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Skjold V, Afanasyev S, Burgerhout E, Sveen L, Rørvik KA, Mota VFCN, Dessen JE, Krasnov A. Endocrine and Transcriptome Changes Associated with Testicular Growth and Differentiation in Atlantic Salmon ( Salmo salar L.). Curr Issues Mol Biol 2024; 46:5337-5351. [PMID: 38920991 PMCID: PMC11202266 DOI: 10.3390/cimb46060319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/15/2024] [Accepted: 05/21/2024] [Indexed: 06/27/2024] Open
Abstract
Sexual maturation of Atlantic salmon males is marked by dramatic endocrine changes and rapid growth of the testes, resulting in an increase in the gonad somatic index (GSI). We examined the association of gonadal growth with serum sex steroids, as well as pituitary and testicular gene expression levels, which were assessed with a DNA oligonucleotide microarray. The testes transcriptome was stable in males with a GSI < 0.08% despite the large difference between the smallest and the largest gonads. Fish with a GSI ≥ 0.23% had 7-17 times higher serum levels of five male steroids and a 2-fold increase in progesterone, without a change in cortisol and related steroids. The pituitary transcriptome showed an upregulation of the hormone-coding genes that control reproduction and behavior, and structural rearrangement was indicated by the genes involved in synaptic transmission and the differentiation of neurons. The observed changes in the abundance of testicular transcripts were caused by the regulation of transcription and/or disproportional growth, with a greater increase in the germinative compartment. As these factors could not be separated, the transcriptome results are presented as higher or lower specific activities (HSA and LSA). LSA was observed in 4268 genes, including many genes involved in various immune responses and developmental processes. LSA also included genes with roles in female reproduction, germinal cell maintenance and gonad development, responses to endocrine and neural regulation, and the biosynthesis of sex steroids. Two functional groups prevailed among HSA: structure and activity of the cilia (95 genes) and meiosis (34 genes). The puberty of A. salmon testis is marked by the predominance of spermatogenesis, which displaces other processes; masculinization; and the weakening of external regulation. Results confirmed the known roles of many genes involved in reproduction and pointed to uncharacterized genes that deserve attention as possible regulators of sexual maturation.
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Affiliation(s)
- Vetle Skjold
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
- Department of Mechanical Engineering and Technology Management, Norwegian University of Life Sciences, 1433 Ås, Norway;
| | - Sergey Afanasyev
- Sechenov Institute of Evolutionary Physiology and Biochemistry, 194223 Saint Petersburg, Russia;
| | - Erik Burgerhout
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
| | - Lene Sveen
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
| | - Kjell-Arne Rørvik
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
- Department of Mechanical Engineering and Technology Management, Norwegian University of Life Sciences, 1433 Ås, Norway;
| | | | - Jens-Erik Dessen
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
| | - Aleksei Krasnov
- The Norwegian Institute of Aquaculture, Nofima, 9291 Tromsø, Norway; (V.S.); (E.B.); (L.S.); (K.-A.R.); (J.-E.D.)
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Liao C, Hu L, Zhang Q. Von Hippel-Lindau protein signalling in clear cell renal cell carcinoma. Nat Rev Urol 2024:10.1038/s41585-024-00876-w. [PMID: 38698165 DOI: 10.1038/s41585-024-00876-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/26/2024] [Indexed: 05/05/2024]
Abstract
The distinct pathological and molecular features of kidney cancer in adaptation to oxygen homeostasis render this malignancy an attractive model for investigating hypoxia signalling and potentially developing potent targeted therapies. Hypoxia signalling has a pivotal role in kidney cancer, particularly within the most prevalent subtype, known as renal cell carcinoma (RCC). Hypoxia promotes various crucial pathological processes, such as hypoxia-inducible factor (HIF) activation, angiogenesis, proliferation, metabolic reprogramming and drug resistance, all of which contribute to kidney cancer development, growth or metastasis formation. A substantial portion of kidney cancers, in particular clear cell RCC (ccRCC), are characterized by a loss of function of Von Hippel-Lindau tumour suppressor (VHL), leading to the accumulation of HIF proteins, especially HIF2α, a crucial driver of ccRCC. Thus, therapeutic strategies targeting pVHL-HIF signalling have been explored in ccRCC, culminating in the successful development of HIF2α-specific antagonists such as belzutifan (PT2977), an FDA-approved drug to treat VHL-associated diseases including advanced-stage ccRCC. An increased understanding of hypoxia signalling in kidney cancer came from the discovery of novel VHL protein (pVHL) targets, and mechanisms of synthetic lethality with VHL mutations. These breakthroughs can pave the way for the development of innovative and potent combination therapies in kidney cancer.
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Affiliation(s)
- Chengheng Liao
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Lianxin Hu
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Qing Zhang
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
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3
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Sun H, Zhang H. Lysine Methylation-Dependent Proteolysis by the Malignant Brain Tumor (MBT) Domain Proteins. Int J Mol Sci 2024; 25:2248. [PMID: 38396925 PMCID: PMC10889763 DOI: 10.3390/ijms25042248] [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: 12/14/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Lysine methylation is a major post-translational protein modification that occurs in both histones and non-histone proteins. Emerging studies show that the methylated lysine residues in non-histone proteins provide a proteolytic signal for ubiquitin-dependent proteolysis. The SET7 (SETD7) methyltransferase specifically transfers a methyl group from S-Adenosyl methionine to a specific lysine residue located in a methylation degron motif of a protein substrate to mark the methylated protein for ubiquitin-dependent proteolysis. LSD1 (Kdm1a) serves as a demethylase to dynamically remove the methyl group from the modified protein. The methylated lysine residue is specifically recognized by L3MBTL3, a methyl-lysine reader that contains the malignant brain tumor domain, to target the methylated proteins for proteolysis by the CRL4DCAF5 ubiquitin ligase complex. The methylated lysine residues are also recognized by PHF20L1 to protect the methylated proteins from proteolysis. The lysine methylation-mediated proteolysis regulates embryonic development, maintains pluripotency and self-renewal of embryonic stem cells and other stem cells such as neural stem cells and hematopoietic stem cells, and controls other biological processes. Dysregulation of the lysine methylation-dependent proteolysis is associated with various diseases, including cancers. Characterization of lysine methylation should reveal novel insights into how development and related diseases are regulated.
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Affiliation(s)
| | - Hui Zhang
- Department of Chemistry and Biochemistry, Nevada Institute of Personalized Medicine, University of Nevada, Las Vegas, 4505 South Maryland Parkway, P.O. Box 454003, Las Vegas, NV 89154-4003, USA;
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Wang Y, Wang H, Shao W, Chen Y, Gui Y, Hu C, Yi X, Huang L, Li S, Wang D. Large-scale loss-of-function perturbations reveal a comprehensive epigenetic regulatory network in breast cancer. Cancer Biol Med 2023; 21:j.issn.2095-3941.2023.0276. [PMID: 38062748 PMCID: PMC10875281 DOI: 10.20892/j.issn.2095-3941.2023.0276] [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: 07/27/2023] [Accepted: 10/26/2023] [Indexed: 02/16/2024] Open
Abstract
OBJECTIVE Epigenetic abnormalities have a critical role in breast cancer by regulating gene expression; however, the intricate interrelationships and key roles of approximately 400 epigenetic regulators in breast cancer remain elusive. It is important to decipher the comprehensive epigenetic regulatory network in breast cancer cells to identify master epigenetic regulators and potential therapeutic targets. METHODS We employed high-throughput sequencing-based high-throughput screening (HTS2) to effectively detect changes in the expression of 2,986 genes following the knockdown of 400 epigenetic regulators. Then, bioinformatics analysis tools were used for the resulting gene expression signatures to investigate the epigenetic regulations in breast cancer. RESULTS Utilizing these gene expression signatures, we classified the epigenetic regulators into five distinct clusters, each characterized by specific functions. We discovered functional similarities between BAZ2B and SETMAR, as well as CLOCK and CBX3. Moreover, we observed that CLOCK functions in a manner opposite to that of HDAC8 in downstream gene regulation. Notably, we constructed an epigenetic regulatory network based on the gene expression signatures, which revealed 8 distinct modules and identified 10 master epigenetic regulators in breast cancer. CONCLUSIONS Our work deciphered the extensive regulation among hundreds of epigenetic regulators. The identification of 10 master epigenetic regulators offers promising therapeutic targets for breast cancer treatment.
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Affiliation(s)
- Yumei Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Haiyan Wang
- Department of Pathology, School of Medicine, Qinghai University, Xining 810001, China
| | - Wei Shao
- Omics Biosciences Inc, Beijing 100871, China
| | - Yuhui Chen
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Yu Gui
- Laboratory of Integrative Medicine, Clinical Research Center for Breast, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu 610041, China
| | - Chao Hu
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Xiaohong Yi
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Lijun Huang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
| | - Shasha Li
- Department of Endocrinology and Metabolism, Guangdong Provincial Key Laboratory of Diabetology & Guangzhou Municipal Key Laboratory of Mechanistic and Translational Obesity Research, Medical Center for Comprehensive Weight Control, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Dong Wang
- School of Basic Medical Sciences, State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China
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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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Endocrine resistance and breast cancer plasticity are controlled by CoREST. Nat Struct Mol Biol 2022; 29:1122-1135. [PMID: 36344844 PMCID: PMC9707522 DOI: 10.1038/s41594-022-00856-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 09/29/2022] [Indexed: 11/09/2022]
Abstract
Resistance to cancer treatment remains a major clinical hurdle. Here, we demonstrate that the CoREST complex is a key determinant of endocrine resistance and ER+ breast cancer plasticity. In endocrine-sensitive cells, CoREST is recruited to regulatory regions co-bound to ERα and FOXA1 to regulate the estrogen pathway. In contrast, during temporal reprogramming towards a resistant state, CoREST is recruited to AP-1 sites. In reprogrammed cells, CoREST favors chromatin opening, cJUN binding to chromatin, and gene activation by controlling SWI/SNF recruitment independently of the demethylase activity of the CoREST subunit LSD1. Genetic and pharmacological CoREST inhibition reduces tumorigenesis and metastasis of endocrine-sensitive and endocrine-resistant xenograft models. Consistently, CoREST controls a gene signature involved in invasiveness in clinical breast tumors resistant to endocrine therapies. Our studies reveal CoREST functions that are co-opted to drive cellular plasticity and resistance to endocrine therapies and tumorigenesis, thus establishing CoREST as a potential therapeutic target for the treatment of advanced breast cancer.
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Tian Q, Wang G, Ma X, Shen Q, Ding M, Yang X, Luo X, Li R, Wang Z, Wang X, Fu Z, Yang Q, Tang J, Wang G. Riboflavin integrates cellular energetics and cell cycle to regulate maize seed development. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1487-1501. [PMID: 35426230 PMCID: PMC9342611 DOI: 10.1111/pbi.13826] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 04/10/2022] [Indexed: 05/23/2023]
Abstract
Riboflavin is the precursor of essential cofactors for diverse metabolic processes. Unlike animals, plants can de novo produce riboflavin through an ancestrally conserved pathway, like bacteria and fungi. However, the mechanism by which riboflavin regulates seed development is poorly understood. Here, we report a novel maize (Zea mays L.) opaque mutant o18, which displays an increase in lysine accumulation, but impaired endosperm filling and embryo development. O18 encodes a rate-limiting bifunctional enzyme ZmRIBA1, targeted to plastid where to initiate riboflavin biosynthesis. Loss of function of O18 specifically disrupts respiratory complexes I and II, but also decreases SDH1 flavinylation, and in turn shifts the mitochondrial tricarboxylic acid (TCA) cycle to glycolysis. The deprivation of cellular energy leads to cell-cycle arrest at G1 and S phases in both mitosis and endoreduplication during endosperm development. The unexpected up-regulation of cell-cycle genes in o18 correlates with the increase of H3K4me3 levels, revealing a possible H3K4me-mediated epigenetic back-up mechanism for cell-cycle progression under unfavourable circumstances. Overexpression of O18 increases riboflavin production and confers osmotic tolerance. Altogether, our results substantiate a key role of riboflavin in coordinating cellular energy and cell cycle to modulate maize endosperm development.
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Affiliation(s)
- Qiuzhen Tian
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Gang Wang
- School of Agriculture and BiologyShanghai Jiao Tong UniversityShanghaiChina
| | - Xuexia Ma
- Shanghai Key Laboratory of Bio‐Energy CropsSchool of Life SciencesShanghai UniversityShanghaiChina
| | - Qingwen Shen
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Mengli Ding
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xueyi Yang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiaoli Luo
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Rongrong Li
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhenghui Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Xiangyang Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Zhiyuan Fu
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Qinghua Yang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
| | - Jihua Tang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
- The Shennong LaboratoryZhengzhouChina
| | - Guifeng Wang
- National Key Laboratory of Wheat and Maize Crops ScienceCIMMYT‐Henan Joint Center for Wheat and Maize ImprovementCollaborative Innovation Center of Henan Grain CropsCollege of AgronomyHenan Agricultural UniversityZhengzhouChina
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Pan R, Yu D, Hu J, Yang X, Wang C, Zhang L, Xue P, Sun J, Zhang X, Cai W. SFMBT1 facilitates colon cancer cell metastasis and drug resistance combined with HMG20A. Cell Death Dis 2022; 8:263. [PMID: 35577773 PMCID: PMC9110378 DOI: 10.1038/s41420-022-01057-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 04/30/2022] [Accepted: 05/04/2022] [Indexed: 12/24/2022]
Abstract
In colorectal cancer (CRC), the development of reagents that increase sensitivity to chemotherapeutic agents could prevent drug resistance and improve patient survival. Scm-like with four malignant brain tumor domains 1 (SFMBT1) is up-regulated in CRC tumor tissues and cells and may be associated with drug resistance. We detected the expression of SFMBT1 in CRC tissue microarrays by immunohistochemistry. The role of SFMBT1 in the migration, proliferation and invasion of CRC or resistance to 5-fluorouracil (5-FU) was determined using scratch assay, colony formation and Transwell assay. Fluorescence co-localization and immunoprecipitation were used to analyze the correlation between SFMBT1 and high mobility group domain-containing protein 20 A (HMG20A). Xenograft experiments were conducted to investigate the role of SFMBT1 and HMG20A in tumor growth and metastasis in vivo. We found that SFMBT1 is up-regulated in CRC and its expression is further amplified in 5-FU resistance. SFMBT1 drives 5-FU resistance and CRC proliferation, migration and invasion. Correlation analysis shows that SFMBT1 and HMG20A are positively correlated. Mechanistically, fluorescence co-localization and immunoprecipitation assay indicate an interaction between SFMBT1 and HMG20A. Depletion of SFMBT1 down-regulates HMG20A downstream. These results were verified by murine xenograft and lung metastasis models. Our results indicate that the SFMBT1/HMG20A axis could be targeted to increase the resistance of CRC cells to 5-FU.
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Affiliation(s)
- Ruijun Pan
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Dingye Yu
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Jiajia Hu
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiao Yang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Chenxing Wang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Luyang Zhang
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Pei Xue
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Jing Sun
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Shanghai Minimally Invasive Surgery Center, Shanghai, China
| | - Xiaoping Zhang
- Department of Interventional & Vascular Surgery, Tenth People's Hospital of Tongji University, Shanghai, 200072, China. .,Institute of Interventional & Vascular Surgery, Tongji University, Shanghai, 200072, China.
| | - Wei Cai
- Department of General Surgery, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Minimally Invasive Surgery Center, Shanghai, China.
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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: 1] [Impact Index Per Article: 0.5] [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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10
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Miltiadous A, Demetriou P, Kyriakou M, Gerasimou P, Herodotou G, Elpidoforou A, Kyprianou Y, Iacovou M, Chi J, Costeas P, Tanteles GA. A de novo SFMBT1 pathogenic variant identified in a boy with Poland syndrome. Cold Spring Harb Mol Case Stud 2022; 8:mcs.a006168. [PMID: 35483874 PMCID: PMC9059785 DOI: 10.1101/mcs.a006168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 04/01/2022] [Indexed: 11/24/2022] Open
Abstract
Poland syndrome is a rare developmental disorder characterized by unilateral, complete or partial, absence of the pectoralis major (and often minor) muscle, accompanied with ipsilateral hand malformations. To date, no clear genetic cause has been associated with Poland syndrome, although familial cases have been reported. We report the employment of trio exome investigation and the identification of a heterozygous de novo pathogenic variant in the SFMBT1 gene, a transcription factor associated with transcriptional repression during development, in a 14-yr-old boy with Poland syndrome. We further demonstrate by means of cDNA sequencing and western blot analysis that this variant results in SFMBT1 exon 10 skipping and a lower concentration of the SFMBT1 wild-type protein. To our knowledge, the heterozygous pathogenic SFMBT1 variant identified in association with this condition is novel as it has not been elsewhere described in the literature and it can be incorporated to the limited reported cases published.
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Affiliation(s)
- Andri Miltiadous
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | | | - Maria Kyriakou
- The Center for the Study of Haematological Malignancies, Nicosia, Cyprus
| | | | - George Herodotou
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | | | - Yiannos Kyprianou
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | - Maria Iacovou
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus
| | - Jianxiang Chi
- The Center for the Study of Haematological Malignancies, Nicosia, Cyprus
| | - Paul Costeas
- Molecular Hematology-Oncology, Karaiskakio Foundation, Nicosia, Cyprus;,The Center for the Study of Haematological Malignancies, Nicosia, Cyprus
| | - George A. Tanteles
- Department of Clinical Genetics, The Cyprus Institute of Neurology and Genetics Nicosia, Cyprus;,Cyprus School of Molecular Medicine, The Cyprus Institute of Neurology and Genetics Nicosia, Cyprus
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11
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Afrashteh F, Ghafoury R, Almasi-Doghaee M. Cerebrospinal fluid biomarkers and genetic factors associated with normal pressure hydrocephalus and Alzheimer’s disease: a narrative review. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2022. [DOI: 10.1186/s43042-022-00247-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Normal pressure hydrocephalus is a neurologic disease leading to enlargement of ventricles which is presented with gait and balance disturbance, cognitive decline, and urinary incontinence. Diagnosis of normal pressure hydrocephalus is challenging due to the late onset of signs and symptoms. In this review, we summarize the cerebrospinal fluid, plasma, pathology, and genetic biomarkers of normal pressure hydrocephalus and related disorders.
Body
Recently, cerebrospinal fluid and serum biomarkers analysis alongside gene analysis has received a lot of attention. Interpreting a set of serum and cerebrospinal fluid biomarkers along with genetic testing for candidate genes could differentiate NPH from other neurological diseases such as Alzheimer's disease, Parkinson's disease with dementia, and other types of dementia.
Conclusion
Better understanding the pathophysiology of normal pressure hydrocephalus through genetic studies can aid in evolving preventative measures and the early treatment of normal pressure hydrocephalus patients.
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12
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Li Y, Ma C, Li S, Wang J, Li W, Yang Y, Li X, Liu J, Yang J, Liu Y, Li K, Li J, Huang D, Chen R, Lv L, Xiao X, Li M, Luo X. Regulatory Variant rs2535629 in ITIH3 Intron Confers Schizophrenia Risk By Regulating CTCF Binding and SFMBT1 Expression. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2104786. [PMID: 34978167 PMCID: PMC8867204 DOI: 10.1002/advs.202104786] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 11/16/2021] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies have identified 3p21.1 as a robust risk locus for schizophrenia. However, the underlying molecular mechanisms remain elusive. Here a functional regulatory variant (rs2535629) is identified that disrupts CTCF binding at 3p21.1. It is confirmed that rs2535629 is also significantly associated with schizophrenia in Chinese population and the regulatory effect of rs2535629 is validated. Expression quantitative trait loci analysis indicates that rs2535629 is associated with the expression of three distal genes (GLT8D1, SFMBT1, and NEK4) in the human brain, and CRISPR-Cas9-mediated genome editing confirmed the regulatory effect of rs2535629 on GLT8D1, SFMBT1, and NEK4. Interestingly, differential expression analysis of GLT8D1, SFMBT1, and NEK4 suggested that rs2535629 may confer schizophrenia risk by regulating SFMBT1 expression. It is further demonstrated that Sfmbt1 regulates neurodevelopment and dendritic spine density, two key pathological characteristics of schizophrenia. Transcriptome analysis also support the potential role of Sfmbt1 in schizophrenia pathogenesis. The study identifies rs2535629 as a plausibly causal regulatory variant at the 3p21.1 risk locus and demonstrates the regulatory mechanism and biological effect of this functional variant, indicating that this functional variant confers schizophrenia risk by altering CTCF binding and regulating expression of SFMBT1, a distal gene which plays important roles in neurodevelopment and synaptic morphogenesis.
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Affiliation(s)
- Yifan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Changguo Ma
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Yunnan Key Laboratory for Basic Research on Bone and Joint Diseases & Yunnan Stem Cell Translational Research CenterKunming UniversityKunmingYunnan650214China
| | - Shiwu Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Junyang Wang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Wenqiang Li
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangHenan453002China
- Henan Key Lab of Biological PsychiatryInternational Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangHenan453002China
| | - Yongfeng Yang
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangHenan453002China
- Henan Key Lab of Biological PsychiatryInternational Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangHenan453002China
| | - Xiaoyan Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of EducationInstitutes of Physical Science and Information TechnologyAnhui UniversityHefeiAnhui230601China
| | - Jiewei Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
| | - Jinfeng Yang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Yixing Liu
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Kaiqin Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Jiao Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Di Huang
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
| | - Rui Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
| | - Luxian Lv
- Henan Mental HospitalThe Second Affiliated Hospital of Xinxiang Medical UniversityXinxiangHenan453002China
- Henan Key Lab of Biological PsychiatryInternational Joint Research Laboratory for Psychiatry and Neuroscience of HenanXinxiang Medical UniversityXinxiangHenan453002China
| | - Xiao Xiao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
| | - Ming Li
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
| | - Xiong‐Jian Luo
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences & Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
- Kunming College of Life ScienceUniversity of Chinese Academy of SciencesKunmingYunnan650204China
- Center for Excellence in Animal Evolution and GeneticsChinese Academy of SciencesKunmingYunnan650204China
- KIZ‐CUHK Joint Laboratory of Bioresources and Molecular Research in Common DiseasesKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan650204China
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13
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Barnes CE, English DM, Broderick M, Collins MO, Cowley SM. Proximity-dependent biotin identification (BioID) reveals a dynamic LSD1-CoREST interactome during embryonic stem cell differentiation. Mol Omics 2022; 18:31-44. [PMID: 34709266 PMCID: PMC8763317 DOI: 10.1039/d1mo00236h] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/14/2021] [Indexed: 12/19/2022]
Abstract
Lysine specific demethylase 1 (LSD1) regulates gene expression as part of the CoREST complex, along with co-repressor of REST (CoREST) and histone deacetylase 1 (HDAC1). CoREST is recruited to specific genomic loci by core components and numerous transient interactions with chromatin-associated factors and transcription factors. We hypothesise that many of these weaker and transient associations may be difficult to identify using traditional co-immunoprecipitation methods. We have therefore employed proximity-dependent biotin-identification (BioID) with four different members of the CoREST complex, in three different cell types, to identify a comprehensive network of LSD1/CoREST associated proteins. In HEK293T cells, we identified 302 CoREST-associated proteins. Among this group were 16 of 18 known CoREST components and numerous novel associations, including readers (CHD3, 4, 6, 7 and 8), writers (KMT2B and KMT2D) and erasers (KDM2B) of histone methylation. However, components of other HDAC1 containing complexes (e.g. Sin3) were largely absent. To examine the dynamic nature of the CoREST interactome in a primary cell type, we replaced endogenous LSD1 with BirA*-LSD1 in embryonic stem (ES) cells and performed BioID in pluripotent, early- and late-differentiating environments. We identified 156 LSD1-associated proteins of which 67 were constitutively associated across all three time-points (43%), including novel associations with the MMB and ChAHP complexes, implying that the majority of interactors are both dynamic and cell type dependent. In total, we have performed 16 independent BioID experiments for LSD1 in three different cell types, producing a definitive network of LSD1-assoicated proteins that should provide a major resource for the field.
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Affiliation(s)
- Claire E Barnes
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - David M English
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Megan Broderick
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
- Faculty of Science Mass Spectrometry Centre, University of Sheffield, Brook Hill Road, Sheffield, S3 7HF, UK
| | - Shaun M Cowley
- Department of Molecular and Cell biology, University of Leicester, Henry Wellcome Building, Leicester LE1 7RH, UK.
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14
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DNA methylation and histone variants in aging and cancer. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2021; 364:1-110. [PMID: 34507780 DOI: 10.1016/bs.ircmb.2021.06.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging-related diseases such as cancer can be traced to the accumulation of molecular disorder including increased DNA mutations and epigenetic drift. We provide a comprehensive review of recent results in mice and humans on modifications of DNA methylation and histone variants during aging and in cancer. Accumulated errors in DNA methylation maintenance lead to global decreases in DNA methylation with relaxed repression of repeated DNA and focal hypermethylation blocking the expression of tumor suppressor genes. Epigenetic clocks based on quantifying levels of DNA methylation at specific genomic sites is proving to be a valuable metric for estimating the biological age of individuals. Histone variants have specialized functions in transcriptional regulation and genome stability. Their concentration tends to increase in aged post-mitotic chromatin, but their effects in cancer are mainly determined by their specialized functions. Our increased understanding of epigenetic regulation and their modifications during aging has motivated interventions to delay or reverse epigenetic modifications using the epigenetic clocks as a rapid readout for efficacity. Similarly, the knowledge of epigenetic modifications in cancer is suggesting new approaches to target these modifications for cancer therapy.
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15
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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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16
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Stielow B, Zhou Y, Cao Y, Simon C, Pogoda HM, Jiang J, Ren Y, Phanor SK, Rohner I, Nist A, Stiewe T, Hammerschmidt M, Shi Y, Bulyk ML, Wang Z, Liefke R. The SAM domain-containing protein 1 (SAMD1) acts as a repressive chromatin regulator at unmethylated CpG islands. SCIENCE ADVANCES 2021; 7:7/20/eabf2229. [PMID: 33980486 PMCID: PMC8115922 DOI: 10.1126/sciadv.abf2229] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 03/25/2021] [Indexed: 05/06/2023]
Abstract
CpG islands (CGIs) are key regulatory DNA elements at most promoters, but how they influence the chromatin status and transcription remains elusive. Here, we identify and characterize SAMD1 (SAM domain-containing protein 1) as an unmethylated CGI-binding protein. SAMD1 has an atypical winged-helix domain that directly recognizes unmethylated CpG-containing DNA via simultaneous interactions with both the major and the minor groove. The SAM domain interacts with L3MBTL3, but it can also homopolymerize into a closed pentameric ring. At a genome-wide level, SAMD1 localizes to H3K4me3-decorated CGIs, where it acts as a repressor. SAMD1 tethers L3MBTL3 to chromatin and interacts with the KDM1A histone demethylase complex to modulate H3K4me2 and H3K4me3 levels at CGIs, thereby providing a mechanism for SAMD1-mediated transcriptional repression. The absence of SAMD1 impairs ES cell differentiation processes, leading to misregulation of key biological pathways. Together, our work establishes SAMD1 as a newly identified chromatin regulator acting at unmethylated CGIs.
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Affiliation(s)
- Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
| | - Yuqiao Zhou
- 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
| | - Yinghua Cao
- 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
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
| | - Hans-Martin Pogoda
- Institute of Zoology, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - 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
| | - 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
| | - Sabrina Keita Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, 35043 Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, 35043 Marburg, Germany
| | - Matthias Hammerschmidt
- Institute of Zoology, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Yang Shi
- Division of Newborn Medicine and Epigenetics Program, Department of Pediatrics, Boston Children's Hospital, Boston, Harvard Medical School, Boston, MA 02115, USA
- Ludwig Institute for Cancer Research, Oxford University, Oxford, UK
| | - 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, 19 Xinjiekouwai Avenue, Beijing 100875, China.
| | - 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
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17
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Yu M, Lun J, Zhang H, Zhu L, Zhang G, Fang J. The non-canonical functions of HIF prolyl hydroxylases and their dual roles in cancer. Int J Biochem Cell Biol 2021; 135:105982. [PMID: 33894356 DOI: 10.1016/j.biocel.2021.105982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 12/20/2022]
Abstract
The hypoxia-inducible factor (HIF) prolyl hydroxylases (PHDs) are dioxygenases using oxygen and 2-oxoglutarate as co-substrates. Under normoxia, PHDs hydroxylate the conserved prolyl residues of HIFα, leading to HIFα degradation. In hypoxia PHDs are inactivated, which results in HIFα accumulation. The accumulated HIFα enters nucleus and initiates gene transcription. Many studies have shown that PHDs have substrates other than HIFα, implying that they have HIF-independent non-canonical functions. Besides modulating protein stability, the PHDs-mediated prolyl hydroxylation affects protein-protein interaction and protein activity for alternative substrates. Increasing evidence indicates that PHDs also have hydroxylase-independent functions. They influence protein stability, enzyme activity, and protein-protein interaction in a hydroxylase-independent manner. These findings highlight the functional diversity and complexity of PHDs. Due to having inhibitory activity on HIFα, PHDs are proposed to act as tumor suppressors. However, research shows that PHDs exert either tumor-promoting or tumor-suppressing features. Here, we try to summarize the current understanding of PHDs hydroxylase-dependent and -independent functions and their roles in cancer.
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Affiliation(s)
- Mengchao Yu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Cancer Institute, Qingdao University, Qingdao, 266061, China
| | - Jie Lun
- Cancer Institute, The Affiliated Hospital of Qingdao University, Cancer Institute, Qingdao University, Qingdao, 266061, China
| | - Hongwei Zhang
- Shandong Provincial Maternal and Child Health Care Hospital, Jinan, 250014, China
| | - Lei Zhu
- Cancer Institute, The Affiliated Hospital of Qingdao University, Cancer Institute, Qingdao University, Qingdao, 266061, China
| | - Gang Zhang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Cancer Institute, Qingdao University, Qingdao, 266061, China.
| | - Jing Fang
- Cancer Institute, The Affiliated Hospital of Qingdao University, Cancer Institute, Qingdao University, Qingdao, 266061, China.
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18
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Mattar P, Jolicoeur C, Dang T, Shah S, Clark BS, Cayouette M. A Casz1-NuRD complex regulates temporal identity transitions in neural progenitors. Sci Rep 2021; 11:3858. [PMID: 33594190 PMCID: PMC7886867 DOI: 10.1038/s41598-021-83395-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 02/02/2021] [Indexed: 12/14/2022] Open
Abstract
Neural progenitor cells undergo identity transitions during development to ensure the generation different types of neurons and glia in the correct sequence and proportions. A number of temporal identity factors that control these transitions in progenitor competence have been identified, but the molecular mechanisms underlying their function remain unclear. Here, we asked how Casz1, the mammalian orthologue of Drosophila castor, regulates competence during retinal development. We show that Casz1 is required to control the transition between neurogenesis and gliogenesis. Using BioID proteomics, we reveal that Casz1 interacts with the nucleosome remodeling and deacetylase (NuRD) complex in retinal cells. Finally, we show that both the NuRD and the polycomb repressor complexes are required for Casz1 to promote the rod fate and suppress gliogenesis. As additional temporal identity factors have been found to interact with the NuRD complex in other contexts, we propose that these factors might act through this common biochemical process to regulate neurogenesis.
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Affiliation(s)
- Pierre Mattar
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada. .,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada.
| | - Christine Jolicoeur
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada
| | - Thanh Dang
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Sujay Shah
- Department of Cell and Molecular Medicine, University of Ottawa, Ottawa, ON, K1H 8M5, Canada.,Ottawa Health Research Institute (OHRI), Ottawa, ON, K1H 8L6, Canada
| | - Brian S Clark
- John F. Hardesty, MD, Department of Ophthalmology and Visual Sciences, Washington University School of Medicine, St. Louis, MO, 63110, USA.,Department of Developmental Biology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Michel Cayouette
- Cellular Neurobiology Research Unit, Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC, H2W 1R7, Canada. .,Department of Anatomy and Cell Biology, and Division of Experimental Medicine, McGill University, Montreal, QC, H3A 0G4, Canada. .,Department of Medicine, Université de Montréal, Montreal, QC, H3T 1J4, Canada.
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19
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Yu T, Fan K, Özata DM, Zhang G, Fu Y, Theurkauf WE, Zamore PD, Weng Z. Long first exons and epigenetic marks distinguish conserved pachytene piRNA clusters from other mammalian genes. Nat Commun 2021; 12:73. [PMID: 33397987 PMCID: PMC7782496 DOI: 10.1038/s41467-020-20345-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 11/17/2020] [Indexed: 02/06/2023] Open
Abstract
In the male germ cells of placental mammals, 26-30-nt-long PIWI-interacting RNAs (piRNAs) emerge when spermatocytes enter the pachytene phase of meiosis. In mice, pachytene piRNAs derive from ~100 discrete autosomal loci that produce canonical RNA polymerase II transcripts. These piRNA clusters bear 5' caps and 3' poly(A) tails, and often contain introns that are removed before nuclear export and processing into piRNAs. What marks pachytene piRNA clusters to produce piRNAs, and what confines their expression to the germline? We report that an unusually long first exon (≥ 10 kb) or a long, unspliced transcript correlates with germline-specific transcription and piRNA production. Our integrative analysis of transcriptome, piRNA, and epigenome datasets across multiple species reveals that a long first exon is an evolutionarily conserved feature of pachytene piRNA clusters. Furthermore, a highly methylated promoter, often containing a low or intermediate level of CG dinucleotides, correlates with germline expression and somatic silencing of pachytene piRNA clusters. Pachytene piRNA precursor transcripts bind THOC1 and THOC2, THO complex subunits known to promote transcriptional elongation and mRNA nuclear export. Together, these features may explain why the major sources of pachytene piRNA clusters specifically generate these unique small RNAs in the male germline of placental mammals.
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Affiliation(s)
- Tianxiong Yu
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Kaili Fan
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Deniz M Özata
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Gen Zhang
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Yu Fu
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
- Bioinformatics Program, Boston University, 44 Cummington Mall, Boston, MA, 02215, USA
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals, Cambridge, MA, 02139, USA
| | - William E Theurkauf
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Phillip D Zamore
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
| | - Zhiping Weng
- Department of Thoracic Surgery, Clinical Translational Research Center, Shanghai Pulmonary Hospital, The School of Life Sciences and Technology, Tongji University, 200092, Shanghai, China.
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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20
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Lismer A, Siklenka K, Lafleur C, Dumeaux V, Kimmins S. Sperm histone H3 lysine 4 trimethylation is altered in a genetic mouse model of transgenerational epigenetic inheritance. Nucleic Acids Res 2020; 48:11380-11393. [PMID: 33068438 PMCID: PMC7672453 DOI: 10.1093/nar/gkaa712] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 08/11/2020] [Accepted: 10/15/2020] [Indexed: 12/30/2022] Open
Abstract
Advancing the molecular knowledge surrounding fertility and inheritance has become critical given the halving of sperm counts in the last 40 years, and the rise in complex disease which cannot be explained by genetics alone. The connection between both these trends may lie in alterations to the sperm epigenome and occur through environmental exposures. Changes to the sperm epigenome are also associated with health risks across generations such as metabolic disorders and cancer. Thus, it is imperative to identify the epigenetic modifications that escape reprogramming during spermatogenesis and embryogenesis. Here, we aimed to identify the chromatin signature(s) involved in transgenerational phenotypes in our genetic mouse model of epigenetic inheritance that overexpresses the histone demethylase KDM1A in their germ cells. We used sperm-specific chromatin immunoprecipitation followed by in depth sequencing (ChIP-seq), and computational analysis to identify whether differential enrichment of histone H3 lysine 4 trimethylation (H3K4me3), and histone H3 lysine 27 trimethylation (H3K27me3) serve as mechanisms for transgenerational epigenetic inheritance through the paternal germline. Our analysis on the sperm of KDM1A transgenic males revealed specific changes in H3K4me3 enrichment that predominantly occurred independently from bivalent H3K4me3/H3K27me3 regions. Many regions with altered H3K4me3 enrichment in sperm were identified on the paternal allele of the pre-implantation embryo. These findings suggest that sperm H3K4me3 functions in the transmission of non-genetic phenotypes transgenerationally.
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Affiliation(s)
- Ariane Lismer
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Canada
| | - Keith Siklenka
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
| | - Vanessa Dumeaux
- PERFORM Center and Department of Biology, Concordia University, Montreal, Canada
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Canada
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Canada
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21
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Chetverina DA, Lomaev DV, Erokhin MM. Polycomb and Trithorax Group Proteins: The Long Road from Mutations in Drosophila to Use in Medicine. Acta Naturae 2020; 12:66-85. [PMID: 33456979 PMCID: PMC7800605 DOI: 10.32607/actanaturae.11090] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/30/2020] [Indexed: 12/12/2022] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) proteins are evolutionarily conserved factors responsible for the repression and activation of the transcription of multiple genes in Drosophila and mammals. Disruption of the PcG/TrxG expression is associated with many pathological conditions, including cancer, which makes them suitable targets for diagnosis and therapy in medicine. In this review, we focus on the major PcG and TrxG complexes, the mechanisms of PcG/TrxG action, and their recruitment to chromatin. We discuss the alterations associated with the dysfunction of a number of factors of these groups in oncology and the current strategies used to develop drugs based on small-molecule inhibitors.
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Affiliation(s)
- D. A. Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - D. V. Lomaev
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
| | - M. M. Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334 Russia
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22
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Coutinho Carneiro V, de Abreu da Silva IC, Amaral MS, Pereira ASA, Silveira GO, Pires DDS, Verjovski-Almeida S, Dekker FJ, Rotili D, Mai A, Lopes-Torres EJ, Robaa D, Sippl W, Pierce RJ, Borrello MT, Ganesan A, Lancelot J, Thiengo S, Fernandez MA, Vicentino ARR, Mourão MM, Coelho FS, Fantappié MR. Pharmacological inhibition of lysine-specific demethylase 1 (LSD1) induces global transcriptional deregulation and ultrastructural alterations that impair viability in Schistosoma mansoni. PLoS Negl Trop Dis 2020; 14:e0008332. [PMID: 32609727 PMCID: PMC7329083 DOI: 10.1371/journal.pntd.0008332] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/28/2020] [Indexed: 02/06/2023] Open
Abstract
Treatment and control of schistosomiasis still rely on only one effective drug, praziquantel (PZQ) and, due to mass treatment, the increasing risk of selecting for schistosome strains that are resistant to PZQ has alerted investigators to the urgent need to develop novel therapeutic strategies. The histone-modifying enzymes (HMEs) represent promising targets for the development of epigenetic drugs against Schistosoma mansoni. In the present study, we targeted the S. mansoni lysine-specific demethylase 1 (SmLSD1), a transcriptional corepressor, using a novel and selective synthetic inhibitor, MC3935, which was used to treat schistosomula and adult worms in vitro. By using cell viability assays and optical and electron microscopy, we showed that treatment with MC3935 affected parasite motility, egg-laying, tegument, and cellular organelle structures, culminating in the death of schistosomula and adult worms. In silico molecular modeling and docking analysis suggested that MC3935 binds to the catalytic pocket of SmLSD1. Western blot analysis revealed that MC3935 inhibited SmLSD1 demethylation activity of H3K4me1/2. Knockdown of SmLSD1 by RNAi recapitulated MC3935 phenotypes in adult worms. RNA-Seq analysis of MC3935-treated parasites revealed significant differences in gene expression related to critical biological processes. Collectively, our findings show that SmLSD1 is a promising drug target for the treatment of schistosomiasis and strongly support the further development and in vivo testing of selective schistosome LSD1 inhibitors.
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Affiliation(s)
- Vitor Coutinho Carneiro
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Isabel Caetano de Abreu da Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Adriana S. A. Pereira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Gilbert Oliveira Silveira
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | | | - Sergio Verjovski-Almeida
- Laboratório de Parasitologia, Instituto Butantan, São Paulo, Brazil
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brasil
| | - Frank J. Dekker
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan, AV Groningen, Netherlands
| | - Dante Rotili
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Antonello Mai
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Rome, Italy
| | - Eduardo José Lopes-Torres
- Laboratório de Helmintologia Romero Lascasas Porto, Faculdade de Ciências Médicas, Universidade do Estado do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle-Wittenberg, Germany
| | - Raymond J. Pierce
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - M. Teresa Borrello
- Centre de Recherche en Cancérologie de Marseille (CRCM), INSERM U1068, CNRS UMR 7258, Aix-Marseille Université and Institut Paoli-Calmettes, Parc Scientifique et Technologique de Luminy, Marseille, France
| | - A. Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Julien Lancelot
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Centre d’Infection et d’Immunité de Lille, Lille, France
| | - Silvana Thiengo
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Monica Ammon Fernandez
- Laboratório de Malacologia, Fundação Oswaldo Cruz, Instituto Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Amanda Roberta Revoredo Vicentino
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marina Moraes Mourão
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Fernanda Sales Coelho
- Grupo de Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Brazil
| | - Marcelo Rosado Fantappié
- Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Molecular e Biotecnologia, Centro de Ciências da Saúde, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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23
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Liu X, Simon JM, Xie H, Hu L, Wang J, Zurlo G, Fan C, Ptacek TS, Herring L, Tan X, Li M, Baldwin AS, Kim WY, Wu T, Kirschner MW, Gong K, Zhang Q. Genome-wide Screening Identifies SFMBT1 as an Oncogenic Driver in Cancer with VHL Loss. Mol Cell 2020; 77:1294-1306.e5. [PMID: 32023483 DOI: 10.1016/j.molcel.2020.01.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/09/2019] [Accepted: 01/01/2020] [Indexed: 11/15/2022]
Abstract
von Hippel-Lindau (VHL) is a critical tumor suppressor in clear cell renal cell carcinomas (ccRCCs). It is important to identify additional therapeutic targets in ccRCC downstream of VHL loss besides hypoxia-inducible factor 2α (HIF2α). By performing a genome-wide screen, we identified Scm-like with four malignant brain tumor domains 1 (SFMBT1) as a candidate pVHL target. SFMBT1 was considered to be a transcriptional repressor but its role in cancer remains unclear. ccRCC patients with VHL loss-of-function mutations displayed elevated SFMBT1 protein levels. SFMBT1 hydroxylation on Proline residue 651 by EglN1 mediated its ubiquitination and degradation governed by pVHL. Depletion of SFMBT1 abolished ccRCC cell proliferation in vitro and inhibited orthotopic tumor growth in vivo. Integrated analyses of ChIP-seq, RNA-seq, and patient prognosis identified sphingosine kinase 1 (SPHK1) as a key SFMBT1 target gene contributing to its oncogenic phenotype. Therefore, the pVHL-SFMBT1-SPHK1 axis serves as a potential therapeutic avenue for ccRCC.
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Affiliation(s)
- Xijuan Liu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Jeremy M Simon
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Haibiao Xie
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Lianxin Hu
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jun Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Giada Zurlo
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Cheng Fan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Travis S Ptacek
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Laura Herring
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC 27599, USA; UNC Proteomics Core Facility, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Xianming Tan
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Mingjie Li
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Albert S Baldwin
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - William Y Kim
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA
| | - Tao Wu
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Marc W Kirschner
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115
| | - Kan Gong
- Department of Urology, Peking University First Hospital, Beijing, China
| | - Qing Zhang
- Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC 27599, USA; Department of Pathology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
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24
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Mačinković I, Theofel I, Hundertmark T, Kovač K, Awe S, Lenz J, Forné I, Lamp B, Nist A, Imhof A, Stiewe T, Renkawitz-Pohl R, Rathke C, Brehm A. Distinct CoREST complexes act in a cell-type-specific manner. Nucleic Acids Res 2019; 47:11649-11666. [PMID: 31701127 PMCID: PMC7145674 DOI: 10.1093/nar/gkz1050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 10/16/2019] [Accepted: 10/23/2019] [Indexed: 01/10/2023] Open
Abstract
CoREST has been identified as a subunit of several protein complexes that generate transcriptionally repressive chromatin structures during development. However, a comprehensive analysis of the CoREST interactome has not been carried out. We use proteomic approaches to define the interactomes of two dCoREST isoforms, dCoREST-L and dCoREST-M, in Drosophila. We identify three distinct histone deacetylase complexes built around a common dCoREST/dRPD3 core: A dLSD1/dCoREST complex, the LINT complex and a dG9a/dCoREST complex. The latter two complexes can incorporate both dCoREST isoforms. By contrast, the dLSD1/dCoREST complex exclusively assembles with the dCoREST-L isoform. Genome-wide studies show that the three dCoREST complexes associate with chromatin predominantly at promoters. Transcriptome analyses in S2 cells and testes reveal that different cell lineages utilize distinct dCoREST complexes to maintain cell-type-specific gene expression programmes: In macrophage-like S2 cells, LINT represses germ line-related genes whereas other dCoREST complexes are largely dispensable. By contrast, in testes, the dLSD1/dCoREST complex prevents transcription of germ line-inappropriate genes and is essential for spermatogenesis and fertility, whereas depletion of other dCoREST complexes has no effect. Our study uncovers three distinct dCoREST complexes that function in a lineage-restricted fashion to repress specific sets of genes thereby maintaining cell-type-specific gene expression programmes.
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Affiliation(s)
- Igor Mačinković
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ina Theofel
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Tim Hundertmark
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Kristina Kovač
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Stephan Awe
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Jonathan Lenz
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
| | - Ignasi Forné
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Boris Lamp
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Axel Imhof
- Protein Analysis Unit, BioMedical Center, Faculty of Medicine, Ludwig-Maximilians-University Munich, Großhadernerstrasse 9, 82152 Martinsried, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Philipps-University, Hans-Meerwein-Strasse 3, 35043 Marburg, Germany
| | - Renate Renkawitz-Pohl
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Christina Rathke
- Department of Biology, Philipps-University, Karl-von-Frisch-Strasse 8, 35043, Marburg, Germany
| | - Alexander Brehm
- Institute of Molecular Biology and Tumor Research, Biomedical Research Center, Philipps-University, Hans-Meerwein-Strasse 2, 35043, Marburg, Germany
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25
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Mao W, Salzberg AC, Uchigashima M, Hasegawa Y, Hock H, Watanabe M, Akbarian S, Kawasawa YI, Futai K. Activity-Induced Regulation of Synaptic Strength through the Chromatin Reader L3mbtl1. Cell Rep 2019; 23:3209-3222. [PMID: 29898393 DOI: 10.1016/j.celrep.2018.05.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 04/12/2018] [Accepted: 05/10/2018] [Indexed: 01/02/2023] Open
Abstract
Homeostatic synaptic downscaling reduces neuronal excitability by modulating the number of postsynaptic receptors. Histone modifications and the subsequent chromatin remodeling play critical roles in activity-dependent gene expression. Histone modification codes are recognized by chromatin readers that affect gene expression by altering chromatin structure. We show that L3mbtl1 (lethal 3 malignant brain tumor-like 1), a polycomb chromatin reader, is downregulated by neuronal activity and is essential for synaptic response and downscaling. Genome-scale mapping of L3mbtl1 occupancies identified Ctnnb1 as a key gene downstream of L3mbtl1. Importantly, the occupancy of L3mbtl1 on the Ctnnb1 gene was regulated by neuronal activity. L3mbtl1 knockout neurons exhibited reduced Ctnnb1 expression. Partial knockdown of Ctnnb1 in wild-type neurons reduced excitatory synaptic transmission and abolished homeostatic downscaling, and transfecting Ctnnb1 in L3mbtl1 knockout neurons enhanced synaptic transmission and restored homeostatic downscaling. These results highlight a role for L3mbtl1 in regulating homeostasis of synaptic efficacy.
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Affiliation(s)
- Wenjie Mao
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA
| | - Anna C Salzberg
- Department of Pharmacology, Department of Biochemistry and Molecular Biology, and Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Motokazu Uchigashima
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA; Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Yuto Hasegawa
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA
| | - Hanno Hock
- Cancer Center and Center for Regenerative Medicine, Massachusetts General Hospital, Harvard Medical School,185 Cambridge Street, Boston, MA 02114, USA
| | - Masahiko Watanabe
- Department of Anatomy, Hokkaido University Graduate School of Medicine, Sapporo, Hokkaido 060-8638, Japan
| | - Schahram Akbarian
- Mount Sinai Department of Psychiatry, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, New York, NY 10029, USA
| | - Yuka Imamura Kawasawa
- Department of Pharmacology, Department of Biochemistry and Molecular Biology, and Institute for Personalized Medicine, Pennsylvania State University College of Medicine, 500 University Drive, Hershey, PA 17033, USA
| | - Kensuke Futai
- Brudnick Neuropsychiatric Research Institute, Department of Neurobiology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-2324, USA.
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Abstract
Though genetic data suggest that Polycomb group proteins (PcGs) are central chromatin modifiers and repressors that have been implicated in control of embryonic stem cell (ESC) pluripotency, the precise mechanism of PcG complex recruitment remains elusive, especially in mammals. We now report that the first and second MBT repeats of L3mbtl2 are important structural and functional features that are necessary and sufficient for L3mbtl2-mediated recruitment of PRC1.6 complex to target promoters. Interestingly, this region of L3mbtl2 harbors the evolutionarily conserved Pho-binding pocket also present in Drosophila Sfmbt, and mutation of the critical residues within this pocket completely abolishes its interaction with target promoters. Additionally, decreased PRC1.6 chromatin occupancy was observed following loss of individual components (L3mbtl2, Pcgf6, and Max) of the complex. Our findings suggest that the recruitment of noncanonical PRC1.6 complex in ESCs might be the result of L3mbtl2's interaction with multiple components of the complex.
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27
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Maezawa S, Yukawa M, Alavattam KG, Barski A, Namekawa SH. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Res 2019; 46:593-608. [PMID: 29126117 PMCID: PMC5778473 DOI: 10.1093/nar/gkx1052] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/02/2017] [Indexed: 12/14/2022] Open
Abstract
During spermatogenesis, germ cells undergo massive cellular reconstruction and dynamic chromatin remodeling to facilitate highly diverse transcriptomes, which are required for the production of functional sperm. However, it remains unknown how germline chromatin is organized to promote the dynamic, complex transcriptomes of spermatogenesis. Here, using ATAC-seq, we establish the varied landscape of open chromatin during spermatogenesis. We identify the reorganization of accessible chromatin in intergenic and intronic regions during the mitosis-to-meiosis transition. During the transition, mitotic-type open chromatin is closed while the de novo formation of meiotic-type open chromatin takes place. Contrastingly, differentiation processes such as spermatogonial differentiation and the meiosis-to-postmeiosis transition involve chromatin closure without the de novo formation of accessible chromatin. In spermiogenesis, the germline-specific Polycomb protein SCML2 promotes the closure of open chromatin at autosomes for gene suppression. Paradoxically, we identify the massive de novo formation of accessible chromatin when the sex chromosomes undergo meiotic sex chromosome inactivation, and this is also mediated by SCML2. These results reveal meiotic sex chromosome inactivation as an active process for chromatin organization. Together, our results unravel the genome-wide, dynamic reorganization of open chromatin and reveal mechanisms that underlie diverse transcriptomes during spermatogenesis.
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Affiliation(s)
- So Maezawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Masashi Yukawa
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Kris G Alavattam
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
| | - Artem Barski
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA.,Division of Allergy and Immunology, Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Satoshi H Namekawa
- Division of Reproductive Sciences, Division of Developmental Biology, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA.,Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH 49267, USA
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28
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Martignago D, Bernardini B, Polticelli F, Salvi D, Cona A, Angelini R, Tavladoraki P. The Four FAD-Dependent Histone Demethylases of Arabidopsis Are Differently Involved in the Control of Flowering Time. FRONTIERS IN PLANT SCIENCE 2019; 10:669. [PMID: 31214214 PMCID: PMC6558185 DOI: 10.3389/fpls.2019.00669] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/02/2019] [Indexed: 05/18/2023]
Abstract
In Arabidopsis thaliana, four FAD-dependent lysine-specific histone demethylases (LDL1, LDL2, LDL3, and FLD) are present, bearing both a SWIRM and an amine oxidase domain. In this study, a comparative analysis of gene structure, evolutionary relationships, tissue- and organ-specific expression patterns, physiological roles and target genes for the four Arabidopsis LDL/FLDs is reported. Phylogenetic analysis evidences a different evolutionary history for the four LDL/FLDs, while promoter activity data show that LDL/FLDs are strongly expressed during plant development and embryogenesis, with some gene-specific expression patterns. Furthermore, phenotypical analysis of loss-of-function mutants indicates a role of all four Arabidopsis LDL/FLD genes in the control of flowering time, though for some of them with opposing effects. This study contributes toward a better understanding of the LDL/FLD physiological roles and may provide biotechnological strategies for crop improvement.
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Affiliation(s)
- Damiano Martignago
- Department of Science, Roma Tre University, Rome, Italy
- Centre for Research in Agricultural Genomics, Spanish National Research Council–Institute for Food and Agricultural Research and Technology–Autonomous University of Barcelona–University of Barcelona, Barcelona, Spain
| | | | - Fabio Polticelli
- Department of Science, Roma Tre University, Rome, Italy
- ‘Roma Tre’ Section, National Institute of Nuclear Physics, Rome, Italy
| | - Daniele Salvi
- Department of Life, Health and Environmental Sciences, University of L’Aquila, L’Aquila, Italy
| | | | | | - Paraskevi Tavladoraki
- Department of Science, Roma Tre University, Rome, Italy
- *Correspondence: Paraskevi Tavladoraki,
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Korhonen VE, Helisalmi S, Jokinen A, Jokinen I, Lehtola JM, Oinas M, Lönnrot K, Avellan C, Kotkansalo A, Frantzen J, Rinne J, Ronkainen A, Kauppinen M, Junkkari A, Hiltunen M, Soininen H, Kurki M, Jääskeläinen JE, Koivisto AM, Sato H, Kato T, Remes AM, Eide PK, Leinonen V. Copy number loss in SFMBT1 is common among Finnish and Norwegian patients with iNPH. NEUROLOGY-GENETICS 2018; 4:e291. [PMID: 30584596 PMCID: PMC6283454 DOI: 10.1212/nxg.0000000000000291] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/09/2018] [Indexed: 12/16/2022]
Abstract
Objective To evaluate the role of the copy number loss in SFMBT1 in a Caucasian population. Methods Five hundred sixty-seven Finnish and 377 Norwegian patients with idiopathic normal pressure hydrocephalus (iNPH) were genotyped and compared with 508 Finnish elderly, neurologically healthy controls. The copy number loss in intron 2 of SFMBT1 was determined using quantitative PCR. Results The copy number loss in intron 2 of SFMBT1 was detected in 10% of Finnish (odds ratio [OR] = 1.9, p = 0.0078) and in 21% of Norwegian (OR = 4.7, p < 0.0001) patients with iNPH compared with 5.4% in Finnish controls. No copy number gains in SFMBT1 were detected in patients with iNPH or healthy controls. The carrier status did not provide any prognostic value for the effect of shunt surgery in either population. Moreover, no difference was detected in the prevalence of hypertension or T2DM between SFMBT1 copy number loss carriers and noncarriers. Conclusions This is the largest and the first multinational study reporting the increased prevalence of the copy number loss in intron 2 of SFMBT1 among patients with iNPH, providing further evidence of its role in iNPH. The pathogenic role still remains unclear, requiring further study.
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Affiliation(s)
- Ville E Korhonen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Seppo Helisalmi
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Aleksi Jokinen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Ilari Jokinen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Juha-Matti Lehtola
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Minna Oinas
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Kimmo Lönnrot
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Cecilia Avellan
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Anna Kotkansalo
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Janek Frantzen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Jaakko Rinne
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Antti Ronkainen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Mikko Kauppinen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Antti Junkkari
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Mikko Hiltunen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Hilkka Soininen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Mitja Kurki
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Juha E Jääskeläinen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Anne M Koivisto
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Hidenori Sato
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Takeo Kato
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Anne M Remes
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Per Kristian Eide
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
| | - Ville Leinonen
- Department of Neurosurgery (V.E.K., A. Jokinen, I.J., J.-M.L., A. Junkkari, J.E.J., V.L.), Kuopio University Hospital and University of Eastern Finland; Institute of Clinical Medicine-Neurology (S.H., M.H., H. Soininen, A.M.K.), University of Eastern Finland, Kuopio; Department of Neurosurgery (M.O., K.L.), University of Helsinki and Helsinki University Hospital; Clinical Neurosciences (C.A., A.K., J.F., J.R.), Department of Neurosurgery, University of Turku and Turku University Hospital; Department of Neurosurgery (A.R.), Tampere University Hospital; Unit of Clinical Neuroscience (M. Kauppinen, V.L.), Neurosurgery, University of Oulu and Medical Research Center, Oulu University Hospital; Institute of Biomedicine (M.H.), University of Eastern Finland, Kuopio; Analytical and Translational Genetics Unit (M. Kurki), Department of Medicine, Massachusetts General Hospital; Program in Medical and Population Genetics (M. Kurki), Broad Institute of MIT and Harvard; Stanley Center for Psychiatric Research (M. Kurki), Broad Institute for Harvard and MIT; Department of Neurology (H. Sato, T.K.), Hematology, Metabolism, Endocrinology and Diabetology, Yamagata University Faculty of Medicine, Japan; Medical Research Center (A.M.R.), Oulu University Hospital, Finland; Unit of Clinical Neuroscience (A.M.R.), Neurology, University of Oulu, Finland; Department of Neurosurgery (P.K.E.), Oslo University Hospital-Rikshospitalet; and Institute of Clinical Medicine (P.K.E.), Faculty of Medicine, University of Oslo, Norway
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Association of SHMT1, MAZ, ERG, and L3MBTL3 Gene Polymorphisms with Susceptibility to Multiple Sclerosis. Biochem Genet 2018; 57:355-370. [PMID: 30456721 DOI: 10.1007/s10528-018-9894-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 11/07/2018] [Indexed: 01/08/2023]
Abstract
Multiple sclerosis (MS) is the most common inflammatory and chronic disease of the central nervous system (CNS). A complex interaction between genetic, environmental, and epigenetic factors is involved in the pathogenesis of MS. With the advancement of GWAS, various variants associated with MS have been identified. This study aimed to evaluate the association of single-nucleotide polymorphisms (SNPs) rs4925166 and rs1979277 in the SHMT1, MAZ rs34286592, ERG rs2836425, and L3MBTL3 rs4364506 with MS. In this case-control study, the association of five SNPs in SHMT1, MAZ, ERG, and L3MBTL3 genes with relapsing-remitting MS (RR-MS) was investigated in 190 patients and 200 healthy individuals. Four SNPs including SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and L3MBTL3 rs4364506 were genotyped using PCR-RFLP and genotyping of ERG rs2836425 was performed by tetra-primer ARMS PCR. Our findings showed a significant difference in the allelic frequencies for the four SNPs of SHMT1 rs4925166, SHMT1 rs1979277, MAZ rs34286592, and ERG rs2836425, while there were no differences in the allele and genotype frequencies for L3MBTL3 rs4364506. These significant associations were observed for the following genotypes: TT and GG genotypes of SHMT1 rs4925166 (OR 0.47 and 1.90, respectively) genotype GG of SHMT1 rs1979277 (OR 0.63), genotype GG of MAZ rs34286592 (OR 0.61), TC and CC genotypes of ERG rs2836425 (OR 1.89 and 0.50, respectively). Our study highlighted that people who are carrying genotypes including GG (SHMT1 rs4925166) and TC (ERG rs2836425) have the highest susceptibility chance for MS, respectively. However, genotypes TT (SHMT1 rs4925166), CC (ERG rs2836425), GG (MAZ rs34286592), and GG (SHMT1 rs1979277) had the highest negative association (protective effect) with MS, respectively. L3MBTL3 rs4364506 was found neither as a predisposing nor a protective variant.
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Zhang C, Leng F, Saxena L, Hoang N, Yu J, Alejo S, Lee L, Qi D, Lu F, Sun H, Zhang H. Proteolysis of methylated SOX2 protein is regulated by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. J Biol Chem 2018; 294:476-489. [PMID: 30442713 DOI: 10.1074/jbc.ra118.005336] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 10/22/2018] [Indexed: 01/23/2023] Open
Abstract
SOX2 is a dose-dependent master stem cell protein that controls the self-renewal and pluripotency or multipotency of embryonic stem (ES) cells and many adult stem cells. We have previously found that SOX2 protein is monomethylated at lysine residues 42 and 117 by SET7 methyltransferase to promote SOX2 proteolysis, whereas LSD1 and PHF20L1 act on both methylated Lys-42 and Lys-117 to prevent SOX2 proteolysis. However, the mechanism by which the methylated SOX2 protein is degraded remains unclear. Here, we report that L3MBTL3, a protein with the malignant-brain-tumor (MBT) methylation-binding domain, is required for SOX2 proteolysis. Our studies showed that L3MBTL3 preferentially binds to the methylated Lys-42 in SOX2, although mutation of Lys-117 also partially reduces the interaction between SOX2 and L3MBTL3. The direct binding of L3MBTL3 to the methylated SOX2 protein leads to the recruitment of the CRL4DCAF5 ubiquitin E3 ligase to target SOX2 protein for ubiquitin-dependent proteolysis. Whereas loss of either LSD1 or PHF20L1 destabilizes SOX2 protein and impairs the self-renewal and pluripotency of mouse ES cells, knockdown of L3MBTL3 or DCAF5 is sufficient to restore the protein levels of SOX2 and rescue the defects of mouse ES cells caused by LSD1 or PHF20L1 deficiency. We also found that retinoic acid-induced differentiation of mouse ES cells is accompanied by the enhanced degradation of the methylated SOX2 protein at both Lys-42 and Lys-117. Our studies provide novel insights into the mechanism by which the methylation-dependent degradation of SOX2 protein is controlled by the L3MBTL3-CRL4DCAF5 ubiquitin ligase complex.
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Affiliation(s)
- Chunxiao Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and.,the School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Feng Leng
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Lovely Saxena
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Nam Hoang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Jiekai Yu
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Salvador Alejo
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Logan Lee
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Dandan Qi
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Fei Lu
- the School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, Guangdong, China
| | - Hong Sun
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
| | - Hui Zhang
- From the Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, Nevada 89154 and
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Abstract
Eukaryotic cells depend on precise genome organization within the nucleus to maintain an appropriate gene-expression profile. Critical to this process is the packaging of functional domains of open and closed chromatin to specific regions of the nucleus, but how this is regulated remains unclear. In this study, we show that the zinc finger protein Casz1 regulates higher-order nuclear organization of rod photoreceptors in the mouse retina by repressing nuclear lamina function, which leads to central localization of heterochromatin. Loss of Casz1 in rods leads to an abnormal transcriptional profile followed by degeneration. These results identify Casz1 as a regulator of higher-order genome organization. Genome organization plays a fundamental role in the gene-expression programs of numerous cell types, but determinants of higher-order genome organization are poorly understood. In the developing mouse retina, rod photoreceptors represent a good model to study this question. They undergo a process called “chromatin inversion” during differentiation, in which, as opposed to classic nuclear organization, heterochromatin becomes localized to the center of the nucleus and euchromatin is restricted to the periphery. While previous studies showed that the lamin B receptor participates in this process, the molecular mechanisms regulating lamina function during differentiation remain elusive. Here, using conditional genetics, we show that the zinc finger transcription factor Casz1 is required to establish and maintain the inverted chromatin organization of rod photoreceptors and to safeguard their gene-expression profile and long-term survival. At the mechanistic level, we show that Casz1 interacts with the polycomb repressor complex in a splice variant-specific manner and that both are required to suppress the expression of the nuclear envelope intermediate filament lamin A/C in rods. Lamin A is in turn sufficient to regulate heterochromatin organization and nuclear position. Furthermore, we show that Casz1 is sufficient to expand and centralize the heterochromatin of fibroblasts, suggesting a general role for Casz1 in nuclear organization. Together, these data support a model in which Casz1 cooperates with polycomb to control rod genome organization, in part by silencing lamin A/C.
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Methylated DNMT1 and E2F1 are targeted for proteolysis by L3MBTL3 and CRL4 DCAF5 ubiquitin ligase. Nat Commun 2018; 9:1641. [PMID: 29691401 PMCID: PMC5915600 DOI: 10.1038/s41467-018-04019-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/27/2018] [Indexed: 01/29/2023] Open
Abstract
Many non-histone proteins are lysine methylated and a novel function of this modification is to trigger the proteolysis of methylated proteins. Here, we report that the methylated lysine 142 of DNMT1, a major DNA methyltransferase that preserves epigenetic inheritance of DNA methylation patterns during DNA replication, is demethylated by LSD1. A novel methyl-binding protein, L3MBTL3, binds the K142-methylated DNMT1 and recruits a novel CRL4DCAF5 ubiquitin ligase to degrade DNMT1. Both LSD1 and PHF20L1 act primarily in S phase to prevent DNMT1 degradation by L3MBTL3-CRL4DCAF5. Mouse L3MBTL3/MBT-1 deletion causes accumulation of DNMT1 protein, increased genomic DNA methylation, and late embryonic lethality. DNMT1 contains a consensus methylation motif shared by many non-histone proteins including E2F1, a key transcription factor for S phase. We show that the methylation-dependent E2F1 degradation is also controlled by L3MBTL3-CRL4DCAF5. Our studies elucidate for the first time a novel mechanism by which the stability of many methylated non-histone proteins are regulated.
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Gwak J, Shin JY, Lee K, Hong SK, Oh S, Goh SH, Kim WS, Ju BG. SFMBT2 (Scm-like with four mbt domains 2) negatively regulates cell migration and invasion in prostate cancer cells. Oncotarget 2018; 7:48250-48264. [PMID: 27340776 PMCID: PMC5217015 DOI: 10.18632/oncotarget.10198] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 06/04/2016] [Indexed: 12/12/2022] Open
Abstract
Metastatic prostate cancer is the leading cause of morbidity and mortality in men. In this study, we found that expression level of SFMBT2 is altered during prostate cancer progression and has been associated with the migration and invasion of prostate cancer cells. The expression level of SFMBT2 is high in poorly metastatic prostate cancer cells compared to highly metastatic prostate cancer cells. We also found that SFMBT2 knockdown elevates MMP-2, MMP-3, MMP-9, and MMP-26 expression, leading to increased cell migration and invasion in LNCaP and VCaP cells. SFMBT2 interacts with YY1, RNF2, N-CoR and HDAC1/3, as well as repressive histone marks such as H3K9me2, H4K20me2, and H2AK119Ub which are associated with transcriptional repression. In addition, SFMBT2 knockdown decreased KAI1 gene expression through up-regulation of N-CoR gene expression. Expression of SFMBT2 in prostate cancer was strongly associated with clinicopathological features. Patients having higher Gleason score (≥ 8) had substantially lower SFMBT2 expression than patients with lower Gleason score. Moreover, tail vein or intraprostatic injection of SFMBT2 knockdown LNCaP cells induced metastasis. Taken together, our findings suggest that regulation of SFMBT2 may provide a new therapeutic strategy to control prostate cancer metastasis as well as being a potential biomarker of metastatic prostate cancer.
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Affiliation(s)
- Jungsug Gwak
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Jee Yoon Shin
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Kwanghyun Lee
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Soon Ki Hong
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Sangtaek Oh
- Department of Bio and Fermentation Convergence Technology, Kookmin University, Seoul 136-702, Republic of Korea
| | - Sung-Ho Goh
- Research Institute, National Cancer Center, Goyang, Gyeonggi-do 410-769, Republic of Korea
| | - Won Sun Kim
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
| | - Bong Gun Ju
- Department of Life Science, Sogang University, Seoul 121-742, Republic of Korea
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Spruijt CG, Luijsterburg MS, Menafra R, Lindeboom RGH, Jansen PWTC, Edupuganti RR, Baltissen MP, Wiegant WW, Voelker-Albert MC, Matarese F, Mensinga A, Poser I, Vos HR, Stunnenberg HG, van Attikum H, Vermeulen M. ZMYND8 Co-localizes with NuRD on Target Genes and Regulates Poly(ADP-Ribose)-Dependent Recruitment of GATAD2A/NuRD to Sites of DNA Damage. Cell Rep 2017; 17:783-798. [PMID: 27732854 DOI: 10.1016/j.celrep.2016.09.037] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Revised: 08/10/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
NuRD (nucleosome remodeling and histone deacetylase) is a versatile multi-protein complex with roles in transcription regulation and the DNA damage response. Here, we show that ZMYND8 bridges NuRD to a number of putative DNA-binding zinc finger proteins. The MYND domain of ZMYND8 directly interacts with PPPLΦ motifs in the NuRD subunit GATAD2A. Both GATAD2A and GATAD2B exclusively form homodimers and define mutually exclusive NuRD subcomplexes. ZMYND8 and NuRD share a large number of genome-wide binding sites, mostly active promoters and enhancers. Depletion of ZMYND8 does not affect NuRD occupancy genome-wide and only slightly affects expression of NuRD/ZMYND8 target genes. In contrast, the MYND domain in ZMYND8 facilitates the rapid, poly(ADP-ribose)-dependent recruitment of GATAD2A/NuRD to sites of DNA damage to promote repair by homologous recombination. Thus, these results show that a specific substoichiometric interaction with a NuRD subunit paralogue provides unique functionality to distinct NuRD subcomplexes.
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Affiliation(s)
- Cornelia G Spruijt
- Department of Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands; Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Martijn S Luijsterburg
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Roberta Menafra
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Rik G H Lindeboom
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Pascal W T C Jansen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Raghu Ram Edupuganti
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Wouter W Wiegant
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands
| | - Moritz C Voelker-Albert
- Department of Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands
| | - Anneloes Mensinga
- Department of Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Ina Poser
- Max Planck Institute for Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Harmjan R Vos
- Department of Molecular Cancer Research, University Medical Center Utrecht, 3584 CG Utrecht, the Netherlands
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC Leiden, the Netherlands.
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525 GA Nijmegen, the Netherlands.
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Marzluff WF, Koreski KP. Birth and Death of Histone mRNAs. Trends Genet 2017; 33:745-759. [PMID: 28867047 DOI: 10.1016/j.tig.2017.07.014] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/24/2017] [Accepted: 07/28/2017] [Indexed: 12/22/2022]
Abstract
In metazoans, histone mRNAs are not polyadenylated but end in a conserved stem-loop. Stem-loop binding protein (SLBP) binds to the stem-loop and is required for all steps in histone mRNA metabolism. The genes for the five histone proteins are linked. A histone locus body (HLB) forms at each histone gene locus. It contains factors essential for transcription and processing of histone mRNAs, and couples transcription and processing. The active form of U7 snRNP contains the HLB component FLASH (FLICE-associated huge protein), the histone cleavage complex (HCC), and a subset of polyadenylation factors including the endonuclease CPSF73. Histone mRNAs are rapidly degraded when DNA replication is inhibited by a 3' to 5' pathway that requires extensive uridylation of mRNA decay intermediates.
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Affiliation(s)
- William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Kaitlin P Koreski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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Myrick DA, Christopher MA, Scott AM, Simon AK, Donlin-Asp PG, Kelly WG, Katz DJ. KDM1A/LSD1 regulates the differentiation and maintenance of spermatogonia in mice. PLoS One 2017; 12:e0177473. [PMID: 28498828 PMCID: PMC5428937 DOI: 10.1371/journal.pone.0177473] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 04/27/2017] [Indexed: 11/18/2022] Open
Abstract
The proper regulation of spermatogenesis is crucial to ensure the continued production of sperm and fertility. Here, we investigated the function of the H3K4me2 demethylase KDM1A/LSD1 during spermatogenesis in developing and adult mice. Conditional deletion of Kdm1a in the testis just prior to birth leads to fewer spermatogonia and germ cell loss before 3 weeks of age. These results demonstrate that KDM1A is required for spermatogonial differentiation, as well as germ cell survival, in the developing testis. In addition, inducible deletion of Kdm1a in the adult testis results in the abnormal accumulation of meiotic spermatocytes, as well as apoptosis and progressive germ cell loss. These results demonstrate that KDM1A is also required during adult spermatogenesis. Furthermore, without KDM1A, the stem cell factor OCT4 is ectopically maintained in differentiating germ cells. This requirement for KDM1A is similar to what has been observed in other stem cell populations, suggesting a common function. Taken together, we propose that KDM1A is a key regulator of spermatogenesis and germ cell maintenance in the mouse.
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Affiliation(s)
- Dexter A. Myrick
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
- Graduate Division of Biological and Biomedical Science, Emory University, Atlanta, Georgia, United States of America
| | - Michael A. Christopher
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
- Graduate Division of Biological and Biomedical Science, Emory University, Atlanta, Georgia, United States of America
| | - Alyssa M. Scott
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
- Graduate Division of Biological and Biomedical Science, Emory University, Atlanta, Georgia, United States of America
| | - Ashley K. Simon
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
| | - Paul G. Donlin-Asp
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
- Graduate Division of Biological and Biomedical Science, Emory University, Atlanta, Georgia, United States of America
| | - William G. Kelly
- Biology Department, Emory University, Atlanta, Georgia, United States of America
| | - David J. Katz
- Cell Biology Department, Emory University, Atlanta, Georgia, United States of America
- * E-mail:
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Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC. Genes Dev 2017; 30:1116-27. [PMID: 27151979 PMCID: PMC4863741 DOI: 10.1101/gad.279141.116] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 04/13/2016] [Indexed: 12/11/2022]
Abstract
Here, Frey et al. report the structural basis by which the Drosophila Pho-repressive complex (PhoRC), the only Polycomb group protein complex with sequence-specific DNA-binding activity, binds to Polycomb-repressive complex 1 (PRC1) and thereby recruits it to Polycomb response elements in target genes. Polycomb group (PcG) protein complexes repress transcription by modifying target gene chromatin. In Drosophila, this repression requires association of PcG protein complexes with cis-regulatory Polycomb response elements (PREs), but the interactions permitting formation of these assemblies are poorly understood. We show that the Sfmbt subunit of the DNA-binding Pho-repressive complex (PhoRC) and the Scm subunit of the canonical Polycomb-repressive complex 1 (PRC1) directly bind each other through their SAM domains. The 1.9 Å crystal structure of the Scm-SAM:Sfmbt-SAM complex reveals the recognition mechanism and shows that Sfmbt-SAM lacks the polymerization capacity of the SAM domains of Scm and its PRC1 partner subunit, Ph. Functional analyses in Drosophila demonstrate that Sfmbt-SAM and Scm-SAM are essential for repression and that PhoRC DNA binding is critical to initiate PRC1 association with PREs. Together, this suggests that PRE-tethered Sfmbt-SAM nucleates PRC1 recruitment and that Scm-SAM/Ph-SAM-mediated polymerization then results in the formation of PRC1-compacted chromatin.
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Jin Y, Huo B, Fu X, Hao T, Zhang Y, Guo Y, Hu X. LSD1 collaborates with EZH2 to regulate expression of interferon-stimulated genes. Biomed Pharmacother 2017; 88:728-737. [PMID: 28152483 DOI: 10.1016/j.biopha.2017.01.055] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 10/20/2022] Open
Abstract
Histone methylation is a complicate and dynamic epigenetic modification that regulates gene transcription, chromosomal structure and cell differentiation. Here, we discovered the interaction between the H3K4 demethylase, lysine specific demethylase 1 (LSD1, an important component of CoREST repressor complex) and the H3K27 methyltransferase, enhancer of zeste homolog 2 (EZH2, an essential component of PRC2). Immuno-precipitation and GST-pull down assay were performed to observe the interaction between the proteins. The MCF-7 cells were cultured and transfected with the siRNA. The mRNA and proteins were examined by using the real-time polymerase chain reaction (RT-PCR) and western blot assay, respectively. HPLC and LC-MS/MS analysis were performed to purify the proteins. RT-PCR-based quantitative ChIP analysis were performed. LSD1 interacts with histone modification protein EZH2 in MCF-7 cells. LSD1 and EZH2 target a few common genes. LSD1 knockdown and EZH2 knockdown affect protein expression. LSD1 knockdown and EZH2 knockdown affect the proteins involving in IFN signaling pathway. LSD1 and EZH2 modify histone methylation at IRF9 gene locus. We systematically analyzed the proteins that are affected by either LSD1 or EZH2 knockdown with proteomic approaches and identified that the interferon pathway and some other pathways are commonly affected. The interaction between LSD1 and EZH2 stabilizes the binding of LSD1 to the promoter region of IRF9, which is a key transcription factor of the interferon pathway. In conclusion, our study revealed that the coordination between histone demethylases and methyl-transferases might serve as a double lock system to suppress the expression of interferon stimulated genes.
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Affiliation(s)
- Yue Jin
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Bo Huo
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Xueqi Fu
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Tian Hao
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Yu Zhang
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Yidi Guo
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China
| | - Xin Hu
- School of Life Sciences, Jilin University, Changchun 130012, China; Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun 130012, China.
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40
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Genomic structural variations for cardiovascular and metabolic comorbidity. Sci Rep 2017; 7:41268. [PMID: 28120895 PMCID: PMC5264603 DOI: 10.1038/srep41268] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
The objective of this study was to identify genes targeted by both copy number and copy-neutral changes in the right coronary arteries in the area of advanced atherosclerotic plaques and intact internal mammary arteries derived from the same individuals with comorbid coronary artery disease and metabolic syndrome. The artery samples from 10 patients were screened for genomic imbalances using array comparative genomic hybridization. Ninety high-confidence, identical copy number variations (CNVs) were detected. We also identified eight copy-neutral changes (cn-LOHs) > 1.5 Mb in paired arterial samples in 4 of 10 individuals. The frequencies of the two gains located in the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions were evaluated in 33 paired arteries and blood samples. Two patients contained the gain in 10q24.31 (ERLIN1) and one patient contained the gain in 12q24.11 (UNG, ACACB) that affected only the blood DNA. An additional two patients harboured these CNVs in both the arteries and blood. In conclusion, we discovered and confirmed a gain of the 10q24.31 (ERLIN1) and 12q24.11 (UNG, ACACB) genomic regions in patients with coronary artery disease and metabolic comorbidity. Analysis of DNA extracted from blood indicated a possible somatic origin for these CNVs.
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Branco MR, King M, Perez-Garcia V, Bogutz AB, Caley M, Fineberg E, Lefebvre L, Cook SJ, Dean W, Hemberger M, Reik W. Maternal DNA Methylation Regulates Early Trophoblast Development. Dev Cell 2016; 36:152-63. [PMID: 26812015 PMCID: PMC4729543 DOI: 10.1016/j.devcel.2015.12.027] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 11/27/2015] [Accepted: 12/23/2015] [Indexed: 02/06/2023]
Abstract
Critical roles for DNA methylation in embryonic development are well established, but less is known about its roles during trophoblast development, the extraembryonic lineage that gives rise to the placenta. We dissected the role of DNA methylation in trophoblast development by performing mRNA and DNA methylation profiling of Dnmt3a/3b mutants. We find that oocyte-derived methylation plays a major role in regulating trophoblast development but that imprinting of the key placental regulator Ascl2 is only partially responsible for these effects. We have identified several methylation-regulated genes associated with trophoblast differentiation that are involved in cell adhesion and migration, potentially affecting trophoblast invasion. Specifically, trophoblast-specific DNA methylation is linked to the silencing of Scml2, a Polycomb Repressive Complex 1 protein that drives loss of cell adhesion in methylation-deficient trophoblast. Our results reveal that maternal DNA methylation controls multiple differentiation-related and physiological processes in trophoblast via both imprinting-dependent and -independent mechanisms. Oocyte-derived DNA methylation is an important regulator of trophoblast transcription DNA methylation controls trophoblast cell adhesion Silencing of Polycomb gene Scml2 is necessary for normal trophoblast development
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Affiliation(s)
- Miguel R Branco
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK.
| | - Michelle King
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Vicente Perez-Garcia
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Aaron B Bogutz
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Matthew Caley
- Blizard Institute, Barts and The London School of Medicine and Dentistry, QMUL, London E1 2AT, UK
| | - Elena Fineberg
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Louis Lefebvre
- Department of Medical Genetics, Life Sciences Institute, University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Simon J Cook
- Signalling Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Wendy Dean
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK
| | - Myriam Hemberger
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Wolf Reik
- Epigenetics Programme, Babraham Institute, Cambridge CB22 3AT, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK; The Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
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42
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Luo H, Shenoy A, Li X, Jin Y, Jin L, Cai Q, Tang M, Liu Y, Chen H, Reisman D, Wu L, Seto E, Qiu Y, Dou Y, Casero R, Lu J. MOF Acetylates the Histone Demethylase LSD1 to Suppress Epithelial-to-Mesenchymal Transition. Cell Rep 2016; 15:2665-78. [DOI: 10.1016/j.celrep.2016.05.050] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Revised: 03/22/2016] [Accepted: 05/12/2016] [Indexed: 12/22/2022] Open
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Sadiq I, Keren I, Citovsky V. Plant homologs of mammalian MBT-domain protein-regulated KDM1 histone lysine demethylases do not interact with plant Tudor/PWWP/MBT-domain proteins. Biochem Biophys Res Commun 2016; 470:913-6. [PMID: 26826387 DOI: 10.1016/j.bbrc.2016.01.151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 01/23/2016] [Indexed: 11/17/2022]
Abstract
Histone lysine demethylases of the LSD1/KDM1 family play important roles in epigenetic regulation of eukaryotic chromatin, and they are conserved between plants and animals. Mammalian LSD1 is thought to be targeted to its substrates, i.e., methylated histones, by an MBT-domain protein SFMBT1 that represents a component of the LSD1-based repressor complex and binds methylated histones. Because MBT-domain proteins are conserved between different organisms, from animals to plants, we examined whether the KDM1-type histone lysine demethylases KDM1C and FLD of Arabidopsis interact with the Arabidopsis Tudor/PWWP/MBT-domain SFMBT1-like proteins SL1, SL2, SL3, and SL4. No such interaction was detected using the bimolecular fluorescence complementation assay in living plant cells. Thus, plants most likely direct their KDM1 chromatin-modifying enzymes to methylated histones of the target chromatin by a mechanism different from that employed by the mammalian cells.
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Affiliation(s)
- Irfan Sadiq
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA; Department of Biosciences, COMSATS Institute of Information Technology Islamabad, Park Road, Islamabad, 44000, Pakistan.
| | - Ido Keren
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA.
| | - Vitaly Citovsky
- Department of Biochemistry and Cell Biology, State University of New York, Stony Brook, NY, 11794-5215, USA.
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Li W, Park JY, Zheng D, Hoque M, Yehia G, Tian B. Alternative cleavage and polyadenylation in spermatogenesis connects chromatin regulation with post-transcriptional control. BMC Biol 2016; 14:6. [PMID: 26801249 PMCID: PMC4724118 DOI: 10.1186/s12915-016-0229-6] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Most mammalian genes display alternative cleavage and polyadenylation (APA). Previous studies have indicated preferential expression of APA isoforms with short 3’ untranslated regions (3’UTRs) in testes. Results By deep sequencing of the 3’ end region of poly(A) + transcripts, we report widespread shortening of 3’UTR through APA during the first wave of spermatogenesis in mouse, with 3’UTR size being the shortest in spermatids. Using genes without APA as a control, we show that shortening of 3’UTR eliminates destabilizing elements, such as U-rich elements and transposable elements, which appear highly potent during spermatogenesis. We additionally found widespread regulation of APA events in introns and exons that can affect the coding sequence of transcripts and global activation of antisense transcripts upstream of the transcription start site, suggesting modulation of splicing and initiation of transcription during spermatogenesis. Importantly, genes that display significant 3’UTR shortening tend to have functions critical for further sperm maturation, and testis-specific genes display greater 3’UTR shortening than ubiquitously expressed ones, indicating functional relevance of APA to spermatogenesis. Interestingly, genes with shortened 3’UTRs tend to have higher RNA polymerase II and H3K4me3 levels in spermatids as compared to spermatocytes, features previously known to be associated with open chromatin state. Conclusions Our data suggest that open chromatin may create a favorable cis environment for 3’ end processing, leading to global shortening of 3’UTR during spermatogenesis. mRNAs with shortened 3’UTRs are relatively stable thanks to evasion of powerful mRNA degradation mechanisms acting on 3’UTR elements. Stable mRNAs generated in spermatids may be important for protein production at later stages of sperm maturation, when transcription is globally halted. Electronic supplementary material The online version of this article (doi:10.1186/s12915-016-0229-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wencheng Li
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ji Yeon Park
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Mainul Hoque
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Ghassan Yehia
- Transgenic Core Facility, Rutgers New Jersey Medical School, Newark, NJ, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ, USA. .,Rutgers Cancer Institute of New Jersey, Newark, NJ, USA.
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Mattar P, Cayouette M. Mechanisms of temporal identity regulation in mouse retinal progenitor cells. NEUROGENESIS 2015; 2:e1125409. [PMID: 27606333 PMCID: PMC4973599 DOI: 10.1080/23262133.2015.1125409] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 10/29/2022]
Abstract
While much progress has been made in recent years toward elucidating the transcription factor codes controlling how neural progenitor cells generate the various glial and neuronal cell types in a particular spatial domain, much less is known about how these progenitors alter their output over time. In the past years, work in the developing mouse retina has provided evidence that a transcriptional cascade similar to the one used in Drosophila neuroblasts might control progenitor temporal identity in vertebrates. The zinc finger transcription factor Ikzf1 (Ikaros), an ortholog of Drosophila hunchback, was reported to confer early temporal identity in retinal progenitors and, more recently, the ortholog of Drosophila castor, Casz1, was found to function as a mid/late temporal identity factor that is negatively regulated by Ikzf1. The molecular mechanisms by which these temporal identity factors function in retinal progenitors, however, remain unknown. Here we briefly review previous work on the vertebrate temporal identity factors in the retina, and propose a model by which they might operate.
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Affiliation(s)
- Pierre Mattar
- Cellular Neurobiology Research Unit; Institut de recherches cliniques de Montréal Montréal, QC, Canada
| | - Michel Cayouette
- Cellular Neurobiology Research Unit; Institut de recherches cliniques de Montréal Montréal, QC, Canada; Department of Medicine; Université de Montréal Montréal, QC, Canada; Department of Anatomy and Cell Biology and Division of Experimental Medicine; McGill University Montréal, QC, Canada
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46
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LSD1 is essential for oocyte meiotic progression by regulating CDC25B expression in mice. Nat Commun 2015; 6:10116. [PMID: 26626423 PMCID: PMC4686821 DOI: 10.1038/ncomms10116] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 11/04/2015] [Indexed: 12/13/2022] Open
Abstract
Mammalian oocytes are arrested at prophase I until puberty when hormonal signals induce the resumption of meiosis I and progression to meiosis II. Meiotic progression is controlled by CDK1 activity and is accompanied by dynamic epigenetic changes. Although the signalling pathways regulating CDK1 activity are well defined, the functional significance of epigenetic changes remains largely unknown. Here we show that LSD1, a lysine demethylase, regulates histone H3 lysine 4 di-methylation (H3K4me2) in mouse oocytes and is essential for meiotic progression. Conditional deletion of Lsd1 in growing oocytes results in precocious resumption of meiosis and spindle and chromosomal abnormalities. Consequently, most Lsd1-null oocytes fail to complete meiosis I and undergo apoptosis. Mechanistically, upregulation of CDC25B, a phosphatase that activates CDK1, is responsible for precocious meiotic resumption and also contributes to subsequent spindle and chromosomal defects. Our findings uncover a functional link between LSD1 and the major signalling pathway governing meiotic progression.
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47
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Siklenka K, Erkek S, Godmann M, Lambrot R, McGraw S, Lafleur C, Cohen T, Xia J, Suderman M, Hallett M, Trasler J, Peters AHFM, Kimmins S. Disruption of histone methylation in developing sperm impairs offspring health transgenerationally. Science 2015; 350:aab2006. [PMID: 26449473 DOI: 10.1126/science.aab2006] [Citation(s) in RCA: 326] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 09/18/2015] [Indexed: 12/28/2022]
Abstract
A father's lifetime experiences can be transmitted to his offspring to affect health and development. However, the mechanisms underlying paternal epigenetic transmission are unclear. Unlike in somatic cells, there are few nucleosomes in sperm, and their function in epigenetic inheritance is unknown. We generated transgenic mice in which overexpression of the histone H3 lysine 4 (H3K4) demethylase KDM1A (also known as LSD1) during spermatogenesis reduced H3K4 dimethylation in sperm. KDM1A overexpression in one generation severely impaired development and survivability of offspring. These defects persisted transgenerationally in the absence of KDM1A germline expression and were associated with altered RNA profiles in sperm and offspring. We show that epigenetic inheritance of aberrant development can be initiated by histone demethylase activity in developing sperm, without changes to DNA methylation at CpG-rich regions.
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Affiliation(s)
- Keith Siklenka
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Serap Erkek
- Friedrich Miescher Institute for Biomedical Research (FMI), CH-4058 Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland
| | - Maren Godmann
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Romain Lambrot
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Serge McGraw
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Tamara Cohen
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Jianguo Xia
- Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada. Institute of Parasitology, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada
| | - Matthew Suderman
- MRC Integrative Epidemiology Unity, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Michael Hallett
- McGill Centre for Bioinformatics, School of Computer Science, Faculty of Science, McGill University, Montreal, Quebec, Canada
| | - Jacquetta Trasler
- Department of Pediatrics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. Department of Human Genetics and Department of Pharmacology and Therapeutics, Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Antoine H F M Peters
- Friedrich Miescher Institute for Biomedical Research (FMI), CH-4058 Basel, Switzerland. Faculty of Sciences, University of Basel, Basel, Switzerland.
| | - Sarah Kimmins
- Department of Pharmacology and Therapeutics, Faculty of Medicine, McGill University, Montreal, Quebec, Canada. Department of Animal Science, Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, Quebec, Canada.
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48
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Kang H, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI. Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 2015; 29:1136-50. [PMID: 26063573 PMCID: PMC4470282 DOI: 10.1101/gad.260562.115] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
In this study, Kang et al. investigate how PcG complexes form repressive chromatin domains. The findings show that Scm, a transcriptional repressor, is an important regulator of PRC1, PRC2, and transcriptional silencing and suggest that Scm coordinates PcG complexes and polymerizes, resulting in PcG silencing. The Polycomb group (PcG) proteins are key regulators of development in Drosophila and are strongly implicated in human health and disease. How PcG complexes form repressive chromatin domains remains unclear. Using cross-linked affinity purifications of BioTAP-Polycomb (Pc) or BioTAP-Enhancer of zeste [E(z)], we captured all PcG-repressive complex 1 (PRC1) or PRC2 core components and Sex comb on midleg (Scm) as the only protein strongly enriched with both complexes. Although previously not linked to PRC2, we confirmed direct binding of Scm and PRC2 using recombinant protein expression and colocalization of Scm with PRC1, PRC2, and H3K27me3 in embryos and cultured cells using ChIP-seq (chromatin immunoprecipitation [ChIP] combined with deep sequencing). Furthermore, we found that RNAi knockdown of Scm and overexpression of the dominant-negative Scm-SAM (sterile α motif) domain both affected the binding pattern of E(z) on polytene chromosomes. Aberrant localization of the Scm-SAM domain in long contiguous regions on polytene chromosomes revealed its independent ability to spread on chromatin, consistent with its previously described ability to oligomerize in vitro. Pull-downs of BioTAP-Scm captured PRC1 and PRC2 and additional repressive complexes, including PhoRC, LINT, and CtBP. We propose that Scm is a key mediator connecting PRC1, PRC2, and transcriptional silencing. Combined with previous structural and genetic analyses, our results strongly suggest that Scm coordinates PcG complexes and polymerizes to produce broad domains of PcG silencing.
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Affiliation(s)
- Hyuckjoon Kang
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kyle A McElroy
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Youngsook Lucy Jung
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Artyom A Alekseyenko
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Barry M Zee
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Peter J Park
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Mitzi I Kuroda
- Division of Genetics, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA; Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA;
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Lambrot R, Lafleur C, Kimmins S. The histone demethylase KDM1A is essential for the maintenance and differentiation of spermatogonial stem cells and progenitors. FASEB J 2015; 29:4402-16. [PMID: 26243864 DOI: 10.1096/fj.14-267328] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 06/22/2015] [Indexed: 12/22/2022]
Abstract
Little is known of the fundamental processes governed by epigenetic mechanisms in the supplier cells of spermatogenesis, the spermatogonial stem cells (SSCs). The histone H3 lysine demethylase KDM1A is expressed in spermatogonia. We hypothesized that KDM1A serves in transcriptional regulation of SSCs and fertility. Using a conditional deletion of Kdm1a [conditional knockout (cKO)] in mouse spermatogonia, we determined that Kdm1a is essential for spermatogenesis as adult cKO males completely lack germ cells. Analysis of postnatal testis development revealed that undifferentiated and differentiating spermatogonial populations form in Kdm1a-cKO animals, yet the majority fail to enter meiosis. Loss of germ cells in the cKO was rapid with none remaining by postnatal day (PND) 21. To gain insight into the mechanistic implications of Kdm1a ablation, we isolated PND 6 spermatogonia enriched for SSCs and analyzed their transcriptome by RNA sequencing. Loss of Kdm1a was associated with altered transcription of 1206 genes. Importantly, differentially expressed genes between control and Kdm1a-cKO animals included those that are essential for SSC and progenitor maintenance and spermatogonial differentiation. The complete loss of fertility and failure to establish spermatogenesis indicate that Kdm1a is a master controller of gene transcription in spermatogonia and is required for SSC and progenitor maintenance and differentiation.
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Affiliation(s)
- Romain Lambrot
- *Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada; and Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Christine Lafleur
- *Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada; and Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
| | - Sarah Kimmins
- *Department of Animal Science, McGill University, Sainte Anne de Bellevue, Quebec, Canada; and Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
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LAMTOR1-PRKCD and NUMA1-SFMBT1 fusion genes identified by RNA sequencing in aneurysmal benign fibrous histiocytoma with t(3;11)(p21;q13). Cancer Genet 2015; 208:545-51. [PMID: 26432191 DOI: 10.1016/j.cancergen.2015.07.007] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/24/2015] [Accepted: 07/29/2015] [Indexed: 12/30/2022]
Abstract
RNA sequencing of an aneurysmal benign fibrous histiocytoma with the karyotype 46,XY,t(3;11)(p21;q13),del(6)(p23)[17]/46,XY[2] showed that the t(3;11) generated two fusion genes: LAMTOR1-PRKCD and NUMA1-SFMBT1. RT-PCR together with Sanger sequencing verified the presence of fusion transcripts from both fusion genes. In the LAMTOR1-PRKCD fusion, the part of the PRKCD gene coding for the catalytic domain of the serine/threonine kinase is under control of the LAMTOR1 promoter. In the NUMA1-SFMBT1 fusion, the part of the SFMBT1 gene coding for two of four malignant brain tumor domains and the sterile alpha motif domain is controlled by the NUMA1 promoter. The data support a neoplastic genesis of aneurysmal benign fibrous histiocytoma and indicate a pathogenetic role for LAMTOR1-PRKCD and NUMA1-SFMBT1.
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