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Hamilton DJ, Hein AE, Wuttke DS, Batey RT. The DNA binding high mobility group box protein family functionally binds RNA. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1778. [PMID: 36646476 PMCID: PMC10349909 DOI: 10.1002/wrna.1778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023]
Abstract
Nucleic acid binding proteins regulate transcription, splicing, RNA stability, RNA localization, and translation, together tailoring gene expression in response to stimuli. Upon discovery, these proteins are typically classified as either DNA or RNA binding as defined by their in vivo functions; however, recent evidence suggests dual DNA and RNA binding by many of these proteins. High mobility group box (HMGB) proteins have a DNA binding HMGB domain, act as transcription factors and chromatin remodeling proteins, and are increasingly understood to interact with RNA as means to regulate gene expression. Herein, multiple layers of evidence that the HMGB family are dual DNA and RNA binding proteins is comprehensively reviewed. For example, HMGB proteins directly interact with RNA in vitro and in vivo, are localized to RNP granules involved in RNA processing, and their protein interactors are enriched in RNA binding proteins involved in RNA metabolism. Importantly, in cell-based systems, HMGB-RNA interactions facilitate protein-protein interactions, impact splicing outcomes, and modify HMGB protein genomic or cellular localization. Misregulation of these HMGB-RNA interactions are also likely involved in human disease. This review brings to light that as a family, HMGB proteins are likely to bind RNA which is essential to HMGB protein biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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2
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Zhang Y, Zhang N. The role of RNA methyltransferase METTL3 in gynecologic cancers: Results and mechanisms. Front Pharmacol 2023; 14:1156629. [PMID: 37007040 PMCID: PMC10060645 DOI: 10.3389/fphar.2023.1156629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/06/2023] [Indexed: 03/18/2023] Open
Abstract
N6-methyladenosine (m6A) methylation is the most prevalent mRNA modification in eukaryotes, and it is defined as the methylation of nitrogen atoms on the six adenine (A) bases of RNA in the presence of methyltransferases. Methyltransferase-like 3 (Mettl3), one of the components of m6A methyltransferase, plays a decisive catalytic role in m6A methylation. Recent studies have confirmed that m6A is associated with a wide spectrum of biological processes and it significantly affects disease progression and prognosis of patients with gynecologic tumors, in which the role of Mettl3 cannot be ignored. Mettl3 is involved in numerous pathophysiological functions, such as embryonic development, fat accumulation, and tumor progression. Moreover, Mettl3 may serve as a potential target for treating gynecologic malignancies, thus, it may benefit the patients and prolong survival. However, there is a need to further study the role and mechanism of Mettl3 in gynecologic malignancies. This paper reviews the recent progression on Mettl3 in gynecologic malignancies, hoping to provide a reference for further research.
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Affiliation(s)
- Yuxiang Zhang
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
- Department of Cancer Hospital, China Medical University, Shenyang, China
| | - Na Zhang
- Department of Radiation Oncology, Cancer Hospital of China Medical University, Liaoning Cancer Hospital and Institute, Shenyang, China
- *Correspondence: Na Zhang,
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3
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Wang QY, Liu HH, Dong YJ, Liang ZY, Yin Y, Liu W, Wang QY, Wang Q, Sun YH, Xu WL, Han N, Li Y, Ren HY. Low-Dose 5-Aza and DZnep Alleviate Acute Graft- Versus-Host Disease With Less Side Effects Through Altering T-Cell Differentiation. Front Immunol 2022; 13:780708. [PMID: 35281001 PMCID: PMC8907421 DOI: 10.3389/fimmu.2022.780708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 01/26/2022] [Indexed: 11/29/2022] Open
Abstract
Objective Previous studies showed that hypomethylating agents (HMAs) could alleviate acute graft-versus-host disease (aGvHD), but affect engraftment after allogeneic hematopoietic stem cell transplantation (allo-HSCT). The combination of two different HMAs in lower doses might overcome this problem. This study aimed to evaluate the treatment effect of the combination of two HMAs—azacitidine (5-Aza) and histone H3K27 methyltransferase inhibitor 3-deazaneplanocin (DZNep)—for the prophylaxis of aGvHD after allo-HSCT and to explore the possible mechanisms. Methods We first optimized the concentrations of individual and combinational 5-Aza and DZNep treatments to ensure no obvious toxicities on activated T cells by evaluating T-cell proliferation, viability, and differentiation. A mouse model of aGvHD was then established to assess the prophylactic efficacy of 5-Aza, DZNep, and their combination on aGvHD. The immunomodulatory effect on T cells and the hematopoietic reconstruction were assessed. Additionally, RNA sequencing (RNA-seq) was performed to identify the underlying molecular mechanisms. Results Compared with single treatments, the in vitro application of 5-Aza with DZNep could more powerfully reduce the production of T helper type 1 (Th1)/T cytotoxic type 1 (Tc1) cells and increase the production of regulatory T cells (Tregs). In an allo-HSCT mouse model, in vivo administration of 5-Aza with DZNep could enhance the prophylactic effect for aGvHD compared with single agents. The mechanism study demonstrated that the combination of 5-Aza and DZNep in vivo had an enhanced effect to inhibit the production of Th1/Tc1, increase the proportions of Th2/Tc2, and induce the differentiation of Tregs as in vitro. RNA-seq analysis revealed the cytokine and chemokine pathways as one mechanism for the alleviation of aGvHD with the combination of 5-Aza and DZNep. Conclusion The combination of 5-Aza and DZNep could enhance the prophylactic effect for aGvHD by influencing donor T-cell differentiation through affecting cytokine and chemokine pathways. This study shed light on the effectively prophylactic measure for aGvHD using different epigenetic agent combinations.
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Affiliation(s)
- Qing Ya Wang
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Hui Hui Liu
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Yu Jun Dong
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Ze Yin Liang
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Yue Yin
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Wei Liu
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Qing Yun Wang
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Qian Wang
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Yu Hua Sun
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Wei Lin Xu
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Na Han
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Yuan Li
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
| | - Han Yun Ren
- Department of Hematology, Peking University First Hospital, Peking University, Beijing, China
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4
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Osman N, Shawky AEM, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure. BMC Genom Data 2022; 23:13. [PMID: 35176995 PMCID: PMC8851830 DOI: 10.1186/s12863-021-01021-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 12/23/2021] [Indexed: 12/31/2022] Open
Abstract
Background Numerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. Results In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Conclusions Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-021-01021-x.
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Affiliation(s)
- Noha Osman
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA.,Department of Cell Biology, National Research Centre, Giza, 12622, Egypt.,Department of Medicine, Baylor College of Medicine, Houston, Texas, 77030, USA
| | - Abd-El-Monsif Shawky
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA. .,Center for Computation and Technology, Louisiana State University, Baton Rouge, LA, 70803, USA.
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Leung HY, Yeung MHY, Leung WT, Wong KH, Tang WY, Cho WCS, Wong HT, Tsang HF, Wong YKE, Pei XM, Cheng HYL, Chan AKC, Wong SCC. The current and future applications of in situ hybridization technologies in anatomical pathology. Expert Rev Mol Diagn 2021; 22:5-18. [PMID: 34779317 DOI: 10.1080/14737159.2022.2007076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION In situ hybridization (ISH) plays an important role in the field of molecular diagnostics, especially in an anatomical pathology laboratory. ISH is a technique that can detect the targeted DNA or RNA sequences in tissue sections from frozen or fixed materials with labeled DNA or RNA probes. Radioactive and non-radioactive probes are the two major probes that can be used to label the targeted nucleic acids. AREAS COVERED Two decades after the Human Genome Project, ISH has not only simply been applied to identify the chromosomal location of a human gene but has also been extensively applied to gene expressions studies and utilized for clinical diagnosis, especially for the determination of biomarkers for breast and ovarian cancers - human epidermal growth factor receptor 2. Duchenne muscular dystrophy, Cri-du-chat syndrome, Angelman syndrome, PraderWilli syndrome, cystic fibrosis, and trisomy are diseases that can also be detected by ISH. In this review, the basic principles, historical development, advantages and disadvantages, enhancement in reporting molecules and probes, advancement in detection methods, in situ PCR, clinical applications and novel applications of ISH will be discussed. EXPERT OPINION With the advancement in ISH technologies and appropriate training, diagnosis can be improved in Anatomical Pathology.
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Affiliation(s)
- Hoi Yi Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Wai Tung Leung
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - King Hin Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Wai Yan Tang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - William Chi Shing Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Heong Ting Wong
- Department of Pathology, Kiang Wu Hospital, Santo António, Macau Special Administrative Region, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Yin Kwan Evelyn Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Xiao Meng Pei
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Hennie Yuk Lin Cheng
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
| | - Amanda Kit Ching Chan
- Department of Pathology, Queen Elizabeth Hospital, Kowloon, Hong Kong Special Administrative Region, China
| | - Sze Chuen Cesar Wong
- Department of Health Technology and Informatics, Faculty of Health and Social Sciences, The Hong Kong Polytechnic University, Kowloon, Hong Kong Special Administrative Region, China
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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] [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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7
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Lange M, Begolli R, Giakountis A. Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine. Noncoding RNA 2021; 7:47. [PMID: 34449663 PMCID: PMC8395730 DOI: 10.3390/ncrna7030047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 07/26/2021] [Accepted: 08/01/2021] [Indexed: 12/11/2022] Open
Abstract
The cancer genome is characterized by extensive variability, in the form of Single Nucleotide Polymorphisms (SNPs) or structural variations such as Copy Number Alterations (CNAs) across wider genomic areas. At the molecular level, most SNPs and/or CNAs reside in non-coding sequences, ultimately affecting the regulation of oncogenes and/or tumor-suppressors in a cancer-specific manner. Notably, inherited non-coding variants can predispose for cancer decades prior to disease onset. Furthermore, accumulation of additional non-coding driver mutations during progression of the disease, gives rise to genomic instability, acting as the driving force of neoplastic development and malignant evolution. Therefore, detection and characterization of such mutations can improve risk assessment for healthy carriers and expand the diagnostic and therapeutic toolbox for the patient. This review focuses on functional variants that reside in transcribed or not transcribed non-coding regions of the cancer genome and presents a collection of appropriate state-of-the-art methodologies to study them.
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Affiliation(s)
- Marios Lange
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Rodiola Begolli
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
| | - Antonis Giakountis
- Department of Biochemistry and Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece; (M.L.); (R.B.)
- Institute for Fundamental Biomedical Research, B.S.R.C “Alexander Fleming”, 34 Fleming Str., 16672 Vari, Greece
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Paakinaho V, Palvimo JJ. Genome-wide crosstalk between steroid receptors in breast and prostate cancers. Endocr Relat Cancer 2021; 28:R231-R250. [PMID: 34137734 PMCID: PMC8345902 DOI: 10.1530/erc-21-0038] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 06/16/2021] [Indexed: 12/18/2022]
Abstract
Steroid receptors (SRs) constitute an important class of signal-dependent transcription factors (TFs). They regulate a variety of key biological processes and are crucial drug targets in many disease states. In particular, estrogen (ER) and androgen receptors (AR) drive the development and progression of breast and prostate cancer, respectively. Thus, they represent the main specific drug targets in these diseases. Recent evidence has suggested that the crosstalk between signal-dependent TFs is an important step in the reprogramming of chromatin sites; a signal-activated TF can expand or restrict the chromatin binding of another TF. This crosstalk can rewire gene programs and thus alter biological processes and influence the progression of disease. Lately, it has been postulated that there may be an important crosstalk between the AR and the ER with other SRs. Especially, progesterone (PR) and glucocorticoid receptor (GR) can reprogram chromatin binding of ER and gene programs in breast cancer cells. Furthermore, GR can take the place of AR in antiandrogen-resistant prostate cancer cells. Here, we review the current knowledge of the crosstalk between SRs in breast and prostate cancers. We emphasize how the activity of ER and AR on chromatin can be modulated by other SRs on a genome-wide scale. We also highlight the knowledge gaps in the interplay of SRs and their complex interactions with other signaling pathways and suggest how to experimentally fill in these gaps.
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Affiliation(s)
- Ville Paakinaho
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jorma J Palvimo
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
- Correspondence should be addressed to J J Palvimo:
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9
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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] [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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10
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Papale A, Holcman D. Chromatin stability generated by stochastic binding and unbinding of cross-linkers at looping sites revealed by Markov models. Phys Biol 2021; 18:046006. [PMID: 33871383 DOI: 10.1088/1478-3975/abf93a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 03/16/2021] [Indexed: 11/11/2022]
Abstract
Chromatin loops inside the nucleus can be stable for a very long time, which remains poorly understood. Such a time is crucial for chromatin organization maintenance and stability. We explore here several physical scenarios, where loop maintenance is due to diffusing cross-linkers (cohesin stabilized by two CTCF molecules) that can bind and unbind at the base of chromatin loops. Using a Markov chain approach to coarse-grain the binding and unbinding, we consider that a stable loop disappears when the last cross-linker is unbound. We derive expressions for this last passage time that we use to quantify the loop stability for various parameters, such as the chemical rate constant or the number of cross-linkers. The present analysis suggests that the balance between binding and unbinding events regulates the number of cross-linkers in place, based on a positive feed-back mechanism that stabilizes the loop over long-time. To conclude, we found that short- and long-lasting stable loops can vary from minutes to the entire cell cycle lifetime, when the number of cross-linkers increases from 1 to 10. This result suggests that a large spectrum of loop time scales is expected with such a few numbers of cross-linkers per local binding sites.
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Affiliation(s)
- Andrea Papale
- Group of Computational Biology and Applied Mathematics, Ecole Normale Supérieure, IBENS, Université PSL, 75005 Paris, France
| | - David Holcman
- Group of Computational Biology and Applied Mathematics, Ecole Normale Supérieure, IBENS, Université PSL, 75005 Paris, France
- Churchill College, University of Cambridge, CB30DS, United Kingdom
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11
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Li GH, Qu Q, Qi TT, Teng XQ, Zhu HH, Wang JJ, Lu Q, Qu J. Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. J Exp Clin Cancer Res 2021; 40:174. [PMID: 34011395 PMCID: PMC8132395 DOI: 10.1186/s13046-021-01974-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Although new developments of surgery, chemotherapy, radiotherapy, and immunotherapy treatments for cancer have improved patient survival, the emergence of chemoresistance in cancer has significant impacts on treatment effects. The development of chemoresistance involves several polygenic, progressive mechanisms at the molecular and cellular levels, as well as both genetic and epigenetic heterogeneities. Chemotherapeutics induce epigenetic reprogramming in cancer cells, converting a transient transcriptional state into a stably resistant one. Super-enhancers (SEs) are central to the maintenance of identity of cancer cells and promote SE-driven-oncogenic transcriptions to which cancer cells become highly addicted. This dependence on SE-driven transcription to maintain chemoresistance offers an Achilles' heel for chemoresistance. Indeed, the inhibition of SE components dampens oncogenic transcription and inhibits tumor growth to ultimately achieve combined sensitization and reverse the effects of drug resistance. No reviews have been published on SE-related mechanisms in the cancer chemoresistance. In this review, we investigated the structure, function, and regulation of chemoresistance-related SEs and their contributions to the chemotherapy via regulation of the formation of cancer stem cells, cellular plasticity, the microenvironment, genes associated with chemoresistance, noncoding RNAs, and tumor immunity. The discovery of these mechanisms may aid in the development of new drugs to improve the sensitivity and specificity of cancer cells to chemotherapy drugs.
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Affiliation(s)
- Guo-Hua Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Ting-Ting Qi
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Hai-Hong Zhu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiao-Jiao Wang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
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12
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H3K27me3-rich genomic regions can function as silencers to repress gene expression via chromatin interactions. Nat Commun 2021; 12:719. [PMID: 33514712 PMCID: PMC7846766 DOI: 10.1038/s41467-021-20940-y] [Citation(s) in RCA: 112] [Impact Index Per Article: 37.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/04/2021] [Indexed: 12/29/2022] Open
Abstract
The mechanisms underlying gene repression and silencers are poorly understood. Here we investigate the hypothesis that H3K27me3-rich regions of the genome, defined from clusters of H3K27me3 peaks, may be used to identify silencers that can regulate gene expression via proximity or looping. We find that H3K27me3-rich regions are associated with chromatin interactions and interact preferentially with each other. H3K27me3-rich regions component removal at interaction anchors by CRISPR leads to upregulation of interacting target genes, altered H3K27me3 and H3K27ac levels at interacting regions, and altered chromatin interactions. Chromatin interactions did not change at regions with high H3K27me3, but regions with low H3K27me3 and high H3K27ac levels showed changes in chromatin interactions. Cells with H3K27me3-rich regions knockout also show changes in phenotype associated with cell identity, and altered xenograft tumor growth. Finally, we observe that H3K27me3-rich regions-associated genes and long-range chromatin interactions are susceptible to H3K27me3 depletion. Our results characterize H3K27me3-rich regions and their mechanisms of functioning via looping.
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Osman N, Shawky A, Brylinski M. Exploring the effects of genetic variation on gene regulation in cancer in the context of 3D genome structure.. [DOI: 10.1101/2020.10.06.328567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractNumerous genome-wide association studies (GWAS) conducted to date revealed genetic variants associated with various diseases, including breast and prostate cancers. Despite the availability of these large-scale data, relatively few variants have been functionally characterized, mainly because the majority of single-nucleotide polymorphisms (SNPs) map to the non-coding regions of the human genome. The functional characterization of these non-coding variants and the identification of their target genes remain challenging. In this communication, we explore the potential functional mechanisms of non-coding SNPs by integrating GWAS with the high-resolution chromosome conformation capture (Hi-C) data for breast and prostate cancers. We show that more genetic variants map to regulatory elements through the 3D genome structure than the 1D linear genome lacking physical chromatin interactions. Importantly, the association of enhancers, transcription factors, and their target genes with breast and prostate cancers tends to be higher when these regulatory elements are mapped to high-risk SNPs through spatial interactions compared to simply using a linear proximity. Finally, we demonstrate that topologically associating domains (TADs) carrying high-risk SNPs also contain gene regulatory elements whose association with cancer is generally higher than those belonging to control TADs containing no high-risk variants. Our results suggest that many SNPs may contribute to the cancer development by affecting the expression of certain tumor-related genes through long-range chromatin interactions with gene regulatory elements. Integrating large-scale genetic datasets with the 3D genome structure offers an attractive and unique approach to systematically investigate the functional mechanisms of genetic variants in disease risk and progression.
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14
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Zheng C, Liu M, Fan H. Targeting complexes of super-enhancers is a promising strategy for cancer therapy. Oncol Lett 2020; 20:2557-2566. [PMID: 32782573 PMCID: PMC7400756 DOI: 10.3892/ol.2020.11855] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/27/2020] [Indexed: 12/16/2022] Open
Abstract
The hyperactivation and overexpression of critical oncogenes is a common occurrence in multiple types of malignant tumors. Recently, the abnormal activation mechanism of an oncogene by a super-enhancer (SE) has attracted significant attention. A series of changes (insertion, deletion, translocation and rearrangement) in the genome occurring in cancer cells may generate new SEs, leading to the overexpression of SE-driven oncogenes. SEs are composed of typical enhancers densely loaded with mediator complexes, transcription factors, and chromatin regulators, and drive the overexpression of oncogenes associated with cellular identity and disease. Cyclin-dependent kinase 7 (CDK7) and bromodomain protein 4 (BRD4) are critical mediator complexes associated with SE-mediated transcription. Clinical trials have shown that emerging small-molecule inhibitors (CDK7 and BRD4 inhibitor), targeting the SE exert a notable effect on cancer treatment. Increasing evidences has illustrated that the SE and its associated complexes play a critical role in the development of various types of cancer. The present review discusses the composition, function and regulation of SEs and their contribution to oncogenic transcription. In addition, creative therapeutic approaches that target SE, their advantages and disadvantages, as well as the problems with their clinical application are discussed. It was found that targeting SE may be used in conventional treatment and establish more access for patients with cancer.
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Affiliation(s)
- Chuqian Zheng
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
| | - Min Liu
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China.,School of Life Science and Technology, Southeast University, Nanjing, Jiangsu 210018, P.R. China
| | - Hong Fan
- Department of Medical Genetics and Developmental Biology, School of Medicine, The Key Laboratory of Developmental Genes and Human Diseases, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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15
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Hou Y, Zhang R, Sun X. Enhancer LncRNAs Influence Chromatin Interactions in Different Ways. Front Genet 2019; 10:936. [PMID: 31681405 PMCID: PMC6807612 DOI: 10.3389/fgene.2019.00936] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/05/2019] [Indexed: 12/14/2022] Open
Abstract
More than 98% of the human genome does not encode proteins, and the vast majority of the noncoding regions have not been well studied. Some of these regions contain enhancers and functional non-coding RNAs. Previous research suggested that enhancer transcripts could be potent independent indicators of enhancer activity, and some enhancer lncRNAs (elncRNAs) have been proven to play critical roles in gene regulation. Here, we identified enhancer–promoter interactions from high-throughput chromosome conformation capture (Hi-C) data. We found that elncRNAs were highly enriched surrounding chromatin loop anchors. Additionally, the interaction frequency of elncRNA-associated enhancer–promoter pairs was significantly higher than the interaction frequency of other enhancer–promoter pairs, suggesting that elncRNAs may reinforce the interactions between enhancers and promoters. We also found that elncRNA expression levels were positively correlated with the interaction frequency of enhancer–promoter pairs. The promoters interacting with elncRNA-associated enhancers were rich in RNA polymerase II and YY1 transcription factor binding sites. We clustered enhancer–promoter pairs into different groups to reflect the different ways in which elncRNAs could influence enhancer–promoter pairs. Interestingly, G-quadruplexes were found to potentially mediate some enhancer–promoter interaction pairs, and the interaction frequency of these pairs was significantly higher than that of other enhancer–promoter pairs. We also found that the G-quadruplexes on enhancers were highly related to the expression of elncRNAs. G-quadruplexes located in the promoters of elncRNAs led to high expression of elncRNAs, whereas G-quadruplexes located in the gene bodies of elncRNAs generally resulted in low expression of elncRNAs.
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Affiliation(s)
- Yue Hou
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Rongxin Zhang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
| | - Xiao Sun
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China
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16
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Fufa TD, Baxter LL, Wedel JC, Gildea DE, Loftus SK, Pavan WJ. MEK inhibition remodels the active chromatin landscape and induces SOX10 genomic recruitment in BRAF(V600E) mutant melanoma cells. Epigenetics Chromatin 2019; 12:50. [PMID: 31399133 PMCID: PMC6688322 DOI: 10.1186/s13072-019-0297-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/28/2019] [Indexed: 01/03/2023] Open
Abstract
Background The MAPK/ERK signaling pathway is an essential regulator of numerous cell processes that are crucial for normal development as well as cancer progression. While much is known regarding MAPK/ERK signal conveyance from the cell membrane to the nucleus, the transcriptional and epigenetic mechanisms that govern gene expression downstream of MAPK signaling are not fully elucidated. Results This study employed an integrated epigenome analysis approach to interrogate the effects of MAPK/ERK pathway inhibition on the global transcriptome, the active chromatin landscape, and protein–DNA interactions in 501mel melanoma cells. Treatment of these cells with the small-molecule MEK inhibitor AZD6244 induces hyperpigmentation, widespread gene expression changes including alteration of genes linked to pigmentation, and extensive epigenomic reprogramming of transcriptionally distinct regulatory regions associated with the active chromatin mark H3K27ac. Regulatory regions with differentially acetylated H3K27ac regions following AZD6244 treatment are enriched in transcription factor binding motifs of ETV/ETS and ATF family members as well as the lineage-determining factors MITF and SOX10. H3K27ac-dense enhancer clusters known as super-enhancers show similar transcription factor motif enrichment, and furthermore, these super-enhancers are associated with genes encoding MITF, SOX10, and ETV/ETS proteins. Along with genome-wide resetting of the active enhancer landscape, MEK inhibition also results in widespread SOX10 recruitment throughout the genome, including increased SOX10 binding density at H3K27ac-marked enhancers. Importantly, these MEK inhibitor-responsive enhancers marked by H3K27ac and occupied by SOX10 are located near melanocyte lineage-specific and pigmentation genes and overlap numerous human SNPs associated with pigmentation and melanoma phenotypes, highlighting the variants located within these regions for prioritization in future studies. Conclusions These results reveal the epigenetic reprogramming underlying the re-activation of melanocyte pigmentation and developmental transcriptional programs in 501mel cells in response to MEK inhibition and suggest extensive involvement of a MEK-SOX10 axis in the regulation of these processes. The dynamic chromatin changes identified here provide a rich genomic resource for further analyses of the molecular mechanisms governing the MAPK pathway in pigmentation- and melanocyte-associated diseases. Electronic supplementary material The online version of this article (10.1186/s13072-019-0297-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Temesgen D Fufa
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.,Ophthalmic Genetics and Visual Function Branch, National Eye Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Laura L Baxter
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Julia C Wedel
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Derek E Gildea
- Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Stacie K Loftus
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William J Pavan
- Genetic Disease Research Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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