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Peters L, Venkatachalam A, Ben-Neriah Y. Tissue-Predisposition to Cancer Driver Mutations. Cells 2024; 13:106. [PMID: 38247798 PMCID: PMC10814991 DOI: 10.3390/cells13020106] [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: 12/08/2023] [Revised: 01/02/2024] [Accepted: 01/03/2024] [Indexed: 01/23/2024] Open
Abstract
Driver mutations are considered the cornerstone of cancer initiation. They are defined as mutations that convey a competitive fitness advantage, and hence, their mutation frequency in premalignant tissue is expected to exceed the basal mutation rate. In old terms, that translates to "the survival of the fittest" and implies that a selective process underlies the frequency of cancer driver mutations. In that sense, each tissue is its own niche that creates a molecular selective pressure that may favor the propagation of a mutation or not. At the heart of this stands one of the biggest riddles in cancer biology: the tissue-predisposition to cancer driver mutations. The frequency of cancer driver mutations among tissues is non-uniform: for instance, mutations in APC are particularly frequent in colorectal cancer, and 99% of chronic myeloid leukemia patients harbor the driver BCR-ABL1 fusion mutation, which is rarely found in solid tumors. Here, we provide a mechanistic framework that aims to explain how tissue-specific features, ranging from epigenetic underpinnings to the expression of viral transposable elements, establish a molecular basis for selecting cancer driver mutations in a tissue-specific manner.
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Affiliation(s)
| | | | - Yinon Ben-Neriah
- Lautenberg Center for Immunology and Cancer Research, Institute for Medical Research (IMRIC), The Faculty of Medicine, Hebrew University of Jerusalem, P.O. Box 12272, Jerusalem 91120, Israel; (L.P.); (A.V.)
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2
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Han J, Wang S, Wu H, Zhao T, Guan X, Fang L. An upgraded method of high-throughput chromosome conformation capture (Hi-C 3.0) in cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1223591. [PMID: 37469786 PMCID: PMC10353440 DOI: 10.3389/fpls.2023.1223591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 06/12/2023] [Indexed: 07/21/2023]
Abstract
High-throughput chromosome conformation capture (Hi-C) technology has been applied to explore the chromatin interactions and shed light on the biological functions of three-dimensional genomic features. However, it remains challenging to guarantee the high quality of Hi-C library in plants and hence the reliable capture of chromatin structures, especially loops, due to insufficient fragmentation and low efficiency of proximity ligations. To overcome these deficiencies, we optimized the parameters of the Hi-C protocol, principally the cross-linking agents and endonuclease fragmentation strategy. The double cross-linkers (FA+DSG) and double restriction enzymes (DpnII+DdeI) were utilized. Thus, a systematic in situ Hi-C protocol was designed using plant tissues embedded with comprehensive quality controls to monitor the library construction. This upgraded method, termed Hi-C 3.0, was applied to cotton leaves for trial. In comparison with the conventional Hi-C 2.0, Hi-C 3.0 can obtain more than 50% valid contacts at a given sequencing depth to improve the signal-to-noise ratio. Hi-C 3.0 can furthermore enhance the capturing of loops almost as twice as that of Hi-C 2.0. In addition, Hi-C 3.0 showed higher efficiency of compartment detection and identified compartmentalization more accurately. In general, Hi-C 3.0 contributes to the advancement of the Hi-C method in plants by promoting its capability on decoding the chromatin organization.
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Affiliation(s)
- Jin Han
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Siyuan Wang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongyu Wu
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Ting Zhao
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Xueying Guan
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
| | - Lei Fang
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, The Advanced Seed Institute, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Yongyou Industry Park, Yazhou Bay Sci-Tech City, Sanya, China
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3
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Gupta K, Wang G, Zhang S, Gao X, Zheng R, Zhang Y, Meng Q, Zhang L, Cao Q, Chen K. StripeDiff: Model-based algorithm for differential analysis of chromatin stripe. SCIENCE ADVANCES 2022; 8:eabk2246. [PMID: 36475785 PMCID: PMC9728969 DOI: 10.1126/sciadv.abk2246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/28/2022] [Indexed: 05/27/2023]
Abstract
Multiple recent studies revealed stripes as an architectural feature of three-dimensional chromatin and found stripes connected to epigenetic regulation of transcription. Whereas a couple of tools are available to define stripes in a single sample, there is yet no reported method to quantitatively measure the dynamic change of each stripe between samples. Here, we developed StripeDiff, a bioinformatics tool that delivers a set of statistical methods to detect differential stripes between samples. StripeDiff showed optimal performance in both simulation data analysis and real Hi-C data analysis. Applying StripeDiff to 12 sets of Hi-C data revealed new insights into the connection between change of chromatin stripe and change of chromatin modification, transcriptional regulation, and cell differentiation. StripeDiff will be a robust tool for the community to facilitate understanding of stripes and their function in numerous biological models.
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Affiliation(s)
- Krishan Gupta
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Guangyu Wang
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Shuo Zhang
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Xinlei Gao
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Rongbin Zheng
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Yanchun Zhang
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Qingshu Meng
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lili Zhang
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
| | - Qi Cao
- Department of Urology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Kaifu Chen
- Department of Cardiology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
- Houston Methodist Hospital Research Institute, Houston, TX 77030, USA
- Broad Institute of MIT and Harvard, Boston, MA 02115, USA
- Dana-Farber/Harvard Cancer Center, Boston, MA 02115, USA
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4
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Sun X, Zhang J, Cao C. CTCF and Its Partners: Shaper of 3D Genome during Development. Genes (Basel) 2022; 13:genes13081383. [PMID: 36011294 PMCID: PMC9407368 DOI: 10.3390/genes13081383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 07/27/2022] [Accepted: 07/29/2022] [Indexed: 02/06/2023] Open
Abstract
The 3D genome organization and its dynamic modulate genome function, playing a pivotal role in cell differentiation and development. CTCF and cohesin, acting as the core architectural components involved in chromatin looping and genome folding, can also recruit other protein or RNA partners to fine-tune genome structure during development. Moreover, systematic screening for partners of CTCF has been performed through high-throughput approaches. In particular, several novel protein and RNA partners, such as BHLHE40, WIZ, MAZ, Aire, MyoD, YY1, ZNF143, and Jpx, have been identified, and these partners are mostly implicated in transcriptional regulation and chromatin remodeling, offering a unique opportunity for dissecting their roles in higher-order chromatin organization by collaborating with CTCF and cohesin. Here, we review the latest advancements with an emphasis on features of CTCF partners and also discuss the specific functions of CTCF-associated complexes in chromatin structure modulation, which may extend our understanding of the functions of higher-order chromatin architecture in developmental processes.
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Affiliation(s)
- Xiaoyue Sun
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Jing Zhang
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
| | - Chunwei Cao
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China; (X.S.); (J.Z.)
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Center for Reproductive Genetics and Reproductive Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510275, China
- Guangzhou Laboratory, Guangzhou 510320, China
- Correspondence:
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5
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Wu S, Yin Y, Wang X. The epigenetic regulation of the germinal center response. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194828. [PMID: 35643396 DOI: 10.1016/j.bbagrm.2022.194828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
In response to T-cell-dependent antigens, antigen-experienced B cells migrate to the center of the B-cell follicle to seed the germinal center (GC) response after cognate interactions with CD4+ T cells. These GC B cells eventually mature into memory and long-lived antibody-secreting plasma cells, thus generating long-lived humoral immunity. Within GC, B cells undergo somatic hypermutation of their B cell receptors (BCR) and positive selection for the emergence of high-affinity antigen-specific B-cell clones. However, this process may be dangerous, as the accumulation of aberrant mutations could result in malignant transformation of GC B cells or give rise to autoreactive B cell clones that can cause autoimmunity. Because of this, better understanding of GC development provides diagnostic and therapeutic clues to the underlying pathologic process. A productive GC response is orchestrated by multiple mechanisms. An emerging important regulator of GC reaction is epigenetic modulation, which has key transcriptional regulatory properties. In this review, we summarize the current knowledge on the biology of epigenetic mechanisms in the regulation of GC reaction and outline its importance in identification of immunotherapy decision making.
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Affiliation(s)
- Shusheng Wu
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Yuye Yin
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoming Wang
- Department of Immunology, State Key Laboratory of Reproductive Medicine, NHC Key Laboratory of Antibody Technique, Nanjing Medical University, Nanjing, Jiangsu, China.
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6
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Li D, Ning C, Zhang J, Wang Y, Tang Q, Kui H, Wang T, He M, Jin L, Li J, Lin Y, Zeng B, Yin H, Zhao X, Zhang Y, Xu H, Zhu Q, Li M. Dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis. Nat Commun 2022; 13:131. [PMID: 35013308 PMCID: PMC8748434 DOI: 10.1038/s41467-021-27800-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 12/07/2021] [Indexed: 12/30/2022] Open
Abstract
Folliculogenesis is a complex biological process involving a central oocyte and its surrounding somatic cells. Three-dimensional chromatin architecture is an important transcription regulator; however, little is known about its dynamics and role in transcriptional regulation of granulosa cells during chicken folliculogenesis. We investigate the transcriptomic dynamics of chicken granulosa cells over ten follicular stages and assess the chromatin architecture dynamics and how it influences gene expression in granulosa cells at three key stages: the prehierarchical small white follicles, the first largest preovulatory follicles, and the postovulatory follicles. Our results demonstrate the consistency between the global reprogramming of chromatin architecture and the transcriptomic divergence during folliculogenesis, providing ample evidence for compartmentalization rearrangement, variable organization of topologically associating domains, and rewiring of the long-range interaction between promoter and enhancers. These results provide key insights into avian reproductive biology and provide a foundational dataset for the future in-depth functional characterization of granulosa cells. The domestic chicken Gallus gallus domesticus is a classic model for the study of folliculogenesis. Here the authors integrate multi-omics analyses characterizing the dynamic transcriptome and chromatin architecture in granulosa cells during chicken folliculogenesis.
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Affiliation(s)
- Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Chunyou Ning
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jiaman Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yujie Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qianzi Tang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Hua Kui
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Tao Wang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mengnan He
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Long Jin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jing Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yu Lin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Bo Zeng
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Huadong Yin
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xiaoling Zhao
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yao Zhang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Huailiang Xu
- College of Life Science, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Qing Zhu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Mingzhou Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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7
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Kim J, Jimenez DS, Ragipani B, Zhang B, Street LA, Kramer M, Albritton SE, Winterkorn LH, Morao AK, Ercan S. Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans. eLife 2022; 11:68745. [PMID: 36331876 PMCID: PMC9635877 DOI: 10.7554/elife.68745] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 10/23/2022] [Indexed: 11/06/2022] Open
Abstract
Condensins are molecular motors that compact DNA via linear translocation. In Caenorhabditis elegans, the X-chromosome harbors a specialized condensin that participates in dosage compensation (DC). Condensin DC is recruited to and spreads from a small number of recruitment elements on the X-chromosome (rex) and is required for the formation of topologically associating domains (TADs). We take advantage of autosomes that are largely devoid of condensin DC and TADs to address how rex sites and condensin DC give rise to the formation of TADs. When an autosome and X-chromosome are physically fused, despite the spreading of condensin DC into the autosome, no TAD was created. Insertion of a strong rex on the X-chromosome results in the TAD boundary formation regardless of sequence orientation. When the same rex is inserted on an autosome, despite condensin DC recruitment, there was no spreading or features of a TAD. On the other hand, when a 'super rex' composed of six rex sites or three separate rex sites are inserted on an autosome, recruitment and spreading of condensin DC led to the formation of TADs. Therefore, recruitment to and spreading from rex sites are necessary and sufficient for recapitulating loop-anchored TADs observed on the X-chromosome. Together our data suggest a model in which rex sites are both loading sites and bidirectional barriers for condensin DC, a one-sided loop-extruder with movable inactive anchor.
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Affiliation(s)
- Jun Kim
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - David S Jimenez
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Bhavana Ragipani
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Bo Zhang
- UCSF HSWSan FranciscoUnited States
| | - Lena A Street
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Maxwell Kramer
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Sarah E Albritton
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Lara H Winterkorn
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Ana K Morao
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
| | - Sevinc Ercan
- Department of Biology and Center for Genomics and Systems Biology, New York UniversityNew YorkUnited States
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8
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The BAF chromatin remodeling complexes: structure, function, and synthetic lethalities. Biochem Soc Trans 2021; 49:1489-1503. [PMID: 34431497 DOI: 10.1042/bst20190960] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
Abstract
BAF complexes are multi-subunit chromatin remodelers, which have a fundamental role in genomic regulation. Large-scale sequencing efforts have revealed frequent BAF complex mutations in many human diseases, particularly in cancer and neurological disorders. These findings not only underscore the importance of the BAF chromatin remodelers in cellular physiological processes, but urge a more detailed understanding of their structure and molecular action to enable the development of targeted therapeutic approaches for diseases with BAF complex alterations. Here, we review recent progress in understanding the composition, assembly, structure, and function of BAF complexes, and the consequences of their disease-associated mutations. Furthermore, we highlight intra-complex subunit dependencies and synthetic lethal interactions, which have emerged as promising treatment modalities for BAF-related diseases.
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9
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Retis-Resendiz AM, González-García IN, León-Juárez M, Camacho-Arroyo I, Cerbón M, Vázquez-Martínez ER. The role of epigenetic mechanisms in the regulation of gene expression in the cyclical endometrium. Clin Epigenetics 2021; 13:116. [PMID: 34034824 PMCID: PMC8146649 DOI: 10.1186/s13148-021-01103-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/13/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND The human endometrium is a highly dynamic tissue whose function is mainly regulated by the ovarian steroid hormones estradiol and progesterone. The serum levels of these and other hormones are associated with three specific phases that compose the endometrial cycle: menstrual, proliferative, and secretory. Throughout this cycle, the endometrium exhibits different transcriptional networks according to the genes expressed in each phase. Epigenetic mechanisms are crucial in the fine-tuning of gene expression to generate such transcriptional networks. The present review aims to provide an overview of current research focused on the epigenetic mechanisms that regulate gene expression in the cyclical endometrium and discuss the technical and clinical perspectives regarding this topic. MAIN BODY The main epigenetic mechanisms reported are DNA methylation, histone post-translational modifications, and non-coding RNAs. These epigenetic mechanisms induce the expression of genes associated with transcriptional regulation, endometrial epithelial growth, angiogenesis, and stromal cell proliferation during the proliferative phase. During the secretory phase, epigenetic mechanisms promote the expression of genes associated with hormone response, insulin signaling, decidualization, and embryo implantation. Furthermore, the global content of specific epigenetic modifications and the gene expression of non-coding RNAs and epigenetic modifiers vary according to the menstrual cycle phase. In vitro and cell type-specific studies have demonstrated that epithelial and stromal cells undergo particular epigenetic changes that modulate their transcriptional networks to accomplish their function during decidualization and implantation. CONCLUSION AND PERSPECTIVES Epigenetic mechanisms are emerging as key players in regulating transcriptional networks associated with key processes and functions of the cyclical endometrium. Further studies using next-generation sequencing and single-cell technology are warranted to explore the role of other epigenetic mechanisms in each cell type that composes the endometrium throughout the menstrual cycle. The application of this knowledge will definitively provide essential information to understand the pathological mechanisms of endometrial diseases, such as endometriosis and endometrial cancer, and to identify potential therapeutic targets and improve women's health.
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Affiliation(s)
- Alejandra Monserrat Retis-Resendiz
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Ixchel Nayeli González-García
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Moisés León-Juárez
- Departamento de Inmunobioquímica, Instituto Nacional de Perinatología, Ciudad de México, Mexico
| | - Ignacio Camacho-Arroyo
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Marco Cerbón
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico
| | - Edgar Ricardo Vázquez-Martínez
- Unidad de Investigación en Reproducción Humana, Instituto Nacional de Perinatología-Facultad de Química, Universidad Nacional Autónoma de México, Montes Urales 800, Lomas Virreyes, Miguel Hidalgo, 11000, Ciudad de México, Mexico.
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10
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Qiu GH, Zheng X, Fu M, Huang C, Yang X. The decreased exclusion of nuclear eccDNA: From molecular and subcellular levels to human aging and age-related diseases. Ageing Res Rev 2021; 67:101306. [PMID: 33610814 DOI: 10.1016/j.arr.2021.101306] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 12/11/2022]
Abstract
Extrachromosomal circular DNA (eccDNA) accumulates within the nucleus of eukaryotic cells during physiological aging and in age-related diseases (ARDs) and the accumulation could be caused by the declined exclusion of nuclear eccDNA in these states. This review focuses on the formation of eccDNA and the roles of some main factors, such as nuclear pore complexes (NPCs), nucleoplasmic reticulum (NR), and nuclear actin, in eccDNA exclusion. eccDNAs are mostly formed from non-coding DNA during DNA damage repair. They move to NPCs along nuclear actin and are excluded out of the nucleus through functional NPCs in young and healthy cells. However, it has been demonstrated that defective NPCs, abnormal NPC components and nuclear actin rods are increased in aged cells, various cancers and certain other ARDs such as cardiovascular diseases, premature aging, neurodegenerative diseases and myopathies. Therefore, mainly resulting from the increase of dysfunctional NPCs, the exclusion of nuclear eccDNAs may be reduced and eccDNAs thus accumulate within the nucleus in aging and the aforementioned ARDs. In addition, the protective function of non-coding DNA in tumorigenesis is further discussed.
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Affiliation(s)
- Guo-Hua Qiu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province Universities, College of Life Sciences, Longyan University, Longyan 364012, People's Republic of China.
| | - Xintian Zheng
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province Universities, College of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Mingjun Fu
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province Universities, College of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Cuiqin Huang
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province Universities, College of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
| | - Xiaoyan Yang
- Fujian Provincial Key Laboratory for the Prevention and Control of Animal Infectious Diseases and Biotechnology, Key Laboratory of Preventive Veterinary Medicine and Biotechnology, Fujian Province Universities, College of Life Sciences, Longyan University, Longyan 364012, People's Republic of China
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11
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Ohnishi T, Kiyama Y, Arima‐Yoshida F, Kadota M, Ichikawa T, Yamada K, Watanabe A, Ohba H, Tanaka K, Nakaya A, Horiuchi Y, Iwayama Y, Toyoshima M, Ogawa I, Shimamoto‐Mitsuyama C, Maekawa M, Balan S, Arai M, Miyashita M, Toriumi K, Nozaki Y, Kurokawa R, Suzuki K, Yoshikawa A, Toyota T, Hosoya T, Okuno H, Bito H, Itokawa M, Kuraku S, Manabe T, Yoshikawa T. Cooperation of LIM domain-binding 2 (LDB2) with EGR in the pathogenesis of schizophrenia. EMBO Mol Med 2021; 13:e12574. [PMID: 33656268 PMCID: PMC8033514 DOI: 10.15252/emmm.202012574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 01/21/2021] [Accepted: 01/25/2021] [Indexed: 01/15/2023] Open
Abstract
Genomic defects with large effect size can help elucidate unknown pathologic architecture of mental disorders. We previously reported on a patient with schizophrenia and a balanced translocation between chromosomes 4 and 13 and found that the breakpoint within chromosome 4 is located near the LDB2 gene. We show here that Ldb2 knockout (KO) mice displayed multiple deficits relevant to mental disorders. In particular, Ldb2 KO mice exhibited deficits in the fear-conditioning paradigm. Analysis of the amygdala suggested that dysregulation of synaptic activities controlled by the immediate early gene Arc is involved in the phenotypes. We show that LDB2 forms protein complexes with known transcription factors. Consistently, ChIP-seq analyses indicated that LDB2 binds to > 10,000 genomic sites in human neurospheres. We found that many of those sites, including the promoter region of ARC, are occupied by EGR transcription factors. Our previous study showed an association of the EGR family genes with schizophrenia. Collectively, the findings suggest that dysregulation in the gene expression controlled by the LDB2-EGR axis underlies a pathogenesis of subset of mental disorders.
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12
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Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation. Nat Commun 2021; 12:651. [PMID: 33510161 PMCID: PMC7844026 DOI: 10.1038/s41467-020-20849-y] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/21/2020] [Indexed: 02/06/2023] Open
Abstract
To investigate the three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia and mantle cell lymphoma patients, here we integrate in situ Hi-C and nine additional omics layers. Beyond conventional active (A) and inactive (B) compartments, we uncover a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, 28% of the compartments change, mostly involving a widespread chromatin activation from naive to germinal center B cells and a reversal to the naive state upon further maturation into memory B cells. B cell neoplasms are characterized by both entity and subtype-specific alterations in 3D genome organization, including large chromatin blocks spanning key disease-specific genes. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.
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Abstract
The discovery of the DNA double helix by Watson and Crick in 1953 was the first report showing that the genomic information is not contained in a stretched linear molecule. After that, a huge advance in the knowledge of the structure of the eukaryotic genome in the nuclear space has been made over the last decades, bringing us to the widely accepted concept that the genome is packaged into hierarchical levels of higher-order three-dimensional structures. The spatial organization of the eukaryotic genome has direct influence on fundamental nuclear processes that include transcription, replication, and DNA repair. The idea that structural alterations of chromosomes may cause disease goes back to the early nineteenth century. Big effort has been devoted to the study of the three-dimensional architecture of the genome and its functional implications. In this chapter, I will describe the chromosome conformation capture (3C), one of the first techniques used to detect and measure the frequency of interactions between genomic sequences that are kept in spatial proximity in the nucleus.
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14
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Ouyang W, Xiong D, Li G, Li X. Unraveling the 3D Genome Architecture in Plants: Present and Future. MOLECULAR PLANT 2020; 13:1676-1693. [PMID: 33065269 DOI: 10.1016/j.molp.2020.10.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 08/09/2020] [Accepted: 10/08/2020] [Indexed: 05/02/2023]
Abstract
The eukaryotic genome has a hierarchical three-dimensional (3D) organization with functional implications for DNA replication, DNA repair, and transcriptional regulation. Over the past decade, scientists have endeavored to elucidate the spatial characteristics and functions of plant genome architecture using high-throughput chromatin conformation capturing technologies such as Hi-C, ChIA-PET, and HiChIP. Here, we systematically review current understanding of chromatin organization in plants at multiple scales. We also discuss the emerging opinions and concepts in 3D genome research, focusing on state-of-the-art 3D genome techniques, RNA-chromatin interactions, liquid-liquid phase separation, and dynamic chromatin alterations. We propose the application of single-cell/single-molecule multi-omics, multiway (DNA-DNA, DNA-RNA, and RNA-RNA interactions) chromatin conformation capturing methods, and proximity ligation-independent 3D genome-mapping technologies to explore chromatin organization structure and function in plants. Such methods could reveal the spatial interactions between trait-related SNPs and their target genes at various spatiotemporal resolutions, and elucidate the molecular mechanisms of the interactions among DNA elements, RNA molecules, and protein factors during the formation of key traits in plants.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Dan Xiong
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
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15
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Meluzzi D, Arya G. Computational approaches for inferring 3D conformations of chromatin from chromosome conformation capture data. Methods 2020; 181-182:24-34. [PMID: 31470090 PMCID: PMC7044057 DOI: 10.1016/j.ymeth.2019.08.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/24/2019] [Accepted: 08/23/2019] [Indexed: 02/08/2023] Open
Abstract
Chromosome conformation capture (3C) and its variants are powerful experimental techniques for probing intra- and inter-chromosomal interactions within cell nuclei at high resolution and in a high-throughput, quantitative manner. The contact maps derived from such experiments provide an avenue for inferring the 3D spatial organization of the genome. This review provides an overview of the various computational methods developed in the past decade for addressing the very important but challenging problem of deducing the detailed 3D structure or structure population of chromosomal domains, chromosomes, and even entire genomes from 3C contact maps.
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Affiliation(s)
- Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, United States
| | - Gaurav Arya
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, NC 27708, United States.
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16
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Chromatin architecture reorganization in murine somatic cell nuclear transfer embryos. Nat Commun 2020; 11:1813. [PMID: 32286279 PMCID: PMC7156422 DOI: 10.1038/s41467-020-15607-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 03/14/2020] [Indexed: 01/03/2023] Open
Abstract
The oocyte cytoplasm can reprogram the somatic cell nucleus into a totipotent state, but with low efficiency. The spatiotemporal chromatin organization of somatic cell nuclear transfer (SCNT) embryos remains elusive. Here, we examine higher order chromatin structures of mouse SCNT embryos using a low-input Hi-C method. We find that donor cell chromatin transforms to the metaphase state rapidly after SCNT along with the dissolution of typical 3D chromatin structure. Intriguingly, the genome undergoes a mitotic metaphase-like to meiosis metaphase II-like transition following activation. Subsequently, weak chromatin compartments and topologically associating domains (TADs) emerge following metaphase exit. TADs are further removed until the 2-cell stage before being progressively reestablished. Obvious defects including stronger TAD boundaries, aberrant super-enhancer and promoter interactions are found in SCNT embryos. These defects are partially caused by inherited H3K9me3, and can be rescued by Kdm4d overexpression. These observations provide insight into chromatin architecture reorganization during SCNT embryo development. The organisation of chromatin in somatic cell nuclear transfer (SCNT) embryos remains poorly understood. Here, the authors examine higher order chromatin structures of mouse SCNT embryos and provide insights into chromatin architecture reorganisation during SCNT embryo development.
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17
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Akhtar MS, Akhter N, Najm MZ, Deo SVS, Shukla NK, Almalki SSR, Alharbi RA, Sindi AAA, Alruwetei A, Ahmad A, Husain SA. Association of mutation and low expression of the CTCF gene with breast cancer progression. Saudi Pharm J 2020; 28:607-614. [PMID: 32435142 PMCID: PMC7229322 DOI: 10.1016/j.jsps.2020.03.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 03/29/2020] [Indexed: 12/15/2022] Open
Abstract
Background CTCF encodes 11-zinc finger protein which is implicated in multiple tumors including the carcinoma of the breast. The Present study investigates the association of CTCF mutations and their expression in breast cancer cases. Methods A total of 155 breast cancer and an equal number of adjacent normal tissue samples from 155 breast cancer patients were examined for CTCF mutation(s) by PCR-SSCP and automated DNA sequencing. Immunohistochemistry (IHC) method was used to analyze CTCF expression. Molecular findings were statistically analyzed with various clinicopathological features to identify associations of clinical relevance. Results Of the total, 16.1% (25/155) cases exhibited mutation in the CTCF gene. Missense mutations Gln > His (G > T) in exon 1 and silent mutations Ser > Ser (C > T) in exon 4 of CTCF gene were analyzed. A significant association was observed between CTCF mutations and some clinicopathological parameters namely menopausal status (p = 0.02) tumor stage (p = 0.03) nodal status (p = 0.03) and ER expression (p = 0.04). Protein expression analysis showed 42.58% samples having low or no expression (+), 38.0% with moderate (++) expression and 19.35% having high (+++) expression for CTCF. A significant association was found between CTCF protein expression and clinicopathological parameters include histological grade (p = 0.04), tumor stage (p = 0.04), nodal status (p = 0.03) and ER status (p = 0.04). Conclusions The data suggest that CTCF mutations leading to its inactivation significantly contribute to the progression of breast cancer.
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Affiliation(s)
- Md Salman Akhtar
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.,Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | - Naseem Akhter
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India.,Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | | | - S V S Deo
- Department of Surgical Oncology, DR. BRA-IRCH, AIIMS, New Delhi 110029, India
| | - N K Shukla
- Department of Surgical Oncology, DR. BRA-IRCH, AIIMS, New Delhi 110029, India
| | | | - Raed A Alharbi
- Faculty of Applied Medical Sciences, Albaha University, Albaha, Saudi Arabia
| | | | - Abdulmohsen Alruwetei
- Department of Medical Laboratory, College of Applied Medical Sciences, Qassim University, Qassim, Saudi Arabia
| | - Abrar Ahmad
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Syed Akhtar Husain
- Human Genetics Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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18
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Babbs C, Brown J, Horsley SW, Slater J, Maifoshie E, Kumar S, Ooijevaar P, Kriek M, Dixon-McIver A, Harteveld CL, Traeger-Synodinos J, Wilkie AOM, Higgs DR, Buckle VJ. ATR-16 syndrome: mechanisms linking monosomy to phenotype. J Med Genet 2020; 57:414-421. [PMID: 32005695 PMCID: PMC7279195 DOI: 10.1136/jmedgenet-2019-106528] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 11/29/2019] [Accepted: 12/05/2019] [Indexed: 12/16/2022]
Abstract
Background Deletions removing 100s–1000s kb of DNA, and variable numbers of poorly characterised genes, are often found in patients with a wide range of developmental abnormalities. In such cases, understanding the contribution of the deletion to an individual’s clinical phenotype is challenging. Methods Here, as an example of this common phenomenon, we analysed 41 patients with simple deletions of ~177 to ~2000 kb affecting one allele of the well-characterised, gene dense, distal region of chromosome 16 (16p13.3), referred to as ATR-16 syndrome. We characterised deletion extents and screened for genetic background effects, telomere position effect and compensatory upregulation of hemizygous genes. Results We find the risk of developmental and neurological abnormalities arises from much smaller distal chromosome 16 deletions (~400 kb) than previously reported. Beyond this, the severity of ATR-16 syndrome increases with deletion size, but there is no evidence that critical regions determine the developmental abnormalities associated with this disorder. Surprisingly, we find no evidence of telomere position effect or compensatory upregulation of hemizygous genes; however, genetic background effects substantially modify phenotypic abnormalities. Conclusions Using ATR-16 as a general model of disorders caused by CNVs, we show the degree to which individuals with contiguous gene syndromes are affected is not simply related to the number of genes deleted but depends on their genetic background. We also show there is no critical region defining the degree of phenotypic abnormalities in ATR-16 syndrome and this has important implications for genetic counselling.
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Affiliation(s)
- Christian Babbs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Jill Brown
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Sharon W Horsley
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joanne Slater
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Evie Maifoshie
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Paul Ooijevaar
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marjolein Kriek
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Cornelis L Harteveld
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Traeger-Synodinos
- Department of Medical Genetics, National and Kapodistrian University of Athens, Athens, Greece
| | - Andrew O M Wilkie
- Clinical Genetics Group, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Craniofacial Unit, Oxford University Hospitals NHS Trust, John Radcliffe Hospital, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Veronica J Buckle
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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19
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Aldersey JE, Sonstegard TS, Williams JL, Bottema CDK. Understanding the effects of the bovine POLLED variants. Anim Genet 2020; 51:166-176. [PMID: 31999853 DOI: 10.1111/age.12915] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/31/2022]
Abstract
Horns are paired appendages on the head of bovine species, comprising an inner bony core and outer keratin sheath. The horn bud forms during early fetal development but ossification of the developing horn does not occur until approximately 1 month after birth. Little is known about the genetic pathways that lead to horn growth. Hornless, or polled, animals are found in all domestic bovids. Histological studies of bovine fetuses have shown that the horn bud does not form in polled individuals. There are currently four known genetic variants for polledness in cattle on BTA1. All of the variants are intergenic, but probably affect regulation of nearby genes or long non-coding RNAs. Transcriptomic studies suggest that the expression of two nearby long non-coding RNAs are affected by the Celtic POLLED variant, but further studies are required to confirm these data. Candidate genes located elsewhere in the genome are involved in regulating bone formation and epithelial-to-mesenchymal transition. Expression of one of these candidate genes, RXFP2, appears to be reduced in the fetal horn bud of polled animals carrying the Celtic variant compared with horned individuals. Investigating horn ontogenesis and the genetic pathway by which the POLLED variants prevent horn development has implications for cattle breeding. If the genetic basis of horn bud formation and polledness is better understood, then new targets may be identified for precision genome editing to create polled individuals.
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Affiliation(s)
- J E Aldersey
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Adelaide, SA, 5371, Australia
| | | | - J L Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Adelaide, SA, 5371, Australia
| | - C D K Bottema
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy Campus, Adelaide, SA, 5371, Australia
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20
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Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol 2019; 20:535-550. [DOI: 10.1038/s41580-019-0132-4] [Citation(s) in RCA: 282] [Impact Index Per Article: 56.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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21
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Qian M, Cheng Y, Wang X. The methodology study of three-dimensional (3D) genome research. Semin Cell Dev Biol 2019; 90:12-18. [DOI: 10.1016/j.semcdb.2018.07.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 12/12/2022]
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22
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Lazniewski M, Dawson WK, Rusek AM, Plewczynski D. One protein to rule them all: The role of CCCTC-binding factor in shaping human genome in health and disease. Semin Cell Dev Biol 2019; 90:114-127. [PMID: 30096365 PMCID: PMC6642822 DOI: 10.1016/j.semcdb.2018.08.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 08/06/2018] [Indexed: 12/12/2022]
Abstract
The eukaryotic genome, constituting several billion base pairs, must be contracted to fit within the volume of a nucleus where the diameter is on the scale of μm. The 3D structure and packing of such a long sequence cannot be left to pure chance, as DNA must be efficiently used for its primary roles as a matrix for transcription and replication. In recent years, methods like chromatin conformation capture (including 3C, 4C, Hi-C, ChIA-PET and Multi-ChIA) and optical microscopy have advanced substantially and have shed new light on how eukaryotic genomes are hierarchically organized; first into 10-nm fiber, next into DNA loops, topologically associated domains and finally into interphase or mitotic chromosomes. This knowledge has allowed us to revise our understanding regarding the mechanisms governing the process of DNA organization. Mounting experimental evidence suggests that the key element in the formation of loops is the binding of the CCCTC-binding factor (CTCF) to DNA; a protein that can be referred to as the chief organizer of the genome. However, CTCF does not work alone but in cooperation with other proteins, such as cohesin or Yin Yang 1 (YY1). In this short review, we briefly describe our current understanding of the structure of eukaryotic genomes, how they are established and how the formation of DNA loops can influence gene expression. We discuss the recent discoveries describing the 3D structure of the CTCF-DNA complex and the role of CTCF in establishing genome structure. Finally, we briefly explain how various genetic disorders might arise as a consequence of mutations in the CTCF target sequence or alteration of genomic imprinting.
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Affiliation(s)
- Michal Lazniewski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Wayne K Dawson
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 103-8657, Japan
| | - Anna Maria Rusek
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Clinical Molecular Biology Department, Medical University of Bialystok, Bialystok, Poland
| | - Dariusz Plewczynski
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland; Centre for Innovative Research, Medical University of Bialystok, Bialystok, Poland; Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.
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23
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Wang DC, Wang W, Zhang L, Wang X. A tour of 3D genome with a focus on CTCF. Semin Cell Dev Biol 2019; 90:4-11. [PMID: 30031214 DOI: 10.1016/j.semcdb.2018.07.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 07/17/2018] [Indexed: 12/19/2022]
Abstract
The complex three-dimensional (3D) structure of the genome plays critical roles in the maintenance of genome stability, organization, and dynamics and in regulation of gene expression for understanding molecular mechanisms and diseases. Chromatin maintains biological functions and transcriptional activities through long distance interaction and interactions between loops and enhancers-promoters. We firstly overview the architecture and biology of chromatin and loops, topologically associated domains (TADs) and interactions, and compartments and functions. We specifically focus on CCCTC-binding factor (CTCF) in 3D genome organization and function to furthermore understand the significance of CTCF biology, transcriptional regulations, interactions with cohesin, roles in DNA binding, influences of CTCF degradation, and communication with wings-apart like (Wapl) protein. We also summarize the advanced single cell approaches to further monitor dynamics of CTCF functions and structures in the maintenance of 3D genome organization and function at single cell level.
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Affiliation(s)
- Diane C Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - William Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Zhongshan Hospital, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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24
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Fu S, Zhang L, Lv J, Zhu B, Wang W, Wang X. Two main stream methods analysis and visual 3D genome architecture. Semin Cell Dev Biol 2019; 90:43-53. [DOI: 10.1016/j.semcdb.2018.07.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 07/10/2018] [Indexed: 01/07/2023]
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25
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26
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Definition of clinical gene tests. Cell Biol Toxicol 2019; 35:83-87. [DOI: 10.1007/s10565-019-09464-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 01/28/2019] [Indexed: 01/20/2023]
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27
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Kong S, Zhang Y. Deciphering Hi-C: from 3D genome to function. Cell Biol Toxicol 2019; 35:15-32. [PMID: 30610495 DOI: 10.1007/s10565-018-09456-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 12/02/2018] [Indexed: 12/11/2022]
Abstract
Hi-C is a commonly used technology in 3D genomics which can depict global chromatin interactions across eukaryotic genome. Integrating with different datasets, it can also be applied to studying various biological questions, such as nuclear organization, gene transcription regulation, spatiotemporal development, genome assembly, and cancer genomics. During the last decade, the development and application of Hi-C have dramatically changed the view of genome architecture, chromatin conformation, and gene interaction. So far, Hi-C-related studies remain vivacious and controversial; thus, a unified standard of library construction and bioinformatics analysis are urgently needed. In this review, we have summarized its history, development, methodologies, advances, applications, shortages, and future perspectives. We discuss a few limitations of the current Hi-C technologies and future directions for improvement and highlight how Hi-C can bridge 3D structure to gene function. This review will be helpful for scientists who want to engage in the 3D genomics field; it also shows some future tracks.
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Affiliation(s)
- Siyuan Kong
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China
| | - Yubo Zhang
- Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 7 Pengfei Road, Dapeng District, 518120, Shenzhen, People's Republic of China.
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28
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Abstract
Complexity in genome architecture determines how gene expression programs are established, maintained, and modified from early developmental stages to normal adult phenotypes. Large scale and hierarchical organization of the genome impacts various aspects of cell functions, ranging from X-chromosome inactivation, stem-cell fate determination to transcription, DNA replication, and cellular repair. While chromatin loops and topologically-associated domains represent a basic structural or fundamental unit of chromatin organization, spatio-temporal organization of the genome further creates a complex network of interacting genome patterns, forming chromosomal compartments and chromosome territories. The understanding of human diseases, including cancers, auto-immune disorders, Alzheimer's, and cardiovascular diseases, relies on the associated molecular and epigenetic mechanisms. There is a growing interest in the impact of three-dimensional chromatin folding upon the genome structure and function, which gives rise to the question "What's in the fold?" and is the main focus of this review. Here we discuss the principles determining the spatial and regulatory relationships between gene regulation and three-dimensional chromatin landscapes, and how changes in chromatin-folding could influence the outcome of genome function in healthy and disease states.
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29
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The advances in CRISPR technology and 3D genome. Semin Cell Dev Biol 2018; 90:54-61. [PMID: 30004018 DOI: 10.1016/j.semcdb.2018.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2018] [Accepted: 07/08/2018] [Indexed: 12/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) system is a prokaryotic immune system that used to resist foreign genetic factors. It rapidly becomes the hot technology in life sciences and is applies for genome editing to solve the problem of genome-derived diseases. Using CRISPR/Cas technique, the biological DNA sequence can be repaired, cut, replaced, or added. It can effectively change the human stem cells and is expected to achieve results in the treatment. Compared with ZFN and TALEN genome editing techniques, CRISPR is more effective, accurate, and convenient. The application of CRISPR technique in three dimensional (3D) genome structure makes us understand the relationship between linear DNA sequence and 3D chromatin structure. Utilizing CRISPR/Cas9 genome editing to reverse or delete CTCF binding sites, to recognize changes of topological isomerism of the genome and interactions between chromatin loops. The purpose of this review is to introduce the characteristics and classification of the current CRISPR/Cas system, multiple functions, and potential therapeutic uses, as well as to outline the effect of the technique on chromatin loops by changing CTCF sites in 3D genomes. We will also briefly describe the importance of ethical dilemmas to be faced in CRISPR applications and provide a perspective for potential CRISPR considerations.
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Wen Z, Huang ZT, Zhang R, Peng C. ZNF143 is a regulator of chromatin loop. Cell Biol Toxicol 2018; 34:471-478. [PMID: 30120652 DOI: 10.1007/s10565-018-9443-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 08/08/2018] [Indexed: 11/30/2022]
Abstract
It is known that transcription factor ZNF143 frequently co-binds with CTCF-Cohesin complex in the anchor regions of chromatin loops. However, there is currently no genome-wide experiment to explore the functional roles of ZNF143 in chromatin loops. In this work, we used both computational and experimental analyses to investigate the regulatory effect of ZNF143 on chromatin loops. By jointly analyzing the ZNF143 and CTCF motifs underlying the isolated ZNF143-binding sites, ZNF143-CTCF co-binding sites and ZNF143-CTCF-RAD21 co-binding sites, our result shows that the ZNF143-CTCF-RAD21 co-binding sites are enriched with CTCF motifs but depleted of Znf143 motifs, implying that the CTCF but not ZNF143 may directly binds to the genome and thus ZNF143 may act as a cofactor instead of pioneer factor of ZNF143-CTCF-Cohesin complex. To explore the regulatory effect of ZNF143 on chromatin loops, we conducted siRNA experiment to knock down the expression level of ZNF143 in HEK293T cell line, and then performed in situ Hi-C on the negative control and ZNF143-silenced HEK293T cells. Comparison shows that the majority of chromatin loops are lost or at least weakened in the ZNF143-silenced HEK293T cells. However, a small proportion of chromatin loops are gained or strengthened, indicating the complicated roles of ZNF143 reduction in regulating chromatin loops. To further validate the loop analyses, we thoroughly investigated the chromatin loop changes between negative control and ZNF143-silenced cells by using aggregate peak analysis. The calculation shows that the lost and gained chromatin loops do undergo loop strength changes after ZNF143 silencing. Altogether, our work shows that ZNF143 can regulate chromatin loops by acting as a cofactor of CTCF-Cohesin complex, and knocking down ZNF143 expression level mainly eliminates or destabilizes chromatin loops.
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Affiliation(s)
- Zi Wen
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhi-Tao Huang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ran Zhang
- College of Life Sciences, Hebei Normal University, Shijiazhuang, 050024, China
| | - Cheng Peng
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, China.
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Gao D, Zhu B, Cao X, Zhang M, Wang X. Roles of NIPBL in maintenance of genome stability. Semin Cell Dev Biol 2018; 90:181-186. [PMID: 30096364 DOI: 10.1016/j.semcdb.2018.08.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 08/06/2018] [Indexed: 12/24/2022]
Abstract
A cohesin-loading factor (NIPBL) is one of important regulatory factors in the maintenance of 3D genome organization and function, by interacting with a large number of factors, e.g. cohesion, CCCTC-binding factor (CTCF) or cohesin complex component. The present article overviews the critical and regulatory roles of NIBPL in cohesion loading on chromotin and in gene expression and transcriptional signaling. We explore molecular mechanisms by which NIPBL recruits endogenous histone deacetylase (HDAC) to induce histone deacetylation and influence multi-dimensions of genome, through which NIPBL "hop" movement in chromatin regulates gene expression and alters genome folding. NIPBL regulates the process of CTCF and cohesion into chromatin loops and topologically associated domains, binding of cohesion and H3K4mes3 through interaction among promoters and enhancers. HP1 recruits NIPBL to DNA damage site through RNF8/RNF168 ubiquitylation pathway. NIPBL contributes to regulation of genome-controlled gene expression through the influence of cohesin in chromosome structure. NIPBL interacts with cohesin and then increases transcriptional activities of REC8 promoter, leading to up-regulation of gene expression. NIPBL movement among chromosomal loops regulates gene expression through dynamic alterations of genome organization. Thus, we expect a new and deep insight to understand dynamics of chromosome and explore potential strategies of therapiesc on basis of NIPBL.
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Affiliation(s)
- Danyan Gao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xin Cao
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Miaomiao Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics Shanghai, China.
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Zhang L, Song D, Zhu B, Wang X. The role of nuclear matrix protein HNRNPU in maintaining the architecture of 3D genome. Semin Cell Dev Biol 2018; 90:161-167. [PMID: 29981443 DOI: 10.1016/j.semcdb.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 07/03/2018] [Indexed: 02/07/2023]
Abstract
The complexity of higher eukaryote genomes is far from being explained by linear information. There is a need to understand roles of genome regulation at the organism level through defining a comprehensive profile of chromosomal organization. Chromosome conformation capture (3C)-based studies reveal that higher-order of chromatin include not only long-range chromatin loops, but also compartments and topologically associating domains as the basis of genome structure and functions. However, the molecular machinery how the genome is spatially organized is still inadequate. Exciting progress has been made with the development of today's technology, we find that heterogeneous nuclear ribonucleoprotein U, initially identified as a structural nuclear protein, plays important role in three-dimensional (3D) genome organization by high-throughput assays. The disruption of this protein not only results in compartment switching on of the genome, it also reduces of TAD boundary strengths at borders between two types of compartments, and regulates chromatin loop by decrease its intensities. In addition, HNRNPU mainly binds to active chromatin. Most of HNRNPU peaks is consistent with CTCF or RAD21.It also plays an irreplaceable role in the processes of mitosis. This review aims to discuss the role of HNRNPU in maintaining the 3D chromatin architecture, as well as the recent development and human diseases involved in this nuclear matrix (NM)-associated protein.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Dongli Song
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Bijun Zhu
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University Medical School, Shanghai Institute of Clinical Bioinformatics, Shanghai, China.
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Wang DC, Wang X. Genome dimensions control biological and toxicological functions; myth or reality? Cell Biol Toxicol 2018; 34:333-336. [DOI: 10.1007/s10565-018-9440-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 07/09/2018] [Indexed: 10/28/2022]
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