1
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Kim HM, Kang B, Park S, Park H, Kim C, Lee H, Yoo M, Kweon MN, Im SH, Kim T, Roh TY. Forkhead box protein D2 suppresses colorectal cancer by reprogramming enhancer interactions. Nucleic Acids Res 2023; 51:6143-6155. [PMID: 37158258 PMCID: PMC10325893 DOI: 10.1093/nar/gkad361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/10/2023] Open
Abstract
Somatic stem cells contribute to normal tissue homeostasis, and their epigenomic features play an important role in regulating tissue identities or developing disease states. Enhancers are one of the key players controlling chromatin context-specific gene expression in a spatial and temporal manner while maintaining tissue homeostasis, and their dysregulation leads to tumorigenesis. Here, epigenomic and transcriptomic analyses reveal that forkhead box protein D2 (FOXD2) is a hub for the gene regulatory network exclusive to large intestinal stem cells, and its overexpression plays a significant role in colon cancer regression. FOXD2 is positioned at the closed chromatin and facilitates mixed-lineage leukemia protein-4 (MLL4/KMT2D) binding to deposit H3K4 monomethylation. De novo FOXD2-mediated chromatin interactions rewire the regulation of p53-responsive genes and induction of apoptosis. Taken together, our findings illustrate the novel mechanistic details of FOXD2 in suppressing colorectal cancer growth and suggest its function as a chromatin-tuning factor and a potential therapeutic target for colorectal cancer.
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Affiliation(s)
- Hyo-Min Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Byunghee Kang
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Sohyun Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyorim Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Chan Johng Kim
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Hyeonji Lee
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mijoung Yoo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Mi-Na Kweon
- Department of Convergence Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul 05505, Republic of Korea
| | - Sin-Hyeog Im
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, Seoul 03722, Republic of Korea
- ImmunoBiome, Inc., Pohang 37666, Republic of Korea
| | - Tae Il Kim
- Department of Internal Medicine, Institute of Gastroenterology, Yonsei University College of Medicine, Seoul 03722, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Ewha Womans University, Seoul 03760, Republic of Korea
- Sysgenlab Inc., Pohang 37673, Republic of Korea
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2
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Creation of bladder assembloids mimicking tissue regeneration and cancer. Nature 2020; 588:664-669. [PMID: 33328632 DOI: 10.1038/s41586-020-3034-x] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 10/13/2020] [Indexed: 12/30/2022]
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3
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A novel role of metal response element binding transcription factor 2 at the Hox gene cluster in the regulation of H3K27me3 by polycomb repressive complex 2. Oncotarget 2018; 9:26572-26585. [PMID: 29899877 PMCID: PMC5995182 DOI: 10.18632/oncotarget.25505] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 05/07/2018] [Indexed: 11/25/2022] Open
Abstract
Polycomb repressive complex 2 (PRC2) is known to play an important role in the regulation of early embryonic development, differentiation, and cellular proliferation by introducing methyl groups onto lysine 27 of histone H3 (H3K27me3). PRC2 is tightly associated with silencing of Hox gene clusters and their sequential activation, leading to normal development and differentiation. To investigate epigenetic changes induced by PRC2 during differentiation, deposition of PRC2 components and levels of H3K27me3 were extensively examined using mouse F9 cells as a model system. Contrary to positive correlation between PRC2 deposition and H3K27me3 level, down-regulation of PRC2 components by shRNA and inhibition of EZH1/2 resulted in unexpected elevation of H3K27me3 level at the Hox gene cluster despite its global decrease. We found that metal response element binding transcriptional factor 2 (MTF2), one of sub-stoichiometric components of PRC2, was stably bound to Hox genes. Its binding capability was dependent on other core PRC2 components. A high level of H3K27me3 at Hox genes in Suz12-knock out cells was reversed by knockdown of Mtf2.This shows that MTF2 is necessary to consolidate PRC2-mediated histone methylation. Taken together, our results indicate that expression of Hox gene clusters during differentiation is strictly modulated by the activity of PRC2 secured by MTF2.
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4
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Cho JG, Park S, Lim CH, Kim HS, Song SY, Roh TY, Sung JH, Suh W, Ham SJ, Lim KH, Park SG. ZNF224, Krüppel like zinc finger protein, induces cell growth and apoptosis-resistance by down-regulation of p21 and p53 via miR-663a. Oncotarget 2018; 7:31177-90. [PMID: 27105517 PMCID: PMC5058748 DOI: 10.18632/oncotarget.8870] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/31/2016] [Indexed: 11/25/2022] Open
Abstract
ZNF224 is a Krüppel-associated box-containing zinc-finger protein which represses gene transcription by interacting with various co-repressors. However, its consensus DNA sequences and target genes are not fully identified. In this study, we identified and characterized consensus DNA sequences containing 5′-CAGC-3′; recognized by ZNF224 through ChIP-sequencing, which further confirmed by ELISA, SPR, qPCR, and luciferase activity assay. ZNF224 increased miR-663a transcription by binding to miR-663a promoter, which in turn binds to 3′; UTR of p53 and p21 to decrease their expression. miR-663a antagonist abolished ZNF224-mediated suppression of p21 and p53, resulting in the enhanced apoptosis by CPT. The analyses using human breast ductal carcinoma tissues exhibited that the expression of ZNF224 and miR-663a was increased in cancer compared to non-cancer region. Consequently, ZNF224 increases cell survival and decreases apoptosis by decreasing the expression of p53 and p21 via miR-663a as a transcriptional activator. Taken together, we identified and characterized DNA binding element of ZNF224, and its target genes, miR-663a, which provides a novel insight in the down-regulation of p21 and p53 via miR-663a by ZNF224 in breast cancer.
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Affiliation(s)
- Jin Gu Cho
- Department of Biomedical Science, CHA University, Sungnam-si, Gyunggi-do, Korea.,Laboratory for Tracing of Gene Function, Department of Pharmacy, College of Pharmacy, Ajou University, Suwon, Gyunggi-do, Korea
| | - Seho Park
- Department of Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Chae Hyun Lim
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Hong Sook Kim
- Laboratory for Tracing of Gene Function, Department of Pharmacy, College of Pharmacy, Ajou University, Suwon, Gyunggi-do, Korea
| | - Seung Yong Song
- Department of Plastic and Reconstructive Surgery, Yonsei University College of Medicine, Seoul, Korea
| | - Tae-Young Roh
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Jong-Hyuk Sung
- Department of Pharmacy, College of Pharmacy, Yonsei University, Incheon, Korea
| | - Wonhee Suh
- Department of Pharmacy, College of Pharmacy, Chung-Ang University, Seoul, Korea
| | - Seok-Jin Ham
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk, Korea
| | - Key-Hwan Lim
- Laboratory for Tracing of Gene Function, Department of Pharmacy, College of Pharmacy, Ajou University, Suwon, Gyunggi-do, Korea
| | - Sang Gyu Park
- Laboratory for Tracing of Gene Function, Department of Pharmacy, College of Pharmacy, Ajou University, Suwon, Gyunggi-do, Korea
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5
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Xue Y, Chen R, Du W, Yang F, Wei X. RIZ1 and histone methylation status in pituitary adenomas. Tumour Biol 2017; 39:1010428317711794. [PMID: 28718376 DOI: 10.1177/1010428317711794] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
RIZ1 displays strong tumor-suppressive activities, which has a potential histone methyltransferase activity. The objective of the study was to evaluate the level and the methylation status of RIZ1 and analyze its association with clinicopathological features and the histone in the pituitary adenomas. We found that RIZ1-positive cases were 11/50 and H-Scores 22.75 ± 11.83 in invasive pituitary adenomas and 26/53 and 66.3 ± 21.7 in non-invasive pituitary adenomas (χ2 = 8.182, p = 0.004). RIZ1 and C-myc showed the opposite trend in these cases. The methylation levels of RIZ1 were more than 50% in 30.4% (7/23) CpG sites through MALDI-TOF Mass array. There was significant difference (p < 0.01) in 4 CpG sites between invasive pituitary adenoma group and non-invasive pituitary adenoma group; furthermore, the relieved methylation levels of H3K4/H3K9 and enhanced methylation levels of H3K27 in the patients' serum were found. Furthermore, there was statistic difference of H3K4 and H3K27 methylation between invasive pituitary adenoma and non-invasive pituitary adenoma group (p < 0.01). The average progression-free survival in high RIZ1 group was 52.63 ± 7.62 months and 26.06 ± 4.23 months in low RIZ1 group (p < 0.05). Promoter region methylation of RIZ1 may play an important role in the epigenetic silencing of RIZ1 expression in pituitary adenomas, which may translate into important diagnostic and therapeutic applications.
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Affiliation(s)
- Yake Xue
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Ruokun Chen
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Wei Du
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Fengdong Yang
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xinting Wei
- Department of Neurosurgery, The First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
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6
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Park J, Kwon YW, Ham S, Hong CP, Seo S, Choe MK, Shin SI, Lee CS, Kim HS, Roh TY. Identification of the early and late responder genes during the generation of induced pluripotent stem cells from mouse fibroblasts. PLoS One 2017; 12:e0171300. [PMID: 28152015 PMCID: PMC5289558 DOI: 10.1371/journal.pone.0171300] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/19/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The generation of induced pluripotent stem cell (iPSC), a substitute for embryonic stem cell (ESC), requires the proper orchestration of a transcription program at the chromatin level. Our recent approach for the induction of pluripotent stem cells from fibroblasts using protein extracts from mouse ESCs could overcome the potential tumorigenicity risks associated with random retroviral integration. Here, we examine the epigenetic modifications and the transcriptome of two types of iPSC and of partially reprogrammed iPSCs (iPSCp) generated independently from adult cardiac and skin fibroblasts to assess any perturbations of the transcription program during reprogramming. RESULTS The comparative dissection of the transcription profiles and histone modification patterns at lysines 4 and 27 of histone H3 of the iPSC, iPSCp, ESC, and somatic cells revealed that the iPSC was almost completely comparable to the ESC, regardless of their origins, whereas the genes of the iPSCp were dysregulated to a larger extent. Regardless of the origins of the somatic cells, the fibroblasts induced using the ESC protein extracts appear to be completely reprogrammed into pluripotent cells, although they show unshared marginal differences in their gene expression programs, which may not affect the maintenance of stemness. A comparative investigation of the iPSCp generated by unwanted reprogramming showed that the two groups of genes on the pathway from somatic cells to iPSC might function as sequential reprogramming-competent early and late responders to the induction stimulus. Moreover, some of the divergent genes expressed only in the iPSCp were associated with many tumor-related pathways. CONCLUSIONS Faithful transcriptional reprogramming should follow epigenetic alterations to generate induced pluripotent stem cells from somatic cells. This genome-wide comparison enabled us to define the early and late responder genes during the cell reprogramming process to iPSC. Our results indicate that the cellular responsiveness to external stimuli should be pre-determined and sequentially orchestrated through the tight modulation of the chromatin environment during cell reprogramming to prevent unexpected reprogramming.
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Affiliation(s)
- Jihwan Park
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Yoo-Wook Kwon
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seokjin Ham
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Chang-Pyo Hong
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Seonghye Seo
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Moon Kyung Choe
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - So-I Shin
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | - Choon-Soo Lee
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Hyo-Soo Kim
- National Research Laboratory for Stem Cell Niche, Seoul National University College of Medicine, Seoul, Republic of Korea
- Innovative Research Institute for Cell Therapy and Cardiovascular Center & Department of Internal Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine or College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
- * E-mail:
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7
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Choi N, Park J, Lee JS, Yoe J, Park GY, Kim E, Jeon H, Cho YM, Roh TY, Lee Y. miR-93/miR-106b/miR-375-CIC-CRABP1: a novel regulatory axis in prostate cancer progression. Oncotarget 2016; 6:23533-47. [PMID: 26124181 PMCID: PMC4695135 DOI: 10.18632/oncotarget.4372] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 05/30/2015] [Indexed: 11/25/2022] Open
Abstract
Capicua (CIC) has been implicated in pathogenesis of spinocerebellar ataxia type-1 (SCA1) neurodegenerative disease and some types of cancer; however, the role of CIC in prostate cancer remains unknown. Here we show that CIC suppresses prostate cancer progression. CIC expression was markedly decreased in human prostatic carcinoma. CIC overexpression suppressed prostate cancer cell proliferation, invasion, and migration, whereas CIC RNAi exerted opposite effects. We found that knock-down of CIC derepresses expression of ETV5 and CRABP1 in LNCaP and PC-3 cells, respectively, thereby promoting cell proliferation and invasion. We also discovered that miR-93, miR-106b, and miR-375, which are known to be frequently overexpressed in prostate cancer patients, cooperatively down-regulate CIC levels to promote cancer progression. Altogether, we suggest miR-93/miR-106b/miR-375-CIC-CRABP1 as a novel key regulatory axis in prostate cancer progression.
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Affiliation(s)
- Nahyun Choi
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Jongmin Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Jeon-Soo Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Jeehyun Yoe
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Guk Yeol Park
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Eunjeong Kim
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Hyeongrin Jeon
- Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Yong Mee Cho
- Department of Pathology, University of Ulsan College of Medicine, Asan Medical Center, Seoul, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea.,Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
| | - Yoontae Lee
- Department of Life Sciences, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea.,Division of Integrative Bioscience and Biotechnology, Pohang University of Science and Technology, Pohang, Kyungbuk, Republic of Korea
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8
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Shin SI, Ham S, Park J, Seo SH, Lim CH, Jeon H, Huh J, Roh TY. Z-DNA-forming sites identified by ChIP-Seq are associated with actively transcribed regions in the human genome. DNA Res 2016; 23:477-486. [PMID: 27374614 PMCID: PMC5066173 DOI: 10.1093/dnares/dsw031] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 06/03/2016] [Indexed: 01/08/2023] Open
Abstract
Z-DNA, a left-handed double helical DNA is structurally different from the most abundant B-DNA. Z-DNA has been known to play a significant role in transcription and genome stability but the biological meaning and positions of Z-DNA-forming sites (ZFSs) in the human genome has not been fully explored. To obtain genome-wide map of ZFSs, Zaa with two Z-DNA-binding domains was used for ChIP-Seq analysis. A total of 391 ZFSs were found and their functions were examined in vivo. A large portion of ZFSs was enriched in the promoter regions and contain sequences with high potential to form Z-DNA. Genes containing ZFSs were occupied by RNA polymerase II at the promoters and showed high levels of expression. Moreover, ZFSs were significantly related to active histone marks such as H3K4me3 and H3K9ac. The association of Z-DNA with active transcription was confirmed by the reporter assay system. Overall, our results suggest that Z-DNA formation depends on chromatin structure as well as sequence composition, and is associated with active transcription in human cells. The global information about ZFSs positioning will provide a useful resource for further understanding of DNA structure-dependent transcriptional regulation.
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Affiliation(s)
| | | | - Jihwan Park
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | - Chae Hyun Lim
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
| | | | | | - Tae-Young Roh
- Department of Life Sciences.,Division of Integrative Biosciences & Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Republic of Korea
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9
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Min H, Kong KA, Lee JY, Hong CP, Seo SH, Roh TY, Bae SS, Kim MH. CTCF-mediated Chromatin Loop for the Posterior Hoxc Gene Expression in MEF Cells. IUBMB Life 2016; 68:436-44. [PMID: 27080371 DOI: 10.1002/iub.1504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/15/2016] [Accepted: 03/25/2016] [Indexed: 01/06/2023]
Abstract
Modulation of chromatin structure has been proposed as a molecular mechanism underlying the spatiotemporal collinear expression of Hox genes during development. CCCTC-binding factor (CTCF)-mediated chromatin organization is now recognized as a crucial epigenetic mechanism for transcriptional regulation. Thus, we examined whether CTCF-mediated chromosomal conformation is involved in Hoxc gene expression by comparing wild-type mouse embryonic fibroblast (MEF) cells expressing anterior Hoxc genes with Akt1 null MEFs expressing anterior as well as posterior Hoxc genes. We found that CTCF binding between Hoxc11 and -c12 is important for CTCF-mediated chromosomal loop formation and concomitant posterior Hoxc gene expression. Hypomethylation at this site increased CTCF binding and recapitulated the chromosomal conformation and posterior Hoxc gene expression patterns observed in Akt1 null MEFs. From this work we found that CTCF at the C12|11 does not function as a barrier/boundary, instead let the posterior Hoxc genes switch their interaction from inactive centromeric to active telomeric genomic niche, and concomitant posterior Hoxc gene expression. Although it is not clear whether CTCF affects Hoxc gene expression solely through its looping activity, CTCF-mediated chromatin structural modulation could be an another tier of Hox gene regulation during development. © 2016 IUBMB Life, 68(6):436-444, 2016.
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Affiliation(s)
- Hyehyun Min
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Kyoung-Ah Kong
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Ji-Yeon Lee
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Chang-Pyo Hong
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Seong-Hye Seo
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Tae-Young Roh
- Department of Life Sciences and Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk, Republic of Korea
| | - Sun Sik Bae
- Department of Pharmacology, MRC For Ischemic Tissue Regeneration, Pusan National University School of Medicine, Yangsan, Republic of Korea
| | - Myoung Hee Kim
- Department of Anatomy, Embryology Laboratory, Brain Korea 21 Plus Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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10
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Holmes KA, Brown GD, Carroll JS. Chromatin Immunoprecipitation-Sequencing (ChIP-seq) for Mapping of Estrogen Receptor-Chromatin Interactions in Breast Cancer. Methods Mol Biol 2016; 1366:79-98. [PMID: 26585129 DOI: 10.1007/978-1-4939-3127-9_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chromatin immunoprecipitation-sequencing (ChIP-Seq) is a powerful tool which combines the established method of ChIP with next-generation sequencing (NGS) to determine DNA-binding sites of a protein of interest on a genome-wide level, importantly, allowing for de novo discovery of binding events. Here we describe ChIP-seq using the well-established example of estrogen receptor-α mapping in the MCF7 breast cancer cell line.
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Affiliation(s)
- Kelly A Holmes
- Cambridge Research Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Gordon D Brown
- Cambridge Research Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Jason S Carroll
- Cambridge Research Institute, Cancer Research UK, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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11
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Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) 2015; 7:1925-58. [PMID: 26404381 PMCID: PMC4586802 DOI: 10.3390/cancers7030869] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies and data have revolutionized cancer research and are increasingly being deployed to guide clinicians in treatment decision-making. NGS technologies have allowed us to take an “omics” approach to cancer in order to reveal genomic, transcriptomic, and epigenomic landscapes of individual malignancies. Integrative multi-platform analyses are increasingly used in large-scale projects that aim to fully characterize individual tumours as well as general cancer types and subtypes. In this review, we examine how NGS technologies in particular have contributed to “omics” approaches in cancer research, allowing for large-scale integrative analyses that consider hundreds of tumour samples. These types of studies have provided us with an unprecedented wealth of information, providing the background knowledge needed to make small-scale (including “N of 1”) studies informative and relevant. We also take a look at emerging opportunities provided by NGS and state-of-the-art third-generation sequencing technologies, particularly in the context of translational research. Cancer research and care are currently poised to experience significant progress catalyzed by accessible sequencing technologies that will benefit both clinical- and research-based efforts.
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12
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Khan AA, Lee AJ, Roh TY. Polycomb group protein-mediated histone modifications during cell differentiation. Epigenomics 2015; 7:75-84. [PMID: 25687468 DOI: 10.2217/epi.14.61] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins play an important role in the regulation of gene expression, especially genes encoding lineage-specific factors. Perturbations in PcG protein expression may trigger an unexpected developmental pathway, resulting in birth defects and developmental disabilities. Two Polycomb repressive complexes, PRC1 and PRC2, have been identified and are related with diverse cellular processes through histone modifications. Many developmental genes are trimethylated at histone H3 lysine 27 (H3K27me3) mediated by PRC2, which provides a binding site for PRC1. These processes contribute to chromatin compaction and transcriptional repression. In this review, we discuss about the complex formation of PcG proteins, the mechanism through which they are recruited to target sites and their functional roles in cell differentiation.
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Affiliation(s)
- Abdul Aziz Khan
- Division of Integrative Biosciences & Biotechnology, Pohang University of Science & Technology (POSTECH), Pohang, Gyeongbuk 790-784, Republic of Korea
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13
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Karsli-Ceppioglu S, Dagdemir A, Judes G, Ngollo M, Penault-Llorca F, Pajon A, Bignon YJ, Bernard-Gallon D. Epigenetic mechanisms of breast cancer: an update of the current knowledge. Epigenomics 2015; 6:651-64. [PMID: 25531258 DOI: 10.2217/epi.14.59] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Epigenetic alterations are heritable changes in gene expression that occur without causing any change in DNA sequence. They are important key factors for cancer development and prognosis. Breast cancer is induced by the accumulation of altered gene regulation. Besides genetic mutations, epigenetics mechanisms have an important role in breast cancer tumorigenesis. Investigations related with aberrant epigenetic regulations in breast cancer focus on initiating molecular mechanisms in cancer development, identification of new biomarkers to predict breast cancer aggressiveness and the potential of epigenetic therapy. In this review, we will summarize the recent knowledge about the role of epigenetic alterations related with DNA methylation and histone modification in breast cancer. In addition, altered regulation of breast cancer specific genes and the potential of epigenetic therapy will be discussed according to epigenetic mechanisms.
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Griffon A, Barbier Q, Dalino J, van Helden J, Spicuglia S, Ballester B. Integrative analysis of public ChIP-seq experiments reveals a complex multi-cell regulatory landscape. Nucleic Acids Res 2014; 43:e27. [PMID: 25477382 PMCID: PMC4344487 DOI: 10.1093/nar/gku1280] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The large collections of ChIP-seq data rapidly accumulating in public data warehouses provide genome-wide binding site maps for hundreds of transcription factors (TFs). However, the extent of the regulatory occupancy space in the human genome has not yet been fully apprehended by integrating public ChIP-seq data sets and combining it with ENCODE TFs map. To enable genome-wide identification of regulatory elements we have collected, analysed and retained 395 available ChIP-seq data sets merged with ENCODE peaks covering a total of 237 TFs. This enhanced repertoire complements and refines current genome-wide occupancy maps by increasing the human genome regulatory search space by 14% compared to ENCODE alone, and also increases the complexity of the regulatory dictionary. As a direct application we used this unified binding repertoire to annotate variant enhancer loci (VELs) from H3K4me1 mark in two cancer cell lines (MCF-7, CRC) and observed enrichments of specific TFs involved in biological key functions to cancer development and proliferation. Those enrichments of TFs within VELs provide a direct annotation of non-coding regions detected in cancer genomes. Finally, full access to this catalogue is available online together with the TFs enrichment analysis tool (http://tagc.univ-mrs.fr/remap/).
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Affiliation(s)
- Aurélien Griffon
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Quentin Barbier
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Jordi Dalino
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Jacques van Helden
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Salvatore Spicuglia
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
| | - Benoit Ballester
- INSERM, UMR1090 TAGC, Marseille, F-13288, France Aix-Marseille Université, UMR1090 TAGC, Marseille, F-13288, France
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Kim HY, Choi BS, Kim SS, Roh TY, Park J, Yoon CH. NUCKS1, a novel Tat coactivator, plays a crucial role in HIV-1 replication by increasing Tat-mediated viral transcription on the HIV-1 LTR promoter. Retrovirology 2014; 11:67. [PMID: 25116364 PMCID: PMC4181878 DOI: 10.1186/s12977-014-0067-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 07/28/2014] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Human immunodeficiency virus-1 (HIV-1) Tat protein plays an essential role in HIV gene transcription from the HIV-1 long terminal repeat (LTR) and replication. Transcriptional activity of Tat is modulated by several host factors, but the mechanism responsible for Tat regulation by host factors is not understood fully. RESULTS Using a yeast two-hybrid screening system, we identified Nuclear ubiquitous casein and cyclin-dependent kinase substrate 1 (NUCKS1) as a novel Tat-interacting partner. Here, we report its function as a positive regulator of Tat. In a coimmunoprecipitation assay, HIV-1 Tat interacted sufficiently with both endogenous and ectopically expressed NUCKS1. In a reporter assay, ectopic expression of NUCKS1 significantly increased Tat-mediated transcription of the HIV-1 LTR, whereas knockdown of NUCKS1 by small interfering RNA diminished Tat-mediated transcription of the HIV-1 LTR. We also investigated which mechanism contributes to NUCKS1-mediated Tat activation. In a chromatin immunoprecipitation assay (ChIP), knockdown of NUCKS1 interrupted the accumulation of Tat in the transactivation-responsive (TAR) region on the LTR, which then led to suppression of viral replication. However, NUCKS1 expression did not increase Tat nuclear localization and interaction with Cyclin T1. Interestingly, the NUCKS1 expression level was lower in latently HIV-1-infected cells than in uninfected parent cells. Besides, expression level of NUCKS1 was markedly induced, which then facilitated HIV-1 reactivation in latently infected cells. CONCLUSION Taken together, our data demonstrate clearly that NUCKS1 is a novel Tat coactivator that is required for Tat-mediated HIV-1 transcription and replication, and that it may contribute to HIV-1 reactivation in latently HIV-1 infected cells.
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Affiliation(s)
- Hye-Young Kim
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Byeong-Sun Choi
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Sung Soon Kim
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
| | - Tae-Young Roh
- />Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Republic of Korea
| | - Jihwan Park
- />Department of Life Sciences, Pohang University of Science and Technology (POSTECH), Pohang, 790-784 Republic of Korea
| | - Cheol-Hee Yoon
- />Division of AIDS, Korean National Institute of Health, Chungbuk, Republic of Korea
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Zane L, Sharma V, Misteli T. Common features of chromatin in aging and cancer: cause or coincidence? Trends Cell Biol 2014; 24:686-94. [PMID: 25103681 DOI: 10.1016/j.tcb.2014.07.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Revised: 06/30/2014] [Accepted: 07/01/2014] [Indexed: 02/06/2023]
Abstract
Age is a major risk factor for cancer. Alterations in DNA methylation, histone modifications, chromatin structure, and epigenetic regulatory mechanisms are prominent hallmarks of both the aging process and cancer. Intriguingly--or possibly coincidentally--several chromatin features are common between aging and cancer. Here we ask whether, and if so how, aging-associated chromatin modifications contribute to tumor susceptibility and tumorigenesis.
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Affiliation(s)
- Linda Zane
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Vivek Sharma
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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Abstract
Objectives: The transcriptional silencing of HIV type 1 (HIV-1) provirus in latently infected cells is a major hurdle on the pathway to HIV-1 elimination. The epigenetic mechanisms established by histone modifications may affect the transcriptional silencing of HIV-1 and viral latency. A systematic epigenome profiling could be applicable to develop new epigenetic diagnostic markers for detecting HIV-1 latency. Design: The HIV-1 latency cell lines (NCHA1, NCHA2 and ACH2] were compared with CD4+ T-cell line (A3.01). Methods: The histone modification profiles obtained from chromatin immunoprecipiation followed by sequencing (ChIP-Seq) for histone H3K4me3 and H3K9ac were systematically examined and differential gene expression patterns along with levels of histone modifications were used for network analysis. Results: The HIV-1 latency gave rise to downregulation of histone H3K4me3 and H3K9ac levels in 387 and 493 regions and upregulation in 451 and 962 sites, respectively. By network analysis, five gene clusters were associated with downregulated histone modifications and six gene clusters came up with upregulated histone modifications. Integration of gene expression with epigenetic information revealed that the cell cycle regulatory genes such as CDKN1A (p21) and cyclin D2 (CCND2) identified by differentially modified histones might play an important role in maintaining the HIV-1 latency. Conclusion: The transcriptional regulation by epigenetic memory should play a key role in the evolution and maintenance of HIV-1 latency accompanied by modulation of signalling molecules in the host cells.
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Lee HT, Kim SK, Choi MR, Park JH, Jung KH, Chai YG. Effects of the activated mitogen-activated protein kinase pathway via the c-ros receptor tyrosine kinase on the T47D breast cancer cell line following alcohol exposure. Oncol Rep 2012; 29:868-74. [PMID: 23292247 PMCID: PMC3597588 DOI: 10.3892/or.2012.2209] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2012] [Accepted: 11/28/2012] [Indexed: 12/13/2022] Open
Abstract
Compared to other cancers affecting women, breast cancer is significantly associated with alcohol consumption. However, the principles underlying the carcinogenesis of alcohol-induced breast cancer and the related metastatic mechanisms have yet to be established. To observe the effect of alcohol on the growth regulation in breast cancer cells, we identified differentially expressed proteins in alcohol-exposed human breast cancer T47D cells using gel-based proteomics analysis. The expression of c-ros receptor tyrosine kinase (ROS1) was increased and activated by autophosphorylation, thereby activating mitogen- and stress-activated protein kinase 1 (MSK1) through the mitogen-activated protein kinase (MAPK) pathway; activated MSK1, in turn, phosphorylated histone 3 serine 10 (H3S10p) residues in the nucleus. The increase in H3S10 phosphorylation consequently increased the level of expression of immediate-early gene such as c-fos. This study demonstrated that when breast cancer cells are exposed to alcohol, phosphorylated ROS1 activates MSK1 via ERK1/2 in the MAPK pathway, which then induces modifications to histone residues that regulate gene expression by 14-3-3 protein recruitment, leading to a lack of control of breast cancer cell proliferation.
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Affiliation(s)
- Hyung Tae Lee
- Department of Molecular and Life Science, Hanyang University, Ansan, Republic of Korea
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Hong CP, Choe MK, Roh TY. Characterization of Chromatin Structure-associated Histone Modifications in Breast Cancer Cells. Genomics Inform 2012; 10:145-52. [PMID: 23166525 PMCID: PMC3492650 DOI: 10.5808/gi.2012.10.3.145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 08/22/2012] [Accepted: 08/24/2012] [Indexed: 12/30/2022] Open
Abstract
Chromatin structure and dynamics that are influenced by epigenetic marks, such as histone modification and DNA methylation, play a crucial role in modulating gene transcription. To understand the relationship between histone modifications and regulatory elements in breast cancer cells, we compared our chromatin immunoprecipitation sequencing (ChIP-Seq) histone modification patterns for histone H3K4me1, H3K4me3, H3K9/16ac, and H3K27me3 in MCF-7 cells with publicly available formaldehyde-assisted isolation of regulatory elements (FAIRE)-chip signals in human chromosomes 8, 11, and 12, identified by a method called FAIRE. Active regulatory elements defined by FAIRE were highly associated with active histone modifications, like H3K4me3 and H3K9/16ac, especially near transcription start sites. The H3K9/16ac-enriched genes that overlapped with FAIRE signals (FAIRE-H3K9/14ac) were moderately correlated with gene expression levels. We also identified functional sequence motifs at H3K4me1-enriched FAIRE sites upstream of putative promoters, suggesting that regulatory elements could be associated with H3K4me1 to be regarded as distal regulatory elements. Our results might provide an insight into epigenetic regulatory mechanisms explaining the association of histone modifications with open chromatin structure in breast cancer cells.
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Affiliation(s)
- Chang Pyo Hong
- Division of Molecular and Life Sciences, Pohang University of Science and Technology, Pohang 790-784, Korea. ; Theragen Etex Bio Institute, Suwon 443-270, Korea
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