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Dhahri H, Saintilnord WN, Chandler D, Fondufe-Mittendorf YN. Beyond the Usual Suspects: Examining the Role of Understudied Histone Variants in Breast Cancer. Int J Mol Sci 2024; 25:6788. [PMID: 38928493 PMCID: PMC11203562 DOI: 10.3390/ijms25126788] [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: 05/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
The incorporation of histone variants has structural ramifications on nucleosome dynamics and stability. Due to their unique sequences, histone variants can alter histone-histone or histone-DNA interactions, impacting the folding of DNA around the histone octamer and the overall higher-order structure of chromatin fibers. These structural modifications alter chromatin compaction and accessibility of DNA by transcription factors and other regulatory proteins to influence gene regulatory processes such as DNA damage and repair, as well as transcriptional activation or repression. Histone variants can also generate a unique interactome composed of histone chaperones and chromatin remodeling complexes. Any of these perturbations can contribute to cellular plasticity and the progression of human diseases. Here, we focus on a frequently overlooked group of histone variants lying within the four human histone gene clusters and their contribution to breast cancer.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
| | - Wesley N. Saintilnord
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA or (H.D.); (W.N.S.)
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
- Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA
- The Edison Family Center of Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Darrell Chandler
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, MI 49503, USA;
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Jung H, Sokolova V, Lee G, Stevens VR, Tan D. Structural and Biochemical Characterization of the Nucleosome Containing Variants H3.3 and H2A.Z. EPIGENOMES 2024; 8:21. [PMID: 38920622 PMCID: PMC11203148 DOI: 10.3390/epigenomes8020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/08/2024] [Accepted: 05/22/2024] [Indexed: 06/27/2024] Open
Abstract
Variant H3.3, along with H2A.Z, is notably enriched at promoter regions and is commonly associated with transcriptional activation. However, the specific molecular mechanisms through which H3.3 influences chromatin dynamics at transcription start sites, and its role in gene regulation, remain elusive. Using a combination of biochemistry and cryo-electron microscopy (cryo-EM), we show that the inclusion of H3.3 alone does not induce discernible changes in nucleosome DNA dynamics. Conversely, the presence of both H3.3 and H2A.Z enhances DNA's flexibility similarly to H2A.Z alone. Interestingly, our findings suggest that the presence of H3.3 in the H2A.Z nucleosome provides slightly increased protection to DNA at internal sites within the nucleosome. These results imply that while H2A.Z at active promoters promotes the formation of more accessible nucleosomes with increased DNA accessibility to facilitate transcription, the simultaneous presence of H3.3 offers an additional mechanism to fine-tune nucleosome accessibility and the chromatin environment.
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Affiliation(s)
- Harry Jung
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, NY 11794, USA; (H.J.); (V.S.); (G.L.); (V.R.S.)
- Department of Pharmacology, Yale University, New Haven, CT 06520, USA
| | - Vladyslava Sokolova
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, NY 11794, USA; (H.J.); (V.S.); (G.L.); (V.R.S.)
| | - Gahyun Lee
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, NY 11794, USA; (H.J.); (V.S.); (G.L.); (V.R.S.)
| | - Victoria Rose Stevens
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, NY 11794, USA; (H.J.); (V.S.); (G.L.); (V.R.S.)
- Chembio Diagnostics Inc., Medford, NY 11763, USA
| | - Dongyan Tan
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, New York, NY 11794, USA; (H.J.); (V.S.); (G.L.); (V.R.S.)
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Hao H, Lian Y, Ren C, Yang S, Zhao M, Bo T, Xu J, Wang W. RebL1 is required for macronuclear structure stability and gametogenesis in Tetrahymena thermophila. MARINE LIFE SCIENCE & TECHNOLOGY 2024; 6:183-197. [PMID: 38827131 PMCID: PMC11136921 DOI: 10.1007/s42995-024-00219-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 03/01/2024] [Indexed: 06/04/2024]
Abstract
Histone modification and nucleosome assembly play important roles in chromatin-related processes. Histone chaperones form different complexes and coordinate histone transportation and assembly. Various histone chaperone complexes have been identified in different organisms. The ciliate protozoa (ciliates) have various chromatin structures and different nuclear morphology. However, histone chaperone components and functions of different subunits remain unclear in ciliates. Tetrahymema thermophila contains a transcriptionally active macronucleus (MAC) and a transcriptionally inactive micronucleus (MIC) which exhibit multiple replication and various chromatin remodeling progresses during vegetative growth and sexual developmental stages. Here, we found histone chaperone RebL1 not only localized evenly in the transcriptionally active MAC but also dynamically changed in the MIC during vegetative growth and sexual developmental stages. REBL1 knockdown inhibited cellular proliferation. The macronuclear morphology became bigger in growing mutants. The abnormal macronuclear structure also occurred in the starvation stage. Furthermore, micronuclear meiosis was disturbed during sexual development, leading to a failure to generate new gametic nuclei. RebL1 potentially interacted with various factors involved in histone-modifying complexes and chromatin remodeling complexes in different developmental stages. REBL1 knockdown affected expression levels of the genes involved in chromatin organization and transcription. Taken together, RebL1 plays a vital role in maintaining macronuclear structure stability and gametogenesis in T. thermophila. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-024-00219-z.
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Affiliation(s)
- Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Chenhui Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Sitong Yang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Min Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
- School of Life Science, Shanxi University, Taiyuan, 030006 China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, 030006 China
- Shanxi Key Laboratory of Biotechnology, Taiyuan, 030006 China
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Hao H, Ren C, Lian Y, Zhao M, Bo T, Xu J, Wang W. Independent and Complementary Functions of Caf1b and Hir1 for Chromatin Assembly in Tetrahymena thermophila. Cells 2023; 12:2828. [PMID: 38132148 PMCID: PMC10741905 DOI: 10.3390/cells12242828] [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: 11/17/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/23/2023] Open
Abstract
Histones and DNA associate to form the nucleosomes of eukaryotic chromatin. Chromatin assembly factor 1 (CAF-1) complex and histone regulatory protein A (HIRA) complex mediate replication-couple (RC) and replication-independent (RI) nucleosome assembly, respectively. CHAF1B and HIRA share a similar domain but play different roles in nucleosome assembly by binding to the different interactors. At present, there is limited understanding for the similarities and differences in their respective functions. Tetrahymena thermophila contains transcriptionally active polyploid macronuclei (MAC) and transcriptionally silent diploid micronuclei (MIC). Here, the distribution patterns of Caf1b and Hir1 exhibited both similarities and distinctions. Both proteins localized to the MAC and MIC during growth, and to the MIC during conjugation. However, Hir1 exhibited additional signaling on parental MAC and new MAC during sexual reproduction and displayed a punctate signal on developing anlagen. Caf1b and Hir1 only co-localized in the MIC with Pcna1 during conjugation. Knockdown of CAF1B impeded cellular growth and arrested sexual reproductive development. Loss of HIR1 led to MIC chromosome defects and aborted sexual development. Co-interference of CAF1B and HIR1 led to a more severe phenotype. Moreover, CAF1B knockdown led to the up-regulation of HIR1 expression, while knockdown of HIR1 also led to an increase in CAF1B expression. Furthermore, Caf1b and Hir1 interacted with different interactors. These results showed that CAF-1 and Hir1 have independent and complementary functions for chromatin assembly in T. thermophila.
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Affiliation(s)
- Huijuan Hao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Chenhui Ren
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Yinjie Lian
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Min Zhao
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Tao Bo
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
| | - Jing Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- School of Life Science, Shanxi University, Taiyuan 030006, China
| | - Wei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan 030006, China; (H.H.); (C.R.); (Y.L.); (M.Z.); (T.B.)
- Shanxi Key Laboratory of Biotechnology, Taiyuan 030006, China
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Morozov VM, Riva A, Sarwar S, Kim WJ, Li J, Zhou L, Licht J, Daaka Y, Ishov A. HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. Nucleic Acids Res 2023; 51:10194-10217. [PMID: 37638746 PMCID: PMC10602887 DOI: 10.1093/nar/gkad700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/21/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growth in vitro and in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. In addition, HIRA KO deregulates glucocorticoid- (GR) driven transcription of genes co-regulated by AR and GR, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity.
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Affiliation(s)
- Viacheslav M Morozov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, USA
| | - Sadia Sarwar
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Wan-Ju Kim
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Jianping Li
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
| | - Lei Zhou
- Department of Molecular Genetics & Microbiology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Jonathan D Licht
- Division of Hematology/Oncology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Yehia Daaka
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
| | - Alexander M Ishov
- Department of Anatomy and Cell Biology, University of Florida College of Medicine, Gainesville, FL, USA
- University of Florida Health Cancer Center, Gainesville, FL, USA
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Wang Y, Peng J, Song C, Yang Y, Qin T. Zinc finger and SCAN domain-containing 18 suppresses the proliferation, self-renewal, and drug resistance of glioblastoma cells. Heliyon 2023; 9:e17000. [PMID: 37389038 PMCID: PMC10300323 DOI: 10.1016/j.heliyon.2023.e17000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 06/02/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023] Open
Abstract
Elucidation of cellular and molecular mechanisms key to glioblastoma growth, self-renewal, survival, and metastasis is important for developing novel therapeutic strategies. In this study, the expression and function of zinc finger and SCAN domain-containing 18 (ZSCAN18) in human glioblastoma cell lines were characterized. Compared with normal astrocytes, ZSCAN18 was significantly down-regulated in all tested glioblastoma cell lines, with the LN-229 cell line having the lowest ZSCAN18 expression. Lentivirus-mediated ZSCAN18 overexpression suppressed glioblastoma cell proliferation, sphere formation, and SOX2 and OCT4 expression, implying the negative role of ZSCAN18 in glioblastoma development. ZSCAN18 overexpression enhanced the sensitivity of glioblastoma cells to Temozolomide. The glioblastoma implantation model showed a consistent inhibitory effect of ZSCAN18 on the proliferation and self-renewal of glioblastoma cells in vivo. Notably, ZSCAN18 overexpression resulted in the down-regulation of glioma-associated oncogene homolog 1 (GLI1) which is the terminal component of the Hedgehog signaling. Lentivirus-mediated GLI1 overexpression restored the proliferation and promoted the resistance of glioblastoma cells to Temozolomide. However, GLI1 overexpression did not affect the self-renewal of ZSCAN18-overexpressing glioblastoma cells. Taken together, this research uncovers the role of ZSCAN18 in regulating glioblastoma cell growth and maintenance. ZSCAN18 could be a potential glioblastoma biomarker.
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Affiliation(s)
- Yan Wang
- The Pediatric Care and Rehabilitation Division at Affiliated Renhe Hospital of China Three Gorges University, Yichang City, Hubei Province, 443000, China
| | - Jingwei Peng
- The Department of Pediatrics at Affiliated Renhe Hospital of China Three Gorges University, Yichang City, Hubei Province, 443000, China
| | - Chenchen Song
- The Pediatric Care and Rehabilitation Division at Affiliated Renhe Hospital of China Three Gorges University, Yichang City, Hubei Province, 443000, China
| | - Yining Yang
- The Pediatric Care and Rehabilitation Division at Affiliated Renhe Hospital of China Three Gorges University, Yichang City, Hubei Province, 443000, China
| | - Tao Qin
- The Department of Radiology and Radiotherapy at Xingshan County People's Hospital, Yichang City, Hubei Province, 443700, China
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Morozov VM, Riva A, Sarwar S, Kim W, Li J, Zhou L, Licht JD, Daaka Y, Ishov AM. HIRA-mediated loading of histone variant H3.3 controls androgen-induced transcription by regulation of AR/BRD4 complex assembly at enhancers. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.536256. [PMID: 37214820 PMCID: PMC10197601 DOI: 10.1101/2023.05.08.536256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Incorporation of histone variant H3.3 comprises active territories of chromatin. Exploring the function of H3.3 in prostate cancer (PC), we found that knockout (KO) of H3.3 chaperone HIRA suppresses PC growth in vitro and in xenograft settings, deregulates androgen-induced gene expression and alters androgen receptor (AR) binding within enhancers of target genes. H3.3 affects transcription in multiple ways, including activation of p300 by phosphorylated H3.3 at Ser-31 (H3.3S31Ph), which results in H3K27 acetylation (H3K27Ac) at enhancers. In turn, H3K27Ac recruits bromodomain protein BRD4 for enhancer-promoter interaction and transcription activation. We observed that HIRA KO reduces H3.3 incorporation, diminishes H3.3S31Ph and H3K27Ac, modifies recruitment of BRD4. These results suggest that H3.3-enriched enhancer chromatin serves as a platform for H3K27Ac-mediated BRD4 recruitment, which interacts with and retains AR at enhancers, resulting in transcription reprogramming. AR KO reduced levels of H3.3 at enhancers, indicating feedback mechanism. In addition, HIRA KO deregulates glucocorticoid-driven transcription, suggesting a common H3.3/HIRA-dependent mechanism of nuclear receptors function. Expression of HIRA complex proteins is increased in PC compared with normal prostate tissue, especially in high-risk PC groups, and is associated with a negative prognosis. Collectively, our results demonstrate function of HIRA-dependent H3.3 pathway in regulation of nuclear receptors activity. Key points *H3.3 at enhancers promotes acetylation of H3K27Ac and retention of AR/BRD4 complex for transcription regulation*Knockout of H3.3 chaperone HIRA suppresses PC cells growth and deregulates androgen-induced transcription*H3.3/HIRA pathway regulates both AR and GR, suggesting a common HIRA/H3.3 mechanism of nuclear receptors function.
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