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Ren J, Wang J, Ren Y, Zhang Y, Wei P, Wang M, Zhang Y, Li M, Yuan C, Gong H, Jiang J, Wang Z. Structural basis of DNA recognition by BEN domain proteins reveals a role for oligomerization in unmethylated DNA selection by BANP. Nucleic Acids Res 2024:gkae762. [PMID: 39225042 DOI: 10.1093/nar/gkae762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 08/17/2024] [Accepted: 08/21/2024] [Indexed: 09/04/2024] Open
Abstract
The BEN domain is a newly discovered type of DNA-binding domain that exists in a variety of species. There are nine BEN domain-containing proteins in humans, and most have been shown to have chromatin-related functions. NACC1 preferentially binds to CATG motif-containing sequences and functions primarily as a transcriptional coregulator. BANP and BEND3 preferentially bind DNA bearing unmethylated CpG motifs, and they function as CpG island-binding proteins. To date, the DNA recognition mechanism of quite a few of these proteins remains to be determined. In this study, we solved the crystal structures of the BEN domains of NACC1 and BANP in complex with their cognate DNA substrates. We revealed the details of DNA binding by these BEN domain proteins and unexpectedly revealed that oligomerization is required for BANP to select unmethylated CGCG motif-containing DNA substrates. Our study clarifies the controversies surrounding DNA recognition by BANP and demonstrates a new mechanism by which BANP selects unmethylated CpG motifs and functions as a CpG island-binding protein. This understanding will facilitate further exploration of the physiological functions of the BEN domain proteins in the future.
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Affiliation(s)
- Jiahao Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Junmeng Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Yuyang Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 30 Shuangqing Road, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, 30 Shuangqing Road, Beijing 100084, China
| | - Pengshuai Wei
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Meng Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Yimeng Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Meng Li
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Chuyan Yuan
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Haipeng Gong
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, 30 Shuangqing Road, Beijing 100084, China
- Beijing Frontier Research Center for Biological Structure, Tsinghua University, 30 Shuangqing Road, Beijing 100084, China
| | - Junyi Jiang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, 19 Xinjiekouwai Avenue, Beijing 100875, China
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Simon C, Brunke ID, Stielow B, Forné I, Steitz AM, Geller M, Rohner I, Weber LM, Fischer S, Jeude LM, Huber T, Nist A, Stiewe T, Huber M, Buchholz M, Liefke R. SAMD1 suppresses epithelial-mesenchymal transition pathways in pancreatic ductal adenocarcinoma. PLoS Biol 2024; 22:e3002739. [PMID: 39137238 PMCID: PMC11343471 DOI: 10.1371/journal.pbio.3002739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 08/23/2024] [Accepted: 07/05/2024] [Indexed: 08/15/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) poses a significant threat due to its tendency to evade early detection, frequent metastasis, and the subsequent challenges in devising effective treatments. Processes that govern epithelial-mesenchymal transition (EMT) in PDAC hold promise for advancing novel therapeutic strategies. SAMD1 (SAM domain-containing protein 1) is a CpG island-binding protein that plays a pivotal role in the repression of its target genes. Here, we revealed that SAMD1 acts as a repressor of genes associated with EMT. Upon deletion of SAMD1 in PDAC cells, we observed significantly increased migration rates. SAMD1 exerts its effects by binding to specific genomic targets, including CDH2, encoding N-cadherin, which emerged as a driver of enhanced migration upon SAMD1 knockout. Furthermore, we discovered the FBXO11-containing E3 ubiquitin ligase complex as an interactor and negative regulator of SAMD1, which inhibits SAMD1 chromatin-binding genome-wide. High FBXO11 expression in PDAC is associated with poor prognosis and increased expression of EMT-related genes, underlining an antagonistic relationship between SAMD1 and FBXO11. In summary, our findings provide insights into the regulation of EMT-related genes in PDAC, shedding light on the intricate role of SAMD1 and its interplay with FBXO11 in this cancer type.
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Affiliation(s)
- Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Inka D. Brunke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried, Germany
| | - Anna Mary Steitz
- Translational Oncology Group, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, Marburg, Germany
| | - Merle Geller
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Lea Marie Jeude
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Theresa Huber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg, Germany
- Institute for Lung Health (ILH), Justus Liebig University, Giessen, Germany
| | - Magdalena Huber
- Institute of Systems Immunology, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, Marburg, Germany
| | - Malte Buchholz
- Department of Gastroenterology, Endocrinology, Metabolism and Infection, Center for Tumor Biology and Immunology (ZTI), Philipps University of Marburg, Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg, Germany
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3
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Wang X, Li QQ, Tang YX, Li Y, Zhang L, Xu FF, Fu XL, Ye K, Ma JQ, Guo SM, Ma FY, Liu ZY, Shi XH, Li XM, Sun HM, Wu Y, Zhang WY, Ye LH. Oncoprotein LAMTOR5-mediated CHOP silence via DNA hypermethylation and miR-182/miR-769 in promotion of liver cancer growth. Acta Pharmacol Sin 2024:10.1038/s41401-024-01310-y. [PMID: 38942954 DOI: 10.1038/s41401-024-01310-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/08/2024] [Indexed: 06/30/2024] Open
Abstract
C/EBP homologous protein (CHOP) triggers the death of multiple cancers via endoplasmic reticulum (ER) stress. However, the function and regulatory mechanism of CHOP in liver cancer remain elusive. We have reported that late endosomal/lysosomal adapter, mitogen-activated protein kinase and mTOR activator 5 (LAMTOR5) suppresses apoptosis in various cancers. Here, we show that the transcriptional and posttranscriptional inactivation of CHOP mediated by LAMTOR5 accelerates liver cancer growth. Clinical bioinformatic analysis revealed that the expression of CHOP was low in liver cancer tissues and that its increased expression predicted a good prognosis. Elevated CHOP contributed to destruction of LAMTOR5-induced apoptotic suppression and proliferation. Mechanistically, LAMTOR5-recruited DNA methyltransferase 1 (DNMT1) to the CpG3 region (-559/-429) of the CHOP promoter and potentiated its hypermethylation to block its interaction with general transcription factor IIi (TFII-I), resulting in its inactivation. Moreover, LAMTOR5-enhanced miR-182/miR-769 reduced CHOP expression by targeting its 3'UTR. Notably, lenvatinib, a first-line targeted therapy for liver cancer, could target the LAMTOR5/CHOP axis to prevent liver cancer progression. Accordingly, LAMTOR5-mediated silencing of CHOP via the regulation of ER stress-related apoptosis promotes liver cancer growth, providing a theoretical basis for the use of lenvatinib for the treatment of liver cancer.
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Affiliation(s)
- Xue Wang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Qian-Qian Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yan-Xin Tang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Ye Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Lu Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
- Chinese Academy of Medical Sciences & Peking Union Medical College Institute of Biomedical Engineering, Tianjin, 300192, China
| | - Fei-Fei Xu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
- Institute of Radiation Medicine, Peking Union Medical College & Chinese Academy of Medical Sciences, Tianjin, 300192, China
| | - Xue-Li Fu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Kai Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Jia-Qi Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Shi-Man Guo
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Fang-Yuan Ma
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Zhi-Yu Liu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xu-He Shi
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Xian-Meng Li
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Hui-Min Sun
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
| | - Yue Wu
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, Collaborative Innovation Center of Cell Biology in Universities of Shandong, College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Wei-Ying Zhang
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
| | - Li-Hong Ye
- State Key Laboratory of Medicinal Chemical Biology, Tianjin Key Laboratory of Protein Sciences, Department of Biochemistry and Molecular Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.
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Olasz B, Smithers L, Evans GL, Anandan A, Murcha MW, Vrielink A. Structural analysis of the SAM domain of the Arabidopsis mitochondrial tRNA import receptor. J Biol Chem 2024; 300:107258. [PMID: 38582448 PMCID: PMC11063897 DOI: 10.1016/j.jbc.2024.107258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/10/2024] [Accepted: 03/19/2024] [Indexed: 04/08/2024] Open
Abstract
Mitochondria are membrane-bound organelles of endosymbiotic origin with limited protein-coding capacity. The import of nuclear-encoded proteins and nucleic acids is required and essential for maintaining organelle mass, number, and activity. As plant mitochondria do not encode all the necessary tRNA types required, the import of cytosolic tRNA is vital for organelle maintenance. Recently, two mitochondrial outer membrane proteins, named Tric1 and Tric2, for tRNA import component, were shown to be involved in the import of cytosolic tRNA. Tric1/2 binds tRNAalavia conserved residues in the C-terminal Sterile Alpha Motif (SAM) domain. Here we report the X-ray crystal structure of the Tric1 SAM domain. We identified the ability of the SAM domain to form a helical superstructure with six monomers per helical turn and key amino acid residues responsible for its formation. We determined that the oligomerization of the Tric1 SAM domain may play a role in protein function whereby mutation of Gly241 introducing a larger side chain at this position disrupted the oligomer and resulted in the loss of RNA binding capability. Furthermore, complementation of Arabidopsis thaliana Tric1/2 knockout lines with a mutated Tric1 failed to restore the defective plant phenotype. AlphaFold2 structure prediction of both the SAM domain and Tric1 support a cyclic pentameric or hexameric structure. In the case of a hexameric structure, a pore of sufficient dimensions to transfer tRNA across the mitochondrial membrane is observed. Our results highlight the importance of oligomerization of Tric1 for protein function.
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Affiliation(s)
- Bence Olasz
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Luke Smithers
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Genevieve L Evans
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Anandhi Anandan
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia
| | - Monika W Murcha
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
| | - Alice Vrielink
- School of Molecular Sciences, The University of Western Australia, Perth, Western Australia, Australia.
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Helbrecht I, Heiter D, Yang W, Vincze T, Hanneman A, Lutz T, Ettwiller L, Bochtler M, Xu SY. Characterization of winged helix domain fusion endonucleases as N6-methyladenine-dependent type IV restriction systems. Front Microbiol 2024; 15:1286822. [PMID: 38655080 PMCID: PMC11037411 DOI: 10.3389/fmicb.2024.1286822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 02/08/2024] [Indexed: 04/26/2024] Open
Abstract
Winged helix (wH) domains, also termed winged helix-turn-helix (wHTH) domains, are widespread in all kingdoms of life and have diverse roles. In the context of DNA binding and DNA modification sensing, some eukaryotic wH domains are known as sensors of non-methylated CpG. In contrast, the prokaryotic wH domains in DpnI and HhiV4I act as sensors of adenine methylation in the 6mApT (N6-methyladenine, 6mA, or N6mA) context. DNA-binding modes and interactions with the probed dinucleotide are vastly different in the two cases. Here, we show that the role of the wH domain as a sensor of adenine methylation is widespread in prokaryotes. We present previously uncharacterized examples of PD-(D/E)XK-wH (FcyTI, Psp4BI), PUA-wH-HNH (HtuIII), wH-GIY-YIG (Ahi29725I, Apa233I), and PLD-wH (Aba4572I, CbaI) fusion endonucleases that sense adenine methylation in the Dam+ Gm6ATC sequence contexts. Representatives of the wH domain endonuclease fusion families with the exception of the PLD-wH family could be purified, and an in vitro preference for adenine methylation in the Dam context could be demonstrated. Like most other modification-dependent restriction endonucleases (MDREs, also called type IV restriction systems), the new fusion endonucleases except those in the PD-(D/E)XK-wH family cleave close to but outside the recognition sequence. Taken together, our data illustrate the widespread combinatorial use of prokaryotic wH domains as adenine methylation readers. Other potential 6mA sensors in modified DNA are also discussed.
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Affiliation(s)
- Igor Helbrecht
- New England Biolabs, Inc., Ipswich, MA, United States
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Daniel Heiter
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Weiwei Yang
- New England Biolabs, Inc., Ipswich, MA, United States
| | - Tamas Vincze
- New England Biolabs, Inc., Ipswich, MA, United States
| | | | - Thomas Lutz
- New England Biolabs, Inc., Ipswich, MA, United States
| | | | - Matthias Bochtler
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- International Institute of Molecular and Cell Biology, Warsaw, Poland
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An R, Yang Y, Liu L, Li P. SAMD1 attenuates antiphospholipid syndrome-induced pregnancy complications. Immun Inflamm Dis 2023; 11:e1006. [PMID: 37904675 PMCID: PMC10614121 DOI: 10.1002/iid3.1006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 11/01/2023] Open
Abstract
OBJECTIVE This study was intended to investigate the effect of SAMD1 on antiphospholipid syndrome (APS)-induced pregnancy complications in mice. METHODS The mRNA and protein expression of SAMD1 in APS patients and healthy controls was detected by qRT-PCR and western blot. Anti-B2 GPI and ACA levels were tested by ELISA, MMP-9, iNOS, ICAM-1 and MCP-1 mRNA and protein levels determined by qRT-PCR and western blot, cellular senescence detected by β-galactosidase staining, cell proliferation ability detected by CCK-8 assay, cell viability detected by trypan blue staining, cell mobility detected by Transwell, and cell angiogenesis ability detected by matrigel tube formation assay. An APS pregnant mouse model was constructed, and the embryo absorption rate was calculated. RESULTS SAMD1 expression was low in serum of APS patients, which was correlated with the history of thrombosis and the number of adverse pregnancies. Anti-B2 GPI and ACA levels were increased in APS. The expressions of MMP-9, iNOS, ICAM-1, and MCP-1 were also significantly upregulated in HUVECs treated with APS serum. APS promoted HUVEC senescence and inhibited cell proliferation, migration and angiogenesis. Overexpression of SAMD1 reversed the above results. Experiments on the APS pregnant mouse model confirmed that overexpression of SAMD1 reduced the rate of fetal loss. CONCLUSION SAMD1 may reduce APS-induced embryo loss by regulating cellular senescence, proliferation, migration, and angiogenesis.
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Affiliation(s)
- Ran An
- Department of Obstetrics and GynecologyThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangP.R. China
| | - Yanqi Yang
- Department of Obstetrics and GynecologyThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangP.R. China
| | - Lei Liu
- Department of Obstetrics and GynecologyThe Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangP.R. China
| | - Peiling Li
- Department of Obstetrics and GynecologyThe Second Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangP.R. China
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Ray S, Hewitt K. Sticky, Adaptable, and Many-sided: SAM protein versatility in normal and pathological hematopoietic states. Bioessays 2023; 45:e2300022. [PMID: 37318311 PMCID: PMC10527593 DOI: 10.1002/bies.202300022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
With decades of research seeking to generalize sterile alpha motif (SAM) biology, many outstanding questions remain regarding this multi-tool protein module. Recent data from structural and molecular/cell biology has begun to reveal new SAM modes of action in cell signaling cascades and biomolecular condensation. SAM-dependent mechanisms underlie blood-related (hematologic) diseases, including myelodysplastic syndromes and leukemias, prompting our focus on hematopoiesis for this review. With the increasing coverage of SAM-dependent interactomes, a hypothesis emerges that SAM interaction partners and binding affinities work to fine tune cell signaling cascades in developmental and disease contexts, including hematopoiesis and hematologic disease. This review discusses what is known and remains unknown about the standard mechanisms and neoplastic properties of SAM domains and what the future might hold for developing SAM-targeted therapies.
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Affiliation(s)
- Suhita Ray
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
| | - Kyle Hewitt
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, 68198, United States
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8
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Deep A, Singh L, Kaur J, Velusamy M, Bhardwaj P, Singh R, Thakur KG. Structural insights into DarT toxin neutralization by cognate DarG antitoxin: ssDNA mimicry by DarG C-terminal domain keeps the DarT toxin inhibited. Structure 2023; 31:780-789.e4. [PMID: 37167974 DOI: 10.1016/j.str.2023.04.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 03/20/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
In the DarTG toxin-antitoxin system, the DarT toxin ADP-ribosylates single-stranded DNA (ssDNA), which stalls DNA replication and plays a crucial role in controlling bacterial growth and bacteriophage infection. This toxic activity is reversed by the N-terminal macrodomain of the cognate antitoxin DarG. DarG also binds DarT, but the role of these interactions in DarT neutralization is unknown. Here, we report that the C-terminal domain of DarG (DarG toxin-binding domain [DarGTBD]) interacts with DarT to form a 1:1 stoichiometric heterodimeric complex. We determined the 2.2 Å resolution crystal structure of the Mycobacterium tuberculosis DarT-DarGTBD complex. The comparative structural analysis reveals that DarGTBD interacts with DarT at the DarT/ssDNA interaction interface, thus sterically occluding substrate ssDNA binding and consequently inactivating toxin by direct protein-protein interactions. Our data support a unique two-layered DarT toxin neutralization mechanism of DarG, which is important in keeping the toxin molecules in check under normal growth conditions.
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Affiliation(s)
- Amar Deep
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Latika Singh
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Japleen Kaur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Maheshwaran Velusamy
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Pushpanjali Bhardwaj
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India
| | - Ramandeep Singh
- Infection and Immunology Group, Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR-Biotech Science Cluster, 3rd Milestone, Faridabad Gurugram Expressway, Faridabad-121001, India
| | - Krishan Gopal Thakur
- Structural Biology Laboratory, Council of Scientific and Industrial Research-Institute of Microbial Technology (CSIR-IMTECH), Chandigarh 160036, India.
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9
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Barruet E, Striedinger K, Marangoni P, Pomerantz JH. Loss of transcriptional heterogeneity in aged human muscle stem cells. PLoS One 2023; 18:e0285018. [PMID: 37192223 PMCID: PMC10187936 DOI: 10.1371/journal.pone.0285018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Age-related loss of muscle mass and function negatively impacts healthspan and lifespan. Satellite cells function as muscle stem cells in muscle maintenance and regeneration by self-renewal, activation, proliferation and differentiation. These processes are perturbed in aging at the stem cell population level, contributing to muscle loss. However, how representation of subpopulations within the human satellite cell pool change during aging remains poorly understood. We previously reported a comprehensive baseline of human satellite cell (Hu-MuSCs) transcriptional activity in muscle homeostasis describing functional heterogenous human satellite cell subpopulations such as CAV1+ Hu-MUSCs. Here, we sequenced additional satellite cells from new healthy donors and performed extended transcriptomic analyses with regard to aging. We found an age-related loss of global transcriptomic heterogeneity and identified new markers (CAV1, CXCL14, GPX3) along with previously described ones (FN1, ITGB1, SPRY1) that are altered during aging in human satellite cells. These findings describe new transcriptomic changes that occur during aging in human satellite cells and provide a foundation for understanding functional impact.
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Affiliation(s)
- Emilie Barruet
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California, United States of America
| | - Katharine Striedinger
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Pauline Marangoni
- Program in Craniofacial Biology and Department of Orofacial Sciences, University of California, San Francisco, California, United States of America
| | - Jason H. Pomerantz
- Departments of Surgery and Orofacial Sciences, Division of Plastic and Reconstructive Surgery, Program in Craniofacial Biology, Eli and Edythe Broad Center of Regeneration Medicine, University of California San Francisco, San Francisco, California, United States of America
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10
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Investigation of SAMD1 ablation in mice. Sci Rep 2023; 13:3000. [PMID: 36810619 PMCID: PMC9944271 DOI: 10.1038/s41598-023-29779-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 02/10/2023] [Indexed: 02/23/2023] Open
Abstract
SAM domain-containing protein 1 (SAMD1) has been implicated in atherosclerosis, as well as in chromatin and transcriptional regulation, suggesting a versatile and complex biological function. However, its role at an organismal level is currently unknown. Here, we generated SAMD1-/- and SAMD1+/- mice to explore the role of SAMD1 during mouse embryogenesis. Homozygous loss of SAMD1 was embryonic lethal, with no living animals seen after embryonic day 18.5. At embryonic day 14.5, organs were degrading and/or incompletely developed, and no functional blood vessels were observed, suggesting failed blood vessel maturation. Sparse red blood cells were scattered and pooled, primarily near the embryo surface. Some embryos had malformed heads and brains at embryonic day 15.5. In vitro, SAMD1 absence impaired neuronal differentiation processes. Heterozygous SAMD1 knockout mice underwent normal embryogenesis and were born alive. Postnatal genotyping showed a reduced ability of these mice to thrive, possibly due to altered steroidogenesis. In summary, the characterization of SAMD1 knockout mice suggests a critical role of SAMD1 during developmental processes in multiple organs and tissues.
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11
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Becht DC, Klein BJ, Kanai A, Jang SM, Cox KL, Zhou BR, Phanor SK, Zhang Y, Chen RW, Ebmeier CC, Lachance C, Galloy M, Fradet-Turcotte A, Bulyk ML, Bai Y, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain. Nat Commun 2023; 14:697. [PMID: 36754959 PMCID: PMC9908889 DOI: 10.1038/s41467-023-36368-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Human acetyltransferases MOZ and MORF are implicated in chromosomal translocations associated with aggressive leukemias. Oncogenic translocations involve the far amino terminus of MOZ/MORF, the function of which remains unclear. Here, we identified and characterized two structured winged helix (WH) domains, WH1 and WH2, in MORF and MOZ. WHs bind DNA in a cooperative manner, with WH1 specifically recognizing unmethylated CpG sequences. Structural and genomic analyses show that the DNA binding function of WHs targets MORF/MOZ to gene promoters, stimulating transcription and H3K23 acetylation, and WH1 recruits oncogenic fusions to HOXA genes that trigger leukemogenesis. Cryo-EM, NMR, mass spectrometry and mutagenesis studies provide mechanistic insight into the DNA-binding mechanism, which includes the association of WH1 with the CpG-containing linker DNA and binding of WH2 to the dyad of the nucleosome. The discovery of WHs in MORF and MOZ and their DNA binding functions could open an avenue in developing therapeutics to treat diseases associated with aberrant MOZ/MORF acetyltransferase activities.
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Affiliation(s)
- Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Ruo-Wen Chen
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | | | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Maxime Galloy
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Amelie Fradet-Turcotte
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada.
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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12
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Weber LM, Jia Y, Stielow B, Gisselbrecht S, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forné I, Nist A, Stiewe T, Bulyk M, Wang Z, Liefke R. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res 2023; 51:574-594. [PMID: 36537216 PMCID: PMC9881136 DOI: 10.1093/nar/gkac1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
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Affiliation(s)
- Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Yulin Jia
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yinghua Cao
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Jessica King
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried 82152, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
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13
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An R, Yang Y, Liu L, Li P. SAMD1 attenuates antiphospholipid syndrome-induced vascular injury and pregnancy complications. Immun Inflamm Dis 2022; 10:e678. [PMID: 36039649 PMCID: PMC9382866 DOI: 10.1002/iid3.678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/22/2022] [Accepted: 07/04/2022] [Indexed: 01/28/2023] Open
Abstract
OBJECTIVE This study was intended to investigate the effect of SAMD1 on antiphospholipid syndrome (APS)-induced vascular injury in human umbilical vein endothelial cells (HUVECs) and pregnancy complications in mice. METHODS The expression of SAMD1 in APS patients and healthy controls was detected by quantitative real-time polymerase chain reaction (qRT-PCR). Anti-B2 GPI and anticardiolipin antibody (ACA) levels were tested by enzyme-linked immunosorbent assay, MMP-9, iNOS, ICAM-1, and MCP-1 mRNA and protein levels determined by qRT-PCR and Western blot, cellular senescence detected by β-galactosidase staining, cell proliferation ability detected by CCK-8 assay, cell viability detected by trypan blue staining, cell mobility detected by Transwell, and cell angiogenesis ability detected by matrigel tube formation assay. An APS pregnant mouse model was constructed, and the embryo absorption rate was calculated. RESULTS SAMD1 expression was low in serum of APS patients, which was correlated with the history of thrombosis and the number of adverse pregnancies. Anti-B2 GPI and ACA levels were increased in APS. The expressions of MMP-9, iNOS, ICAM-1, and MCP-1 were also significantly upregulated in HUVECs treated with APS serum. APS promoted HUVEC senescence and inhibited cell proliferation, migration, and angiogenesis. Overexpression of SAMD1 reversed the above results. Experiments on the APS pregnant mouse model confirmed that overexpression of SAMD1 reduced the rate of fetal loss. CONCLUSION SAMD1 may reduce APS-induced vascular injury and embryo loss by regulating cellular senescence, proliferation, migration, and angiogenesis.
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Affiliation(s)
- Ran An
- Department of Obstetrics and Gynecology, the Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Yanqi Yang
- Department of Obstetrics and Gynecology, the Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Lei Liu
- Department of Obstetrics and Gynecology, the Fourth Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
| | - Peiling Li
- Department of Obstetrics and Gynecology, the Second Affiliated Hospital of Harbin Medical UniversityHarbinHeilongjiangChina
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14
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Biedermannová L, Černý J, Malý M, Nekardová M, Schneider B. Knowledge-based prediction of DNA hydration using hydrated dinucleotides as building blocks. Acta Crystallogr D Struct Biol 2022; 78:1032-1045. [PMID: 35916227 PMCID: PMC9344474 DOI: 10.1107/s2059798322006234] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/14/2022] [Indexed: 11/19/2022] Open
Abstract
Water plays an important role in stabilizing the structure of DNA and mediating its interactions. Here, the hydration of DNA was analyzed in terms of dinucleotide fragments from an ensemble of 2727 nonredundant DNA chains containing 41 853 dinucleotides and 316 265 associated first-shell water molecules. The dinucleotides were classified into categories based on their 16 sequences and the previously determined structural classes known as nucleotide conformers (NtCs). The construction of hydrated dinucleotide building blocks allowed dinucleotide hydration to be calculated as the probability of water density distributions. Peaks in the water densities, known as hydration sites (HSs), uncovered the interplay between base and sugar-phosphate hydration in the context of sequence and structure. To demonstrate the predictive power of hydrated DNA building blocks, they were then used to predict hydration in an independent set of crystal and NMR structures. In ten tested crystal structures, the positions of predicted HSs and experimental waters were in good agreement (more than 40% were within 0.5 Å) and correctly reproduced the known features of DNA hydration, for example the `spine of hydration' in B-DNA. Therefore, it is proposed that hydrated building blocks can be used to predict DNA hydration in structures solved by NMR and cryo-EM, thus providing a guide to the interpretation of experimental data and computer models. The data for the hydrated building blocks and the predictions are available for browsing and visualization at the website https://watlas.datmos.org/watna/.
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Affiliation(s)
- Lada Biedermannová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Jiří Černý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michal Malý
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Michaela Nekardová
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Bohdan Schneider
- Institute of Biotechnology of the Czech Academy of Sciences, BIOCEV, Průmyslová 595, 252 50 Vestec, Czech Republic
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15
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Isbel L, Grand RS, Schübeler D. Generating specificity in genome regulation through transcription factor sensitivity to chromatin. Nat Rev Genet 2022; 23:728-740. [PMID: 35831531 DOI: 10.1038/s41576-022-00512-6] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2022] [Indexed: 12/11/2022]
Abstract
Cell type-specific gene expression relies on transcription factors (TFs) binding DNA sequence motifs embedded in chromatin. Understanding how motifs are accessed in chromatin is crucial to comprehend differential transcriptional responses and the phenotypic impact of sequence variation. Chromatin obstacles to TF binding range from DNA methylation to restriction of DNA access by nucleosomes depending on their position, composition and modification. In vivo and in vitro approaches now enable the study of TF binding in chromatin at unprecedented resolution. Emerging insights suggest that TFs vary in their ability to navigate chromatin states. However, it remains challenging to link binding and transcriptional outcomes to molecular characteristics of TFs or the local chromatin substrate. Here, we discuss our current understanding of how TFs access DNA in chromatin and novel techniques and directions towards a better understanding of this critical step in genome regulation.
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Affiliation(s)
- Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Sciences, University of Basel, Basel, Switzerland.
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16
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Dungan CM, Brightwell CR, Wen Y, Zdunek CJ, Latham CM, Thomas NT, Zagzoog AM, Brightwell BD, Nolt GL, Keeble AR, Watowich SJ, Murach KA, Fry CS. Muscle-Specific Cellular and Molecular Adaptations to Late-Life Voluntary Concurrent Exercise. FUNCTION 2022; 3:zqac027. [PMID: 35774589 PMCID: PMC9233305 DOI: 10.1093/function/zqac027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/06/2022] [Accepted: 05/08/2022] [Indexed: 01/07/2023] Open
Abstract
Murine exercise models can provide information on factors that influence muscle adaptability with aging, but few translatable solutions exist. Progressive weighted wheel running (PoWeR) is a simple, voluntary, low-cost, high-volume endurance/resistance exercise approach for training young mice. In the current investigation, aged mice (22-mo-old) underwent a modified version of PoWeR for 8 wk. Muscle functional, cellular, biochemical, transcriptional, and myonuclear DNA methylation analyses provide an encompassing picture of how muscle from aged mice responds to high-volume combined training. Mice run 6-8 km/d, and relative to sedentary mice, PoWeR increases plantarflexor muscle strength. The oxidative soleus of aged mice responds to PoWeR similarly to young mice in every parameter measured in previous work; this includes muscle mass, glycolytic-to-oxidative fiber type transitioning, fiber size, satellite cell frequency, and myonuclear number. The oxidative/glycolytic plantaris adapts according to fiber type, but with modest overall changes in muscle mass. Capillarity increases markedly with PoWeR in both muscles, which may be permissive for adaptability in advanced age. Comparison to published PoWeR RNA-sequencing data in young mice identified conserved regulators of adaptability across age and muscles; this includes Aldh1l1 which associates with muscle vasculature. Agrn and Samd1 gene expression is upregulated after PoWeR simultaneous with a hypomethylated promoter CpG in myonuclear DNA, which could have implications for innervation and capillarization. A promoter CpG in Rbm10 is hypomethylated by late-life exercise in myonuclei, consistent with findings in muscle tissue. PoWeR and the data herein are a resource for uncovering cellular and molecular regulators of muscle adaptation with aging.
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Affiliation(s)
- Cory M Dungan
- Department of Physical Therapy, University of Kentucky, Lexington 40536, KY, USA
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
| | - Camille R Brightwell
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
| | - Yuan Wen
- Department of Physical Therapy, University of Kentucky, Lexington 40536, KY, USA
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
| | | | - Christine M Latham
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
| | - Nicholas T Thomas
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
| | - Alyaa M Zagzoog
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
| | - Benjamin D Brightwell
- Kinesiology and Health Promotion Graduate Program, University of Kentucky, Lexington 40536, KY, USA
| | - Georgia L Nolt
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
| | - Alexander R Keeble
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
| | - Stanley J Watowich
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston 77555, TX, USA
| | - Kevin A Murach
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville 72701, AR, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville 72701, AR, USA
| | - Christopher S Fry
- Center for Muscle Biology, University of Kentucky, Lexington 40536, KY, USA
- Department of Athletic Training and Clinical Nutrition, University of Kentucky, Lexington 40536, KY, USA
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17
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Simon C, Stielow B, Nist A, Rohner I, Weber LM, Geller M, Fischer S, Stiewe T, Liefke R. The CpG Island-Binding Protein SAMD1 Contributes to an Unfavorable Gene Signature in HepG2 Hepatocellular Carcinoma Cells. BIOLOGY 2022; 11:557. [PMID: 35453756 PMCID: PMC9032685 DOI: 10.3390/biology11040557] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/23/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
The unmethylated CpG island-binding protein SAMD1 is upregulated in many human cancer types, but its cancer-related role has not yet been investigated. Here, we used the hepatocellular carcinoma cell line HepG2 as a cancer model and investigated the cellular and transcriptional roles of SAMD1 using ChIP-Seq and RNA-Seq. SAMD1 targets several thousand gene promoters, where it acts predominantly as a transcriptional repressor. HepG2 cells with SAMD1 deletion showed slightly reduced proliferation, but strongly impaired clonogenicity. This phenotype was accompanied by the decreased expression of pro-proliferative genes, including MYC target genes. Consistently, we observed a decrease in the active H3K4me2 histone mark at most promoters, irrespective of SAMD1 binding. Conversely, we noticed an increase in interferon response pathways and a gain of H3K4me2 at a subset of enhancers that were enriched for IFN-stimulated response elements (ISREs). We identified key transcription factor genes, such as IRF1, STAT2, and FOSL2, that were directly repressed by SAMD1. Moreover, SAMD1 deletion also led to the derepression of the PI3K-inhibitor PIK3IP1, contributing to diminished mTOR signaling and ribosome biogenesis pathways. Our work suggests that SAMD1 is involved in establishing a pro-proliferative setting in hepatocellular carcinoma cells. Inhibiting SAMD1's function in liver cancer cells may therefore lead to a more favorable gene signature.
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Affiliation(s)
- Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Andrea Nist
- Genomics Core Facility, Faculty of Medicine, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany; (A.N.); (T.S.)
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Merle Geller
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
| | - Thorsten Stiewe
- Genomics Core Facility, Faculty of Medicine, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany; (A.N.); (T.S.)
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Faculty of Medicine, Philipps University of Marburg, 35043 Marburg, Germany; (C.S.); (B.S.); (I.R.); (L.M.W.); (M.G.); (S.F.)
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany
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18
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Murach KA, Dungan CM, von Walden F, Wen Y. Epigenetic evidence for distinct contributions of resident and acquired myonuclei during long-term exercise adaptation using timed in vivo myonuclear labeling. Am J Physiol Cell Physiol 2022; 322:C86-C93. [PMID: 34817266 PMCID: PMC8765804 DOI: 10.1152/ajpcell.00358.2021] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Muscle fibers are syncytial postmitotic cells that can acquire exogenous nuclei from resident muscle stem cells, called satellite cells. Myonuclei are added to muscle fibers by satellite cells during conditions such as load-induced hypertrophy. It is difficult to dissect the molecular contributions of resident versus satellite cell-derived myonuclei during adaptation due to the complexity of labeling distinct nuclear populations in multinuclear cells without label transference between nuclei. To sidestep this barrier, we used a genetic mouse model where myonuclear DNA can be specifically and stably labeled via nonconstitutive H2B-GFP at any point in the lifespan. Resident myonuclei (Mn) were GFP-tagged in vivo before 8 wk of progressive weighted wheel running (PoWeR) in adult mice (>4-mo-old). Resident + satellite cell-derived myonuclei (Mn+SC Mn) were labeled at the end of PoWeR in a separate cohort. Following myonuclear isolation, promoter DNA methylation profiles acquired with low-input reduced representation bisulfite sequencing (RRBS) were compared to deduce epigenetic contributions of satellite cell-derived myonuclei during adaptation. Resident myonuclear DNA has hypomethylated promoters in genes related to protein turnover, whereas the addition of satellite cell-derived myonuclei shifts myonuclear methylation profiles to favor transcription factor regulation and cell-cell signaling. By comparing myonucleus-specific methylation profiling to previously published single-nucleus transcriptional analysis in the absence (Mn) versus the presence of satellite cells (Mn+SC Mn) with PoWeR, we provide evidence that satellite cell-derived myonuclei may preferentially supply specific ribosomal proteins to growing myofibers and retain an epigenetic "memory" of prior stem cell identity. These data offer insights on distinct epigenetic myonuclear characteristics and contributions during adult muscle growth.
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Affiliation(s)
- Kevin A. Murach
- 1Molecular Muscle Mass Regulation Laboratory, Exercise Science Research Center, Department of Health, Human Performance, and Recreation, University of Arkansas, Fayetteville, Arkansas,2Cell and Molecular Biology Program, University of Arkansas, Fayetteville, Arkansas,3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky
| | - Cory M. Dungan
- 3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky,4Department of Physical Therapy, College of Health Sciences, University of Kentucky, Lexington, Kentucky
| | - Ferdinand von Walden
- 5Department of Women’s and Children’s Health, Karolinska Institute, Stockholm, Sweden
| | - Yuan Wen
- 3The Center for Muscle Biology, University of Kentucky, Lexington, Kentucky,6Department of Physiology, College of Medicine, University of Kentucky, Lexington, Kentucky,7Myoanalytics, LLC, Lexington, Kentucky
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19
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Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. BANP opens chromatin and activates CpG-island-regulated genes. Nature 2021; 596:133-137. [PMID: 34234345 DOI: 10.1038/s41586-021-03689-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3-5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6-8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.
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Affiliation(s)
- Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Sevi Durdu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marco Pregnolato
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
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20
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Stielow B, Simon C, Liefke R. Making fundamental scientific discoveries by combining information from literature, databases, and computational tools - An example. Comput Struct Biotechnol J 2021; 19:3027-3033. [PMID: 34136100 PMCID: PMC8175269 DOI: 10.1016/j.csbj.2021.04.052] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 04/21/2021] [Accepted: 04/22/2021] [Indexed: 11/18/2022] Open
Abstract
In recent years, the amount of available literature, data and computational tools has increased exponentially, providing opportunities and challenges to make use of this vast amount of material. Here, we describe how we utilized publicly available information to identify the previously hardly characterized protein SAMD1 (SAM domain-containing protein 1) as a novel unmethylated CpG island-binding protein. This discovery is an example, how the richness of material and tools on the internet can be used to make scientific breakthroughs, but also the hurdles that may occur. Specifically, we discuss how the misrepresentation of SAMD1 in literature and databases may have prevented an earlier characterization of this protein and we address what can be learned from this example.
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Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
- Department of Hematology, Oncology and Immunology, University Hospital Giessen and Marburg, 35043 Marburg, Germany
- Corresponding author at: Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany.
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