1
|
Yao Y, Lv H, Zhang M, Li Y, Herman JG, Brock MV, Gao A, Wang Q, Fuks F, Zhang L, Guo M. Epigenetic silencing of BEND4, a novel DNA damage repair gene, is a synthetic lethal marker for ATM inhibitor in pancreatic cancer. Front Med 2024; 18:721-734. [PMID: 38926248 DOI: 10.1007/s11684-023-1053-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 12/04/2023] [Indexed: 06/28/2024]
Abstract
Synthetic lethality is a novel model for cancer therapy. To understand the function and mechanism of BEN domain-containing protein 4 (BEND4) in pancreatic cancer, eight cell lines and a total of 492 cases of pancreatic neoplasia samples were included in this study. Methylation-specific polymerase chain reaction, CRISPR/Cas9, immunoprecipitation assay, comet assay, and xenograft mouse model were used. BEND4 is a new member of the BEN domain family. The expression of BEND4 is regulated by promoter region methylation. It is methylated in 58.1% (176/303) of pancreatic ductal adenocarcinoma (PDAC), 33.3% (14/42) of intraductal papillary mucinous neoplasm, 31.0% (13/42) of pancreatic neuroendocrine tumor, 14.3% (3/21) of mucinous cystic neoplasm, 4.3% (2/47) of solid pseudopapillary neoplasm, and 2.7% (1/37) of serous cystic neoplasm. BEND4 methylation is significantly associated with late-onset PDAC (> 50 years, P < 0.01) and tumor differentiation (P < 0.0001), and methylation of BEND4 is an independent poor prognostic marker (P < 0.01) in PDAC. Furthermore, BEND4 plays tumor-suppressive roles in vitro and in vivo. Mechanistically, BEND4 involves non-homologous end joining signaling by interacting with Ku80 and promotes DNA damage repair. Loss of BEND4 increased the sensitivity of PDAC cells to ATM inhibitor. Collectively, the present study revealed an uncharacterized tumor suppressor BEND4 and indicated that methylation of BEND4 may serve as a potential synthetic lethal marker for ATM inhibitor in PDAC treatment.
Collapse
Affiliation(s)
- Yuanxin Yao
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Honghui Lv
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Meiying Zhang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Yuan Li
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
- Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, China
| | - James G Herman
- UPMC Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Malcolm V Brock
- Department of surgery, School of Medicine, Johns Hopkins School of Medicine, Baltimore, MD, 21287, USA
| | - Aiai Gao
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Qian Wang
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China
| | - Francois Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Center (U-CRC), Universite Libre de Bruxelles (ULB), Brussels, 1070, Belgium
| | - Lirong Zhang
- Department of Pharmacology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China.
| | - Mingzhou Guo
- Department of Gastroenterology and Hepatology, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
- National Key Laboratory of Kidney Diseases, the First Medical Center, Chinese PLA General Hospital, Beijing, 100853, China.
| |
Collapse
|
2
|
Messias TS, Silva KCP, Silva TC, Soares S. Potential of Viruses as Environmental Etiological Factors for Non-Syndromic Orofacial Clefts. Viruses 2024; 16:511. [PMID: 38675854 PMCID: PMC11053622 DOI: 10.3390/v16040511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/20/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
In this study, we analyzed the potential of viral infections in the species Homo sapiens as environmental causes of orofacial clefts (OFCs). A scoring system was adapted for qualitatively assessing the potential of viruses to cause cleft lip and/or palate (CL/P). This assessment considered factors such as information from the literature, nucleotide and amino acid similarities, and the presence of Endogenous Viral Elements (EVEs). The analysis involved various algorithm packages within Basic Local Alignment Search Tool 2.13.0 software and databases from the National Center for Biotechnology Information and the International Committee on Taxonomy of Viruses. Twenty significant viral species using different biosynthesis strategies were identified: Human coronavirus NL63, Rio Negro virus, Alphatorquevirus homin9, Brisavirus, Cosavirus B, Torque teno mini virus 4, Bocaparvovirus primate2, Human coronavirus HKU1, Monkeypox virus, Mammarenavirus machupoense, Volepox virus, Souris mammarenavirus, Gammapapillomavirus 7, Betainfluenzavirus influenzae, Lymphocytic choriomeningitis mammarenavirus, Ledantevirus kern, Gammainfluenzavirus influenzae, Betapolyomavirus hominis, Vesiculovirus perinet, and Cytomegalovirus humanbeta5. The evident viral etiological potential in relation to CL/P varies depending on the Baltimore class to which the viral species belongs. Given the multifactorial nature of CL/P, this relationship appears to be dynamic.
Collapse
Affiliation(s)
- Thiago S. Messias
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
| | - Kaique C. P. Silva
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Faculty of Medicine, Nove de Julho University, Bauru 17011-102, SP, Brazil
| | - Thiago C. Silva
- Faculty of Architecture, Arts, Communication and Design, São Paulo State University, Bauru 17033-360, SP, Brazil;
| | - Simone Soares
- Hospital for Rehabilitation of Craniofacial Anomalies, University of São Paulo, Bauru 17012-901, SP, Brazil; (T.S.M.); (K.C.P.S.)
- Department of Prosthodontics and Periodontology, Bauru School of Dentistry, University of São Paulo, 9-75, Bauru 17012-901, SP, Brazil
| |
Collapse
|
3
|
Gao G, Sumrall ES, Pitchiaya S, Bitzer M, Alberti S, Walter NG. Biomolecular condensates in kidney physiology and disease. Nat Rev Nephrol 2023; 19:756-770. [PMID: 37752323 DOI: 10.1038/s41581-023-00767-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/27/2023] [Indexed: 09/28/2023]
Abstract
The regulation and preservation of distinct intracellular and extracellular solute microenvironments is crucial for the maintenance of cellular homeostasis. In mammals, the kidneys control bodily salt and water homeostasis. Specifically, the urine-concentrating mechanism within the renal medulla causes fluctuations in extracellular osmolarity, which enables cells of the kidney to either conserve or eliminate water and electrolytes, depending on the balance between intake and loss. However, relatively little is known about the subcellular and molecular changes caused by such osmotic stresses. Advances have shown that many cells, including those of the kidney, rapidly (within seconds) and reversibly (within minutes) assemble membraneless, nano-to-microscale subcellular assemblies termed biomolecular condensates via the biophysical process of hyperosmotic phase separation (HOPS). Mechanistically, osmotic cell compression mediates changes in intracellular hydration, concentration and molecular crowding, rendering HOPS one of many related phase-separation phenomena. Osmotic stress causes numerous homo-multimeric proteins to condense, thereby affecting gene expression and cell survival. HOPS rapidly regulates specific cellular biochemical processes before appropriate protective or corrective action by broader stress response mechanisms can be initiated. Here, we broadly survey emerging evidence for, and the impact of, biomolecular condensates in nephrology, where initial concentration buffering by HOPS and its subsequent cellular escalation mechanisms are expected to have important implications for kidney physiology and disease.
Collapse
Affiliation(s)
- Guoming Gao
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily S Sumrall
- Biophysics Graduate Program, University of Michigan, Ann Arbor, MI, USA
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA
| | | | - Markus Bitzer
- Department of Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany
| | - Nils G Walter
- Department of Chemistry and Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
| |
Collapse
|
4
|
Gräwe C, Hernandez-Quiles M, Jansen PWTC, Brimmers A, Vermeulen M. Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy. J Proteome Res 2023; 22:2683-2693. [PMID: 37466164 PMCID: PMC10407929 DOI: 10.1021/acs.jproteome.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Indexed: 07/20/2023]
Abstract
In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.
Collapse
Affiliation(s)
- Cathrin Gräwe
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Miguel Hernandez-Quiles
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| | - Pascal W. T. C. Jansen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Annika Brimmers
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department
of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute,
Radboud University Nijmegen, 6525 GA Nijmegen, The Netherlands
- Division
of Molecular Genetics, The Netherlands Cancer
Institute, 1066CX Amsterdam, the Netherlands
| |
Collapse
|
5
|
Khan A, Prasanth S. BENDing with Polycomb in pluripotency and cancer. Bioessays 2023; 45:e2300046. [PMID: 37194980 PMCID: PMC10524657 DOI: 10.1002/bies.202300046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/18/2023]
Abstract
Three recent publications on BEND3 firmly establish its role as a novel sequence-specific transcription factor that is essential for PRC2 recruitment and maintenance of pluripotency. Here, we briefly review our current understanding of the BEND3-PRC2 axis in the regulation of pluripotency and also explore the possibility of a similar connection in cancer.
Collapse
Affiliation(s)
- Abid Khan
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599-7260
| | - Supriya Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
- Cancer center at Illinois, UIUC
| |
Collapse
|
6
|
Naiyer S, Dwivedi L, Singh N, Phulera S, Mohan V, Kamran M. Role of Transcription Factor BEND3 and Its Potential Effect on Cancer Progression. Cancers (Basel) 2023; 15:3685. [PMID: 37509346 PMCID: PMC10377563 DOI: 10.3390/cancers15143685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
BEND3 is a transcription factor that plays a critical role in the regulation of gene expression in mammals. While there is limited research on the role of BEND3 as a tumor suppressor or an oncogene and its potential role in cancer therapy is still emerging, several studies suggest that it may be involved in both the processes. Its interaction and regulation with multiple other factors via p21 have already been reported to play a significant role in cancer development, which serves as an indication of its potential role in oncogenesis. Its interaction with chromatin modifiers such as NuRD and NoRC and its role in the recruitment of polycomb repressive complex 2 (PRC2) are some of the additional events indicative of its potential role in cancer development. Moreover, a few recent studies indicate BEND3 as a potential target for cancer therapy. Since the specific mechanisms by which BEND3 may contribute to cancer progression are not yet fully elucidated, in this review, we have discussed the possible pathways BEND3 may take to serve as an oncogenic driver or suppressor.
Collapse
Affiliation(s)
- Sarah Naiyer
- Department of Biomedical Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Lalita Dwivedi
- Faculty of Science, Department of Biotechnology, Invertis University, Bareilly 243122, UP, India
| | - Nishant Singh
- Cell and Gene Therapy Division Absorption System, Exton, PA 19341, USA
| | - Swastik Phulera
- Initium Therapeutics, 22 Strathmore Rd., STE 453, Natick, MA 01760, USA
| | - Vijay Mohan
- Department of Biosciences, School of Basic and Applied Sciences, Galgotias University, Greater Noida 203201, UP, India
| | - Mohammad Kamran
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| |
Collapse
|
7
|
Yang N, Wang Y, Dai P, Li T, Zierhut C, Tan A, Zhang T, Xiang JZ, Ordureau A, Funabiki H, Chen Z, Deng L. Vaccinia E5 is a major inhibitor of the DNA sensor cGAS. Nat Commun 2023; 14:2898. [PMID: 37217469 PMCID: PMC10201048 DOI: 10.1038/s41467-023-38514-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 05/05/2023] [Indexed: 05/24/2023] Open
Abstract
The DNA sensor cyclic GMP-AMP synthase (cGAS) is critical in host antiviral immunity. Vaccinia virus (VACV) is a large cytoplasmic DNA virus that belongs to the poxvirus family. How vaccinia virus antagonizes the cGAS-mediated cytosolic DNA-sensing pathway is not well understood. In this study, we screened 80 vaccinia genes to identify potential viral inhibitors of the cGAS/Stimulator of interferon gene (STING) pathway. We discovered that vaccinia E5 is a virulence factor and a major inhibitor of cGAS. E5 is responsible for abolishing cGAMP production during vaccinia virus (Western Reserve strain) infection of dendritic cells. E5 localizes to the cytoplasm and nucleus of infected cells. Cytosolic E5 triggers ubiquitination of cGAS and proteasome-dependent degradation via interacting with cGAS. Deleting the E5R gene from the Modified vaccinia virus Ankara (MVA) genome strongly induces type I IFN production by dendritic cells (DCs) and promotes DC maturation, and thereby improves antigen-specific T cell responses.
Collapse
Affiliation(s)
- Ning Yang
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
| | - Yi Wang
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Peihong Dai
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Tuo Li
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Christian Zierhut
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY, 10065, USA
- The Institute of Cancer Research, London, SW3 6JB, UK
| | - Adrian Tan
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Tuo Zhang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Jenny Zhaoying Xiang
- Genomic Resources Core Facility, Weill Cornell Medical College, New York, NY, 10065, USA
| | - Alban Ordureau
- Cell Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Zhijian Chen
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Liang Deng
- Dermatology Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Weill Cornell Medical College, New York, NY, 10065, USA.
| |
Collapse
|
8
|
Liu K, Zhang J, Xiao Y, Yang A, Song X, Li Y, Chen Y, Hughes TR, Min J. Structural insights into DNA recognition by the BEN domain of the transcription factor BANP. J Biol Chem 2023; 299:104734. [PMID: 37086783 DOI: 10.1016/j.jbc.2023.104734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/12/2023] [Accepted: 04/15/2023] [Indexed: 04/24/2023] Open
Abstract
The BEN domain-containing transcription factors regulate transcription by recruiting chromatin-modifying factors to specific chromatin regions via their DNA-binding BEN domains. The BEN domain of BANP has been shown to bind to a CGCG DNA sequence or an AAA-containing MARs (matrix attachment regions) DNA sequence. Consistent with these in vivo observations, we identified an optimal DNA binding sequence of AAATCTCG by PBM (protein binding microarray), which was also confirmed by our ITC (Isothermal Titration Calorimetry) and mutagenesis results to uncover additional mechanistic details about DNA binding by the BEN domain of BANP. We then determined crystal structures of the BANP BEN domain in apo form and in complex with a CGCG-containing DNA, respectively, which revealed that the BANP BEN domain mainly used the electrostatic interactions to bind DNA with some base-specific interactions with the TC motifs. Our ITC results also showed that BANP bound to unmethylated and methylated DNAs with comparable binding affinities. Our complex structure of BANP-mCGCG revealed that the BANP BEN domain bound to the unmethylated and methylated DNAs in a similar mode and cytosine methylation did not get involved in binding, which is also consistent with our observations from the complex structures of the BEND6 BEN domain with the CGCG or CGmCG DNAs. Taken together, our results further elucidate the elements important for DNA recognition and transcriptional regulation by the BANP BEN domain-containing transcription factor.
Collapse
Affiliation(s)
- Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.
| | - Jin Zhang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Yuqing Xiao
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Ally Yang
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Xiaosheng Song
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Yanjun Li
- Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Yunxia Chen
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China
| | - Timothy R Hughes
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Jinrong Min
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium and Department of Physiology, University of Toronto, Toronto, Ontario M5S 3E1, Canada.
| |
Collapse
|
9
|
Yu Y. BEND3 takes the rein. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1210-1212. [PMID: 36648610 DOI: 10.1007/s11427-022-2134-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 05/21/2022] [Indexed: 01/18/2023]
Affiliation(s)
- Yang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
10
|
Association analyses of the autosomal genome and mitochondrial DNA with accelerometry-derived sleep parameters in depressed UK biobank subjects. J Psychiatr Res 2023; 157:152-161. [PMID: 36463630 DOI: 10.1016/j.jpsychires.2022.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 09/01/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
BACKGROUND The bidirectional relationship between sleep disturbances and depression is well documented, yet the biology of sleep is not fully understood. Mitochondria have become of interest not only because of the connection between sleep and metabolism but also because of mitochondria's involvement in the production of reactive oxygen species, which are largely scavenged during sleep. METHODS Genome-wide association studies (GWAS) of eight accelerometry-derived sleep measures were performed across both the autosomal and mitochondrial DNA (mtDNA) among two severity levels of depression in UK Biobank participants. We calculated SNP heritability for each of the sleep measures. Linear regression was performed to test associations and mitochondrial haplogroups. RESULTS Variants included in the GWAS accounted for moderate heritability of bedtime (19.6%, p = 4.75 × 10-7), sleep duration (16.6%, p = 8.58 × 10-6) and duration of longest sleep bout (22.6%, p = 4.64 × 10-4). No variants passed genome-wide significance in the autosomal genome. The top hit in the severe depression sample was rs145019802, near GOLGA8B, for sleep efficiency (p = 1.17 × 10-7), and the top hit in the broad depression sample was rs7100859, an intergenic SNP, and nap duration (p = 1.25 × 10-7). Top mtDNA loci were m.12633C > A of MT-ND5 with bedtime (p = 0.002) in the severe sample and m.16186C > T of the control region with nap duration (p = 0.002) in the broad sample. CONCLUSION SNP heritability estimates support the involvement of common SNPs in specific sleep measures among depressed individuals. This is the first study to analyze mtDNA variance in sleep measures in depressed individuals. Our mtDNA findings, although nominally significant, provide preliminary suggestion that mitochondria are involved in sleep.
Collapse
|
11
|
H3K27me3 at pericentromeric heterochromatin is a defining feature of the early mouse blastocyst. Sci Rep 2022; 12:13908. [PMID: 35974030 PMCID: PMC9381757 DOI: 10.1038/s41598-022-17730-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 07/29/2022] [Indexed: 11/09/2022] Open
Abstract
Early mouse development is characterized by structural and epigenetic changes while cells progress towards differentiation. At blastocyst stage, the segregation of the three primordial lineages is accompanied by establishment of differential patterns of DNA methylation and post-translational modifications of histones, such as H3K27me3. Here, we analysed the dynamics of H3K27me3 at pericentromeric heterochromatin (PCH) during early development. We also followed the localization of EZH2 and BEND3, previously shown in ESCs to drive PRC2 to hypomethylated PCH. We show that the location of H3K27me3 at PCH, in addition to H3K9me3, is a defining feature of embryonic cells in vivo. Moreover, it may play an important role in structuring PCH and preserving genomic integrity at a time of globally relaxed chromatin. At peri-implantation stages, while DNA methylation is still low, EZH2 and then H3K27me3, leave PCH in epiblast progenitors at the time of their spatial segregation from primitive endoderm cells, while BEND3 remains there up to implantation. The comparison with stem cells (ESCs and TSCs) reveals that the epigenetic marks (i.e. H3K9me3 and H3K27me3) of PCH are reset during in vitro derivation and only partially restored thereafter. This highlights possible divergences between in vitro and "in embryo" epigenetic regulation regarding constitutive heterochromatin.
Collapse
|
12
|
Kurniawan F, Prasanth SG. A BEN-domain protein and polycomb complex work coordinately to regulate transcription. Transcription 2022; 13:82-87. [PMID: 35904285 PMCID: PMC9467525 DOI: 10.1080/21541264.2022.2105128] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022] Open
Abstract
Transcription regulation is an important mechanism that controls pluripotency and differentiation. Transcription factors dictate cell fate decisions by functioning cooperatively with chromatin regulators. We have recently demonstrated that BEND3 (BANP, E5R and Nac1 domain) protein regulates the expression of differentiation-associated genes by modulating the chromatin architecture at promoters. We highlight the collaboration of BEND3 with the polycomb repressive complex in coordinating transcription repression and propose a model highlighting the relevance of the BEND3-PRC2 axis in gene regulation and chromatin organization.Abbreviations: BEND3, BANP, E5R and Nac1 domain; rDNA, ribosomal DNA; PRC2, Polycomb Repressive Complex 2; H3K27me3, Histone H3 Lysine 27 methylation; PcG, Polycomb group.
Collapse
Affiliation(s)
- Fredy Kurniawan
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL,USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL,USA
| |
Collapse
|
13
|
Ma L, Xie D, Luo M, Lin X, Nie H, Chen J, Gao C, Duo S, Han C. Identification and characterization of BEND2 as a key regulator of meiosis during mouse spermatogenesis. SCIENCE ADVANCES 2022; 8:eabn1606. [PMID: 35613276 PMCID: PMC9132480 DOI: 10.1126/sciadv.abn1606] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/08/2022] [Indexed: 05/07/2023]
Abstract
The chromatin state, which undergoes global changes during spermatogenesis, is critical to meiotic initiation and progression. However, the key regulators involved and the underlying molecular mechanisms remain to be uncovered. Here, we report that mouse BEND2 is specifically expressed in spermatogenic cells around meiotic initiation and that it plays an essential role in meiotic progression. Bend2 gene knockout in male mice arrested meiosis at the transition from zygonema to pachynema, disrupted synapsis and DNA double-strand break repair, and induced nonhomologous chromosomal pairing. BEND2 interacted with chromatin-associated proteins that are components of certain transcription-repressor complexes. BEND2-binding sites were identified in diverse chromatin states and enriched in simple sequence repeats. BEND2 inhibited the expression of genes involved in meiotic initiation and regulated chromatin accessibility and the modification of H3K4me3. Therefore, our study identified BEND2 as a previously unknown key regulator of meiosis, gene expression, and chromatin state during mouse spermatogenesis.
Collapse
Affiliation(s)
- Longfei Ma
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dan Xie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengcheng Luo
- Department of Tissue and Embryology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, Hubei Province, China
| | - Xiwen Lin
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Hengyu Nie
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Chenxu Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuguang Duo
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunsheng Han
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
- Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| |
Collapse
|
14
|
Lehman NL, Spassky N, Sak M, Webb A, Zumbar CT, Usubalieva A, Alkhateeb KJ, McElroy JP, Maclean KH, Fadda P, Liu T, Gangalapudi V, Carver J, Abdullaev Z, Timmers C, Parker JR, Pierson CR, Mobley BC, Gokden M, Hattab EM, Parrett T, Cooke RX, Lehman TD, Costinean S, Parwani A, Williams BJ, Jensen RL, Aldape K, Mistry AM. Astroblastomas exhibit radial glia stem cell lineages and differential expression of imprinted and X-inactivation escape genes. Nat Commun 2022; 13:2083. [PMID: 35440587 PMCID: PMC9018799 DOI: 10.1038/s41467-022-29302-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/07/2022] [Indexed: 02/04/2023] Open
Abstract
Astroblastomas (ABs) are rare brain tumors of unknown origin. We performed an integrative genetic and epigenetic analysis of AB-like tumors. Here, we show that tumors traceable to neural stem/progenitor cells (radial glia) that emerge during early to later brain development occur in children and young adults, respectively. Tumors with MN1-BEND2 fusion appear to present exclusively in females and exhibit overexpression of genes expressed prior to 25 post-conception weeks (pcw), including genes enriched in early ventricular zone radial glia and ependymal tumors. Other, histologically classic ABs overexpress or harbor mutations of mitogen-activated protein kinase pathway genes, outer and truncated radial glia genes, and genes expressed after 25 pcw, including neuronal and astrocyte markers. Findings support that AB-like tumors arise in the context of epigenetic and genetic changes in neural progenitors. Selective gene fusion, variable imprinting and/or chromosome X-inactivation escape resulting in biallelic overexpression may contribute to female predominance of AB molecular subtypes.
Collapse
Affiliation(s)
- Norman L Lehman
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA.
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA.
- The Brown Cancer Center, University of Louisville, Louisville, KY, 40202, USA.
| | - Nathalie Spassky
- Institut de Biologie de l'ENS (IBENS), Inserm, CNRS, École Normale Supérieure, PSL Research University, Paris, France
| | - Müge Sak
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
- Department of Biochemistry and Molecular Genetics, University of Louisville, Louisville, KY, 40202, USA
| | - Amy Webb
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Cory T Zumbar
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Aisulu Usubalieva
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Khaled J Alkhateeb
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Joseph P McElroy
- Center for Biostatistics, Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | | | - Paolo Fadda
- Department of Cancer Biology, The Ohio State University, Columbus, OH, 43210, USA
| | - Tom Liu
- Solid Tumor Translational Science, The Ohio State University, Columbus, OH, 43210, USA
| | - Vineela Gangalapudi
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Jamie Carver
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Cynthia Timmers
- Solid Tumor Translational Science, The Ohio State University, Columbus, OH, 43210, USA
| | - John R Parker
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Christopher R Pierson
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, OH, 43205, USA
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Bret C Mobley
- Department of Pathology, Microbiology and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Murat Gokden
- Department of Pathology and Laboratory Services, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Eyas M Hattab
- Department of Pathology and Laboratory Medicine, University of Louisville, Louisville, KY, 40202, USA
| | - Timothy Parrett
- Department of Pathology and Anatomic Sciences, University of Missouri, Columbia, MO, 65212, USA
| | - Ralph X Cooke
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Trang D Lehman
- Department of Family and Community Medicine, Contra Costa County Health System, Martinez, CA, 94553, USA
| | - Stefan Costinean
- Department of Pathology, Banner Gateway Medical Center, MD Anderson Cancer Center, Tempe, AZ, 85284, USA
| | - Anil Parwani
- Department of Pathology, The Ohio State University, Columbus, OH, 43210, USA
| | - Brian J Williams
- Department of Neurosurgery, University of Louisville, Louisville, KY, 40202, USA
| | - Randy L Jensen
- Department of Neurosurgery, University of Utah, Salt Lake City, UT, 84132, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892, USA
| | - Akshitkumar M Mistry
- Department of Neurological Surgery, Vanderbilt University, Nashville, TN, 37232, USA
| |
Collapse
|
15
|
Roosen M, Odé Z, Bunt J, Kool M. The oncogenic fusion landscape in pediatric CNS neoplasms. Acta Neuropathol 2022; 143:427-451. [PMID: 35169893 PMCID: PMC8960661 DOI: 10.1007/s00401-022-02405-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/31/2022] [Accepted: 01/31/2022] [Indexed: 01/09/2023]
Abstract
Pediatric neoplasms in the central nervous system (CNS) are the leading cause of cancer-related deaths in children. Recent developments in molecular analyses have greatly contributed to a more accurate diagnosis and risk stratification of CNS tumors. Additionally, sequencing studies have identified various, often entity specific, tumor-driving events. In contrast to adult tumors, which often harbor multiple mutated oncogenic drivers, the number of mutated genes in pediatric cancers is much lower and many tumors can have a single oncogenic driver. Moreover, in children, much more than in adults, fusion proteins play an important role in driving tumorigenesis, and many different fusions have been identified as potential driver events in pediatric CNS neoplasms. However, a comprehensive overview of all the different reported oncogenic fusion proteins in pediatric CNS neoplasms is still lacking. A better understanding of the fusion proteins detected in these tumors and of the molecular mechanisms how these proteins drive tumorigenesis, could improve diagnosis and further benefit translational research into targeted therapies necessary to treat these distinct entities. In this review, we discuss the different oncogenic fusions reported in pediatric CNS neoplasms and their structure to create an overview of the variety of oncogenic fusion proteins to date, the tumor entities they occur in and their proposed mode of action.
Collapse
Affiliation(s)
- Mieke Roosen
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Zelda Odé
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Jens Bunt
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands
| | - Marcel Kool
- Princess Máxima Center for Pediatric Oncology, 3584CS, Utrecht, The Netherlands.
- Hopp Children's Cancer Center (KiTZ), 69120, Heidelberg, Germany.
- Division of Pediatric Neurooncology, German Cancer Research Center DKFZ and German Cancer Consortium DKTK, 69120, Heidelberg, Germany.
| |
Collapse
|
16
|
Zhang J, Zhang Y, You Q, Huang C, Zhang T, Wang M, Zhang T, Yang X, Xiong J, Li Y, Liu CP, Zhang Z, Xu RM, Zhu B. Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation. Science 2022; 375:1053-1058. [PMID: 35143257 DOI: 10.1126/science.abm0730] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bivalent genes are ready for activation upon the arrival of developmental cues. Here, we report that BEND3 is a CpG island (CGI)-binding protein that is enriched at regulatory elements. The cocrystal structure of BEND3 in complex with its target DNA reveals the structural basis for its DNA methylation-sensitive binding property. Mouse embryos ablated of Bend3 died at the pregastrulation stage. Bend3 null embryonic stem cells (ESCs) exhibited severe defects in differentiation, during which hundreds of CGI-containing bivalent genes were prematurely activated. BEND3 is required for the stable association of polycomb repressive complex 2 (PRC2) at bivalent genes that are highly occupied by BEND3, which suggests a reining function of BEND3 in maintaining high levels of H3K27me3 at these bivalent genes in ESCs to prevent their premature activation in the forthcoming developmental stage.
Collapse
Affiliation(s)
- Jing Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qinglong You
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chang Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tiantian Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mingzhu Wang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei 230601, Anhui, China
| | - Tianwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaocheng Yang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yingfeng Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
17
|
BEND3 safeguards pluripotency by repressing differentiation-associated genes. Proc Natl Acad Sci U S A 2022; 119:2107406119. [PMID: 35217604 PMCID: PMC8892337 DOI: 10.1073/pnas.2107406119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2022] [Indexed: 12/17/2022] Open
Abstract
The molecular basis of how the BEN domain–containing gene family regulates chromatin function and transcription remains to be elucidated. We report that BEND3 is highly expressed in pluripotent cells and binds to promoters of genes involved in differentiation. BEND3 regulates the expression of differentiation-associated genes by modulating the chromatin architecture at promoters. We propose that transcription repression mediated by BEND3 is essential for normal development and maintenance of pluripotency. BEN domain–containing proteins are emerging rapidly as an important class of factors involved in modulating gene expression, yet the molecular basis of how they regulate chromatin function and transcription remains to be established. BEND3 is a quadruple BEN domain–containing protein that associates with heterochromatin and functions as a transcriptional repressor. We find that BEND3 is highly expressed in pluripotent cells, and the induction of differentiation results in the down-regulation of BEND3. The removal of BEND3 from pluripotent cells results in cells exhibiting upregulation of the differentiation-inducing gene expression signature. We find that BEND3 binds to the promoters of differentiation-associated factors and key cell cycle regulators, including CDKN1A, encoding the cell cycle inhibitor p21, and represses the expression of differentiation-associated genes by enhancing H3K27me3 decoration at these promoters. Our results support a model in which transcription repression mediated by BEND3 is essential for normal development and to prevent differentiation.
Collapse
|
18
|
Zheng L, Liu J, Niu L, Kamran M, Yang AWH, Jolma A, Dai Q, Hughes TR, Patel DJ, Zhang L, Prasanth SG, Yu Y, Ren A, Lai EC. Distinct structural bases for sequence-specific DNA binding by mammalian BEN domain proteins. Genes Dev 2022; 36:225-240. [PMID: 35144965 PMCID: PMC8887127 DOI: 10.1101/gad.348993.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 01/05/2022] [Indexed: 11/24/2022]
Abstract
The BEN domain is a recently recognized DNA binding module that is present in diverse metazoans and certain viruses. Several BEN domain factors are known as transcriptional repressors, but, overall, relatively little is known of how BEN factors identify their targets in humans. In particular, X-ray structures of BEN domain:DNA complexes are only known for Drosophila factors bearing a single BEN domain, which lack direct vertebrate orthologs. Here, we characterize several mammalian BEN domain (BD) factors, including from two NACC family BTB-BEN proteins and from BEND3, which has four BDs. In vitro selection data revealed sequence-specific binding activities of isolated BEN domains from all of these factors. We conducted detailed functional, genomic, and structural studies of BEND3. We show that BD4 is a major determinant for in vivo association and repression of endogenous BEND3 targets. We obtained a high-resolution structure of BEND3-BD4 bound to its preferred binding site, which reveals how BEND3 identifies cognate DNA targets and shows differences with one of its non-DNA-binding BEN domains (BD1). Finally, comparison with our previous invertebrate BEN structures, along with additional structural predictions using AlphaFold2 and RoseTTAFold, reveal distinct strategies for target DNA recognition by different types of BEN domain proteins. Together, these studies expand the DNA recognition activities of BEN factors and provide structural insights into sequence-specific DNA binding by mammalian BEN proteins.
Collapse
Affiliation(s)
- Luqian Zheng
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jingjing Liu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Lijie Niu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
| | - Mohammad Kamran
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Ally W H Yang
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Arttu Jolma
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Qi Dai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Timothy R Hughes
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
- Donnelly Centre, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Dinshaw J Patel
- Structural Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Long Zhang
- The Eighth Affiliated Hospital, Sun Yat-Sen University, Shenzhen, Guangdong 518033, China
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Yang Yu
- State Key Laboratory of Medical Molecular Biology, Department of Molecular Biology and Biochemistry, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| | - Aiming Ren
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, New York 10065, USA
| |
Collapse
|
19
|
Kara B, Uyguner O, Maraş Genç H, İşlek EE, Kasap M, Toksoy G, Akpınar G, Uyur Yalçın E, Anık Y, Üstek D. BEND4 as a Candidate Gene for an Infection-Induced Acute Encephalopathy Characterized by a Cyst and Calcification of the Pons and Cerebellar Atrophy. Mol Syndromol 2021; 13:12-22. [DOI: 10.1159/000517541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 06/01/2021] [Indexed: 11/19/2022] Open
Abstract
Three siblings born to Turkish parents from the same village had normal brain development until acute neurological deterioration between 12 months and 8 years of age. Consequent loss of all acquired motor, social, and language functions following infections was associated with a pontine cyst, calcification, and cerebellar atrophy. Exome sequencing revealed a homozygous c.1297G>A (p.Gly433Ser) alteration in <i>BEND4</i>, which was predicted to be deleterious in in silico analysis tools and segregated in multiple affected individuals in the family. <i>BEND4</i> has not been associated with any existing disease. Immunofluorescence microscopy analysis of wild-type and mutant BEND4 expressing Vero cells showed nuclear and cytoplasmic localization. Wild-type BEND4 displayed a network-like distribution, whereas mutant BEND4 showed a juxtanuclear distribution pattern. Differential proteome analysis of Vero cells expressing BEND4 revealed that mutant BEND4 expression caused selective increase in reticulocalbin-1 and endoplasmic reticulum resident protein-29. Both proteins are associated with the endoplasmic reticulum and are primarily involved in protein processing and folding pathways. Any defect or stress in protein folding creates stress on cells and may cause chronic damage. This is the first study showing that pathogenic <i>BEND4</i> variants may lead to an infection-induced acute necrotizing encephalopathy as demonstrated in characteristic neuroimaging findings.
Collapse
|
20
|
Grand RS, Burger L, Gräwe C, Michael AK, Isbel L, Hess D, Hoerner L, Iesmantavicius V, Durdu S, Pregnolato M, Krebs AR, Smallwood SA, Thomä N, Vermeulen M, Schübeler D. BANP opens chromatin and activates CpG-island-regulated genes. Nature 2021; 596:133-137. [PMID: 34234345 DOI: 10.1038/s41586-021-03689-8] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 06/03/2021] [Indexed: 02/06/2023]
Abstract
The majority of gene transcripts generated by RNA polymerase II in mammalian genomes initiate at CpG island (CGI) promoters1,2, yet our understanding of their regulation remains limited. This is in part due to the incomplete information that we have on transcription factors, their DNA-binding motifs and which genomic binding sites are functional in any given cell type3-5. In addition, there are orphan motifs without known binders, such as the CGCG element, which is associated with highly expressed genes across human tissues and enriched near the transcription start site of a subset of CGI promoters6-8. Here we combine single-molecule footprinting with interaction proteomics to identify BTG3-associated nuclear protein (BANP) as the transcription factor that binds this element in the mouse and human genome. We show that BANP is a strong CGI activator that controls essential metabolic genes in pluripotent stem and terminally differentiated neuronal cells. BANP binding is repelled by DNA methylation of its motif in vitro and in vivo, which epigenetically restricts most binding to CGIs and accounts for differential binding at aberrantly methylated CGI promoters in cancer cells. Upon binding to an unmethylated motif, BANP opens chromatin and phases nucleosomes. These findings establish BANP as a critical activator of a set of essential genes and suggest a model in which the activity of CGI promoters relies on methylation-sensitive transcription factors that are capable of chromatin opening.
Collapse
Affiliation(s)
- Ralph S Grand
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Lukas Burger
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Cathrin Gräwe
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Alicia K Michael
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Luke Isbel
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Daniel Hess
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Leslie Hoerner
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | | | - Sevi Durdu
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marco Pregnolato
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Science, University of Basel, Basel, Switzerland
| | - Arnaud R Krebs
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Nicolas Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Dirk Schübeler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Science, University of Basel, Basel, Switzerland.
| |
Collapse
|
21
|
Visualising G-quadruplex DNA dynamics in live cells by fluorescence lifetime imaging microscopy. Nat Commun 2021; 12:162. [PMID: 33420085 PMCID: PMC7794231 DOI: 10.1038/s41467-020-20414-7] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 11/27/2020] [Indexed: 12/12/2022] Open
Abstract
Guanine rich regions of oligonucleotides fold into quadruple-stranded structures called G-quadruplexes (G4s). Increasing evidence suggests that these G4 structures form in vivo and play a crucial role in cellular processes. However, their direct observation in live cells remains a challenge. Here we demonstrate that a fluorescent probe (DAOTA-M2) in conjunction with fluorescence lifetime imaging microscopy (FLIM) can identify G4s within nuclei of live and fixed cells. We present a FLIM-based cellular assay to study the interaction of non-fluorescent small molecules with G4s and apply it to a wide range of drug candidates. We also demonstrate that DAOTA-M2 can be used to study G4 stability in live cells. Reduction of FancJ and RTEL1 expression in mammalian cells increases the DAOTA-M2 lifetime and therefore suggests an increased number of G4s in these cells, implying that FancJ and RTEL1 play a role in resolving G4 structures in cellulo. Direct observation of G-quadruplexes (G4s) in live cells is challenging. Here the authors report a method to identify G4s within the nuclei of live and fixed cells using a fluorescent probe combined with fluorescence lifetime imaging microscopy.
Collapse
|
22
|
Kong NR, Bassal MA, Tan HK, Kurland JV, Yong KJ, Young JJ, Yang Y, Li F, Lee JD, Liu Y, Wu CS, Stein A, Luo HR, Silberstein LE, Bulyk ML, Tenen DG, Chai L. Zinc Finger Protein SALL4 Functions through an AT-Rich Motif to Regulate Gene Expression. Cell Rep 2021; 34:108574. [PMID: 33406418 PMCID: PMC8197658 DOI: 10.1016/j.celrep.2020.108574] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/29/2020] [Accepted: 12/08/2020] [Indexed: 11/19/2022] Open
Abstract
The zinc finger transcription factor SALL4 is highly expressed in embryonic stem cells, downregulated in most adult tissues, but reactivated in many aggressive cancers. This unique expression pattern makes SALL4 an attractive therapeutic target. However, whether SALL4 binds DNA directly to regulate gene expression is unclear, and many of its targets in cancer cells remain elusive. Here, through an unbiased screen of protein binding microarray (PBM) and cleavage under targets and release using nuclease (CUT&RUN) experiments, we identify and validate the DNA binding domain of SALL4 and its consensus binding sequence. Combined with RNA sequencing (RNA-seq) analyses after SALL4 knockdown, we discover hundreds of new SALL4 target genes that it directly regulates in aggressive liver cancer cells, including genes encoding a family of histone 3 lysine 9-specific demethylases (KDMs). Taken together, these results elucidate the mechanism of SALL4 DNA binding and reveal pathways and molecules to target in SALL4-dependent tumors. In this paper, Kong et al. elucidate the DNA binding mechanisms of the transcription factor SALL4 and an epigenetic pathway that it regulates. Due to its important role in driving aggressive cancers, better understanding of SALL4 function will lead to strategies to target this protein in cancer.
Collapse
Affiliation(s)
- Nikki R Kong
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Mahmoud A Bassal
- Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Hong Kee Tan
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore 117599, Singapore
| | - Jesse V Kurland
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Kol Jia Yong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore; Department of Biochemistry, Yoon Loo Lin School of Medicine, National University of Singapore, Singapore 117599, Singapore
| | - John J Young
- Department of Biology, Simmons University, Boston, MA 02115, USA
| | - Yang Yang
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Fudong Li
- Hefei National Laboratory for Physical Sciences at Microscale, School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Jonathan D Lee
- Cancer Research Institute, Beth Israel Deaconess Medical Center, Boston, MA 02115, USA
| | - Yue Liu
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA
| | - Chan-Shuo Wu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore
| | - Alicia Stein
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hongbo R Luo
- Joint Program in Transfusion Medicine, Department of Laboratory Medicne, Children's Hospital Boston, Boston, MA 02115, USA
| | - Leslie E Silberstein
- Joint Program in Transfusion Medicine, Department of Laboratory Medicne, Children's Hospital Boston, Boston, MA 02115, USA
| | - Martha L Bulyk
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Daniel G Tenen
- Harvard Stem Cell Institute, Boston, MA 02115, USA; Cancer Science Institute of Singapore, National University of Singapore, Singapore 117599, Singapore.
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Boston, MA 02115, USA.
| |
Collapse
|
23
|
Lyu B, Dong Y, Kang J. A New Case of de novo Variant c.892C>T (p.Arg298Trp) in NACC1: A First Case Report From China. Front Pediatr 2021; 9:754261. [PMID: 34869110 PMCID: PMC8634650 DOI: 10.3389/fped.2021.754261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background: The nucleus accumbens associated 1 (NACC1) gene is a transcription factor member of the BTB/POZ family. A de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 may define a syndrome characterized by intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. Case Presentation: We report a new case with a neurodevelopmental disorder characterized by severe intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. Brain MRI reveals brain dysplasia. We observe a de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 gene in this case. Now, the child regularly goes to the hospital for rehabilitation training (once a month). Sodium Valproate (10 mg/kg/day) and Clobazam (10 mg/kg/day) are used in the treatment of epilepsy. A total of three articles were screened, and two papers were excluded. The search revealed one article related to a syndrome caused by a de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1; they screened the main clinical features of eight cases of a syndrome, which were summarized and analyzed. Conclusions: The NACC1 gene is a member of the BTB/POZ family of transcription factors. A de novo heterozygous c.892C>T (p.Arg298Trp) variant in the NACC1 may define a syndrome characterized by intellectual disability, infantile epilepsy, congenital cataract, and feeding difficulties. At present, there is no effective cure. In the future, we need more cases to determine the phenotype-genotype correlation of NACC1 variants. Many questions remain to be answered, and many challenges remain to be faced. Future transcriptional studies may further clarify this rare, recurrent variant, and could potentially lead to targeted therapies.
Collapse
Affiliation(s)
- Baiyu Lyu
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yan Dong
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Juan Kang
- Department of Pediatrics, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| |
Collapse
|
24
|
Nucleus Accumbens-Associated Protein 1 Binds DNA Directly through the BEN Domain in a Sequence-Specific Manner. Biomedicines 2020; 8:biomedicines8120608. [PMID: 33327466 PMCID: PMC7764960 DOI: 10.3390/biomedicines8120608] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/10/2020] [Accepted: 12/10/2020] [Indexed: 01/03/2023] Open
Abstract
Nucleus accumbens-associated protein 1 (NAC1) is a nuclear protein that harbors an amino-terminal BTB domain and a carboxyl-terminal BEN domain. NAC1 appears to play significant and diverse functions in cancer and stem cell biology. Here we demonstrated that the BEN domain of NAC1 is a sequence-specific DNA-binding domain. We selected the palindromic 6 bp motif ACATGT as a target sequence by using a PCR-assisted random oligonucleotide selection approach. The interaction between NAC1 and target DNA was characterized by gel shift assays, pull-down assays, isothermal titration calorimetry (ITC), chromatin-immunoprecipitation assays, and NMR chemical shifts perturbation (CSP). The solution NMR structure revealed that the BEN domain of human NAC-1 is composed of five conserved α helices and two short β sheets, with an additional hitherto unknown N-terminal α helix. In particular, ITC clarified that there are two sequential events in the titration of the BEN domain of NAC1 into the target DNA. The ITC results were further supported by CSP data and structure analyses. Furthermore, live cell photobleaching analyses revealed that the BEN domain of NAC1 alone was unable to interact with chromatin/other proteins in cells.
Collapse
|
25
|
Ueberschär M, Wang H, Zhang C, Kondo S, Aoki T, Schedl P, Lai EC, Wen J, Dai Q. BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila. Nat Commun 2019; 10:5700. [PMID: 31836703 PMCID: PMC6911014 DOI: 10.1038/s41467-019-13558-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 11/14/2019] [Indexed: 11/08/2022] Open
Abstract
The Drosophila genome encodes three BEN-solo proteins including Insensitive (Insv), Elba1 and Elba2 that possess activities in transcriptional repression and chromatin insulation. A fourth protein-Elba3-bridges Elba1 and Elba2 to form an ELBA complex. Here, we report comprehensive investigation of these proteins in Drosophila embryos. We assess common and distinct binding sites for Insv and ELBA and their genetic interdependencies. While Elba1 and Elba2 binding generally requires the ELBA complex, Elba3 can associate with chromatin independently of Elba1 and Elba2. We further demonstrate that ELBA collaborates with other insulators to regulate developmental patterning. Finally, we find that adjacent gene pairs separated by an ELBA bound sequence become less differentially expressed in ELBA mutants. Transgenic reporters confirm the insulating activity of ELBA- and Insv-bound sites. These findings define ELBA and Insv as general insulator proteins in Drosophila and demonstrate the functional importance of insulators to partition transcription units.
Collapse
Affiliation(s)
- Malin Ueberschär
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Huazhen Wang
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Chun Zhang
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- State Key Laboratory of Developmental Biology of Freshwater Fish College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shu Kondo
- Laboratory of Invertebrate Genetics, National Institute of Genetics, Mishima, Japan
| | - Tsutomu Aoki
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Paul Schedl
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA
| | - Eric C Lai
- Department of Developmental Biology, Memorial Sloan Kettering Institute, New York, NY, USA.
| | - Jiayu Wen
- Department of Genome Sciences, The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
| | - Qi Dai
- Department of Molecular Bioscience, the Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
| |
Collapse
|
26
|
Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003814. [PMID: 31160355 PMCID: PMC6549554 DOI: 10.1101/mcs.a003814] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/06/2019] [Indexed: 01/05/2023] Open
Abstract
Pancreatic neuroendocrine neoplasms (PanNENs) represent a minority of pancreatic neoplasms that exhibit variability in prognosis. Ongoing mutational analyses of PanNENs have found recurrent abnormalities in chromatin remodeling genes (e.g., DAXX and ATRX), and mTOR pathway genes (e.g., TSC2, PTEN PIK3CA, and MEN1), some of which have relevance to patients with related familial syndromes. Most recently, grade 3 PanNENs have been divided into two groups based on differentiation, creating a new group of well-differentiated grade 3 neuroendocrine tumors (PanNETs) that have had a limited whole-genome level characterization to date. In a patient with a metastatic well-differentiated grade 3 PanNET, our study utilized whole-genome sequencing of liver metastases for the comparative analysis and detection of single-nucleotide variants, insertions and deletions, structural variants, and copy-number variants, with their biologic relevance confirmed by RNA sequencing. We found that this tumor most notably exhibited a TSC1-disrupting fusion, showed a novel CHD7–BEND2 fusion, and lacked any somatic variants in ATRX, DAXX, and MEN1.
Collapse
|
27
|
Kang T, Jensen P, Solovyeva V, Brewer JR, Larsen MR. Dynamic Changes in the Protein Localization in the Nuclear Environment in Pancreatic β-Cell after Brief Glucose Stimulation. J Proteome Res 2018. [PMID: 29518335 DOI: 10.1021/acs.jproteome.7b00930] [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] [Indexed: 02/01/2023]
Abstract
Characterization of molecular mechanisms underlying pancreatic β-cell function in relation to glucose-stimulated insulin secretion is incomplete, especially with respect to global response in the nuclear environment. We focus on the characterization of proteins in the nuclear environment of β-cells after brief, high glucose stimulation. We compared purified nuclei derived from β-cells stimulated with 17 mM glucose for 0, 2, and 5 min using quantitative proteomics, a time frame that most likely does not result in translation of new protein in the cell. Among the differentially regulated proteins, we identified 20 components of the nuclear organization processes, including nuclear pore organization, ribonucleoprotein complex, and pre-mRNA transcription. We found alteration of the nuclear pore complex, together with calcium/calmodulin-binding chaperones that facilitate protein and RNA import or export to/from the nucleus to the cytoplasm. Putative insulin mRNA transcription-associated factors were identified among the regulated proteins, and they were cross-validated by Western blotting and confocal immunofluorescence imaging. Collectively, our data suggest that protein translocation between the nucleus and the cytoplasm is an important process, highly involved in the initial molecular mechanism underlying glucose-stimulated insulin secretion in pancreatic β-cells.
Collapse
Affiliation(s)
- Taewook Kang
- Protein Research Group, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Pia Jensen
- Protein Research Group, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Vita Solovyeva
- MEMPHYS-Centre for Biomembrane Physics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Jonathan R Brewer
- MEMPHYS-Centre for Biomembrane Physics, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Martin R Larsen
- Protein Research Group, Department of Biochemistry and Molecular Biology , University of Southern Denmark , DK-5230 Odense M , Denmark
| |
Collapse
|
28
|
Burford A, Mackay A, Popov S, Vinci M, Carvalho D, Clarke M, Izquierdo E, Avery A, Jacques TS, Ingram WJ, Moore AS, Frawley K, Hassall TE, Robertson T, Jones C. The ten-year evolutionary trajectory of a highly recurrent paediatric high grade neuroepithelial tumour with MN1:BEND2 fusion. Sci Rep 2018; 8:1032. [PMID: 29348602 PMCID: PMC5773598 DOI: 10.1038/s41598-018-19389-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Accepted: 12/29/2017] [Indexed: 01/01/2023] Open
Abstract
Astroblastomas are rare brain tumours which predominate in children and young adults, and have a controversial claim as a distinct entity, with no established WHO grade. Reports suggest a better outcome than high grade gliomas, though they frequently recur. Recently, they have been described to overlap with a newly-discovered group of tumours described as'high grade neuroepithelial tumour with MN1 alteration' (CNS HGNET-MN1), defined by global methylation patterns and strongly associated with gene fusions targeting MN1. We have studied a unique case of astroblastoma arising in a 6 year-old girl, with multiple recurrences over a period of 10 years, with the pathognomonic MN1:BEND2 fusion. Exome sequencing allowed for a phylogenetic reconstruction of tumour evolution, which when integrated with clinical, pathological and radiological data provide for a detailed understanding of disease progression, with initial treatment driving tumour dissemination along four distinct trajectories. Infiltration of distant sites was associated with a later genome doubling, whilst there was evidence of convergent evolution of different lesions acquiring distinct alterations targeting NF-κB. These data represent an unusual opportunity to understand the evolutionary history of a highly recurrent childhood brain tumour, and provide novel therapeutic targets for astroblastoma/CNS HGNET-MN1.
Collapse
Affiliation(s)
- Anna Burford
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Alan Mackay
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Sergey Popov
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
- Department of Pathology, Cardiff University School of Medicine, Cardiff, UK
| | - Maria Vinci
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
- Bambino Gesù Children's Hospital, Rome, Italy
| | - Diana Carvalho
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Matthew Clarke
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Elisa Izquierdo
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK
- Division of Molecular Pathology, Institute of Cancer Research, London, UK
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK
| | - Aimee Avery
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Department of Histopathology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
| | - Wendy J Ingram
- UQ Child Health Research Centre, The University of Queensland, Brisbane, Australia
| | - Andrew S Moore
- The University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, Australia
- Oncology Services Group, Children's Health Queensland Hospital and Health Service, Brisbane, Australia
- Medical Imaging and Nuclear Medicine, Children's Health Queensland Hospital and Health Service, Brisbane, Australia
| | - Kieran Frawley
- Medical Imaging and Nuclear Medicine, Children's Health Queensland Hospital and Health Service, Brisbane, Australia
| | - Timothy E Hassall
- Oncology Services Group, Children's Health Queensland Hospital and Health Service, Brisbane, Australia
| | - Thomas Robertson
- Pathology Queensland, Royal Brisbane and Women's Hospital, and School of Medicine, University of Queensland, Brisbane, Australia
| | - Chris Jones
- Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, Institute of Cancer Research, London, UK.
- Division of Cancer Therapeutics, Institute of Cancer Research, London, UK.
| |
Collapse
|
29
|
Pitchai GP, Kaulich M, Bizard AH, Mesa P, Yao Q, Sarlos K, Streicher WW, Nigg EA, Montoya G, Hickson ID. A novel TPR-BEN domain interaction mediates PICH-BEND3 association. Nucleic Acids Res 2017; 45:11413-11424. [PMID: 28977671 PMCID: PMC5737856 DOI: 10.1093/nar/gkx792] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/31/2017] [Indexed: 12/20/2022] Open
Abstract
PICH is a DNA translocase required for the maintenance of chromosome stability in human cells. Recent data indicate that PICH co-operates with topoisomerase IIα to suppress pathological chromosome missegregation through promoting the resolution of ultra-fine anaphase bridges (UFBs). Here, we identify the BEN domain-containing protein 3 (BEND3) as an interaction partner of PICH in human cells in mitosis. We have purified full length PICH and BEND3 and shown that they exhibit a functional biochemical interaction in vitro. We demonstrate that the PICH–BEND3 interaction occurs via a novel interface between a TPR domain in PICH and a BEN domain in BEND3, and have determined the crystal structure of this TPR–BEN complex at 2.2 Å resolution. Based on the structure, we identified amino acids important for the TPR–BEN domain interaction, and for the functional interaction of the full-length proteins. Our data reveal a proposed new function for BEND3 in association with PICH, and the first example of a specific protein–protein interaction mediated by a BEN domain.
Collapse
Affiliation(s)
- Ganesha P Pitchai
- Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark.,Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Manuel Kaulich
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Anna H Bizard
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Pablo Mesa
- Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Qi Yao
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Kata Sarlos
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Werner W Streicher
- Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Erich A Nigg
- Biozentrum, University of Basel, CH-4056, Basel, Switzerland
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research, Protein Structure & Function Programme, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Ian D Hickson
- Center for Chromosome Stability and Center for Healthy Aging, Department of Cellular and Molecular Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| |
Collapse
|
30
|
Lin RK, Hung WY, Huang YF, Chang YJ, Lin CH, Chen WY, Chiu SF, Chang SC, Tsai SF. Hypermethylation of BEND5 contributes to cell proliferation and is a prognostic marker of colorectal cancer. Oncotarget 2017; 8:113431-113443. [PMID: 29371920 PMCID: PMC5768337 DOI: 10.18632/oncotarget.22266] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 05/10/2017] [Indexed: 01/05/2023] Open
Abstract
Aberrant hypermethylation of CpG islands in tumor suppressor genes (TSGs) contributes to colorectal tumorigenesis. To identify new colorectal cancer (CRC) screening marker, we investigated DNA methylation alterations in novel TSGs. Using HumanMethylation450 BeadChip arrays, CpG regions in BEND5 were the most highly methylated among all genomic regions in 26 colorectal tumors compared to paired non-neoplastic tissues from a Taiwan cohort. Therefore, BEND5 was selected for further analysis. Quantitative methylation-specific real-time PCR revealed that 86.7% (117/135) of CRC patients exhibited hypermethylated BEND5. Real-time reverse transcription PCR identified that BEND5 mRNA expression was downregulated in 68% (32/47) of the analyzed samples. BEND5 hypermethylation was associated with poor overall survival (OS) in Taiwan patients with early-stage CRC (P = 0.037). In a CRC tissue set from South Korea, OS was higher in patients with high BEND5 protein expression than in those with low BEND5 protein expression (P = 0.037) by using immunohistochemistry assays. Consistently, BEND5 hypermethylation was associated with poor OS in patients with early-stage CRC in The Cancer Genome Atlas (TCGA) data set (P = 0.003). Multivariate Cox proportional hazards regression analysis further supported that hypermethylation of BEND5 genes was significantly associated with OS in Taiwan and TCGA CRC patients (P = 0.023 and 0.033, respectively). Finally, the cell model assay with transient transfection of BEND5 or si-BEND5 knockdown indicated that BEND5 inhibited cancer cell proliferation. In conclusion, epigenetic alteration in the candidate TSG BEND5 contributes to colorectal cancer development and is a prognostic marker of CRC.
Collapse
Affiliation(s)
- Ruo-Kai Lin
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, R.O.C.,Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, Taipei, Taiwan, R.O.C.,PH.D Program for Clinical Drug Development of Chinese Herbal Medicine, Ph.D Program in Biotechnology Research and Development, College of Pharmacy, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Wan-Yu Hung
- Master Program for Clinical Pharmacogenomics and Pharmacoproteomics, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Yu-Fang Huang
- Graduate Institute of Pharmacognosy, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Yu-Jia Chang
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Chien-Hsing Lin
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| | - Wei-Yu Chen
- Department of Pathology, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan, R.O.C.,Department of Pathology, Wan Fang Hospital, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Shih-Feng Chiu
- Professional Master Program in Pharmaceutics and Biotechnology, Taipei Medical University, Taipei, Taiwan, R.O.C
| | - Shih-Ching Chang
- Division of Colon and Rectal Surgery, Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan, R.O.C
| | - Shih-Feng Tsai
- Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli, Taiwan
| |
Collapse
|
31
|
Sathyan KM, Fachinetti D, Foltz DR. α-amino trimethylation of CENP-A by NRMT is required for full recruitment of the centromere. Nat Commun 2017; 8:14678. [PMID: 28266506 PMCID: PMC5343448 DOI: 10.1038/ncomms14678] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 01/18/2017] [Indexed: 02/07/2023] Open
Abstract
Centromeres are unique chromosomal domains that control chromosome segregation, and are epigenetically specified by the presence of the CENP-A containing nucleosomes. CENP-A governs centromere function by recruiting the constitutive centromere associated network (CCAN) complex. The features of the CENP-A nucleosome necessary to distinguish centromeric chromatin from general chromatin are not completely understood. Here we show that CENP-A undergoes α-amino trimethylation by the enzyme NRMT in vivo. We show that α-amino trimethylation of the CENP-A tail contributes to cell survival. Loss of α-amino trimethylation causes a reduction in the CENP-T and CENP-I CCAN components at the centromere and leads to lagging chromosomes and spindle pole defects. The function of p53 alters the response of cells to defects associated with decreased CENP-A methylation. Altogether we show an important functional role for α-amino trimethylation of the CENP-A nucleosome in maintaining centromere function and faithful chromosomes segregation.
Collapse
Affiliation(s)
- Kizhakke M Sathyan
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA
| | - Daniele Fachinetti
- Department of Cell Biology and Cancer, Institut Curie, PSL Research University, CNRS, UMR 144, 26 rue d'Ulm, Paris 75005, France
| | - Daniel R Foltz
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia 22908, USA.,Northwestern University, Feinberg School of Medicine, Department of Biochemistry and Molecular Genetics, Chicago, Illinois 60611, USA.,Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
| |
Collapse
|
32
|
Teferi WM, Desaulniers MA, Noyce RS, Shenouda M, Umer B, Evans DH. The vaccinia virus K7 protein promotes histone methylation associated with heterochromatin formation. PLoS One 2017; 12:e0173056. [PMID: 28257484 PMCID: PMC5336242 DOI: 10.1371/journal.pone.0173056] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/14/2017] [Indexed: 12/12/2022] Open
Abstract
It has been well established that many vaccinia virus proteins suppress host antiviral pathways by targeting the transcription of antiviral proteins, thus evading the host innate immune system. However, whether viral proteins have an effect on the host’s overall cellular transcription is less understood. In this study we investigated the regulation of heterochromatin during vaccinia virus infection. Heterochromatin is a highly condensed form of chromatin that is less transcriptionally active and characterized by methylation of histone proteins. We examined the change in methylation of two histone proteins, H3 and H4, which are major markers of heterochromatin, during the course of viral infection. Using immunofluorescence microscopy and flow cytometry we were able to track the overall change in the methylated levels of H3K9 and H4K20. Our results suggest that there is significant increase in methylation of H3K9 and H4K20 during Orthopoxviruses infection compared to mock-infected cells. However, this effect was not seen when we infected cells with Leporipoxviruses. We further screened several vaccinia virus single and multi-gene deletion mutant and identified the vaccinia virus gene K7R as a contributor to the increase in cellular histone methylation during infection.
Collapse
Affiliation(s)
- Wondimagegnehu M. Teferi
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Megan A. Desaulniers
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Ryan S. Noyce
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Mira Shenouda
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - Brittany Umer
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
| | - David H. Evans
- Department of Medical Microbiology & Immunology, Li Ka Shing Institute of Virology, University of Alberta, Edmonton, Alberta, Canada
- * E-mail:
| |
Collapse
|
33
|
Sumoylation as an Integral Mechanism in Bacterial Infection and Disease Progression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 963:389-408. [DOI: 10.1007/978-3-319-50044-7_22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
34
|
Unnikrishnan A, Guan YF, Huang Y, Beck D, Thoms JAI, Peirs S, Knezevic K, Ma S, de Walle IV, de Jong I, Ali Z, Zhong L, Raftery MJ, Taghon T, Larsson J, MacKenzie KL, Van Vlierberghe P, Wong JWH, Pimanda JE. A quantitative proteomics approach identifies ETV6 and IKZF1 as new regulators of an ERG-driven transcriptional network. Nucleic Acids Res 2016; 44:10644-10661. [PMID: 27604872 PMCID: PMC5159545 DOI: 10.1093/nar/gkw804] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Revised: 08/31/2016] [Accepted: 09/02/2016] [Indexed: 12/14/2022] Open
Abstract
Aberrant stem cell-like gene regulatory networks are a feature of leukaemogenesis. The ETS-related gene (ERG), an important regulator of normal haematopoiesis, is also highly expressed in T-ALL and acute myeloid leukaemia (AML). However, the transcriptional regulation of ERG in leukaemic cells remains poorly understood. In order to discover transcriptional regulators of ERG, we employed a quantitative mass spectrometry-based method to identify factors binding the 321 bp ERG +85 stem cell enhancer region in MOLT-4 T-ALL and KG-1 AML cells. Using this approach, we identified a number of known binders of the +85 enhancer in leukaemic cells along with previously unknown binders, including ETV6 and IKZF1. We confirmed that ETV6 and IKZF1 were also bound at the +85 enhancer in both leukaemic cells and in healthy human CD34+ haematopoietic stem and progenitor cells. Knockdown experiments confirmed that ETV6 and IKZF1 are transcriptional regulators not just of ERG, but also of a number of genes regulated by a densely interconnected network of seven transcription factors. At last, we show that ETV6 and IKZF1 expression levels are positively correlated with expression of a number of heptad genes in AML and high expression of all nine genes confers poorer overall prognosis.
Collapse
MESH Headings
- Base Sequence
- Binding Sites
- Cell Line, Tumor
- Consensus Sequence
- Enhancer Elements, Genetic
- Gene Expression Regulation, Leukemic
- Gene Regulatory Networks
- Humans
- Ikaros Transcription Factor/physiology
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Prognosis
- Proportional Hazards Models
- Protein Binding
- Proteome
- Proteomics
- Proto-Oncogene Proteins c-ets/physiology
- Repressor Proteins/physiology
- Transcription, Genetic
- Transcriptional Regulator ERG/physiology
- ETS Translocation Variant 6 Protein
Collapse
Affiliation(s)
- Ashwin Unnikrishnan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yi F Guan
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Yizhou Huang
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Dominik Beck
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Center for Medical Genetics, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Julie A I Thoms
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Sofie Peirs
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Kathy Knezevic
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Shiyong Ma
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - Inge V de Walle
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Ineke de Jong
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Zara Ali
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Mark J Raftery
- Bioanalytical Mass Spectrometry Facility, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Tom Taghon
- Department of Clinical Chemistry, Microbiology and Immunology, Ghent University, De Pintelaan 185 9000 Ghent, Belgium
| | - Jonas Larsson
- Division of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, SE-221 00, Lund, Sweden
| | - Karen L MacKenzie
- Children's Cancer Institute Australia, Sydney, New South Wales, 2052 Australia
| | - Pieter Van Vlierberghe
- Centre for Health Technologies and the School of Software, University of Technology, Sydney, 2007, Australia
| | - Jason W H Wong
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
| | - John E Pimanda
- Adult Cancer Program, Prince of Wales Clinical School, Lowy Cancer Research Centre, University of New South Wales, Sydney, 2052, Australia
- Department of Haematology, Prince of Wales Hospital, Sydney, 2031, Australia
| |
Collapse
|
35
|
Pitchai GP, Hickson ID, Streicher W, Montoya G, Mesa P. Characterization of the NTPR and BD1 interacting domains of the human PICH-BEND3 complex. Acta Crystallogr F Struct Biol Commun 2016; 72:646-51. [PMID: 27487930 PMCID: PMC4973307 DOI: 10.1107/s2053230x16010724] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 07/01/2016] [Indexed: 11/10/2022] Open
Abstract
Chromosome integrity depends on DNA structure-specific processing complexes that resolve DNA entanglement between sister chromatids. If left unresolved, these entanglements can generate either chromatin bridging or ultrafine DNA bridging in the anaphase of mitosis. These bridge structures are defined by the presence of the PICH protein, which interacts with the BEND3 protein in mitosis. To obtain structural insights into PICH-BEND3 complex formation at the atomic level, their respective NTPR and BD1 domains were cloned, overexpressed and crystallized using 1.56 M ammonium sulfate as a precipitant at pH 7.0. The protein complex readily formed large hexagonal crystals belonging to space group P6122, with unit-cell parameters a = b = 47.28, c = 431.58 Å and with one heterodimer in the asymmetric unit. A complete multiwavelength anomalous dispersion (MAD) data set extending to 2.2 Å resolution was collected from a selenomethionine-labelled crystal at the Swiss Light Source.
Collapse
Affiliation(s)
- Ganesha P. Pitchai
- Protein Structure and Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Ian D. Hickson
- Department of Cellular and Molecular Medicine, Center for Chromosome Stability and Center for Healthy Aging, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Werner Streicher
- Protein Structure and Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Guillermo Montoya
- Protein Structure and Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| | - Pablo Mesa
- Protein Structure and Function Programme, Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3b, 2200 Copenhagen, Denmark
| |
Collapse
|
36
|
Hiragami-Hamada K, Soeroes S, Nikolov M, Wilkins B, Kreuz S, Chen C, De La Rosa-Velázquez IA, Zenn HM, Kost N, Pohl W, Chernev A, Schwarzer D, Jenuwein T, Lorincz M, Zimmermann B, Walla PJ, Neumann H, Baubec T, Urlaub H, Fischle W. Dynamic and flexible H3K9me3 bridging via HP1β dimerization establishes a plastic state of condensed chromatin. Nat Commun 2016; 7:11310. [PMID: 27090491 PMCID: PMC4838890 DOI: 10.1038/ncomms11310] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 03/13/2016] [Indexed: 12/12/2022] Open
Abstract
Histone H3 trimethylation of lysine 9 (H3K9me3) and proteins of the heterochromatin protein 1 (HP1) family are hallmarks of heterochromatin, a state of compacted DNA essential for genome stability and long-term transcriptional silencing. The mechanisms by which H3K9me3 and HP1 contribute to chromatin condensation have been speculative and controversial. Here we demonstrate that human HP1β is a prototypic HP1 protein exemplifying most basal chromatin binding and effects. These are caused by dimeric and dynamic interaction with highly enriched H3K9me3 and are modulated by various electrostatic interfaces. HP1β bridges condensed chromatin, which we postulate stabilizes the compacted state. In agreement, HP1β genome-wide localization follows H3K9me3-enrichment and artificial bridging of chromatin fibres is sufficient for maintaining cellular heterochromatic conformation. Overall, our findings define a fundamental mechanism for chromatin higher order structural changes caused by HP1 proteins, which might contribute to the plastic nature of condensed chromatin. Heterochromatin protein 1 (HP1), including HP1 α, β and γ, is a family of non-histone chromatin factors thought to be involved in chromatin organization. Here, the authors show that dimeric HP1β interacts dynamically with H3K9me3, a hallmark of heterochromatin, and bridges condensed chromatin.
Collapse
Affiliation(s)
- Kyoko Hiragami-Hamada
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Szabolcs Soeroes
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Miroslav Nikolov
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Bryan Wilkins
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Sarah Kreuz
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Carol Chen
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | - Inti A De La Rosa-Velázquez
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Hans Michael Zenn
- Biaffin GmbH &Co KG, Heinrich-Plett Strasse 40, 34132 Kassel, Germany
| | - Nils Kost
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Wiebke Pohl
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Hoppe-Seyler-Str. 4, 72076 Tübingen, Germany
| | - Thomas Jenuwein
- Department of Epigenetics, Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany
| | - Matthew Lorincz
- Department of Medical Genetics, Life Sciences Institute, The University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z3
| | | | - Peter Jomo Walla
- Biomolecular Spectroscopy and Single-Molecule Detection, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Department of Biophysical Chemistry, Technische Universität Braunschweig, Hans-Sommerstr. 10, 38106 Braunschweig, Germany
| | - Heinz Neumann
- Applied Synthetic Biology, Institute for Microbiology and Genetics, Georg-August University Göttingen, 37077 Göttingen, Germany
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, Robert-Koch-Strasse 40, 37075 Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, Göttingen, Am Fassberg 11, 37077, Germany
| |
Collapse
|
37
|
Khan A, Prasanth SG. BEND3 mediates transcriptional repression and heterochromatin organization. Transcription 2015; 6:102-5. [PMID: 26507581 DOI: 10.1080/21541264.2015.1100228] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Transcription repression plays a central role in gene regulation. Transcription repressors utilize diverse strategies to mediate transcriptional repression. We have recently demonstrated that BEND3 (BANP, E5R and Nac1 domain) protein represses rDNA transcription by stabilizing a NoRC component. We discuss the role of BEND3 as a global regulator of gene expression and propose a model whereby BEND3 associates with chromatin remodeling complexes to modulate gene expression and heterochromatin organization.
Collapse
Affiliation(s)
- Abid Khan
- a Department of Cell and Developmental Biology ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| | - Supriya G Prasanth
- a Department of Cell and Developmental Biology ; University of Illinois at Urbana-Champaign ; Urbana , IL USA
| |
Collapse
|
38
|
Aghajanirefah A, Nguyen LN, Ohadi M. BEND3 is involved in the human-specific repression of calreticulin: Implication for the evolution of higher brain functions in human. Gene 2015; 576:577-80. [PMID: 26481236 DOI: 10.1016/j.gene.2015.10.040] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/01/2015] [Accepted: 10/15/2015] [Indexed: 01/27/2023]
Abstract
Recent emerging evidence indicates that changes in gene expression levels are linked to human evolution. We have previously reported a human-specific nucleotide in the promoter sequence of the calreticulin (CALR) gene at position -220C, which is the site of action of valproic acid. Reversion of this nucleotide to the ancestral A-allele has been detected in patients with degrees of deficit in higher brain cognitive functions. This mutation has since been reported in the 1000 genomes database at an approximate frequency of <0.0004 in humans (rs138452745). In the study reported here, we present update on the status of rs138452745 across evolution, based on the Ensembl and NCBI databases. The DNA pulldown assay was also used to identify the proteins binding to the C- and A-alleles, using two cell lines, SK-N-BE and HeLa. Consistent with our previous findings, the C-allele is human-specific, and the A-allele is the rule across all other species (N=38). This nucleotide resides in a block of 12-nucleotides that is strictly conserved across evolution. The DNA pulldown experiments revealed that in both SK-N-BE and HeLa cells, the transcription repressor BEN domain containing 3 (BEND3) binds to the human-specific C-allele, whereas the nuclear factor I (NFI) family members, NF1A, B, C, and X, specifically bind to the ancestral A-allele. This binding pattern is consistent with a previously reported decreased promoter activity of the C-allele vs. the A-allele. We propose that there is a link between binding of BEND3 to the CALR rs138452745 C-allele and removal of NFI binding site from this nucleotide, and the evolution of human-specific higher brain functions. To our knowledge, CALR rs138452745 is the first instance of enormous nucleotide conservation across evolution, except in the human species.
Collapse
Affiliation(s)
- A Aghajanirefah
- Department of Molecular Biology, Faculty of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - L N Nguyen
- Department of Molecular Biology, Faculty of Science and Medicine, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - M Ohadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran.
| |
Collapse
|
39
|
Abstract
Covalent linkage to members of the small ubiquitin-like (SUMO) family of proteins is an important mechanism by which the functions of many cellular proteins are regulated. Sumoylation has roles in the control of protein stability, activity and localization, and is involved in the regulation of transcription, gene expression, chromatin structure, nuclear transport and RNA metabolism. Sumoylation is also linked, both positively and negatively, with the replication of many different viruses both in terms of modification of viral proteins and modulation of sumoylated cellular proteins that influence the efficiency of infection. One prominent example of the latter is the widespread reduction in the levels of cellular sumoylated species induced by herpes simplex virus type 1 (HSV-1) ubiquitin ligase ICP0. This activity correlates with relief from intrinsic immunity antiviral defence mechanisms. Previous work has shown that ICP0 is selective in substrate choice, with some sumoylated proteins such the promyelocytic leukemia protein PML being extremely sensitive, while RanGAP is completely resistant. Here we present a comprehensive proteomic analysis of changes in the cellular SUMO2 proteome during HSV-1 infection. Amongst the 877 potentially sumoylated species detected, we identified 124 whose abundance was decreased by a factor of 3 or more by the virus, several of which were validated by western blot and expression analysis. We found many previously undescribed substrates of ICP0 whose degradation occurs by a range of mechanisms, influenced or not by sumoylation and/or the SUMO2 interaction motif within ICP0. Many of these proteins are known or are predicted to be involved in the regulation of transcription, chromatin assembly or modification. These results present novel insights into mechanisms and host cell proteins that might influence the efficiency of HSV-1 infection. Proteins are subject to many types of modification that regulate their functions and which are applied after their initial synthesis in the cell. One such modification is known as sumoylation, the covalent linkage of a small ubiquitin-like protein to a wide variety of substrate proteins. Sumoylation is involved in the regulation of many cellular pathways, including transcription, DNA repair, chromatin modification and defence to viral infections. Several viruses have connections with sumoylation, either through modification of their own proteins or in changing the sumoylation status of cellular proteins in ways that may be beneficial for infection. Herpes simplex virus type 1 (HSV-1) causes a widespread reduction in uncharacterized sumoylated cellular protein species, an effect that is caused by one of its key regulatory proteins (ICP0), which also induces the degradation of a number of repressive cellular proteins and thereby stimulates efficient infection. This study describes a comprehensive analysis of cellular proteins whose sumoylation status is altered by HSV-1 infection. Of 877 putative cellular sumoylation substrates, we found 124 whose sumoylation status reduces at least three-fold during infection. We validated the behavior of several such proteins and identified amongst them several novel targets of ICP0 activity with predicted repressive properties.
Collapse
|
40
|
BEND3 represses rDNA transcription by stabilizing a NoRC component via USP21 deubiquitinase. Proc Natl Acad Sci U S A 2015; 112:8338-43. [PMID: 26100909 DOI: 10.1073/pnas.1424705112] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Ribosome biogenesis dictates the translational capacity of cells. Several mechanisms establish and maintain transcriptional output from eukaryotic ribosomal DNA (rDNA) loci. rDNA silencing is one such mechanism that ensures the inactivity and hence the maintenance of a silenced state of a subset of rRNA gene copies. Whereas oncogenic agents stimulate rRNA gene transcription, tumor suppressors decrease rRNA gene transcription. We demonstrate in mammalian cells that BANP, E5R, and Nac1 (BEN) domain 3 (BEND3), a quadruple BEN domain-containing protein, localizes in nucleoli and binds to ribosomal RNA gene promoters to help repress rRNA genes. Loss of BEND3 increases histone H3K4 trimethylation and, correspondingly, decreases rDNA promoter DNA methylation, consistent with a role for BEND3 in rDNA silencing. BEND3 associates with the nucleolar-remodeling complex (NoRC), and SUMOylated BEND3 stabilizes NoRC component TTF-1-interacting protein 5 via association with ubiquitin specific protease 21 (USP21) debiquitinase. Our results provide mechanistic insights into how the novel rDNA transcription repressor BEND3 acts together with NoRC to actively coordinate the establishment of rDNA silencing.
Collapse
|
41
|
Dai Q, Ren A, Westholm JO, Duan H, Patel DJ, Lai EC. Common and distinct DNA-binding and regulatory activities of the BEN-solo transcription factor family. Genes Dev 2015; 29:48-62. [PMID: 25561495 PMCID: PMC4281564 DOI: 10.1101/gad.252122.114] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The BEN domain is recognized as a new class of conserved DNA-binding domain. The fly genome encodes three proteins that bear only a single BEN domain (“BEN-solo” factors); namely, Insensitive (Insv), Bsg25A (Elba1), and CG9883 (Elba2). Dai et al. identify both distinct and overlapping functional properties of these three Drosophila BEN-solo proteins, introducing unexpected complexity in their contributions to gene regulation and development. Recently, the BEN (BANP, E5R, and NAC1) domain was recognized as a new class of conserved DNA-binding domain. The fly genome encodes three proteins that bear only a single BEN domain (“BEN-solo” factors); namely, Insensitive (Insv), Bsg25A (Elba1), and CG9883 (Elba2). Insv homodimers preferentially bind CCAATTGG palindromes throughout the genome to mediate transcriptional repression, whereas Bsg25A and Elba2 heterotrimerize with their obligate adaptor, Elba3 (i.e., the ELBA complex), to recognize a CCAATAAG motif in the Fab-7 insulator. While these data suggest distinct DNA-binding properties of BEN-solo proteins, we performed reporter assays that indicate that both Bsg25A and Elba2 can individually recognize Insv consensus sites efficiently. We confirmed this by solving the structure of Bsg25A complexed to the Insv site, which showed that key aspects of the BEN:DNA recognition strategy are similar between these proteins. We next show that both Insv and ELBA proteins are competent to mediate transcriptional repression via Insv consensus sequences but that the ELBA complex appears to be selective for the ELBA site. Reciprocally, genome-wide analysis reveals that Insv exhibits significant cobinding to class I insulator elements, indicating that it may also contribute to insulator function. Indeed, we observed abundant Insv binding within the Hox complexes with substantial overlaps with class I insulators, many of which bear Insv consensus sites. Moreover, Insv coimmunoprecipitates with the class I insulator factor CP190. Finally, we observed that Insv harbors exclusive activity among fly BEN-solo factors with respect to regulation of Notch-mediated cell fate choices in the peripheral nervous system. This in vivo activity is recapitulated by BEND6, a mammalian BEN-solo factor that conserves the Notch corepressor function of Insv but not its capacity to bind Insv consensus sites. Altogether, our data define an array of common and distinct biochemical and functional properties of this new family of transcription factors.
Collapse
Affiliation(s)
- Qi Dai
- Department of Developmental Biology
| | - Aiming Ren
- Department of Structural Biology, Sloan-Kettering Institute New York, New York 10065, USA
| | | | | | - Dinshaw J Patel
- Department of Structural Biology, Sloan-Kettering Institute New York, New York 10065, USA
| | | |
Collapse
|
42
|
Shiheido H, Shimizu J. Basic amino acid residues located in the N-terminal region of BEND3 are essential for its nuclear localization. Biochem Biophys Res Commun 2015; 457:589-94. [DOI: 10.1016/j.bbrc.2015.01.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 01/09/2015] [Indexed: 12/31/2022]
|
43
|
Saksouk N, Barth TK, Ziegler-Birling C, Olova N, Nowak A, Rey E, Mateos-Langerak J, Urbach S, Reik W, Torres-Padilla ME, Imhof A, Déjardin J, Simboeck E. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Mol Cell 2014; 56:580-94. [PMID: 25457167 DOI: 10.1016/j.molcel.2014.10.001] [Citation(s) in RCA: 159] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 08/22/2014] [Accepted: 09/30/2014] [Indexed: 11/25/2022]
Abstract
Constitutive heterochromatin is typically defined by high levels of DNA methylation and H3 lysine 9 trimethylation (H3K9Me3), whereas facultative heterochromatin displays DNA hypomethylation and high H3 lysine 27 trimethylation (H3K27Me3). The two chromatin types generally do not coexist at the same loci, suggesting mutual exclusivity. During development or in cancer, pericentromeric regions can adopt either epigenetic state, but the switching mechanism is unknown. We used a quantitative locus purification method to characterize changes in pericentromeric chromatin-associated proteins in mouse embryonic stem cells deficient for either the methyltransferases required for DNA methylation or H3K9Me3. DNA methylation controls heterochromatin architecture and inhibits Polycomb recruitment. BEND3, a protein enriched on pericentromeric chromatin in the absence of DNA methylation or H3K9Me3, allows Polycomb recruitment and H3K27Me3, resulting in a redundant pathway to generate repressive chromatin. This suggests that BEND3 is a key factor in mediating a switch from constitutive to facultative heterochromatin.
Collapse
Affiliation(s)
- Nehmé Saksouk
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Teresa K Barth
- Munich Centre of Integrated Protein Science and Adolf Butenandt Institute, Group, Ludwig-Maximillians University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Celine Ziegler-Birling
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France
| | - Nelly Olova
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | - Agnieszka Nowak
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Elodie Rey
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Julio Mateos-Langerak
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Serge Urbach
- Functional Proteomics Facility, Institute of Functional Genomics, 141 rue de la Cardonille, 34000 Montpellier, France
| | - Wolf Reik
- The Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK; Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK; Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK; Centre for Trophoblast Research, University of Cambridge, Cambridge CB2 3EG, UK
| | - Maria-Elena Torres-Padilla
- Institute of Genetics and Molecular and Cellular Biology (IGBMC), 1 rue Laurent Fries, 67404 Illkirch, France
| | - Axel Imhof
- Munich Centre of Integrated Protein Science and Adolf Butenandt Institute, Group, Ludwig-Maximillians University of Munich, Schillerstrasse 44, 80336 Munich, Germany
| | - Jérome Déjardin
- INSERM AVENIR, Institute of Human Genetics CNRS UPR1142, 141 rue de la Cardonille, 34000 Montpellier, France.
| | | |
Collapse
|
44
|
Li M, Pang Z, Xiao W, Liu X, Zhang Y, Yu D, Yang M, Yang Y, Hu J, Luo K. A transcriptome analysis suggests apoptosis-related signaling pathways in hemocytes of Spodoptera litura after parasitization by Microplitis bicoloratus. PLoS One 2014; 9:e110967. [PMID: 25350281 PMCID: PMC4211697 DOI: 10.1371/journal.pone.0110967] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Accepted: 09/19/2014] [Indexed: 01/01/2023] Open
Abstract
Microplitis bicoloratus parasitism induction of apoptotic DNA fragmentation of host Spodoptera litura hemocytes has been reported. However, how M. bicoloratus parasitism regulates the host signaling pathways to induce DNA fragmentation during apoptosis remains unclear. To address this question, we performed a new RNAseq-based comparative analysis of the hemocytes transcriptomes of non-parasitized and parasitized S. litura. We were able to assemble a total of more than 11.63 Gbp sequence, to yield 20,571 unigenes. At least six main protein families encoded by M. bicoloratus bracovirus are expressed in the parasitized host hemocytes: Ankyrin-repeat, Ben domain, C-type lectin, Egf-like and Mucin-like, protein tyrosine phosphatase. The analysis indicated that during DNA fragmentation and cell death, 299 genes were up-regulated and 2,441 genes were down-regulated. Data on five signaling pathways related with cell death, the gap junctions, Ca2+, PI3K/Akt, NF-κB, ATM/p53 revealed that CypD, which is involved in forming a Permeability Transition Pore Complex (PTPC) to alter mitochondrial membrane permeabilization (MMP), was dramatically up-regulated. The qRT-PCR also provided that the key genes for cell survival were down-regulated under M. bicoloratus parasitism, including those encoding Inx1, Inx2 and Inx3 of the gap junction signaling pathway, p110 subunit of the PI3K/Akt signaling pathway, and the p50 and p65 subunit of the NF-κB signaling pathway. These findings suggest that M. bicoloratus parasitism may regulate host mitochondria to trigger internucleosomal DNA fragmentation. This study will facilitate the identification of immunosuppression-related genes and also improves our understanding of molecular mechanisms underlying polydnavirus-parasitoid-host interaction.
Collapse
Affiliation(s)
- Ming Li
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Zunyu Pang
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Wei Xiao
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Xinyi Liu
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Yan Zhang
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Dongshuai Yu
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Minjun Yang
- Shanghai–Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, P. R. China
| | - Yang Yang
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Jiansheng Hu
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
| | - Kaijun Luo
- School of Life Sciences, Yunnan University, Kunming, P. R. China; Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province, Yunnan University, Kunming, P. R. China
- * E-mail:
| |
Collapse
|
45
|
Chakraborty A, Prasanth KV, Prasanth SG. Dynamic phosphorylation of HP1α regulates mitotic progression in human cells. Nat Commun 2014; 5:3445. [PMID: 24619172 PMCID: PMC3982596 DOI: 10.1038/ncomms4445] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/12/2014] [Indexed: 01/09/2023] Open
Abstract
Heterochromatin protein 1α (HP1α), a key player in the establishment and maintenance of higher-order chromatin regulates key cellular processes, including metaphase chromatid cohesion and centromere organization. However, how HP1α controls these processes is not well understood. Here we demonstrate that post-translational modifications of HP1α dictate its mitotic functions. HP1α is constitutively phosphorylated within its amino terminus, whereas phosphorylation within the hinge domain occurs preferentially at G2/M phase of the cell cycle. The hinge-phosphorylated form of HP1α specifically localizes to kinetochores during early mitosis and this phosphorylation mediated by NDR1 kinase is required for mitotic progression and for Sgo1 binding to mitotic centromeres. Cells lacking NDR kinase show loss of mitosis-specific phosphorylation of HP1α leading to prometaphase arrest. Our results reveal that NDR kinase catalyses the hinge-specific phosphorylation of human HP1α during G2/M in vivo and this orchestrates accurate chromosome alignment and mitotic progression.
Collapse
Affiliation(s)
- Arindam Chakraborty
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, Illinois 61801, USA
| | - Supriya G Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, Illinois 61801, USA
| |
Collapse
|
46
|
Shiheido H, Kitagori K, Sasaki C, Kobayashi S, Aoyama T, Urata K, Oku T, Hirayama Y, Yoshitomi H, Hikida M, Yoshifuji H, Mimori T, Watanabe T, Shimizu J. Human T cells expressing BEND3 on their surface represent a novel subpopulation that preferentially produces IL-6 and IL-8. IMMUNITY INFLAMMATION AND DISEASE 2014; 2:35-43. [PMID: 25400923 PMCID: PMC4220666 DOI: 10.1002/iid3.17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Revised: 12/25/2013] [Accepted: 01/16/2014] [Indexed: 02/04/2023]
Abstract
BEN domain-containing protein 3 (BEND3) has no transmembrane region, is localized in the cytoplasm, and is involved in chromatin function and transcription. We here identified a novel subpopulation of human T cells that expressed BEND3 on their cell surface (BEND3+ T cells). BEND3+ T cells consisted of approximately 3% of T cells in the peripheral blood, were present in both CD4+ and CD8+ T cells, and were also observed in cord blood. The stimulation of BEND3+ T cells through the TCR/CD3 complex led to the production of various kinds of cytokines; however, the levels of IL-6 and IL-8 produced by BEND3+ T cells were higher than those by BEND3− T cells. The proportion of BEND3+ T cells was also increased in some patients with inflammatory diseases. Taken together, these results indicate that BEND3+ T cells are a new subpopulation of T cells in terms of their cytokine profile. Further analyses on BEND3+ T cells may be of importance and useful in understanding human T cell immunology.
Collapse
Affiliation(s)
- Hirokazu Shiheido
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Koji Kitagori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Chiyomi Sasaki
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan ; Pharmacology Research Laboratories, Drug Discovery Research, Astellas Pharma Inc. Tsukuba, Japan
| | - Shio Kobayashi
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Takane Aoyama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Kozue Urata
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Takuma Oku
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan ; Pharmacology Research Laboratories, Drug Discovery Research, Astellas Pharma Inc. Tsukuba, Japan
| | - Yoshitaka Hirayama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan ; Pharmacology Research Laboratories, Drug Discovery Research, Astellas Pharma Inc. Tsukuba, Japan
| | - Hiroyuki Yoshitomi
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Masaki Hikida
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Takeshi Watanabe
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| | - Jun Shimizu
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University Kyoto, Japan
| |
Collapse
|
47
|
Identification of telomere-associated molecules by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP). Sci Rep 2013; 3:3171. [PMID: 24201379 PMCID: PMC3821016 DOI: 10.1038/srep03171] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 10/24/2013] [Indexed: 11/09/2022] Open
Abstract
Biochemical analysis of molecular interactions in specific genomic regions requires their isolation while retaining molecular interactions in vivo. Here, we report isolation of telomeres by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using a transcription activator-like (TAL) protein recognizing telomere repeats. Telomeres recognized by the tagged TAL protein were immunoprecipitated with an antibody against the tag and subjected to identification of telomere-binding molecules. enChIP-mass spectrometry (enChIP-MS) targeting telomeres identified known and novel telomere-binding proteins. The data have been deposited to the ProteomeXchange with identifier PXD000461. In addition, we showed that RNA associated with telomeres could be isolated by enChIP. Identified telomere-binding molecules may play important roles in telomere biology. enChIP using TAL proteins would be a useful tool for biochemical analysis of specific genomic regions of interest.
Collapse
|
48
|
Dai Q, Andreu-Agullo C, Insolera R, Wong LC, Shi SH, Lai EC. BEND6 is a nuclear antagonist of Notch signaling during self-renewal of neural stem cells. Development 2013; 140:1892-902. [PMID: 23571214 DOI: 10.1242/dev.087502] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The activity of the Notch pathway revolves around a CSL-class transcription factor, which recruits distinct complexes that activate or repress target gene expression. The co-activator complex is deeply conserved and includes the cleaved Notch intracellular domain (NICD) and Mastermind. By contrast, numerous CSL co-repressor proteins have been identified, and these are mostly different between invertebrate and vertebrate systems. In this study, we demonstrate that mammalian BEND6 is a neural BEN-solo factor that shares many functional attributes with Drosophila Insensitive, a co-repressor for the Drosophila CSL factor. BEND6 binds the mammalian CSL protein CBF1 and antagonizes Notch-dependent target activation. In addition, its association with Notch- and CBF1-regulated enhancers is promoted by CBF1 and antagonized by activated Notch. In utero electroporation experiments showed that ectopic BEND6 inhibited Notch-mediated self-renewal of neocortical neural stem cells and promoted neurogenesis. Conversely, knockdown of BEND6 increased NSC self-renewal in wild-type neocortex, and exhibited genetic interactions with gain and loss of Notch pathway activity. We recapitulated all of these findings in cultured neurospheres, in which overexpression and depletion of BEND6 caused reciprocal effects on neural stem cell renewal and neurogenesis. These data reveal a novel mammalian CSL co-repressor in the nervous system, and show that the Notch-inhibitory activity of certain BEN-solo proteins is conserved between flies and mammals.
Collapse
Affiliation(s)
- Qi Dai
- Department of Developmental Biology, Sloan-Kettering Institute, 1275 York Avenue, New York, NY 10065, USA
| | | | | | | | | | | |
Collapse
|
49
|
Dai Q, Ren A, Westholm JO, Serganov AA, Patel DJ, Lai EC. The BEN domain is a novel sequence-specific DNA-binding domain conserved in neural transcriptional repressors. Genes Dev 2013; 27:602-14. [PMID: 23468431 DOI: 10.1101/gad.213314.113] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We recently reported that Drosophila Insensitive (Insv) promotes sensory organ development and has activity as a nuclear corepressor for the Notch transcription factor Suppressor of Hairless [Su(H)]. Insv lacks domains of known biochemical function but contains a single BEN domain (i.e., a "BEN-solo" protein). Our chromatin immunoprecipitation (ChIP) sequencing (ChIP-seq) analysis confirmed binding of Insensitive to Su(H) target genes in the Enhancer of split gene complex [E(spl)-C]; however, de novo motif analysis revealed a novel site strongly enriched in Insv peaks (TCYAATHRGAA). We validate binding of endogenous Insv to genomic regions bearing such sites, whose associated genes are enriched for neural functions and are functionally repressed by Insv. Unexpectedly, we found that the Insv BEN domain binds specifically to this sequence motif and that Insv directly regulates transcription via this motif. We determined the crystal structure of the BEN-DNA target complex, revealing homodimeric binding of the BEN domain and extensive nucleotide contacts via α helices and a C-terminal loop. Point mutations in key DNA-contacting residues severely impair DNA binding in vitro and capacity for transcriptional regulation in vivo. We further demonstrate DNA-binding and repression activities by the mammalian neural BEN-solo protein BEND5. Altogether, we define novel DNA-binding activity in a conserved family of transcriptional repressors, opening a molecular window on this extensive gene family.
Collapse
Affiliation(s)
- Qi Dai
- Department of Developmental Biology, Sloan-Kettering Institute, New York, New York 10065, USA
| | | | | | | | | | | |
Collapse
|
50
|
Shen Z, Prasanth SG. Orc2 protects ORCA from ubiquitin-mediated degradation. Cell Cycle 2012; 11:3578-89. [PMID: 22935713 DOI: 10.4161/cc.21870] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Origin recognition complex (ORC) is highly dynamic, with several ORC subunits getting posttranslationally modified by phosphorylation or ubiquitination in a cell cycle-dependent manner. We have previously demonstrated that a WD repeat containing protein ORC-associated (ORCA/LRWD1) stabilizes the ORC on chromatin and facilitates pre-RC assembly. Further, ORCA levels are cell cycle-regulated, with highest levels during G(1), and progressively decreasing during S phase, but the mechanism remains to be elucidated. We now demonstrate that ORCA is polyubiquitinated in vivo, with elevated ubiquitination observed at the G(1)/S boundary. ORCA utilizes lysine-48 (K48) ubiquitin linkage, suggesting that ORCA ubiquitination mediates its regulated degradation. Ubiquitinated ORCA is re-localized in the form of nuclear aggregates and is predominantly associated with chromatin. We demonstrate that ORCA associates with the E3 ubiquitin ligase Cul4A-Ddb1. ORCA is ubiquitinated at the WD40 repeat domain, a region that is also recognized by Orc2. Furthermore, Orc2 associates only with the non-ubiquitinated form of ORCA, and Orc2 depletion results in the proteasome-mediated destabilization of ORCA. Based on the results, we suggest that Orc2 protects ORCA from ubiquitin-mediated degradation in vivo.
Collapse
Affiliation(s)
- Zhen Shen
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | | |
Collapse
|