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Mizokami H, Okabe A, Choudhary R, Mima M, Saeda K, Fukuyo M, Rahmutulla B, Seki M, Goh BC, Kondo S, Dochi H, Moriyama-Kita M, Misawa K, Hanazawa T, Tan P, Yoshizaki T, Fullwood MJ, Kaneda A. Enhancer infestation drives tumorigenic activation of inactive B compartment in Epstein-Barr virus-positive nasopharyngeal carcinoma. EBioMedicine 2024; 102:105057. [PMID: 38490101 PMCID: PMC10951899 DOI: 10.1016/j.ebiom.2024.105057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 02/13/2024] [Accepted: 02/28/2024] [Indexed: 03/17/2024] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is an Epstein-Barr virus (EBV)-associated malignant epithelial tumor endemic to Southern China and Southeast Asia. While previous studies have revealed a low frequency of gene mutations in NPC, its epigenomic aberrations are not fully elucidated apart from DNA hypermethylation. Epigenomic rewiring and enhancer dysregulation, such as enhancer hijacking due to genomic structural changes or extrachromosomal DNA, drive cancer progression. METHODS We conducted Hi-C, 4C-seq, ChIP-seq, and RNA-seq analyses to comprehensively elucidate the epigenome and interactome of NPC using C666-1 EBV(+)-NPC cell lines, NP69T immortalized nasopharyngeal epithelial cells, clinical NPC biopsy samples, and in vitro EBV infection in HK1 and NPC-TW01 EBV(-) cell lines. FINDINGS In C666-1, the EBV genome significantly interacted with inactive B compartments of host cells; the significant association of EBV-interacting regions (EBVIRs) with B compartment was confirmed using clinical NPC and in vitro EBV infection model. EBVIRs in C666-1 showed significantly higher levels of active histone modifications compared with NP69T. Aberrant activation of EBVIRs after EBV infection was validated using in vitro EBV infection models. Within the EBVIR-overlapping topologically associating domains, 14 H3K4me3(+) genes were significantly upregulated in C666-1. Target genes of EBVIRs including PLA2G4A, PTGS2 and CITED2, interacted with the enhancers activated in EBVIRs and were highly expressed in NPC, and their knockdown significantly reduced cell proliferation. INTERPRETATION The EBV genome contributes to NPC tumorigenesis through "enhancer infestation" by interacting with the inactive B compartments of the host genome and aberrantly activating enhancers. FUNDING The funds are listed in the Acknowledgements section.
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Affiliation(s)
- Harue Mizokami
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Health and Disease Omics Center, Chiba University, Chiba, 260-8670, Japan
| | - Ruchi Choudhary
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Masato Mima
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Hamamatsu University School of Medicine, Shizuoka, 431-3125, Japan
| | - Kenta Saeda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Motoaki Seki
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Boon-Cher Goh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore; Department of Haematology-Oncology, National University Cancer Institute, Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Blk MD3, 16 Medical Drive, Singapore, 117600, Singapore
| | - Satoru Kondo
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Hirotomo Dochi
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Makiko Moriyama-Kita
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Kiyoshi Misawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Hamamatsu University School of Medicine, Shizuoka, 431-3125, Japan
| | - Toyoyuki Hanazawa
- Department of Otorhinolaryngology/Head and Neck Surgery, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore, 169857, Singapore
| | - Tomokazu Yoshizaki
- Division of Otolaryngology and Head and Neck Surgery, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, 920-8640, Japan
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore; Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, 117599, Singapore; Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan; Health and Disease Omics Center, Chiba University, Chiba, 260-8670, Japan.
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Yeo SJ, Ying C, Fullwood MJ, Tergaonkar V. Emerging regulatory mechanisms of noncoding RNAs in topologically associating domains. Trends Genet 2023; 39:217-232. [PMID: 36642680 DOI: 10.1016/j.tig.2022.12.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 01/15/2023]
Abstract
Topologically associating domains (TADs) are integral to spatial genome organization, instructing gene expression, and cell fate. Recently, several advances have uncovered roles for noncoding RNAs (ncRNAs) in the regulation of the form and function of mammalian TADs. Phase separation has also emerged as a potential arbiter of ncRNAs in the regulation of TADs. In this review we discuss the implications of these novel findings in relation to how ncRNAs might structurally and functionally regulate TADs from two perspectives: moderating loop extrusion through interactions with architectural proteins, and facilitating TAD phase separation. Additionally, we propose future studies and directions to investigate these phenomena.
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Affiliation(s)
- Samuel Jianjie Yeo
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Lee Kong Chian School of Medicine, Nanyang Technological University (NTU), Singapore 308232, Singapore
| | - Chen Ying
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore 117599, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore.
| | - Vinay Tergaonkar
- Laboratory of NFκB Signaling, Institute of Molecular Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore 138673, Singapore; Department of Pathology and the Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore 117597, Singapore.
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3
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Warrier T, El Farran C, Zeng Y, Ho B, Bao Q, Zheng Z, Bi X, Ng HH, Ong D, Chu J, Sanyal A, Fullwood MJ, Collins J, Li H, Xu J, Loh YH. SETDB1 acts as a topological accessory to Cohesin via an H3K9me3-independent, genomic shunt for regulating cell fates. Nucleic Acids Res 2022; 50:7326-7349. [PMID: 35776115 PMCID: PMC9303280 DOI: 10.1093/nar/gkac531] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/30/2022] [Accepted: 06/30/2022] [Indexed: 11/13/2022] Open
Abstract
SETDB1 is a key regulator of lineage-specific genes and endogenous retroviral elements (ERVs) through its deposition of repressive H3K9me3 mark. Apart from its H3K9me3 regulatory role, SETDB1 has seldom been studied in terms of its other potential regulatory roles. To investigate this, a genomic survey of SETDB1 binding in mouse embryonic stem cells across multiple libraries was conducted, leading to the unexpected discovery of regions bereft of common repressive histone marks (H3K9me3, H3K27me3). These regions were enriched with the CTCF motif that is often associated with the topological regulator Cohesin. Further profiling of these non-H3K9me3 regions led to the discovery of a cluster of non-repeat loci that were co-bound by SETDB1 and Cohesin. These regions, which we named DiSCs (domains involving SETDB1 and Cohesin) were seen to be proximal to the gene promoters involved in embryonic stem cell pluripotency and lineage development. Importantly, it was found that SETDB1-Cohesin co-regulate target gene expression and genome topology at these DiSCs. Depletion of SETDB1 led to localized dysregulation of Cohesin binding thereby locally disrupting topological structures. Dysregulated gene expression trends revealed the importance of this cluster in ES cell maintenance as well as at gene 'islands' that drive differentiation to other lineages. The 'unearthing' of the DiSCs thus unravels a unique topological and transcriptional axis of control regulated chiefly by SETDB1.
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Affiliation(s)
- Tushar Warrier
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Chadi El Farran
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
| | - Yingying Zeng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Benedict Shao Quan Ho
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Qiuye Bao
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Zi Hao Zheng
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Xuezhi Bi
- Proteomics Group, Bioprocessing Technology Institute, A*STAR, Singapore 138668, Singapore
| | - Huck Hui Ng
- Gene Regulation Laboratory, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Derrick Sek Tong Ong
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Justin Jang Hann Chu
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- Infectious Disease Translational Research Programme, National University of Singapore, Singapore 117597, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
| | - Melissa Jane Fullwood
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive 637551, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore
| | - James J Collins
- Howard Hughes Medical Institute, Boston, MA 02114, USA
- Institute for Medical Engineering and Science Department of Biological Engineering, and Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA 02114, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Hu Li
- Center for Individualized Medicine, Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jian Xu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Plant Systems Physiology, Radboud Institute for Biological and Environmental Sciences, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, The Netherlands
| | - Yuin-Han Loh
- Cell Fate Engineering and Therapeutics Lab, Cell Biology and Therapies Division, A*STAR Institute of Molecular and Cell Biology, Singapore 138673, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 28 MedicalDrive, Singapore 117456, Singapore
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Animesh S, Choudhary R, Wong BJH, Koh CTJ, Ng XY, Tay JKX, Chong WQ, Jian H, Chen L, Goh BC, Fullwood MJ. Profiling of 3D Genome Organization in Nasopharyngeal Cancer Needle Biopsy Patient Samples by a Modified Hi-C Approach. Front Genet 2021; 12:673530. [PMID: 34539729 PMCID: PMC8446523 DOI: 10.3389/fgene.2021.673530] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 07/31/2021] [Indexed: 11/16/2022] Open
Abstract
Nasopharyngeal cancer (NPC), a cancer derived from epithelial cells in the nasopharynx, is a cancer common in China, Southeast Asia, and Africa. The three-dimensional (3D) genome organization of nasopharyngeal cancer is poorly understood. A major challenge in understanding the 3D genome organization of cancer samples is the lack of a method for the characterization of chromatin interactions in solid cancer needle biopsy samples. Here, we developed Biop-C, a modified in situ Hi-C method using solid cancer needle biopsy samples. We applied Biop-C to characterize three nasopharyngeal cancer solid cancer needle biopsy patient samples. We identified topologically associated domains (TADs), chromatin interaction loops, and frequently interacting regions (FIREs) at key oncogenes in nasopharyngeal cancer from the Biop-C heatmaps. We observed that the genomic features are shared at some important oncogenes, but the patients also display extensive heterogeneity at certain genomic loci. On analyzing the super enhancer landscape in nasopharyngeal cancer cell lines, we found that the super enhancers are associated with FIREs and can be linked to distal genes via chromatin loops in NPC. Taken together, our results demonstrate the utility of our Biop-C method in investigating 3D genome organization in solid cancers.
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Affiliation(s)
- Sambhavi Animesh
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Ruchi Choudhary
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | | | - Charlotte Tze Jia Koh
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Xin Yi Ng
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Joshua Kai Xun Tay
- Department of Otolaryngology - Head and Neck Surgery, National University of Singapore, Singapore, Singapore
| | - Wan-Qin Chong
- Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore
| | - Han Jian
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore
| | - Leilei Chen
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,Department of Anatomy, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Boon Cher Goh
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,Department of Haematology-Oncology, National University Cancer Institute, National University Health System, Singapore, Singapore.,Department of Pharmacology, Yong Loo Lin School of Medicine, National University Health System, Singapore, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, Centre for Translational Medicine, National University of Singapore, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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5
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Zhang Y, Cai Y, Roca X, Kwoh CK, Fullwood MJ. Chromatin loop anchors predict transcript and exon usage. Brief Bioinform 2021; 22:6319936. [PMID: 34263910 PMCID: PMC8575016 DOI: 10.1093/bib/bbab254] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 06/16/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022] Open
Abstract
Epigenomics and transcriptomics data from high-throughput sequencing techniques such as RNA-seq and ChIP-seq have been successfully applied in predicting gene transcript expression. However, the locations of chromatin loops in the genome identified by techniques such as Chromatin Interaction Analysis with Paired End Tag sequencing (ChIA-PET) have never been used for prediction tasks. Here, we developed machine learning models to investigate if ChIA-PET could contribute to transcript and exon usage prediction. In doing so, we used a large set of transcription factors as well as ChIA-PET data. We developed different Gradient Boosting Trees models according to the different tasks with the integrated datasets from three cell lines, including GM12878, HeLaS3 and K562. We validated the models via 10-fold cross validation, chromosome-split validation and cross-cell validation. Our results show that both transcript and splicing-derived exon usage can be effectively predicted with at least 0.7512 and 0.7459 of accuracy, respectively, on all cell lines from all kinds of validations. Examining the predictive features, we found that RNA Polymerase II ChIA-PET was one of the most important features in both transcript and exon usage prediction, suggesting that chromatin loop anchors are predictive of both transcript and exon usage.
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Affiliation(s)
- Yu Zhang
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Yichao Cai
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Dr, Singapore 637551, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore, 639798, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Dr, Singapore 117599, Singapore.,School of Biological Sciences, Nanyang Technological University, 637551, Singapore.,Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Dr, Singapore 138673, Singapore
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6
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Zhou Q, Yu M, Tirado-Magallanes R, Li B, Kong L, Guo M, Tan ZH, Lee S, Chai L, Numata A, Benoukraf T, Fullwood MJ, Osato M, Ren B, Tenen DG. ZNF143 mediates CTCF-bound promoter-enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun 2021; 12:43. [PMID: 33397967 PMCID: PMC7782510 DOI: 10.1038/s41467-020-20282-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 11/23/2020] [Indexed: 12/28/2022] Open
Abstract
CCCTC binding factor (CTCF) is an important factor in the maintenance of chromatin-chromatin interactions, yet the mechanism regulating its binding to chromatin is unknown. We demonstrate that zinc finger protein 143 (ZNF143) is a key regulator for CTCF-bound promoter-enhancer loops. In the murine genome, a large percentage of CTCF and ZNF143 DNA binding motifs are distributed 37 bp apart in the convergent orientation. Furthermore, deletion of ZNF143 leads to loss of CTCF binding on promoter and enhancer regions associated with gene expression changes. CTCF-bound promoter-enhancer loops are also disrupted after excision of ZNF143. ZNF143-CTCF-bound promoter-enhancer loops regulate gene expression patterns essential for maintenance of murine hematopoietic stem and progenitor cell integrity. Our data suggest a common feature of gene regulation is that ZNF143 is a critical factor for CTCF-bound promoter-enhancer loops.
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Affiliation(s)
- Qiling Zhou
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- YLL School of Medicine, National University of Singapore, 119228, Singapore, Singapore
| | - Miao Yu
- School of Life Sciences, Fudan University, Shanghai, China
| | - Roberto Tirado-Magallanes
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Bin Li
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
| | - Lingshi Kong
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Mingrui Guo
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- YLL School of Medicine, National University of Singapore, 119228, Singapore, Singapore
| | - Zi Hui Tan
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Sanghoon Lee
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Li Chai
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA
| | - Akihiko Numata
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Medicine and Biosystemic Science, Kyushu University Graduate School of Medical Science, Fukuoka, Japan
| | - Touati Benoukraf
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, NL, A1B 3V6, Canada
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), 61 Biopolis Drive, Proteos, 138673, Singapore
| | - Motomi Osato
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore
| | - Bing Ren
- Ludwig Institute for Cancer Research, La Jolla, CA, 92093, USA
- Department of Cellular & Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, UCSD School of Medicine, 9500 Gilman Drive, La Jolla, CA, 92093, USA
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, 117599, Singapore, Singapore.
- Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, 02115, USA.
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7
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Zhang Y, Jia C, Fullwood MJ, Kwoh CK. DeepCPP: a deep neural network based on nucleotide bias information and minimum distribution similarity feature selection for RNA coding potential prediction. Brief Bioinform 2020; 22:2073-2084. [PMID: 32227075 DOI: 10.1093/bib/bbaa039] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 12/22/2022] Open
Abstract
The development of deep sequencing technologies has led to the discovery of novel transcripts. Many in silico methods have been developed to assess the coding potential of these transcripts to further investigate their functions. Existing methods perform well on distinguishing majority long noncoding RNAs (lncRNAs) and coding RNAs (mRNAs) but poorly on RNAs with small open reading frames (sORFs). Here, we present DeepCPP (deep neural network for coding potential prediction), a deep learning method for RNA coding potential prediction. Extensive evaluations on four previous datasets and six new datasets constructed in different species show that DeepCPP outperforms other state-of-the-art methods, especially on sORF type data, which overcomes the bottleneck of sORF mRNA identification by improving more than 4.31, 37.24 and 5.89% on its accuracy for newly discovered human, vertebrate and insect data, respectively. Additionally, we also revealed that discontinuous k-mer, and our newly proposed nucleotide bias and minimal distribution similarity feature selection method play crucial roles in this classification problem. Taken together, DeepCPP is an effective method for RNA coding potential prediction.
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Affiliation(s)
- Yu Zhang
- School of Computer Science and Engineering, Nanyang Techonological University, 50 Nanyang Avenue, Singapore
| | - Cangzhi Jia
- School of Mathematical Sciences, Dalian University of Technology, No.2 Linggong Road, Dalian, China
| | - Melissa Jane Fullwood
- School of Computer Science and Engineering, Nanyang Techonological University, 50 Nanyang Avenue, Singapore
| | - Chee Keong Kwoh
- School of Computer Science and Engineering, Nanyang Techonological University, 50 Nanyang Avenue, Singapore
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Lee DP, Tan WLW, Anene-Nzelu CG, Lee CJM, Li PY, Luu TDA, Chan CX, Tiang Z, Ng SL, Huang X, Efthymios M, Autio MI, Jiang J, Fullwood MJ, Prabhakar S, Lieberman Aiden E, Foo RSY. Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response. Circulation 2020; 139:1937-1956. [PMID: 30717603 DOI: 10.1161/circulationaha.118.036726] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
BACKGROUND The human genome folds in 3 dimensions to form thousands of chromatin loops inside the nucleus, encasing genes and cis-regulatory elements for accurate gene expression control. Physical tethers of loops are anchored by the DNA-binding protein CTCF and the cohesin ring complex. Because heart failure is characterized by hallmark gene expression changes, it was recently reported that substantial CTCF-related chromatin reorganization underpins the myocardial stress-gene response, paralleled by chromatin domain boundary changes observed in CTCF knockout. METHODS We undertook an independent and orthogonal analysis of chromatin organization with mouse pressure-overload model of myocardial stress (transverse aortic constriction) and cardiomyocyte-specific knockout of Ctcf. We also downloaded published data sets of similar cardiac mouse models and subjected them to independent reanalysis. RESULTS We found that the cardiomyocyte chromatin architecture remains broadly stable in transverse aortic constriction hearts, whereas Ctcf knockout resulted in ≈99% abolition of global chromatin loops. Disease gene expression changes correlated instead with differential histone H3K27-acetylation enrichment at their respective proximal and distal interacting genomic enhancers confined within these static chromatin structures. Moreover, coregulated genes were mapped out as interconnected gene sets on the basis of their multigene 3D interactions. CONCLUSIONS This work reveals a more stable genome-wide chromatin framework than previously described. Myocardial stress-gene transcription responds instead through H3K27-acetylation enhancer enrichment dynamics and gene networks of coregulation. Robust and intact CTCF looping is required for the induction of a rapid and accurate stress response.
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Affiliation(s)
- Dominic Paul Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Wilson Lek Wen Tan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chukwuemeka George Anene-Nzelu
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Chang Jie Mick Lee
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Peter Yiqing Li
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Tuan Danh Anh Luu
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Cheryl Xueli Chan
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Zenia Tiang
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Shi Ling Ng
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Xingfan Huang
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Motakis Efthymios
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Matias I Autio
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
| | - Jianming Jiang
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
- Department of Biochemistry, School of Medicine (J.J.), National University of Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute (M.J.F.), National University of Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore (M.J.F.)
| | - Shyam Prabhakar
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
| | - Erez Lieberman Aiden
- Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX (X.H., E.L.A.)
- Center for Theoretical Biological Physics and Department of Computer Science, Rice University, Houston, TX (X.H., E.L.A.)
| | - Roger Sik-Yin Foo
- Genome Institute of Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., C.X.C., Z.T., S.L.N., M.E., M.I.A., S.P., R.S.-Y.F.)
- Cardiovascular Research Institute, National University Health System, Centre for Translational Medicine, Singapore (D.P.L., W.L.W.T., C.G.A.-N., C.J.M.L., P.Y.L., T.L.D.A., C.X.C., Z.T., S.L.N., M.E., M.I.A., J.J., R.S.-Y.F.)
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9
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Jadhav SP, Kumari N, Ng L, Tan PF, Yeo-Teh NSL, Goh Y, Fam WN, Tng JQ, Tian JS, Koh BTH, Chun CM, Wang W, Chng WJ, Fullwood MJ, Guccione E, Karnani N, Tenen DG, Jha S. circASXL1-1 regulates BAP1 deubiquitinase activity in leukemia. Haematologica 2019; 105:e343-e348. [PMID: 31780633 DOI: 10.3324/haematol.2019.225961] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Shweta Pradip Jadhav
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Nishi Kumari
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Larry Ng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Pei Fang Tan
- Singapore Institute for Clinical Sciences, A*STAR, Singapore
| | - Nicole Shu Ling Yeo-Teh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,National University of Singapore Graduate School for Integrative Sciences and Engineering, Singapore
| | - Yufen Goh
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Wee Nih Fam
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia Qi Tng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Johann Shane Tian
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bryan T H Koh
- Department of Orthopedic Surgery, National University Health Systems, Singapore
| | - Chan Ming Chun
- Department of Orthopedic Surgery, National University Health Systems, Singapore
| | - Wilson Wang
- Department of Orthopedic Surgery, National University of Singapore, Singapore
| | - Wee Joo Chng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Hematology-Oncology, National University Cancer Institute, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,School of Biological Sciences, Nanyang Technological Institute, Singapore.,Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore.,Tisch Cancer Institute, Department of Oncological Sciences and Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Daniel G Tenen
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Harvard Stem Cell Institute, Harvard Medical School, Boston, MA, USA
| | - Sudhakar Jha
- Cancer Science Institute of Singapore, National University of Singapore, Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
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10
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Yan T, Ooi WF, Qamra A, Cheung A, Ma D, Sundaram GM, Xu C, Xing M, Poon L, Wang J, Loh YP, Ho JHJ, Ng JJQ, Ramlee MK, Aswad L, Rozen SG, Ghosh S, Bard FA, Sampath P, Tergaonkar V, Davies JOJ, Hughes JR, Goh E, Bi X, Fullwood MJ, Tan P, Li S. HoxC5 and miR-615-3p target newly evolved genomic regions to repress hTERT and inhibit tumorigenesis. Nat Commun 2018; 9:100. [PMID: 29311615 PMCID: PMC5758779 DOI: 10.1038/s41467-017-02601-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 12/13/2017] [Indexed: 02/06/2023] Open
Abstract
The repression of telomerase activity during cellular differentiation promotes replicative aging and functions as a physiological barrier for tumorigenesis in long-lived mammals, including humans. However, the underlying mechanisms remain largely unclear. Here we describe how miR-615-3p represses hTERT expression. mir-615-3p is located in an intron of the HOXC5 gene, a member of the highly conserved homeobox family of transcription factors controlling embryogenesis and development. Unexpectedly, we found that HoxC5 also represses hTERT expression by disrupting the long-range interaction between hTERT promoter and its distal enhancer. The 3'UTR of hTERT and its upstream enhancer region are well conserved in long-lived primates. Both mir-615-3p and HOXC5 are activated upon differentiation, which constitute a feed-forward loop that coordinates transcriptional and post-transcriptional repression of hTERT during cellular differentiation. Deregulation of HOXC5 and mir-615-3p expression may contribute to the activation of hTERT in human cancers.
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Affiliation(s)
- TingDong Yan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Wen Fong Ooi
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - Aditi Qamra
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
| | - Alice Cheung
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - DongLiang Ma
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | | | - Chang Xu
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
| | - Manjie Xing
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cancer Therapeutics and Stratified Oncology, Genome Institute of Singapore, 60 Biopolis Street, Singapore, 138672, Singapore
| | - LaiFong Poon
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Jing Wang
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Yan Ping Loh
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Jess Hui Jie Ho
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Joscelyn Jun Quan Ng
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Muhammad Khairul Ramlee
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Luay Aswad
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Steve G Rozen
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Duke-NUS Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Sujoy Ghosh
- Cardiovascular and Metabolic Disorders Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Frederic A Bard
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - Prabha Sampath
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Institute of Medical Biology (IMB), 8A Biomedical Grove, Singapore, 138648, Singapore
| | - Vinay Tergaonkar
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - James O J Davies
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Jim R Hughes
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, Oxford University, Oxford, OX3 9DS, UK
| | - Eyleen Goh
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
- Neuroscience Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Research, National Neuroscience Institute, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | - Xuezhi Bi
- Bioprocessing Technology Institute, 20 Biopolis Street, Singapore, 138669, Singapore
| | - Melissa Jane Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
- Institute of Molecular and Cell Biology (IMCB), Singapore, 138673, Singapore
| | - Patrick Tan
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, 14 Medical Drive, Singapore, 117599, Singapore
- Duke-NUS Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
- Cellular and Molecular Research, National Cancer Centre, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Shang Li
- Cancer and Stem Cell Biology Program, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117597, Singapore.
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11
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Akıncılar SC, Khattar E, Boon PLS, Unal B, Fullwood MJ, Tergaonkar V. Long-Range Chromatin Interactions Drive Mutant TERT Promoter Activation. Cancer Discov 2016; 6:1276-1291. [PMID: 27650951 DOI: 10.1158/2159-8290.cd-16-0177] [Citation(s) in RCA: 114] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 09/13/2016] [Indexed: 11/16/2022]
Abstract
Cancer-specific TERT promoter mutations (-146C>T and -124C>T) have been linked to reactivation of the epigenetically silenced telomerase reverse transcriptase gene (TERT). Understanding how these single-nucleotide alterations drive TERT reactivation is a fundamental unanswered question and is key for making successful therapeutics. We show that unlike wild-type promoters, recruitment of the transcription factor GABPA specifically to mutant TERT promoters mediates long-range chromatin interaction and enrichment of active histone marks, and hence drives TERT transcription. CRISPR-mediated reversal of mutant TERT promoters, or deletion of its long-range interacting chromatin, abrogates GABPA binding and long-range interactions, leading to depletion of active histone marks, loss of POL2 recruitment, and suppression of TERT transcription. In contrast, de novo introduction of a TERT promoter mutation enables GABPA binding and upregulation of TERT via long-range interactions, acquisition of active histone marks, and subsequent POL2 recruitment. This study provides a unifying mechanistic insight into activation of mutant TERT promoters across various human cancers. SIGNIFICANCE This study identifies a key mechanism by which cancer-specific mutant TERT promoters cause reactivation of TERT Because the mechanism uncovered here is not utilized by promoters that drive TERT in normal cells, this mechanism could be exploited to make inhibitors which have the potential to block telomerase function and hence the progression of up to 90% of human cancers. Cancer Discov; 6(11); 1276-91. ©2016 AACR.See related commentary by Min and Shay, p. 1212This article is highlighted in the In This Issue feature, p. 1197.
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Affiliation(s)
- Semih Can Akıncılar
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore
| | - Ekta Khattar
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore
| | | | - Bilal Unal
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore
| | | | - Vinay Tergaonkar
- Division of Cancer Genetics and Therapeutics, Laboratory of NFκB Signaling, Institute of Molecular and Cell Biology (IMCB), A*STAR (Agency for Science, Technology and Research), Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore (NUS), Singapore.,Centre for Cancer Biology, University of South Australia and SA Pathology, Adelaide, Australia
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12
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Sandhu KS, Li G, Poh HM, Quek YLK, Sia YY, Peh SQ, Mulawadi FH, Lim J, Sikic M, Menghi F, Thalamuthu A, Sung WK, Ruan X, Fullwood MJ, Liu E, Csermely P, Ruan Y. Large-scale functional organization of long-range chromatin interaction networks. Cell Rep 2012; 2:1207-19. [PMID: 23103170 PMCID: PMC4181841 DOI: 10.1016/j.celrep.2012.09.022] [Citation(s) in RCA: 90] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Revised: 07/31/2012] [Accepted: 09/24/2012] [Indexed: 11/27/2022] Open
Abstract
Chromatin interactions play important roles in transcription regulation. To better understand the underlying evolutionary and functional constraints of these interactions, we implemented a systems approach to examine RNA polymerase-II-associated chromatin interactions in human cells. We found that 40% of the total genomic elements involved in chromatin interactions converged to a giant, scale-free-like, hierarchical network organized into chromatin communities. The communities were enriched in specific functions and were syntenic through evolution. Disease-associated SNPs from genome-wide association studies were enriched among the nodes with fewer interactions, implying their selection against deleterious interactions by limiting the total number of interactions, a model that we further reconciled using somatic and germline cancer mutation data. The hubs lacked disease-associated SNPs, constituted a nonrandomly interconnected core of key cellular functions, and exhibited lethality in mouse mutants, supporting an evolutionary selection that favored the nonrandom spatial clustering of the least-evolving key genomic domains against random genetic or transcriptional errors in the genome. Altogether, our analyses reveal a systems-level evolutionary framework that shapes functionally compartmentalized and error-tolerant transcriptional regulation of human genome in three dimensions.
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Affiliation(s)
- Kuljeet Singh Sandhu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Knowledge City, Sector 81, Mohali 140306, India
| | - Guoliang Li
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Huay Mei Poh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Yu Ling Kelly Quek
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia 4072, Australia
| | - Yee Yen Sia
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Su Qin Peh
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Joanne Lim
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Mile Sikic
- Bioinformatics Institute, 30 Biopolis Street, Singapore 138671
- Faculty of Electrical Engineering and Computing, University of Zagreb, Unska 3, HR 10000 Zagreb, Croatia
| | - Francesca Menghi
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | | | - Wing Kin Sung
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- School of Computing, National University of Singapore, Singapore 117417
| | - Xiaoan Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
| | - Melissa Jane Fullwood
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- A*STAR-Duke-NUS Neuroscience Research Partnership, 8 College Road, Singapore 169857
| | - Edison Liu
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
| | - Peter Csermely
- Department of Medical Chemistry, School of Medicine, Semmelweis University, Tuzolto Street 37-47, Budapest 1094, Hungary
| | - Yijun Ruan
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609, USA
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