1
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Lee B, Cyrill SL, Lee W, Melchiotti R, Andiappan AK, Poidinger M, Rötzschke O. Analysis of archaic human haplotypes suggests that 5hmC acts as an epigenetic guide for NCO recombination. BMC Biol 2022; 20:173. [PMID: 35927700 PMCID: PMC9354366 DOI: 10.1186/s12915-022-01353-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/17/2022] [Indexed: 11/17/2022] Open
Abstract
Background Non-crossover (NCO) refers to a mechanism of homologous recombination in which short tracks of DNA are copied between homologue chromatids. The allelic changes are typically restricted to one or few SNPs, which potentially allow for the gradual adaptation and maturation of haplotypes. It is assumed to be a stochastic process but the analysis of archaic and modern human haplotypes revealed a striking variability in local NCO recombination rates. Methods NCO recombination rates of 1.9 million archaic SNPs shared with Denisovan hominids were defined by a linkage study and correlated with functional and genomic annotations as well as ChIP-Seq data from modern humans. Results We detected a strong correlation between NCO recombination rates and the function of the respective region: low NCO rates were evident in introns and quiescent intergenic regions but high rates in splice sites, exons, 5′- and 3′-UTRs, as well as CpG islands. Correlations with ChIP-Seq data from ENCODE and other public sources further identified epigenetic modifications that associated directly with these recombination events. A particularly strong association was observed for 5-hydroxymethylcytosine marks (5hmC), which were enriched in virtually all of the functional regions associated with elevated NCO rates, including CpG islands and ‘poised’ bivalent regions. Conclusion Our results suggest that 5hmC marks may guide the NCO machinery specifically towards functionally relevant regions and, as an intermediate of oxidative demethylation, may open a pathway for environmental influence by specifically targeting recently opened gene loci. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01353-9.
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Affiliation(s)
- Bernett Lee
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore.,Present address: Lee Kong Chian School of Medicine, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Samantha Leeanne Cyrill
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore.,Present address: Cold Spring Harbor Laboratory, One Bungtown Road, NY, 11724, Cold Spring Harbor, USA
| | - Wendy Lee
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore
| | - Rossella Melchiotti
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore
| | - Anand Kumar Andiappan
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore
| | - Michael Poidinger
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore.,Present address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road, Parkville, Victoria, 3052, Australia
| | - Olaf Rötzschke
- Singapore Immunology Network (SIgN), Agency of Science Technology and Research (A*STAR), 8A Biomedical Drive, Singapore, 138648, Singapore.
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2
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Abstract
AbstractIn B cells, IgD is expressed together with IgM through alternative splicing of primary VHDJH-Cμ-s-m-Cδ-s-m RNAs, and also through IgD class switch DNA recombination (CSR) via double-strand DNA breaks (DSB) and synapse of Sμ with σδ. How such DSBs are resolved is still unknown, despite our previous report showing that Rad52 effects the ‘short-range’ microhomology-mediated synapsis of intra-Sμ region DSBs. Here we find that induction of IgD CSR downregulates Zfp318, and promotes Rad52 phosphorylation and recruitment to Sμ and σδ, thereby leading to alternative end-joining (A-EJ)-mediated Sμ-σδ recombination with extensive microhomologies, VHDJH-Cδs transcription and sustained IgD secretion. Rad52 ablation in mouse Rad52−/− B cells aborts IgD CSR in vitro and in vivo and dampens the specific IgD antibody response to OVA. Rad52 knockdown in human B cells also abrogates IgD CSR. Finally, Rad52 phosphorylation is associated with high levels of IgD CSR and anti-nuclear IgD autoantibodies in patients with systemic lupus erythematosus and in lupus-prone mice. Our findings thus show that Rad52 mediates IgD CSR through microhomology-mediated A-EJ in concert with Zfp318 downregulation.
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3
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Vander Zanden CM, Czarny RS, Ho EN, Robertson AB, Ho PS. Structural adaptation of vertebrate endonuclease G for 5-hydroxymethylcytosine recognition and function. Nucleic Acids Res 2020; 48:3962-3974. [PMID: 32095813 PMCID: PMC7144941 DOI: 10.1093/nar/gkaa117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/09/2020] [Accepted: 02/19/2020] [Indexed: 01/07/2023] Open
Abstract
Modified DNA bases functionally distinguish the taxonomic forms of life—5-methylcytosine separates prokaryotes from eukaryotes and 5-hydroxymethylcytosine (5hmC) invertebrates from vertebrates. We demonstrate here that mouse endonuclease G (mEndoG) shows specificity for both 5hmC and Holliday junctions. The enzyme has higher affinity (>50-fold) for junctions over duplex DNAs. A 5hmC-modification shifts the position of the cut site and increases the rate of DNA cleavage in modified versus unmodified junctions. The crystal structure of mEndoG shows that a cysteine (Cys69) is positioned to recognize 5hmC through a thiol-hydroxyl hydrogen bond. Although this Cys is conserved from worms to mammals, a two amino acid deletion in the vertebrate relative to the invertebrate sequence unwinds an α-helix, placing the thiol of Cys69 into the mEndoG active site. Mutations of Cys69 with alanine or serine show 5hmC-specificity that mirrors the hydrogen bonding potential of the side chain (C–H < S–H < O–H). A second orthogonal DNA binding site identified in the mEndoG structure accommodates a second arm of a junction. Thus, the specificity of mEndoG for 5hmC and junctions derives from structural adaptations that distinguish the vertebrate from the invertebrate enzyme, thereby thereby supporting a role for 5hmC in recombination processes.
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Affiliation(s)
- Crystal M Vander Zanden
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ryan S Czarny
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Ethan N Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
| | - Adam B Robertson
- Department of Molecular Microbiology, Oslo University Hospital, Sognsvannsveien 20, NO-0027 Oslo, Norway
| | - P Shing Ho
- Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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4
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Zan H, Tat C, Qiu Z, Taylor JR, Guerrero JA, Shen T, Casali P. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends to modulate antibody class-switch DNA recombination. Nat Commun 2017; 8:14244. [PMID: 28176781 PMCID: PMC5309807 DOI: 10.1038/ncomms14244] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/12/2016] [Indexed: 12/13/2022] Open
Abstract
Antibody class-switch DNA recombination (CSR) is initiated by AID-introduced DSBs in the switch (S) regions targeted for recombination, as effected by Ku70/Ku86-mediated NHEJ. Ku-deficient B cells, however, undergo (reduced) CSR through an alternative(A)-NHEJ pathway, which introduces microhomologies in S-S junctions. As microhomology-mediated end-joining requires annealing of single-strand DNA ends, we addressed the contribution of single-strand annealing factors HR Rad52 and translesion DNA polymerase θ to CSR. Compared with their Rad52+/+ counterparts, which display normal CSR, Rad52-/- B cells show increased CSR, fewer intra-Sμ region recombinations, no/minimal microhomologies in S-S junctions, decreased c-Myc/IgH translocations and increased Ku70/Ku86 recruitment to S-region DSB ends. Rad52 competes with Ku70/Ku86 for binding to S-region DSB ends. It also facilitates a Ku-independent DSB repair, which favours intra-S region recombination and mediates, particularly in Ku absence, inter-S-S recombination, as emphasized by the significantly greater CSR reduction in Rad52-/- versus Rad52+/+ B cells on Ku86 knockdown.
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Affiliation(s)
- Hong Zan
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Connie Tat
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Zhifang Qiu
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Julia R. Taylor
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Justin A. Guerrero
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Tian Shen
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
| | - Paolo Casali
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas School of Medicine, UT Health Science Center, San Antonio, Texas 78229, USA
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5
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Pone EJ. Analysis by Flow Cytometry of B-Cell Activation and Antibody Responses Induced by Toll-Like Receptors. Methods Mol Biol 2016; 1390:229-48. [PMID: 26803633 DOI: 10.1007/978-1-4939-3335-8_15] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
Toll-like receptors (TLRs) are expressed in B lymphocytes and contribute to B-cell activation, antibody responses, and their maturation. TLR stimulation of mouse B cells induces class switch DNA recombination (CSR) to isotypes specified by cytokines, and also induces formation of IgM(+) as well as class-switched plasma cells. B-cell receptor (BCR) signaling, while on its own inducing limited B-cell proliferation and no CSR, can enhance CSR driven by TLRs. Particular synergistic or antagonistic interactions among TLR pathways, BCR, and cytokine signaling can have important consequences for B-cell activation, CSR, and plasma cell formation. This chapter outlines protocols for the induction and analysis of B-cell activation and antibody production by TLRs with or without other stimuli.
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Affiliation(s)
- Egest J Pone
- Department of Pharmaceutical Sciences, University of California, Irvine, CA, 92697, USA.
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6
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Lin JLJ, Wu CC, Yang WZ, Yuan HS. Crystal structure of endonuclease G in complex with DNA reveals how it nonspecifically degrades DNA as a homodimer. Nucleic Acids Res 2016; 44:10480-10490. [PMID: 27738134 PMCID: PMC5137453 DOI: 10.1093/nar/gkw931] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 10/05/2016] [Accepted: 10/07/2016] [Indexed: 01/20/2023] Open
Abstract
Endonuclease G (EndoG) is an evolutionarily conserved mitochondrial protein in eukaryotes that digests nucleus chromosomal DNA during apoptosis and paternal mitochondrial DNA during embryogenesis. Under oxidative stress, homodimeric EndoG becomes oxidized and converts to monomers with diminished nuclease activity. However, it remains unclear why EndoG has to function as a homodimer in DNA degradation. Here, we report the crystal structure of the Caenorhabditis elegans EndoG homologue, CPS-6, in complex with single-stranded DNA at a resolution of 2.3 Å. Two separate DNA strands are bound at the ββα-metal motifs in the homodimer with their nucleobases pointing away from the enzyme, explaining why CPS-6 degrades DNA without sequence specificity. Two obligatory monomeric CPS-6 mutants (P207E and K131D/F132N) were constructed, and they degrade DNA with diminished activity due to poorer DNA-binding affinity as compared to wild-type CPS-6. Moreover, the P207E mutant exhibits predominantly 3′-to-5′ exonuclease activity, indicating a possible endonuclease to exonuclease activity change. Thus, the dimer conformation of CPS-6 is essential for maintaining its optimal DNA-binding and endonuclease activity. Compared to other non-specific endonucleases, which are usually monomeric enzymes, EndoG is a unique dimeric endonuclease, whose activity hence can be modulated by oxidation to induce conformational changes.
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Affiliation(s)
- Jason L J Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Chyuan-Chuan Wu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC .,Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan 10048, ROC
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7
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Lin JLJ, Nakagawa A, Skeen-Gaar R, Yang WZ, Zhao P, Zhang Z, Ge X, Mitani S, Xue D, Yuan HS. Oxidative Stress Impairs Cell Death by Repressing the Nuclease Activity of Mitochondrial Endonuclease G. Cell Rep 2016; 16:279-287. [PMID: 27346342 DOI: 10.1016/j.celrep.2016.05.090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 04/28/2016] [Accepted: 05/22/2016] [Indexed: 01/22/2023] Open
Abstract
Endonuclease G (EndoG) is a mitochondrial protein that is released from mitochondria and relocated into the nucleus to promote chromosomal DNA fragmentation during apoptosis. Here, we show that oxidative stress causes cell-death defects in C. elegans through an EndoG-mediated cell-death pathway. In response to high reactive oxygen species (ROS) levels, homodimeric CPS-6-the C. elegans homolog of EndoG-is dissociated into monomers with diminished nuclease activity. Conversely, the nuclease activity of CPS-6 is enhanced, and its dimeric structure is stabilized by its interaction with the worm AIF homolog, WAH-1, which shifts to disulfide cross-linked dimers under high ROS levels. CPS-6 thus acts as a ROS sensor to regulate the life and death of cells. Modulation of the EndoG dimer conformation could present an avenue for prevention and treatment of diseases resulting from oxidative stress.
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Affiliation(s)
- Jason L J Lin
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Akihisa Nakagawa
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Riley Skeen-Gaar
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Wei-Zen Yang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC
| | - Pei Zhao
- School of Life Sciences and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Zhe Zhang
- School of Life Sciences and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Xiao Ge
- School of Life Sciences and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China
| | - Shohei Mitani
- Department of Physiology, Tokyo Women's Medical University School of Medicine, Tokyo 162-8666, Japan; Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Tokyo 162-8666, Japan
| | - Ding Xue
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309, USA; School of Life Sciences and Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Tsinghua University, Beijing 100084, China.
| | - Hanna S Yuan
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan 11529, ROC; Graduate Institute of Biochemistry and Molecular Biology, National Taiwan University, Taiwan 10048, ROC.
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8
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Misic V, El-Mogy M, Haj-Ahmad Y. Role of Endonuclease G in Exogenous DNA Stability in HeLa Cells. BIOCHEMISTRY (MOSCOW) 2016; 81:163-75. [PMID: 27260396 DOI: 10.1134/s0006297916020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Endonuclease G (EndoG) is a well-conserved mitochondrial-nuclear nuclease with dual lethal and vital roles in the cell. The aim of our study was to examine whether EndoG exerts its nuclease activity on exogenous DNA substrates such as plasmid DNA (pDNA), considering their importance in gene therapy applications. The effects of EndoG knockdown on pDNA stability and levels of encoded reporter gene expression were evaluated in the cervical carcinoma HeLa cells. Transfection of pDNA vectors encoding short-hairpin RNAs (shRNAs) reduced levels of EndoG mRNA in HeLa cells. In physiological circumstances, EndoG knockdown did not have an effect on the stability of pDNA or the levels of encoded transgene expression as measured over a four-day time course. However, when endogenous expression of EndoG was induced by an extrinsic stimulus, targeting of EndoG by shRNA improved the perceived stability and transgene expression of pDNA vectors. Therefore, EndoG is not a mediator of exogenous DNA clearance, but in non-physiological circumstances, it may nonspecifically cleave intracellular DNA regardless of its origin. These findings make it unlikely that targeting of EndoG is a viable strategy for improving the duration and level of transgene expression from nonviral DNA vectors in gene therapy efforts.
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Affiliation(s)
- V Misic
- Brock University, Department of Biological Sciences, St. Catharines, ON, L2S 3A1, Canada.
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9
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Misic V, El-Mogy M, Geng S, Haj-Ahmad Y. Effect of endonuclease G depletion on plasmid DNA uptake and levels of homologous recombination in hela cells. Mol Biol 2016. [DOI: 10.1134/s0026893316020175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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10
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Robertson AB, Robertson J, Fusser M, Klungland A. Endonuclease G preferentially cleaves 5-hydroxymethylcytosine-modified DNA creating a substrate for recombination. Nucleic Acids Res 2014; 42:13280-93. [PMID: 25355512 PMCID: PMC4245937 DOI: 10.1093/nar/gku1032] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
5-hydroxymethylcytosine (5hmC) has been suggested to be involved in various nucleic acid transactions and cellular processes, including transcriptional regulation, demethylation of 5-methylcytosine and stem cell pluripotency. We have identified an activity that preferentially catalyzes the cleavage of double-stranded 5hmC-modified DNA. Using biochemical methods we purified this activity from mouse liver extracts and demonstrate that the enzyme responsible for the cleavage of 5hmC-modified DNA is Endonuclease G (EndoG). We show that recombinant EndoG preferentially recognizes and cleaves a core sequence when one specific cytosine within that core sequence is hydroxymethylated. Additionally, we provide in vivo evidence that EndoG catalyzes the formation of double-stranded DNA breaks and that this cleavage is dependent upon the core sequence, EndoG and 5hmC. Finally, we demonstrate that the 5hmC modification can promote conservative recombination in an EndoG-dependent manner.
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Affiliation(s)
- Adam B Robertson
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Julia Robertson
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Markus Fusser
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway
| | - Arne Klungland
- Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, Norway Institute of Basic Medical Sciences, University of Oslo, PO Box 1018 Blindern, N-0315 Oslo, Norway
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11
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Gole B, Baumann C, Mian E, Ireno CI, Wiesmüller L. Endonuclease G initiates DNA rearrangements at the MLL breakpoint cluster upon replication stress. Oncogene 2014; 34:3391-401. [PMID: 25132265 DOI: 10.1038/onc.2014.268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Revised: 07/02/2014] [Accepted: 07/14/2014] [Indexed: 12/31/2022]
Abstract
MLL (myeloid/lymphoid or mixed-lineage leukemia) rearrangements are frequent in therapy-related and childhood acute leukemia, and are associated with poor prognosis. The majority of the rearrangements fall within a 7.3-kb MLL breakpoint cluster region (MLLbcr), particularly in a 0.4-kb hotspot at the intron11-exon12 boundary. The underlying mechanisms are poorly understood, though multiple pathways including early apoptotic signaling, accompanied by high-order DNA fragmentation, have been implicated. We introduced the MLLbcr hotspot in an EGFP-based recombination reporter system and demonstrated enhancement of both spontaneous and genotoxic treatment-induced DNA recombination by the MLLbcr in various human cell types. We identified Endonuclease G (EndoG), an apoptotic nuclease, as an essential factor for MLLbcr-specific DNA recombination after induction of replication stress. We provide evidence for replication stress-induced nuclear accumulation of EndoG, DNA binding by EndoG as well as cleavage of the chromosomal MLLbcr locus in a manner requiring EndoG. We demonstrate additional dependency of MLLbcr breakage on ATM signaling to histone H2B monoubiquitinase RNF20, involved in chromatin relaxation. Altogether our findings provide a novel mechanism underlying MLLbcr destabilization in the cells of origin of leukemogenesis, with replication stress-activated, EndoG-mediated cleavage at the MLLbcr, which may serve resolution of the stalled forks via recombination repair, however, also permits MLL rearrangements.
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Affiliation(s)
- B Gole
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - C Baumann
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - E Mian
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - C I Ireno
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
| | - L Wiesmüller
- Gynecological Oncology, Department of Obstetrics and Gynecology, University of Ulm, Ulm, Germany
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12
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Aleksandrushkina NI, Vanyushin BF. Endonucleases and apoptosis in animals. BIOCHEMISTRY (MOSCOW) 2013; 77:1436-51. [PMID: 23379520 DOI: 10.1134/s0006297912130032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Endonucleases are the main instruments of obligatory DNA degradation in apoptosis. Many endonucleases have marked processive action; initially they split DNA in chromatin into very large domains, and then they perform in it internucleosomal fragmentation of DNA followed by its hydrolysis to small fragments (oligonucleotides). During apoptosis, DNA of chromatin is attacked by many nucleases that are different in activity, specificity, and order of action. The activity of every endonuclease is regulated in the cell through its own regulatory mechanism (metal ions and other effectors, possibly also S-adenosylmethionine). Apoptosis is impossible without endonucleases as far as it leads to accumulation of unnecessary (defective) DNA, disorders in cell differentiation, embryogenesis, the organism's development, and is accompanied by various severe diseases. The interpretation of the structure and functions of endonucleases and of the nature and action of their modulating effectors is important not only for elucidation of mechanisms of apoptosis, but also for regulation and control of programmed cell death, cell differentiation, and development of organisms.
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Affiliation(s)
- N I Aleksandrushkina
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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13
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14
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Xu Z, Zan H, Pone EJ, Mai T, Casali P. Immunoglobulin class-switch DNA recombination: induction, targeting and beyond. Nat Rev Immunol 2012; 12:517-31. [PMID: 22728528 PMCID: PMC3545482 DOI: 10.1038/nri3216] [Citation(s) in RCA: 294] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Class-switch DNA recombination (CSR) of the immunoglobulin heavy chain (IGH) locus is central to the maturation of the antibody response and crucially requires the cytidine deaminase AID. CSR involves changes in the chromatin state and the transcriptional activation of the IGH locus at the upstream and downstream switch (S) regions that are to undergo S-S DNA recombination. In addition, CSR involves the induction of AID expression and the targeting of CSR factors to S regions by 14-3-3 adaptors, and it is facilitated by the transcription machinery and by histone modifications. In this Review, we focus on recent advances regarding the induction and targeting of CSR and outline an integrated model of the assembly of macromolecular complexes that transduce crucial epigenetic information to enzymatic effectors of the CSR machinery.
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Affiliation(s)
- Zhenming Xu
- Institute for Immunology and Department of Medicine, School of Medicine, University of California, Irvine, California 92697-4120, USA
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15
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Pone EJ, Zhang J, Mai T, White CA, Li G, Sakakura JK, Patel PJ, Al-Qahtani A, Zan H, Xu Z, Casali P. BCR-signalling synergizes with TLR-signalling for induction of AID and immunoglobulin class-switching through the non-canonical NF-κB pathway. Nat Commun 2012; 3:767. [PMID: 22473011 PMCID: PMC3337981 DOI: 10.1038/ncomms1769] [Citation(s) in RCA: 180] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 03/01/2012] [Indexed: 12/12/2022] Open
Abstract
By diversifying antibody biological effector functions, class switch DNA recombination has a central role in the maturation of the antibody response. Here we show that BCR-signalling synergizes with Toll-like receptor (TLR) signalling to induce class switch DNA recombination. BCR-signalling activates the non-canonical NF-κB pathway and enhances the TLR-dependent canonical NF-κB pathway, thereby inducing activation-induced cytidine deaminase (AID), which is critical for class switch DNA recombination. Escherichia coli lipopolysaccharide (LPS) triggers dual TLR4/BCR-signalling and induces hallmarks of BCR-signalling, including CD79a phosphorylation and Ca(2+) mobilization, and activates both the NF-κB pathways to induce AID and class switch DNA recombination in a PI(3)K p85α-dependent fashion. CD40-signalling activates the two NF-κB pathways to induce AID and class switch DNA recombination independent of BCR-signalling. Finally, dual BCR/TLR-engaging NP-lipopolysaccharide effectively elicits class-switched NP-specific IgG3 and IgG2b in mice. Thus, by integrating signals of the non-canonical and canonical NF-κB pathways, BCR and TLRs synergize to induce AID and T-cell-independent class switch DNA recombination.
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Affiliation(s)
- Egest J Pone
- Institute for immunology and School of Medicine, University of California, Irvine, 92697-4120, USA
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16
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Non-apoptotic functions of apoptosis-regulatory proteins. EMBO Rep 2012; 13:322-30. [PMID: 22402666 DOI: 10.1038/embor.2012.19] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2011] [Accepted: 01/23/2012] [Indexed: 01/24/2023] Open
Abstract
During the past two decades, apoptotic cell death has been the subject of an intense wave of investigation, leading to the discovery of multiple gene products that govern both its induction and execution. In parallel, it has progressively become evident that most, if not all, proteins that had initially been discovered for their essential role in apoptosis also mediate a wide range of non-apoptotic functions. On the one hand, apoptotic regulators and executioners are involved in non-lethal physiological processes as diverse as cell cycle progression, differentiation, metabolism, autophagy and inflammation. On the other hand, pro-apoptotic proteins can control other modalities of programmed cell death, in particular regulated necrosis. In this review, we summarize the unconventional roles of the apoptotic core machinery from a functional perspective and discuss their pathophysiological implications.
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White CA, Seth Hawkins J, Pone EJ, Yu ES, Al-Qahtani A, Mai T, Zan H, Casali P. AID dysregulation in lupus-prone MRL/Fas(lpr/lpr) mice increases class switch DNA recombination and promotes interchromosomal c-Myc/IgH loci translocations: modulation by HoxC4. Autoimmunity 2011; 44:585-98. [PMID: 21585311 DOI: 10.3109/08916934.2011.577128] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Immunoglobulin gene somatic hypermutation (SHM) and class switch DNA recombination (CSR) play important roles in the generation of autoantibodies in systemic lupus erythematosus. Systemic lupus is characterized by the production of an array of pathogenic high-affinity mutated and class-switched, mainly IgG, antibodies to a variety of self-antigens, including nuclear components, such as dsDNA, histones, and chromatin. We previously found that MRL/Fas(lpr/lpr) mice, which develop a systemic autoimmune syndrome sharing many features with human lupus, display greatly upregulated CSR, particularly to IgG2a, in B cells of the spleen, lymph nodes, and Peyer's patches. In MRL/Fas(lpr/lpr) mice, the significant upregulation of CSR is associated with increased expression of activation-induced cytidine deaminase (AID), which is critical for CSR and SHM. We also found that HoxC4 directly activates the promoter of the AID gene to induce AID expression, CSR and SHM. Here, we show that in both lupus patients and lupus-prone MRL/Fas(lpr/lpr) mice, the expression of HoxC4 and AID is significantly upregulated. To further analyze the role of HoxC4 in lupus, we generated HoxC4(-/-) MRL/Fas(lpr/lpr) mice. In these mice, HoxC4-deficiency resulted in reduced AID expression, impaired CSR, and decreased serum anti-dsDNA IgG, particularly IgG2a, autoantibodies, which were associated with a reduction in IgG deposition in kidney glomeruli. In addition, consistent with our previous findings in MRL/Fas(lpr/lpr) mice that upregulated AID expression is associated with extensive DNA lesions, comprising deletions and insertions in the IgH locus, we found that c-Myc to IgH (c-Myc/IgH) translocations occur frequently in B cells of MRL/Fas(lpr/lpr) mice. The frequency of such translocations was significantly reduced in HoxC4(-/-) MRL/Fas(lpr/lpr) mice. These findings suggest that in lupus B cells, upregulation of HoxC4 plays a major role in dysregulation of AID expression, thereby increasing CSR and autoantibody production and promoting c-Myc/IgH translocations.
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Affiliation(s)
- Clayton A White
- School of Medicine and School of Biological Sciences, Institute for Immunology, University of California, 3028 Hewitt Hall, Irvine, CA 92697-4120, USA
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