPACA6 and IZUMO1 founding members of a superfamily of fertilization-associated proteins, herein dubbed the IST superfamily...
September 17, 2022: Communications Biology
#27
JOURNAL ARTICLE
Su-Jin Lee, Han Byeol Oh, Sung-Il Yoon
Homologous recombination is involved in repairing DNA damage, contributing to maintaining the integrity and stability of viral and cellular genomes. In bacteria, the recombination mediator proteins RecO and RecR are required to load the RecA recombinase on ssDNA for homologous recombination. To structurally and functionally characterize RecO, we determined the crystal structure of RecO from Campylobacter jejuni (cjRecO) at a 1.8 Å resolution and biochemically assessed its capacity to interact with DNA and a metal ion...
August 26, 2022: International Journal of Molecular Sciences
#28
JOURNAL ARTICLE
Hanuman P Kalmode, Izabella Podsiadly, Ashish Kabra, Adam Boulton, Prabhakar Reddy, Yan Gao, Christopher Li, John H Bushweller
The CXXC domain is a reader of DNA methylation which preferentially binds to unmethylated CpG DNA motifs. Chromosomal translocations involving the MLL1 gene produce in-frame fusion proteins in which the N-terminal portion of the MLL1 protein harboring its CXXC domain is fused to the C-terminal portion of multiple partners. For the MLL-AF9 fusion, mutations which disrupt CXXC domain-DNA binding abrogate the ability to cause leukemia in mice. Based on this, we initiated an effort to develop small-molecule inhibitors of the MLL1 CXXC domain as a novel approach to therapy...
August 11, 2022: ACS Medicinal Chemistry Letters
#29
JOURNAL ARTICLE
Natsumi Taka, Yuji Baba, Yuka Iwasaki, Wataru Yoshida
Global hypomethylation of genomic DNA is associated with genomic instability and carcinogenic processes. The loss of DNA methylation has been reported in several cancers; therefore, global methylation levels have been considered as biomarkers for cancer diagnosis. Bisulfite conversion analysis has been widely used as the gold standard method for quantification of DNA methylation levels. However, this method requires cumbersome and time-consuming steps. To quantify global DNA methylation levels in homogeneous solutions, we exemplify a sensing system based on bioluminescence resonance energy transfer (BRET) using methyl-CpG binding domain (MBD)-fused firefly luciferase (MBD-FLuc) and unmethyl-CpG binding domain (CXXC)-fused firefly luciferase (CXXC-FLuc)...
2022: Methods in Molecular Biology
#30
JOURNAL ARTICLE
Kyungjun Uh, Kiho Lee
Enzymes of the Ten-eleven translocation (TET) family are considered to play an important role in the regulation of DNA methylation patterns by converting 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC). Known as a maternal transcript enriched in mature oocytes, TET3 has been suggested to initiate DNA demethylation of the paternal genome in zygotes. Previous studies in mouse cells indicate that the N-terminal CXXC domain of TET3 is important in catalyzing the oxidation of 5mC through its potential DNA binding ability; however, it is not clear whether the DNA binding capacity of CXXC domain is required for the 5hmC conversion in mammalian embryos...
June 29, 2022: Biology of Reproduction
#31
JOURNAL ARTICLE
Tinna Reynisdottir, Kimberley Jade Anderson, Leandros Boukas, Hans Tomas Bjornsson
Wiedemann-Steiner syndrome (WDSTS) is a neurodevelopmental disorder caused by de novo variants in KMT2A, which encodes a multi-domain histone methyltransferase. To gain insight into the currently unknown pathogenesis of WDSTS, we examined the spatial distribution of likely WDSTS-causing variants across the 15 different domains of KMT2A. Compared to variants in healthy controls, WDSTS variants exhibit a 61.9-fold overrepresentation within the CXXC domain-which mediates binding to unmethylated CpGs-suggesting a major role for this domain in mediating the phenotype...
June 2022: PLoS Genetics
#32
JOURNAL ARTICLE
Yingzi Shen, Jiaping Wei, Shuang Wang, Xi Zhang, Kebing Mu, Sushuang Liu, Hao Ma
Abiotic stresses such as high temperature, high humidity, and heavy metals are important factors that affect seed development and quality, and restrict yield in soybean. The ATX1-type copper chaperones are an important type of proteins that are used for maintaining intracellular copper ion homeostasis. In our previous study, a copper chaperone protein GmATX1 was identified in developing seeds of soybean under high temperature and humidity (HTH) stresses. In this study, the GmATX1 gene was isolated, and multiple alignment analysis showed that its encoding protein shared high sequence identities with other plant orthologues of copper chaperone proteins containing the HMA domain, and a conserved metal ion-binding site, CXXC...
May 17, 2022: Plants (Basel, Switzerland)
#33
JOURNAL ARTICLE
Karin Fritz-Wolf, Jochen Bathke, Stefan Rahlfs, Katja Becker
Plasmoredoxin is a 22 kDa thiol-disulfide oxidoreductase involved in cellular redox regulatory processes and antioxidant defense. The 1.6 Å structure of the protein, solved via X-ray crystallography, adopts a modified thioredoxin fold. The structure reveals that plasmoredoxin, unique for malarial parasites, forms a new subgroup of thioredoxin-like proteins together with tryparedoxin, unique for kinetoplastids. Unlike most members of this superfamily, Plrx does not have a proline residue within the CxxC redox motif...
2022: Current research in structural biology
#34
JOURNAL ARTICLE
Yuen Gao, Natalia Duque-Wilckens, Mohammad B Aljazi, Adam J Moeser, George I Mias, Alfred J Robison, Yi Zhang, Jin He
Recent clinical studies report that chromosomal 12q24.31 microdeletions are associated with autism spectrum disorder (ASD) and intellectual disability (ID). However, the causality and underlying mechanisms linking 12q24.31 microdeletions to ASD/ID remain undetermined. Here we show Kdm2b , one gene located in chromosomal 12q24.31, plays a critical role in maintaining neural stem cells (NSCs) in the mouse brain. Loss of the CxxC-ZF domain of KDM2B impairs its function in recruiting Polycomb repressive complex 1 (PRC1) to chromatin, resulting in de-repression of genes involved in cell apoptosis, cell-cycle arrest, NSC senescence, and loss of NSC populations in the brain...
February 18, 2022: IScience
#35
JOURNAL ARTICLE
Zhenguang Zhao, Reem Mousa, Norman Metanis
Human SELENOF is an endoplasmic reticulum (ER) selenoprotein that contains the redox active motif CXU (C is cysteine and U is selenocysteine), resembling the redox motif of thiol-disulfide oxidoreductases (CXXC). Like other selenoproteins, the challenge in accessing SELENOF has somewhat limited its full biological characterization thus far. Here we present the one-pot chemical synthesis of the thioredoxin-like domain of SELENOF, highlighted by the use of Fmoc-protected selenazolidine, native chemical ligations and deselenization reactions...
February 2, 2022: Chemistry: a European Journal
#36
REVIEW
Yu-Ke Wu, Heng-Yu Fan
Putative RNA-binding proteins (RBPs), zygote arrested-1 (ZAR1), and ZAR2 (also known as ZAR1L), have been identified as maternal factors that mainly function in oogenesis and embryogenesis. Despite divergence in their spatio-temporal expression among species, the CxxC structure of the C-terminus of ZAR proteins is highly conserved and is reported to be the functional domain for the activity of the RBPs of ZAR proteins. In oocytes from Xenopus laevis and zebrafish, ZAR proteins have been reported to bind to maternal transcripts and inhibit translation in immature growing oocytes, whereas in fully grown mouse oocytes, they promote the translation during meiotic maturation...
January 24, 2022: Cellular and Molecular Life Sciences: CMLS
#37
JOURNAL ARTICLE
Russell J Jarrott, Emily J Furlong, Guillaume A Petit, David Drew, Jennifer L Martin, Maria A Halili
Suppressor of copper sensitivity (Scs) proteins play a role in the bacterial response to copper stress in many Gram-negative bacteria, including in the human pathogen Proteus mirabilis. Recently, the ScsC protein from P. mirabilis (PmScsC) was characterized as a trimeric protein with isomerase activity that contributes to the ability of the bacterium to swarm in the presence of copper. The CXXC motif catalytic cysteines of PmScsC are maintained in their active reduced state by the action of its membrane-bound partner protein, the Proteus mirabilis ScsB (PmScsB)...
May 2022: Protein Expression and Purification
#38
REVIEW
Atsushi Onodera, Masahiro Kiuchi, Kota Kokubo, Toshinori Nakayama
Epigenetic regulation of gene transcription in the immune system is important for proper control of protective and pathogenic inflammation. Aberrant epigenetic modifications are often associated with dysregulation of the immune cells, including lymphocytes and macrophages, leading to pathogenic inflammation and autoimmune diseases. Two classical epigenetic markers-histone modifications and DNA cytosine methylation, the latter is the 5 position of the cytosine base in the context of CpG dinucleotides-play multiple roles in the immune system...
January 2022: Immunological Reviews
#39
JOURNAL ARTICLE
Min-Kyu Kim, Lei Zhao, Soyoung Jeong, Jing Zhang, Jong-Hyun Jung, Ho Seong Seo, Jong-Il Choi, Sangyong Lim
Thioredoxin (Trx), a ubiquitous protein showing disulfide reductase activity, plays critical roles in cellular redox control and oxidative stress response. Trx is a member of the Trx system, comprising Trx, Trx reductase (TrxR), and a cognate reductant (generally reduced nicotinamide adenine dinucleotide phosphate, NADPH). Bacterial Trx1 contains only the Trx-fold domain, in which the active site CXXC motif that is critical for the disulfide reduction activity is located. Bacterial Trx2 contains an N-terminal extension, which forms a zinc-finger domain, including two additional CXXC motifs...
November 20, 2021: Antioxidants (Basel, Switzerland)
#40
JOURNAL ARTICLE
Desmond Onyeka Agwunobi, Miao Zhang, Xinyue Shi, Shiqi Zhang, Meng Zhang, Tongxuan Wang, Abolfazl Masoudi, Zhijun Yu, Jingze Liu
DNA methylation, mediated by DNA methyltransferases (Dnmts), is a typical epigenetic process that plays an important role in affecting organism acclimatization and adaptation to environmental changes. However, information about Dnmts and their associations with the cold tolerance of ticks remains meager. Hence, in the present study, the Dnmts in important vector ticks Dermacentor silvarum and Haemaphysalis longicornis were cloned and identified, and their functions in cold response were further explored. Results showed that the length of DsDnmt and DsDnmt1 in D...
2021: Frontiers in Veterinary Science
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