1
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EZH2 interacts with HP1BP3 to epigenetically activate WNT7B that promotes temozolomide resistance in glioblastoma. Oncogene 2023; 42:461-470. [PMID: 36517590 DOI: 10.1038/s41388-022-02570-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 12/04/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Glioblastoma (GBM) is the most lethal primary brain tumor in adults and harbors a subpopulation of glioma stem cells (GSCs). Enhancer of Zeste Homolog 2 (EZH2), a histone lysine methyltransferase, deeply involves in the stemness maintenance of GSC. However, the precise mechanism and therapeutic potential remain elusive. We postulated that the interactome of EZH2 in GSC is unique. Therefore, we performed proteomic and transcriptomic research to unveil the oncogenic mechanism of EZH2. Immunoprecipitation and mass spectrometry were used to identify proteins that co-precipitate with EZH2. We show that EZH2 binds to heterochromatin protein 1 binding protein 3 (HP1BP3) in GSCs and impairs the methylation of H3K9. Overexpression of HP1BP3 enhances the proliferation, self-renewal and temozolomide (TMZ) resistance of GBM cells. Furthermore, EZH2 and HP1BP3 co-activate WNT7B expression thereby increasing TMZ resistance and stemness of GBM cells. Importantly, inhibition of WNT7B autocrine via LGK974 effectively reverses the TMZ resistance. Our work clarifies a new oncogenic mechanism of EZH2 by which it interacts with HP1BP3 and epigenetically activates WNT7B thereby promoting TMZ resistance in GSCs. Our results provide a rationale for targeting WNT/β-catenin pathway as a promising strategy to overcome TMZ resistance in GSCs.
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2
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Stochastic chromatin packing of 3D mitotic chromosomes revealed by coherent X-rays. Proc Natl Acad Sci U S A 2021; 118:2109921118. [PMID: 34750262 DOI: 10.1073/pnas.2109921118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/01/2021] [Indexed: 11/18/2022] Open
Abstract
DNA molecules are atomic-scale information storage molecules that promote reliable information transfer via fault-free repetitions of replications and transcriptions. Remarkable accuracy of compacting a few-meters-long DNA into a micrometer-scale object, and the reverse, makes the chromosome one of the most intriguing structures from both physical and biological viewpoints. However, its three-dimensional (3D) structure remains elusive with challenges in observing native structures of specimens at tens-of-nanometers resolution. Here, using cryogenic coherent X-ray diffraction imaging, we succeeded in obtaining nanoscale 3D structures of metaphase chromosomes that exhibited a random distribution of electron density without characteristics of high-order folding structures. Scaling analysis of the chromosomes, compared with a model structure having the same density profile as the experimental results, has discovered the fractal nature of density distributions. Quantitative 3D density maps, corroborated by molecular dynamics simulations, reveal that internal structures of chromosomes conform to diffusion-limited aggregation behavior, which indicates that 3D chromatin packing occurs via stochastic processes.
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3
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Shi G, Hu Y, Zhu X, Jiang Y, Pang J, Wang C, Huang W, Zhao Y, Ma W, Liu D, Huang J, Songyang Z. A critical role of telomere chromatin compaction in ALT tumor cell growth. Nucleic Acids Res 2020; 48:6019-6031. [PMID: 32379321 PMCID: PMC7293046 DOI: 10.1093/nar/gkaa224] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 03/17/2020] [Accepted: 04/18/2020] [Indexed: 01/15/2023] Open
Abstract
ALT tumor cells often contain abundant DNA damage foci at telomeres and rely on the alternative lengthening of telomeres (ALT) mechanism to maintain their telomeres. How the telomere chromatin is regulated and maintained in these cells remains largely unknown. In this study, we present evidence that heterochromatin protein 1 binding protein 3 (HP1BP3) can localize to telomeres and is particularly enriched on telomeres in ALT cells. HP1BP3 inhibition led to preferential growth inhibition of ALT cells, which was accompanied by telomere chromatin decompaction, increased presence of C-circles, more pronounced ALT-associated phenotypes and elongated telomeres. Furthermore, HP1BP3 appeared to participate in regulating telomere histone H3K9me3 epigenetic marks. Taken together, our data suggest that HP1BP3 functions on telomeres to maintain telomere chromatin and represents a novel target for inhibiting ALT cancer cells.
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Affiliation(s)
- Guang Shi
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yang Hu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Xing Zhu
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuanling Jiang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Junjie Pang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Chuanle Wang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenjun Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Zhao
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Wenbin Ma
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Dan Liu
- Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030
| | - Junjiu Huang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
| | - Zhou Songyang
- MOE Key Laboratory of Gene Function and Regulation, Guangzhou Key Laboratory of Healthy Aging Research and SYSU-BCM Joint Research Center, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.,Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Verna and Marrs Mclean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, Houston, TX, USA 77030.,State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangzhou 510060, China
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4
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Chow TT, Shi X, Wei JH, Guan J, Stadler G, Huang B, Blackburn EH. Local enrichment of HP1alpha at telomeres alters their structure and regulation of telomere protection. Nat Commun 2018; 9:3583. [PMID: 30181605 PMCID: PMC6123478 DOI: 10.1038/s41467-018-05840-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 07/26/2018] [Indexed: 12/27/2022] Open
Abstract
Enhanced telomere maintenance is evident in malignant cancers. While telomeres are thought to be inherently heterochromatic, detailed mechanisms of how epigenetic modifications impact telomere protection and structures are largely unknown in human cancers. Here we develop a molecular tethering approach to experimentally enrich heterochromatin protein HP1α specifically at telomeres. This results in increased deposition of H3K9me3 at cancer cell telomeres. Telomere extension by telomerase is attenuated, and damage-induced foci at telomeres are reduced, indicating augmentation of telomere stability. Super-resolution STORM imaging shows an unexpected increase in irregularity of telomeric structure. Telomere-tethered chromo shadow domain (CSD) mutant I165A of HP1α abrogates both the inhibition of telomere extension and the irregularity of telomeric structure, suggesting the involvement of at least one HP1α-ligand in mediating these effects. This work presents an approach to specifically manipulate the epigenetic status locally at telomeres to uncover insights into molecular mechanisms underlying telomere structural dynamics.
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Affiliation(s)
- Tracy T Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Xiaoyu Shi
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Jen-Hsuan Wei
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94143, USA
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Juan Guan
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94143, USA
| | | | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Elizabeth H Blackburn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA, 94143, USA.
- Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
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5
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Becker JS, McCarthy RL, Sidoli S, Donahue G, Kaeding KE, He Z, Lin S, Garcia BA, Zaret KS. Genomic and Proteomic Resolution of Heterochromatin and Its Restriction of Alternate Fate Genes. Mol Cell 2017; 68:1023-1037.e15. [PMID: 29272703 PMCID: PMC5858919 DOI: 10.1016/j.molcel.2017.11.030] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 10/18/2017] [Accepted: 11/21/2017] [Indexed: 12/24/2022]
Abstract
Heterochromatin is integral to cell identity maintenance by impeding the activation of genes for alternate cell fates. Heterochromatic regions are associated with histone 3 lysine 9 trimethylation (H3K9me3) or H3K27me3, but these modifications are also found in euchromatic regions that permit transcription. We discovered that resistance to sonication is a reliable indicator of the heterochromatin state, and we developed a biophysical method (gradient-seq) to discriminate subtypes of H3K9me3 and H3K27me3 domains in sonication-resistant heterochromatin (srHC) versus euchromatin. These classifications are more accurate than the histone marks alone in predicting transcriptional silence and resistance of alternate fate genes to activation during direct cell conversion. Our proteomics of H3K9me3-marked srHC and functional screens revealed diverse proteins, including RBMX and RBMXL1, that impede gene induction during cellular reprogramming. Isolation of srHC with gradient-seq provides a genome-wide map of chromatin structure, elucidating subtypes of repressed domains that are uniquely predictive of diverse other chromatin properties.
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Affiliation(s)
- Justin S Becker
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Ryan L McCarthy
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Simone Sidoli
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Greg Donahue
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kelsey E Kaeding
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Zhiying He
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Shu Lin
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Benjamin A Garcia
- Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA
| | - Kenneth S Zaret
- Institute for Regenerative Medicine , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Epigenetics Program , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology , Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, 3400 Civic Center Boulevard, Philadelphia, PA 19104, USA.
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6
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Liu H, Zhang L, Wei Q, Shi Z, Shi X, Du J, Huang C, Zhang Y, Guo Z. Comprehensive Proteomic Analysis of PGC7-Interacting Proteins. J Proteome Res 2017; 16:3113-3123. [PMID: 28712289 DOI: 10.1021/acs.jproteome.6b00883] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Primordial germ cell 7 (PGC7), a maternal factor essential for early development, plays a critical role in the regulation of DNA methylation, transcriptional repression, chromatin condensation, and cell division and the maintenance of cell pluripotentiality. Despite the fundamental roles of PGC7 in these cellular processes, only a few molecular and functional interactions of PGC7 have been reported. Here, a streptavidin-biotin affinity purification technique combined with LC-MS/MS was used to analyze potential proteins that interact with PGC7. In total, 291 potential PGC7-interacting proteins were identified. Through an in-depth bioinformatic analysis of potential interactors, we linked PGC7 to critical cellular processes including translation, RNA processing, cell cycle, and regulation of heterochromatin structure. To better understand the functional interactions of PGC7 with its potential interactors, we constructed a protein-protein interaction network using the STRING database. In addition, we discussed in detail the interactions between PGC7 and some of its newly validated partners. The identification of these potential interactors of PGC7 expands our knowledge on the PGC7 interactome and provides a valuable resource for understanding the diverse functions of this protein.
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Affiliation(s)
- Hongliang Liu
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Lei Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Qing Wei
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zhaopeng Shi
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Xiaoyan Shi
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medical Experiment Center of Shaanxi University of Chinese Medicine , Xianyang, Shaanxi 712000, China
| | - Juan Du
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China.,Medicine School of Yan'an University , Yan'an, Shaanxi 716000, China
| | - Chenyang Huang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
| | - Zekun Guo
- College of Veterinary Medicine, Northwest A&F University , Yangling, Shaanxi 712100, China.,Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University , Yangling, Shaanxi 712100, China
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7
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Garfinkel BP, Arad S, Neuner SM, Netser S, Wagner S, Kaczorowski CC, Rosen CJ, Gal M, Soreq H, Orly J. HP1BP3 expression determines maternal behavior and offspring survival. GENES BRAIN AND BEHAVIOR 2017; 15:678-88. [PMID: 27470444 DOI: 10.1111/gbb.12312] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 07/03/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022]
Abstract
Maternal care is an indispensable behavioral component necessary for survival and reproductive success in mammals, and postpartum maternal behavior is mediated by an incompletely understood complex interplay of signals including effects of epigenetic regulation. We approached this issue using our recently established mice with targeted deletion of heterochromatin protein 1 binding protein 3 (HP1BP3), which we found to be a novel epigenetic repressor with critical roles in postnatal growth. Here, we report a dramatic reduction in the survival of pups born to Hp1bp3(-/-) deficient mouse dams, which could be rescued by co-fostering with wild-type dams. Hp1bp3(-/-) females failed to retrieve both their own pups and foster pups in a pup retrieval test, and showed reduced anxiety-like behavior in the open-field and elevated-plus-maze tests. In contrast, Hp1bp3(-/-) females showed no deficits in behaviors often associated with impaired maternal care, including social behavior, depression, motor coordination and olfactory capability; and maintained unchanged anxiety-associated hallmarks such as cholinergic status and brain miRNA profiles. Collectively, our results suggest a novel role for HP1BP3 in regulating maternal and anxiety-related behavior in mice and call for exploring ways to manipulate this epigenetic process.
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Affiliation(s)
- B P Garfinkel
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel. .,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - S Arad
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Biomedical Sciences, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - S M Neuner
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - S Netser
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - S Wagner
- Sagol Department of Neurobiology, University of Haifa, Haifa, Israel
| | - C C Kaczorowski
- Department of Anatomy and Neurobiology, University of Tennessee Health Science Center, Memphis, TN, USA
| | - C J Rosen
- Center for Clinical and Translational Research, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - M Gal
- Biomedical Sciences, The Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel.,The IVF Unit - Obstetrics and Gynecology Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - H Soreq
- The Edmond and Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.,Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - J Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
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8
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Xu D, Yang Q, Cui M, Zhang Q. The novel transcriptional factor HP1BP3 negatively regulates Hsp70 transcription in Crassostrea hongkongensis. Sci Rep 2017; 7:1401. [PMID: 28469151 PMCID: PMC5431216 DOI: 10.1038/s41598-017-01573-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 03/29/2017] [Indexed: 11/29/2022] Open
Abstract
ChHP1BP3, a chromatin complex-related protein known with dynamic features, was identified as a ChHsp70 promoter-associated factor in Crassostrea hongkongensis by DNA-affinity purification and mass spectrometry analysis. Direct interaction between purified ChHP1BP3 and the ChHsp70 promoter region was demonstrated using EMSA. ChHp1bp3 depletion led to clear enhancements in ChHsp70 mRNA expression in C. hongkongensis hemocytes. However, ChHp1bp3 overexpression in heterologous HEK293T cells correlated with fluctuations in ChHsp70 transcription. Quantitative RT-PCR analysis showed that both ChHsp70 and ChHp1bp3 transcription were responsive to external physical/chemical stresses by heat, CdCl2 and NP. This indicated a plausible correlation between ChHsp70 and ChHp1bp3 in the stress-induced genetic regulatory pathway. While, the distinctive ChHp1bp3 expression patterns upon physical and chemical stresses suggest that the mechanisms that mediate ChHp1bp3 induction might be stress-specific. This study discovered a novel role for HP1BP3 as a negative regulator in controlling Hsp70 transcription in C. hongkongensis, and contributed to better understanding the complex regulatory mechanisms governing Hsp70 transcription.
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Affiliation(s)
- Delin Xu
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Qin Yang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China
| | - Miao Cui
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
| | - Qizhong Zhang
- Department of Ecology, Institute of Hydrobiology, School of Life Science and Technology, Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering, Ministry of Education, Jinan University, Guangzhou, 510632, P.R. China.
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9
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Phengchat R, Takata H, Morii K, Inada N, Murakoshi H, Uchiyama S, Fukui K. Calcium ions function as a booster of chromosome condensation. Sci Rep 2016; 6:38281. [PMID: 27910894 PMCID: PMC5133622 DOI: 10.1038/srep38281] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/07/2016] [Indexed: 12/14/2022] Open
Abstract
Chromosome condensation is essential for the faithful transmission of genetic information to daughter cells during cell division. The depletion of chromosome scaffold proteins does not prevent chromosome condensation despite structural defects. This suggests that other factors contribute to condensation. Here we investigated the contribution of divalent cations, particularly Ca2+, to chromosome condensation in vitro and in vivo. Ca2+ depletion caused defects in proper mitotic progression, particularly in chromosome condensation after the breakdown of the nuclear envelope. Fluorescence lifetime imaging microscopy-Förster resonance energy transfer and electron microscopy demonstrated that chromosome condensation is influenced by Ca2+. Chromosomes had compact globular structures when exposed to Ca2+ and expanded fibrous structures without Ca2+. Therefore, we have clearly demonstrated a role for Ca2+ in the compaction of chromatin fibres.
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Affiliation(s)
- Rinyaporn Phengchat
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Hideaki Takata
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Kenichi Morii
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Noriko Inada
- The Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916-5 Takayama-Cho Ikoma-shi, Nara 630-0192, Japan
| | - Hideji Murakoshi
- Supportive Center for Brain Research, National Institute for Physiological Sciences, Okazaki, Aichi 444-8585, Japan
| | - Susumu Uchiyama
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
| | - Kiichi Fukui
- Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita 565-0871, Osaka, Japan
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10
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Liu H, Liang C, Kollipara RK, Matsui M, Ke X, Jeong BC, Wang Z, Yoo KS, Yadav GP, Kinch LN, Grishin NV, Nam Y, Corey DR, Kittler R, Liu Q. HP1BP3, a Chromatin Retention Factor for Co-transcriptional MicroRNA Processing. Mol Cell 2016; 63:420-32. [PMID: 27425409 DOI: 10.1016/j.molcel.2016.06.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 04/26/2016] [Accepted: 06/09/2016] [Indexed: 02/08/2023]
Abstract
Recent studies suggest that the microprocessor (Drosha-DGCR8) complex can be recruited to chromatin to catalyze co-transcriptional processing of primary microRNAs (pri-miRNAs) in mammalian cells. However, the molecular mechanism of co-transcriptional miRNA processing is poorly understood. Here we find that HP1BP3, a histone H1-like chromatin protein, specifically associates with the microprocessor and promotes global miRNA biogenesis in human cells. Chromatin immunoprecipitation (ChIP) studies reveal genome-wide co-localization of HP1BP3 and Drosha and HP1BP3-dependent Drosha binding to actively transcribed miRNA loci. Moreover, HP1BP3 specifically binds endogenous pri-miRNAs and facilitates the Drosha/pri-miRNA association in vivo. Knockdown of HP1BP3 compromises pri-miRNA processing by causing premature release of pri-miRNAs from the chromatin. Taken together, these studies suggest that HP1BP3 promotes co-transcriptional miRNA processing via chromatin retention of nascent pri-miRNA transcripts. This work significantly expands the functional repertoire of the H1 family of proteins and suggests the existence of chromatin retention factors for widespread co-transcriptional miRNA processing.
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Affiliation(s)
- Haoming Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Chunyang Liang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rahul K Kollipara
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Masayuki Matsui
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Xiong Ke
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Byung-Cheon Jeong
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhiqiang Wang
- International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan
| | - Kyoung Shin Yoo
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaya P Yadav
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Lisa N Kinch
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Nicholas V Grishin
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yunsun Nam
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - David R Corey
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Ralf Kittler
- McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qinghua Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; International Institute for Integrated Sleep Medicine, University of Tsukuba, Tsukuba 305-8575, Japan; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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11
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Hadac JN, Miller DD, Grimes IC, Clipson L, Newton MA, Schelman WR, Halberg RB. Heterochromatin Protein 1 Binding Protein 3 Expression as a Candidate Marker of Intrinsic 5-Fluorouracil Resistance. Anticancer Res 2016; 36:845-852. [PMID: 26976970 PMCID: PMC4876978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
BACKGROUND Despite receiving post-operative 5-fluorouracil (5-FU)-based chemotherapy, approximately 50% of patients with stage IIIC colon cancer experience recurrence. Currently, no molecular signature can predict response to 5-FU. MATERIALS AND METHODS Mouse models of colon cancer have been developed and characterized. Individual tumors in these mice can be longitudinally monitored and assessed to identify differences between those that are responsive and those that are resistant to therapy. Gene expression was analyzed in serial biopsies that were collected before and after treatment with 5-FU. Colon tumors had heterogeneous responses to treatment with 5-FU. Microarray analysis of pre-treatment biopsies revealed that Hp1bp3, a gene encoding heterochromatin protein 1 binding protein 3, was differentially expressed between sensitive and resistant tumors. CONCLUSION Using mouse models of human colorectal cancer, Hp1bp3 was identified as a candidate marker of intrinsic 5-FU resistance and may represent a potential biomarker for patient stratification or a target of clinical importance.
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Affiliation(s)
- Jamie N Hadac
- Department of Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Devon D Miller
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Ian C Grimes
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Linda Clipson
- Department of Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Michael A Newton
- Departments of Statistics and of Biostatistics and Medical Informatics, 1245a, K6/434 Medical Sciences Center, Madison, WI, U.S.A
| | - William R Schelman
- Department of Medicine, Division of Hematology and Oncology, K4/532 Clinical Science Center, Madison, WI, U.S.A
| | - Richard B Halberg
- Department of Medicine, Division of Gastroenterology and Hepatology, K4/532 Clinical Science Center, Madison, WI, U.S.A. Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI, U.S.A.
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12
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Newhart A, Powers SL, Shastrula PK, Sierra I, Joo LM, Hayden JE, Cohen AR, Janicki SM. RNase P protein subunit Rpp29 represses histone H3.3 nucleosome deposition. Mol Biol Cell 2016; 27:1154-69. [PMID: 26842893 PMCID: PMC4814222 DOI: 10.1091/mbc.e15-02-0099] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 01/28/2016] [Indexed: 11/15/2022] Open
Abstract
RNase P protein subunits Rpp29, POP1, and Rpp21 interact with histone H3.3 upstream of nucleosome deposition, suggesting that a variant of this enzyme regulates H3.3 function. Rpp29 knockdown increases H3.3 chromatin incorporation, suggesting that it represses H3.3 nucleosome deposition, which has important implications for epigenetic regulation. In mammals, histone H3.3 is a critical regulator of transcription state change and heritability at both euchromatin and heterochromatin. The H3.3-specific chaperone, DAXX, together with the chromatin-remodeling factor, ATRX, regulates H3.3 deposition and transcriptional silencing at repetitive DNA, including pericentromeres and telomeres. However, the events that precede H3.3 nucleosome incorporation have not been fully elucidated. We previously showed that the DAXX-ATRX-H3.3 pathway regulates a multi-copy array of an inducible transgene that can be visualized in single living cells. When this pathway is impaired, the array can be robustly activated. H3.3 is strongly recruited to the site during activation where it accumulates in a complex with transcribed sense and antisense RNA, which is distinct from the DNA/chromatin. This suggests that transcriptional events regulate H3.3 recruited to its incorporation sites. Here we report that the nucleolar RNA proteins Rpp29, fibrillarin, and RPL23a are also components of this H3.3/RNA complex. Rpp29 is a protein subunit of RNase P. Of the other subunits, POP1 and Rpp21 are similarly recruited suggesting that a variant of RNase P regulates H3.3 chromatin assembly. Rpp29 knockdown increases H3.3 chromatin incorporation, which suggests that Rpp29 represses H3.3 nucleosome deposition, a finding with implications for epigenetic regulation.
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Affiliation(s)
- Alyshia Newhart
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Sara Lawrence Powers
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Prashanth Krishna Shastrula
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104 Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, PA 19104
| | - Isabel Sierra
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Lucy M Joo
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - James E Hayden
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
| | - Andrew R Cohen
- Electrical and Computer Engineering Department, Drexel University, Philadelphia, PA 19104
| | - Susan M Janicki
- Molecular and Cellular Oncogenesis Program, Wistar Institute, Philadelphia, PA 19104
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13
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Porter LF, Galli GG, Williamson S, Selley J, Knight D, Elcioglu N, Aydin A, Elcioglu M, Venselaar H, Lund AH, Bonshek R, Black GC, Manson FD. A role for repressive complexes and H3K9 di-methylation in PRDM5-associated brittle cornea syndrome. Hum Mol Genet 2015; 24:6565-79. [PMID: 26395458 PMCID: PMC4634368 DOI: 10.1093/hmg/ddv345] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2015] [Revised: 07/29/2015] [Accepted: 08/18/2015] [Indexed: 12/11/2022] Open
Abstract
Type 2 brittle cornea syndrome (BCS2) is an inherited connective tissue disease with a devastating ocular phenotype caused by mutations in the transcription factor PR domain containing 5 (PRDM5) hypothesized to exert epigenetic effects through histone and DNA methylation. Here we investigate clinical samples, including skin fibroblasts and retinal tissue from BCS2 patients, to elucidate the epigenetic role of PRDM5 and mechanisms of its dysregulation in disease. First we report abnormal retinal vascular morphology in the eyes of two cousins with BCS2 (PRDM5 Δ exons 9-14) using immunohistochemistry, and mine data from skin fibroblast expression microarrays from patients with PRDM5 mutations p.Arg590* and Δ exons 9-14, as well as from a PRDM5 ChIP-sequencing experiment. Gene ontology analysis of dysregulated PRDM5-target genes reveals enrichment for extracellular matrix (ECM) genes supporting vascular integrity and development. Q-PCR and ChIP-qPCR confirm upregulation of critical mediators of ECM stability in vascular structures (COL13A1, COL15A1, NTN1, CDH5) in patient fibroblasts. We identify H3K9 di-methylation (H3K9me2) at these PRDM5-target genes in fibroblasts, and demonstrate that the BCS2 mutation p.Arg83Cys diminishes interaction of PRDM5 with repressive complexes, including NuRD complex protein CHD4, and the repressive chromatin interactor HP1BP3, by co-immunoprecipitation combined with mass spectrometry. We observe reduced heterochromatin protein 1 binding protein 3 (HP1BP3) staining in the retinas of two cousins lacking exons 9-14 by immunohistochemistry, and dysregulated H3K9me2 in skin fibroblasts of three patients (p.Arg590*, p.Glu134* and Δ exons 9-14) by western blotting. These findings suggest that defective interaction of PRDM5 with repressive complexes, and dysregulation of H3K9me2, play a role in PRDM5-associated disease.
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Affiliation(s)
- Louise F Porter
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, Department of Eye and Vision Science, Institute of Ageing and Chronic Disease, University of Liverpool, Liverpool, UK
| | - Giorgio G Galli
- Stem Cell Program, Boston Children's Hospital, Harvard Stem Cell and Regenerative Biology Department and Harvard Stem Cell Institute, Harvard University, Boston, MA, USA, Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Sally Williamson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
| | - Julian Selley
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - David Knight
- Faculty of Life Sciences, Michael Smith Building, Manchester, UK
| | - Nursel Elcioglu
- Department of Pediatric Genetics, Marmara University Medical School, Istanbul, Turkey
| | - Ali Aydin
- Department of Ophthalmology, University of Medipol Medical Faculty, Istanbul, Turkey
| | - Mustafa Elcioglu
- Department of Ophthalmology, Okmeydani Research and Training Hospital, Istanbul, Turkey
| | - Hanka Venselaar
- Centre of Molecular and Biomolecular Informatics, Radboudumc Institute for Molecular Life Sciences, Nijmegen, The Netherlands and
| | - Anders H Lund
- Biotech Research and Innovation Centre and Centre for Epigenetics, University of Copenhagen, Copenhagen, Denmark
| | - Richard Bonshek
- Manchester Royal Eye Hospital, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre, Manchester, UK, National Ophthalmic Pathology Service Laboratory, Department of Histopathology, Central Manchester University Hospitals NHS Foundation Trust, Manchester, UK
| | - Graeme C Black
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, MAHSC, Manchester, UK
| | - Forbes D Manson
- Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, Manchester Academic Health Science Centre (MAHSC), Manchester, UK
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14
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Garfinkel BP, Melamed-Book N, Anuka E, Bustin M, Orly J. HP1BP3 is a novel histone H1 related protein with essential roles in viability and growth. Nucleic Acids Res 2015; 43:2074-90. [PMID: 25662603 PMCID: PMC4344522 DOI: 10.1093/nar/gkv089] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 12/17/2014] [Accepted: 01/23/2015] [Indexed: 12/28/2022] Open
Abstract
The dynamic architecture of chromatin is vital for proper cellular function, and is maintained by the concerted action of numerous nuclear proteins, including that of the linker histone H1 variants, the most abundant family of nucleosome-binding proteins. Here we show that the nuclear protein HP1BP3 is widely expressed in most vertebrate tissues and is evolutionarily and structurally related to the H1 family. HP1BP3 contains three globular domains and a highly positively charged C-terminal domain, resembling similar domains in H1. Fluorescence recovery after photobleaching (FRAP) studies indicate that like H1, binding of HP1BP3 to chromatin depends on both its C and N terminal regions and is affected by the cell cycle and post translational modifications. HP1BP3 contains functional motifs not found in H1 histones, including an acidic stretch and a consensus HP1-binding motif. Transcriptional profiling of HeLa cells lacking HP1BP3 showed altered expression of 383 genes, suggesting a role for HP1BP3 in modulation of gene expression. Significantly, Hp1bp3(-/-) mice present a dramatic phenotype with 60% of pups dying within 24 h of birth and the surviving animals exhibiting a lifelong 20% growth retardation. We suggest that HP1BP3 is a ubiquitous histone H1 like nuclear protein with distinct and non-redundant functions necessary for survival and growth.
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Affiliation(s)
- Benjamin P Garfinkel
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Naomi Melamed-Book
- Bio-Imaging Unit, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Eli Anuka
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Michael Bustin
- Protein Section, Laboratory of Metabolism, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joseph Orly
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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15
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Dutta B, Ren Y, Hao P, Sim KH, Cheow E, Adav S, Tam JP, Sze SK. Profiling of the Chromatin-associated Proteome Identifies HP1BP3 as a Novel Regulator of Cell Cycle Progression. Mol Cell Proteomics 2014; 13:2183-97. [PMID: 24830416 DOI: 10.1074/mcp.m113.034975] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Indexed: 12/31/2022] Open
Abstract
The chromatin-associated proteome (chromatome) regulates cellular gene expression by restricting access of transcriptional machinery to template DNA, and dynamic re-modeling of chromatin structure is required to regulate critical cell functions including growth and replication, DNA repair and recombination, and oncogenic transformation in progression to cancer. Central to the control of these processes is efficient regulation of the host cell cycle, which is maintained by rapid changes in chromatin conformation during normal cycle progression. A global overview of chromatin protein organization is therefore essential to fully understand cell cycle regulation, but the influence of the chromatome and chromatin binding topology on host cell cycle progression remains poorly defined. Here we used partial MNase digestion together with iTRAQ-based high-throughput quantitative proteomics to quantify chromatin-associated proteins during interphase progression. We identified a total of 481 proteins with high confidence that were involved in chromatin-dependent events including transcriptional regulation, chromatin re-organization, and DNA replication and repair, whereas the quantitative data revealed the temporal interactions of these proteins with chromatin during interphase progression. When combined with biochemical and functional assays, these data revealed a strikingly dynamic association of protein HP1BP3 with the chromatin complex during different stages of interphase, and uncovered a novel regulatory role for this molecule in transcriptional regulation. We report that HP1BP3 protein maintains heterochromatin integrity during G1-S progression and regulates the duration of G1 phase to critically influence cell proliferative capacity.
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Affiliation(s)
- Bamaprasad Dutta
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Yan Ren
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Piliang Hao
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Kae Hwan Sim
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Esther Cheow
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Sunil Adav
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - James P Tam
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
| | - Siu Kwan Sze
- From the ‡School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551
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16
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Kirkwood KJ, Ahmad Y, Larance M, Lamond AI. Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics. Mol Cell Proteomics 2013; 12:3851-73. [PMID: 24043423 PMCID: PMC3861729 DOI: 10.1074/mcp.m113.032367] [Citation(s) in RCA: 115] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Proteins form a diverse array of complexes that mediate cellular function and regulation. A largely unexplored feature of such protein complexes is the selective participation of specific protein isoforms and/or post-translationally modified forms. In this study, we combined native size-exclusion chromatography (SEC) with high-throughput proteomic analysis to characterize soluble protein complexes isolated from human osteosarcoma (U2OS) cells. Using this approach, we have identified over 71,500 peptides and 1,600 phosphosites, corresponding to over 8,000 proteins, distributed across 40 SEC fractions. This represents >50% of the predicted U2OS cell proteome, identified with a mean peptide sequence coverage of 27% per protein. Three biological replicates were performed, allowing statistical evaluation of the data and demonstrating a high degree of reproducibility in the SEC fractionation procedure. Specific proteins were detected interacting with multiple independent complexes, as typified by the separation of distinct complexes for the MRFAP1-MORF4L1-MRGBP interaction network. The data also revealed protein isoforms and post-translational modifications that selectively associated with distinct subsets of protein complexes. Surprisingly, there was clear enrichment for specific Gene Ontology terms associated with differential size classes of protein complexes. This study demonstrates that combined SEC/MS analysis can be used for the system-wide annotation of protein complexes and to predict potential isoform-specific interactions. All of these SEC data on the native separation of protein complexes have been integrated within the Encyclopedia of Proteome Dynamics, an online, multidimensional data-sharing resource available to the community.
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Affiliation(s)
- Kathryn J Kirkwood
- Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dow St., Dundee, DD1 5EH, United Kingdom
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17
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Soldi M, Bonaldi T. The proteomic investigation of chromatin functional domains reveals novel synergisms among distinct heterochromatin components. Mol Cell Proteomics 2013; 12:764-80. [PMID: 23319141 PMCID: PMC3591667 DOI: 10.1074/mcp.m112.024307] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Chromatin is a highly dynamic, well-structured nucleoprotein complex of DNA and proteins that controls virtually all DNA transactions. Chromatin dynamicity is regulated at specific loci by the presence of various associated proteins, histones, post-translational modifications, histone variants, and DNA methylation. Until now the characterization of the proteomic component of chromatin domains has been held back by the challenge of enriching distinguishable, homogeneous regions for subsequent mass spectrometry analysis. Here we describe a modified protocol for chromatin immunoprecipitation combined with quantitative proteomics based on stable isotope labeling by amino acids in cell culture to identify known and novel histone modifications, variants, and complexes that specifically associate with silent and active chromatin domains. Our chromatin proteomics strategy revealed unique functional interactions among various chromatin modifiers, suggesting new regulatory pathways, such as a heterochromatin-specific modulation of DNA damage response involving H2A.X and WICH, both enriched in silent domains. Chromatin proteomics expands the arsenal of tools for deciphering how all the distinct protein components act together to enforce a given region-specific chromatin status.
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Affiliation(s)
- Monica Soldi
- Department of Experimental Oncology, European Institute of Oncology (IEO), Via Adamello 16, Milan, Italy
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18
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Mitsunobu H, Izumi M, Mon H, Tatsuke T, Lee JM, Kusakabe T. Molecular characterization of heterochromatin proteins 1a and 1b from the silkworm, Bombyx mori. INSECT MOLECULAR BIOLOGY 2012; 21:9-20. [PMID: 22142192 DOI: 10.1111/j.1365-2583.2011.01115.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Heterochromatin protein 1s (HP1s) are nonhistone chromosomal proteins that play a direct role in the formation and maintenance of heterochromatin structure. Similarly to Caenorhabditis elegans, silkworms possess holocentric chromosomes, in which diffused kinetochores extend along the length of each chromosome. We have isolated two silkworm HP1 homologues, BmHP1a and BmHP1b. Cytological analysis showed a unique localization of BmHP1s during cell division, in which these proteins first appear to dissociate from the chromosomes, but then return to enclose the chromosomes during metaphase. BmHP1s formed homo- and hetero-dimers and interacted with BmSu(var)3-9, which is a methyltransferase for histone H3 lysine 9 (H3K9). We further showed, using a silkworm cell-based reporter system, that BmHP1b had higher transcriptional repression activity than BmHP1a, whereas BmHP1a interacted more strongly with BmSu(var)3-9 than did BmHP1b. These results suggest that silkworm HP1a and HP1b may play different roles in heterochromatin formation in holocentric silkworm chromosomes.
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Affiliation(s)
- H Mitsunobu
- Laboratory of Silkworm Science, Kyushu University Graduate School of Bioresource and Bioenvironmental Sciences, Fukuoka, Japan
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19
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Jin B, Li Y, Robertson KD. DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2011; 2:607-17. [PMID: 21941617 DOI: 10.1177/1947601910393957] [Citation(s) in RCA: 437] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic modifications are heritable changes in gene expression not encoded by the DNA sequence. In the past decade, great strides have been made in characterizing epigenetic changes during normal development and in disease states like cancer. However, the epigenetic landscape has grown increasingly complicated, encompassing DNA methylation, the histone code, noncoding RNA, and nucleosome positioning, along with DNA sequence. As a stable repressive mark, DNA methylation, catalyzed by the DNA methyltransferases (DNMTs), is regarded as a key player in epigenetic silencing of transcription. DNA methylation may coordinately regulate the chromatin status via the interaction of DNMTs with other modifications and with components of the machinery mediating those marks. In this review, we will comprehensively examine the current understanding of the connections between DNA methylation and other epigenetic marks and discuss molecular mechanisms of transcriptional repression in development and in carcinogenesis.
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Affiliation(s)
- Bilian Jin
- Department of Biochemistry & Molecular Biology, Medical College of Georgia Cancer Center, Augusta, GA, USA
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