1
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Lu Z, Wang Y, Assumpção ALFV, Liu P, Kopp A, Saka S, Mcilwain SJ, Viny AD, Brand M, Pan X. Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells. Blood Adv 2024; 8:3076-3091. [PMID: 38531064 DOI: 10.1182/bloodadvances.2023011411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 02/16/2024] [Accepted: 02/26/2024] [Indexed: 03/28/2024] Open
Abstract
ABSTRACT Yin Yang 1 (YY1) and structural maintenance of chromosomes 3 (SMC3) are 2 critical chromatin structural factors that mediate long-distance enhancer-promoter interactions and promote developmentally regulated changes in chromatin architecture in hematopoietic stem/progenitor cells (HSPCs). Although YY1 has critical functions in promoting hematopoietic stem cell (HSC) self-renewal and maintaining HSC quiescence, SMC3 is required for proper myeloid lineage differentiation. However, many questions remain unanswered regarding how YY1 and SMC3 interact with each other and affect hematopoiesis. We found that YY1 physically interacts with SMC3 and cooccupies with SMC3 at a large cohort of promoters genome wide, and YY1 deficiency deregulates the genetic network governing cell metabolism. YY1 occupies the Smc3 promoter and represses SMC3 expression in HSPCs. Although deletion of 1 Smc3 allele partially restores HSC numbers and quiescence in YY1 knockout mice, Yy1-/-Smc3+/- HSCs fail to reconstitute blood after bone marrow transplant. YY1 regulates HSC metabolic pathways and maintains proper intracellular reactive oxygen species levels in HSCs, and this regulation is independent of the YY1-SMC3 axis. Our results establish a distinct YY1-SMC3 axis and its impact on HSC quiescence and metabolism.
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Affiliation(s)
- Zhanping Lu
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Yinghua Wang
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Anna L F V Assumpção
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Peng Liu
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Audrey Kopp
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Sahitya Saka
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
| | - Sean J Mcilwain
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Department of Biostatistics and Medical Informatics, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Aaron D Viny
- Division of Hematology & Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
- Columbia Stem Cell Initiative, Columbia University Irving Medical Center, New York, NY
- Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY
| | - Marjorie Brand
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin School of Medicine and Public Health, Madison, WI
| | - Xuan Pan
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin, Madison, WI
- Carbone Cancer Center, University of Wisconsin, Madison, WI
- Wisconsin Blood Cancer Research Institute, University of Wisconsin, Madison, WI
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2
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Wulfridge P, Sarma K. Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization. Nat Cell Biol 2024:10.1038/s41556-024-01437-4. [PMID: 38914786 DOI: 10.1038/s41556-024-01437-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 05/10/2024] [Indexed: 06/26/2024]
Abstract
R-loops are three-stranded nucleic acid structures that are abundant and widespread across the genome and that have important physiological roles in many nuclear processes. Their accumulation is observed in cancers and neurodegenerative disorders. Recent studies have implicated a function for R-loops and G-quadruplex (G4) structures, which can form on the displaced single strand of R-loops, in three-dimensional genome organization in both physiological and pathological contexts. Here we discuss the interconnected functions of DNA:RNA hybrids and G4s within R-loops, their impact on DNA repair and gene regulatory networks, and their emerging roles in genome organization during development and disease.
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Affiliation(s)
- Phillip Wulfridge
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA
| | - Kavitha Sarma
- Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, PA, USA.
- Penn Epigenetics Institute, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Ning M, Song L, Niu X, Wang Y, Liu W, Hu J, Cai H, Song W, Liu L, Li H, Gong D, Smith J, Huang Y. Multiscale 3D genome organization underlies duck fatty liver with no adipose inflammation or serious injury. Int J Biol Macromol 2024; 271:132452. [PMID: 38777007 DOI: 10.1016/j.ijbiomac.2024.132452] [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: 12/18/2023] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 05/25/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common form of chronic liver disease. Little is known about how gene expression and chromatin structure are regulated in NAFLD due to lack of suitable model. Ducks naturally develop fatty liver similar to serious human non-alcoholic fatty liver (NAFL) without adipose inflammation and liver fibrosis, thus serves as a good model for investigating molecular mechanisms of adipose metabolism and anti-inflammation. Here, we constructed a NAFLD model without adipose inflammation and liver fibrosis in ducks. By performing dynamic pathological and transcriptomic analyses, we identified critical genes involving in regulation of the NF-κB and MHCII signaling, which usually lead to adipose inflammation and liver fibrosis. We further generated dynamic three-dimensional chromatin maps during liver fatty formation and recovery. This showed that ducks enlarged hepatocyte cell nuclei to reduce inter-chromosomal interaction, decompress chromatin structure, and alter strength of intra-TAD and loop interactions during fatty liver formation. These changes partially contributed to the tight control the NF-κB and the MHCII signaling. Our analysis uncovers duck chromatin reorganization might be advantageous to maintain liver regenerative capacity and reduce adipose inflammation. These findings shed light on new strategies for NAFLD control.
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Affiliation(s)
- Mengfei Ning
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Linfei Song
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Xinyu Niu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Yiming Wang
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Wenjie Liu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Jiaxiang Hu
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Han Cai
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China
| | - Weitao Song
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Huifang Li
- Jiangsu Institute of Poultry Science, Yangzhou, China
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jacqueline Smith
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - Yinhua Huang
- State Key Laboratory for Farm Animal Biotech Breeding, College of Biology Sciences, China Agricultural University, Beijing, China.
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4
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Zhu H, Liu T, Wang Z. C2c: Predicting Micro-C from Hi-C. Genes (Basel) 2024; 15:673. [PMID: 38927609 DOI: 10.3390/genes15060673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/28/2024] Open
Abstract
MOTIVATION High-resolution Hi-C data, capable of detecting chromatin features below the level of Topologically Associating Domains (TADs), significantly enhance our understanding of gene regulation. Micro-C, a variant of Hi-C incorporating a micrococcal nuclease (MNase) digestion step to examine interactions between nucleosome pairs, has been developed to overcome the resolution limitations of Hi-C. However, Micro-C experiments pose greater technical challenges compared to Hi-C, owing to the need for precise MNase digestion control and higher-resolution sequencing. Therefore, developing computational methods to derive Micro-C data from existing Hi-C datasets could lead to better usage of a large amount of existing Hi-C data in the scientific community and cost savings. RESULTS We developed C2c ("high" or upper case C to "micro" or lower case c), a computational tool based on a residual neural network to learn the mapping between Hi-C and Micro-C contact matrices and then predict Micro-C contact matrices based on Hi-C contact matrices. Our evaluation results show that the predicted Micro-C contact matrices reveal more chromatin loops than the input Hi-C contact matrices, and more of the loops detected from predicted Micro-C match the promoter-enhancer interactions. Furthermore, we found that the mutual loops from real and predicted Micro-C better match the ChIA-PET data compared to Hi-C and real Micro-C loops, and the predicted Micro-C leads to more TAD-boundaries detected compared to the Hi-C data. The website URL of C2c can be found in the Data Availability Statement.
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Affiliation(s)
- Hao Zhu
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245, USA
| | - Tong Liu
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245, USA
| | - Zheng Wang
- Department of Computer Science, University of Miami, 330M Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33124-4245, USA
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Xu J, Xu X, Huang D, Luo Y, Lin L, Bai X, Zheng Y, Yang Q, Cheng Y, Huang A, Shi J, Bo X, Gu J, Chen H. A comprehensive benchmarking with interpretation and operational guidance for the hierarchy of topologically associating domains. Nat Commun 2024; 15:4376. [PMID: 38782890 PMCID: PMC11116433 DOI: 10.1038/s41467-024-48593-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 05/03/2024] [Indexed: 05/25/2024] Open
Abstract
Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.
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Affiliation(s)
- Jingxuan Xu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiang Xu
- Academy of Military Medical Science, Beijing, 100850, China
| | - Dandan Huang
- Department of Oncology, Peking University Shougang Hospital, Beijing, China
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China
| | - Yawen Luo
- Academy of Military Medical Science, Beijing, 100850, China
| | - Lin Lin
- Academy of Military Medical Science, Beijing, 100850, China
- School of Computer Science and Information Technology& KLAS, Northeast Normal University, Changchun, China
| | - Xuemei Bai
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yang Zheng
- Academy of Military Medical Science, Beijing, 100850, China
| | - Qian Yang
- Academy of Military Medical Science, Beijing, 100850, China
| | - Yu Cheng
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - An Huang
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Jingyi Shi
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China
| | - Xiaochen Bo
- Academy of Military Medical Science, Beijing, 100850, China.
| | - Jin Gu
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Department of Gastrointestinal Surgery, Peking University Cancer Hospital & Institute, Beijing, 100142, China.
- Department of Oncology, Peking University Shougang Hospital, Beijing, China.
- Center for Precision Diagnosis and Treatment of Colorectal Cancer and Inflammatory Diseases, Peking University Health Science Center, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
| | - Hebing Chen
- Academy of Military Medical Science, Beijing, 100850, China.
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6
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. Histochem Cell Biol 2024:10.1007/s00418-024-02289-7. [PMID: 38724854 DOI: 10.1007/s00418-024-02289-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2024] [Indexed: 05/21/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are nonrandom, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection of DNA and nascent RNA. These optimized DNA and RNA FISH protocols were implemented in a 384-well plate format alongside automated image and data analysis and enable accurate detection of individual gene alleles and their gene expression status across a large cell population. We successfully visualized MYC and EGFR DNA and nascent RNA with allele-level resolution in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD, 20892, USA.
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7
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Lee KH, Kim J, Kim JH. 3D epigenomics and 3D epigenopathies. BMB Rep 2024; 57:216-231. [PMID: 38627948 PMCID: PMC11139681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/15/2024] [Accepted: 03/18/2024] [Indexed: 05/25/2024] Open
Abstract
Mammalian genomes are intricately compacted to form sophisticated 3-dimensional structures within the tiny nucleus, so called 3D genome folding. Despite their shapes reminiscent of an entangled yarn, the rapid development of molecular and next-generation sequencing technologies (NGS) has revealed that mammalian genomes are highly organized in a hierarchical order that delicately affects transcription activities. An increasing amount of evidence suggests that 3D genome folding is implicated in diseases, giving us a clue on how to identify novel therapeutic approaches. In this review, we will study what 3D genome folding means in epigenetics, what types of 3D genome structures there are, how they are formed, and how the technologies have developed to explore them. We will also discuss the pathological implications of 3D genome folding. Finally, we will discuss how to leverage 3D genome folding and engineering for future studies. [BMB Reports 2024; 57(5): 216-231].
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Affiliation(s)
- Kyung-Hwan Lee
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Jungyu Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - Ji Hun Kim
- Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
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8
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Chang L, Xie Y, Taylor B, Wang Z, Sun J, Tan TR, Bejar R, Chen CC, Furnari FB, Hu M, Ren B. Droplet Hi-C for Fast and Scalable Profiling of Chromatin Architecture in Single Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.18.590148. [PMID: 38712075 PMCID: PMC11071305 DOI: 10.1101/2024.04.18.590148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Comprehensive analysis of chromatin architecture is crucial for understanding the gene regulatory programs during development and in disease pathogenesis, yet current methods often inadequately address the unique challenges presented by analysis of heterogeneous tissue samples. Here, we introduce Droplet Hi-C, which employs a commercial microfluidic device for high-throughput, single-cell chromatin conformation profiling in droplets. Using Droplet Hi-C, we mapped the chromatin architecture at single-cell resolution from the mouse cortex and analyzed gene regulatory programs in major cortical cell types. Additionally, we used this technique to detect copy number variation (CNV), structural variations (SVs) and extrachromosomal DNA (ecDNA) in cancer cells, revealing clonal dynamics and other oncogenic events during treatment. We further refined this technique to allow for joint profiling of chromatin architecture and transcriptome in single cells, facilitating a more comprehensive exploration of the links between chromatin architecture and gene expression in both normal tissues and tumors. Thus, Droplet Hi-C not only addresses critical gaps in chromatin analysis of heterogeneous tissues but also emerges as a versatile tool enhancing our understanding of gene regulation in health and disease.
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Affiliation(s)
- Lei Chang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Yang Xie
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA, USA
| | - Brett Taylor
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA
| | - Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
| | - Jiachen Sun
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
- Department of Systems Biology and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Tuyet R. Tan
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Rafael Bejar
- Moores Cancer Center, UC San Diego, La Jolla, CA, USA
| | - Clark C. Chen
- Department of Neurosurgery, University of Minnesota, Minneapolis, MN, USA
| | - Frank B. Furnari
- Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Ming Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA
- Center for Epigenomics, Institute for Genomic Medicine, Moores Cancer Center, University of California, San Diego, School of Medicine, La Jolla, CA, USA
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9
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Wall BPG, Nguyen M, Harrell JC, Dozmorov MG. Machine and deep learning methods for predicting 3D genome organization. ARXIV 2024:arXiv:2403.03231v1. [PMID: 38495565 PMCID: PMC10942493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene expression. Recent development of chromatin conformation capture technologies has enabled genome-wide profiling of various 3D structures, even with single cells. However, current catalogs of 3D structures remain incomplete and unreliable due to differences in technology, tools, and low data resolution. Machine learning methods have emerged as an alternative to obtain missing 3D interactions and/or improve resolution. Such methods frequently use genome annotation data (ChIP-seq, DNAse-seq, etc.), DNA sequencing information (k-mers, Transcription Factor Binding Site (TFBS) motifs), and other genomic properties to learn the associations between genomic features and chromatin interactions. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and analyze their pros and cons. We also point out obstacles of computational prediction of 3D interactions and suggest future research directions.
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Affiliation(s)
- Brydon P. G. Wall
- Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - My Nguyen
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
| | - J. Chuck Harrell
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
- Massey Comprehensive Cancer Center, Virginia Commonwealth University, Richmond, VA 23298, USA
- Center for Pharmaceutical Engineering, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Mikhail G. Dozmorov
- Department of Biostatistics, Virginia Commonwealth University, Richmond, VA, 23298, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, VA, 23284, USA
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10
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. RESEARCH SQUARE 2024:rs.3.rs-3970096. [PMID: 38464289 PMCID: PMC10925428 DOI: 10.21203/rs.3.rs-3970096/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
| | | | | | - Tom Misteli
- National Cancer Institute, National Institute of Health
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11
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E L, Lyu S, Wang Y, Xiao D, Liu T, Hou X, Li Y, Zhang C. Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in Brassica rapa. Int J Mol Sci 2024; 25:2568. [PMID: 38473815 DOI: 10.3390/ijms25052568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 01/25/2024] [Accepted: 02/09/2024] [Indexed: 03/14/2024] Open
Abstract
Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F1) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F1. Further study revealed that the DEGs detected in the F1 and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of Brassica rapa. The analysis of 3D genome data revealed that hybrid F1 plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F1 had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F1. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in Brassica rapa. This study provides further insight into the molecular mechanism of heterosis in Brassica rapa.
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Affiliation(s)
- Liu E
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Shanwu Lyu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Yaolong Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
| | - Changwei Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China
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12
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Almansour F, Keikhosravi A, Pegoraro G, Misteli T. Allele-level visualization of transcription and chromatin by high-throughput imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.19.580973. [PMID: 38529487 PMCID: PMC10962702 DOI: 10.1101/2024.02.19.580973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
The spatial arrangement of the genome within the nucleus is a pivotal aspect of cellular organization and function with implications for gene expression and regulation. While all genome organization features, such as loops, domains, and radial positioning, are non-random, they are characterized by a high degree of single-cell variability. Imaging approaches are ideally suited to visualize, measure, and study single-cell heterogeneity in genome organization. Here, we describe two methods for the detection of DNA and RNA of individual gene alleles by fluorescence in situ hybridization (FISH) in a high-throughput format. We have optimized combined DNA/RNA FISH approaches either using simultaneous or sequential detection. These optimized DNA and RNA FISH protocols, implemented in a 384-well plate format alongside automated image and data analysis, enable accurate detection of chromatin loci and their gene expression status across a large cell population with allele-level resolution. We successfully visualized MYC and EGFR DNA and RNA in multiple cell types, and we determined the radial position of active and inactive MYC and EGFR alleles. These optimized DNA/RNA detection approaches are versatile and sensitive tools for mapping of chromatin features and gene activity at the single-allele level and at high throughput.
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Affiliation(s)
- Faisal Almansour
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical School, Washington, DC, 20057, USA
| | - Adib Keikhosravi
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Gianluca Pegoraro
- High-Throughput Imaging Facility, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, National Institute of Health, Bethesda, MD 20892, USA
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13
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Zhang F, Bechara S, Nowacki M. Structural maintenance of chromosomes (SMC) proteins are required for DNA elimination in Paramecium. Life Sci Alliance 2024; 7:e202302281. [PMID: 38056908 PMCID: PMC10700549 DOI: 10.26508/lsa.202302281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
Chromosome (SMC) proteins are a large family of ATPases that play important roles in the organization and dynamics of chromatin. They are central regulators of chromosome dynamics and the core component of condensin. DNA elimination during zygotic somatic genome development is a characteristic feature of ciliated protozoa such as Paramecium This process occurs after meiosis, mitosis, karyogamy, and another mitosis, which result in the formation of a new germline and somatic nuclei. The series of nuclear divisions implies an important role of SMC proteins in Paramecium sexual development. The relationship between DNA elimination and SMC has not yet been described. Here, we applied RNA interference, genome sequencing, mRNA sequencing, immunofluorescence, and mass spectrometry to investigate the roles of SMC components in DNA elimination. Our results show that SMC4-2 is required for genome rearrangement, whereas SMC4-1 is not. Functional diversification of SMC4 in Paramecium led to a formation of two paralogues where SMC4-2 acquired a novel, development-specific function and differs from SMC4-1. Moreover, our study suggests a competitive relationship between these two proteins.
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Affiliation(s)
- Fukai Zhang
- https://ror.org/02k7v4d05 Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Sebastian Bechara
- https://ror.org/02k7v4d05 Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Mariusz Nowacki
- https://ror.org/02k7v4d05 Institute of Cell Biology, University of Bern, Bern, Switzerland
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14
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Kocanova S, Raynal F, Goiffon I, Oksuz BA, Baú D, Kamgoué A, Cantaloube S, Zhan Y, Lajoie B, Marti-Renom MA, Dekker J, Bystricky K. Enhancer-driven 3D chromatin domain folding modulates transcription in human mammary tumor cells. Life Sci Alliance 2024; 7:e202302154. [PMID: 37989525 PMCID: PMC10663337 DOI: 10.26508/lsa.202302154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 11/03/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023] Open
Abstract
The genome is organized in functional compartments and structural domains at the sub-megabase scale. How within these domains interactions between numerous cis-acting enhancers and promoters regulate transcription remains an open question. Here, we determined chromatin folding and composition over several hundred kb around estrogen-responsive genes in human breast cancer cell lines after hormone stimulation. Modeling of 5C data at 1.8 kb resolution was combined with quantitative 3D analysis of multicolor FISH measurements at 100 nm resolution and integrated with ChIP-seq data on transcription factor binding and histone modifications. We found that rapid estradiol induction of the progesterone gene expression occurs in the context of preexisting, cell type-specific chromosomal architectures encompassing the 90 kb progesterone gene coding region and an enhancer-spiked 5' 300 kb upstream genomic region. In response to estradiol, interactions between estrogen receptor α (ERα) bound regulatory elements are reinforced. Whereas initial enhancer-gene contacts coincide with RNA Pol 2 binding and transcription initiation, sustained hormone stimulation promotes ERα accumulation creating a regulatory hub stimulating transcript synthesis. In addition to implications for estrogen receptor signaling, we uncover that preestablished chromatin architectures efficiently regulate gene expression upon stimulation without the need for de novo extensive rewiring of long-range chromatin interactions.
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Affiliation(s)
- Silvia Kocanova
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Flavien Raynal
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Isabelle Goiffon
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Betul Akgol Oksuz
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Davide Baú
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
| | - Alain Kamgoué
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Sylvain Cantaloube
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
| | - Ye Zhan
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Bryan Lajoie
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
| | - Marc A Marti-Renom
- Centre Nacional d'Anàlisi Genòmica (CNAG), Barcelona, Spain
- Genome Biology Program, Centre de Regulació Genòmica (CRG), Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Job Dekker
- https://ror.org/0464eyp60 Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kerstin Bystricky
- Molecular, Cellular and Developmental Biology Unit (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, UPS, CNRS, Toulouse, France
- Institut Universitaire de France (IUF), Paris, France
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15
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Lin X, Zhang B. Explicit ion modeling predicts physicochemical interactions for chromatin organization. eLife 2024; 12:RP90073. [PMID: 38289342 PMCID: PMC10945522 DOI: 10.7554/elife.90073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono- and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of TechnologyCambridgeUnited States
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16
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Duan Z, Xu S, Sai Srinivasan S, Hwang A, Lee CY, Yue F, Gerstein M, Luan Y, Girgenti M, Zhang J. scENCORE: leveraging single-cell epigenetic data to predict chromatin conformation using graph embedding. Brief Bioinform 2024; 25:bbae096. [PMID: 38493342 PMCID: PMC10944576 DOI: 10.1093/bib/bbae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 02/01/2024] [Accepted: 02/20/2024] [Indexed: 03/18/2024] Open
Abstract
Dynamic compartmentalization of eukaryotic DNA into active and repressed states enables diverse transcriptional programs to arise from a single genetic blueprint, whereas its dysregulation can be strongly linked to a broad spectrum of diseases. While single-cell Hi-C experiments allow for chromosome conformation profiling across many cells, they are still expensive and not widely available for most labs. Here, we propose an alternate approach, scENCORE, to computationally reconstruct chromatin compartments from the more affordable and widely accessible single-cell epigenetic data. First, scENCORE constructs a long-range epigenetic correlation graph to mimic chromatin interaction frequencies, where nodes and edges represent genome bins and their correlations. Then, it learns the node embeddings to cluster genome regions into A/B compartments and aligns different graphs to quantify chromatin conformation changes across conditions. Benchmarking using cell-type-matched Hi-C experiments demonstrates that scENCORE can robustly reconstruct A/B compartments in a cell-type-specific manner. Furthermore, our chromatin confirmation switching studies highlight substantial compartment-switching events that may introduce substantial regulatory and transcriptional changes in psychiatric disease. In summary, scENCORE allows accurate and cost-effective A/B compartment reconstruction to delineate higher-order chromatin structure heterogeneity in complex tissues.
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Affiliation(s)
- Ziheng Duan
- Department of Computer Science, University of California, Irvine, 92697 CA, USA
| | - Siwei Xu
- Department of Computer Science, University of California, Irvine, 92697 CA, USA
| | | | - Ahyeon Hwang
- Department of Computer Science, University of California, Irvine, 92697 CA, USA
| | - Che Yu Lee
- Department of Computer Science, University of California, Irvine, 92697 CA, USA
| | - Feng Yue
- Department of Pathology, Northwestern University, 60611 IL, USA
| | - Mark Gerstein
- Molecular Biophysics & Biochemistry, Yale, 06519 CT, USA
| | - Yu Luan
- Department of Cell Systems and Anatomy, UT Health San Antonio, 78229 TX, USA
| | - Matthew Girgenti
- Department of Psychiatry, School of Medicine, Yale, 06519 CT, USA
- Clinical Neurosciences Division, National Center for PTSD, U.S. Department of Veterans Affairs, 06477 CT, USA
| | - Jing Zhang
- Department of Computer Science, University of California, Irvine, 92697 CA, USA
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17
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Jehangir M, Ahmad SF, Singchat W, Panthum T, Thong T, Aramsirirujiwet P, Lisachov A, Muangmai N, Han K, Koga A, Duengkae P, Srikulnath K. Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea's muntjac genome. Chromosome Res 2023; 31:34. [PMID: 38017297 DOI: 10.1007/s10577-023-09744-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 10/08/2023] [Accepted: 11/08/2023] [Indexed: 11/30/2023]
Abstract
Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may have been affected by spontaneous genome rearrangements. Chromosome fusion drastically alters karyotypes. However, the mechanisms and consequences of chromosome fusions, particularly in muntjac species, are poorly understood. Recent research-based advancements in three-dimensional (3D) genomics, particularly high-throughput chromatin conformation capture (Hi-C) sequencing, have allowed for the identification of chromosome fusions and provided mechanistic insights into three muntjac species: Muntiacus muntjak, M. reevesi, and M. crinifrons. This study aimed to uncover potential genome rearrangement patterns in the threatened species Fea's muntjac (Muntiacus feae), which have not been previously examined for such characteristics. Deep Hi-C sequencing (31.42 × coverage) was performed to reveal the 3D chromatin architecture of the Fea's muntjac genome. Patterns of repeated chromosome fusions that were potentially mediated by high-abundance transposable elements were identified. Comparative Hi-C maps demonstrated linkage homology between the sex chromosomes in Fea's muntjac and autosomes in M. reevesi, indicating that fusions may have played a crucial role in the evolution of the sex chromosomes of the lineage. The species-level dynamics of topologically associated domains (TADs) suggest that TAD organization could be altered by differential chromosome interactions owing to repeated chromosome fusions. However, research on the effect of TADs on muntjac genome evolution is insufficient. This study generated Hi-C data for the Fea's muntjac, providing a genomic resource for future investigations of the evolutionary patterns of chromatin conformation at the chromosomal level.
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Affiliation(s)
- Maryam Jehangir
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Syed Farhan Ahmad
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
| | - Worapong Singchat
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thitipong Panthum
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Thanyapat Thong
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Pakpoom Aramsirirujiwet
- Deparment of National Park, Wildlife and Plant Conservation, Ministry of Natural Resources and Environment, Bangkok, 10900, Thailand
| | - Artem Lisachov
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Narongrit Muangmai
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, 10900, Thailand
| | - Kyudong Han
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Department of Microbiology, Dankook University, Cheonan, 31116, Korea
- Bio-Medical Engineering Core Facility Research Center, Dankook University, Cheonan, 31116, Korea
| | - Akihiko Koga
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Kornsorn Srikulnath
- Animal Genomics and Bioresource Research Unit (AGB Research Unit), Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics (SRUWG), Department of Forest Biology, Faculty of Forestry, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- The International Undergraduate Program in Bioscience and Technology, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Bangkok, 10900, Thailand.
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18
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Lin X, Zhang B. Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.16.541030. [PMID: 37293007 PMCID: PMC10245791 DOI: 10.1101/2023.05.16.541030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Molecular mechanisms that dictate chromatin organization in vivo are under active investigation, and the extent to which intrinsic interactions contribute to this process remains debatable. A central quantity for evaluating their contribution is the strength of nucleosome-nucleosome binding, which previous experiments have estimated to range from 2 to 14 kBT. We introduce an explicit ion model to dramatically enhance the accuracy of residue-level coarse-grained modeling approaches across a wide range of ionic concentrations. This model allows for de novo predictions of chromatin organization and remains computationally efficient, enabling large-scale conformational sampling for free energy calculations. It reproduces the energetics of protein-DNA binding and unwinding of single nucleosomal DNA, and resolves the differential impact of mono and divalent ions on chromatin conformations. Moreover, we showed that the model can reconcile various experiments on quantifying nucleosomal interactions, providing an explanation for the large discrepancy between existing estimations. We predict the interaction strength at physiological conditions to be 9 kBT, a value that is nonetheless sensitive to DNA linker length and the presence of linker histones. Our study strongly supports the contribution of physicochemical interactions to the phase behavior of chromatin aggregates and chromatin organization inside the nucleus.
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Affiliation(s)
- Xingcheng Lin
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Bin Zhang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Harris RJ, Heer M, Levasseur MD, Cartwright TN, Weston B, Mitchell JL, Coxhead JM, Gaughan L, Prendergast L, Rico D, Higgins JMG. Release of Histone H3K4-reading transcription factors from chromosomes in mitosis is independent of adjacent H3 phosphorylation. Nat Commun 2023; 14:7243. [PMID: 37945563 PMCID: PMC10636195 DOI: 10.1038/s41467-023-43115-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023] Open
Abstract
Histone modifications influence the recruitment of reader proteins to chromosomes to regulate events including transcription and cell division. The idea of a histone code, where combinations of modifications specify unique downstream functions, is widely accepted and can be demonstrated in vitro. For example, on synthetic peptides, phosphorylation of Histone H3 at threonine-3 (H3T3ph) prevents the binding of reader proteins that recognize trimethylation of the adjacent lysine-4 (H3K4me3), including the TAF3 component of TFIID. To study these combinatorial effects in cells, we analyzed the genome-wide distribution of H3T3ph and H3K4me2/3 during mitosis. We find that H3T3ph anti-correlates with adjacent H3K4me2/3 in cells, and that the PHD domain of TAF3 can bind H3K4me2/3 in isolated mitotic chromatin despite the presence of H3T3ph. Unlike in vitro, H3K4 readers are still displaced from chromosomes in mitosis in Haspin-depleted cells lacking H3T3ph. H3T3ph is therefore unlikely to be responsible for transcriptional downregulation during cell division.
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Affiliation(s)
- Rebecca J Harris
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Maninder Heer
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Mark D Levasseur
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Tyrell N Cartwright
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Bethany Weston
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jennifer L Mitchell
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Jonathan M Coxhead
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Luke Gaughan
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Lisa Prendergast
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK
| | - Daniel Rico
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Centro Andaluz de Biología Molecular y Medicina Regenerativa (CABIMER), CSIC-Universidad Sevilla-Universidad Pablo de Olavide-Junta de Andalucía, 41092, Seville, Spain.
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
- Newcastle University Centre for Cancer, Faculty of Medical Sciences, Framlington Place, Newcastle Upon Tyne, NE2 1HH, UK.
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20
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Milevskiy MJ, Coughlan HD, Kane SR, Johanson TM, Kordafshari S, Chan WF, Tsai M, Surgenor E, Wilcox S, Allan RS, Chen Y, Lindeman GJ, Smyth GK, Visvader JE. Three-dimensional genome architecture coordinates key regulators of lineage specification in mammary epithelial cells. CELL GENOMICS 2023; 3:100424. [PMID: 38020976 PMCID: PMC10667557 DOI: 10.1016/j.xgen.2023.100424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 06/20/2023] [Accepted: 09/20/2023] [Indexed: 12/01/2023]
Abstract
Although lineage-specific genes have been identified in the mammary gland, little is known about the contribution of the 3D genome organization to gene regulation in the epithelium. Here, we describe the chromatin landscape of the three major epithelial subsets through integration of long- and short-range chromatin interactions, accessibility, histone modifications, and gene expression. While basal genes display exquisite lineage specificity via distal enhancers, luminal-specific genes show widespread promoter priming in basal cells. Cell specificity in luminal progenitors is largely mediated through extensive chromatin interactions with super-enhancers in gene-body regions in addition to interactions with polycomb silencer elements. Moreover, lineage-specific transcription factors appear to be controlled through cell-specific chromatin interactivity. Finally, chromatin accessibility rather than interactivity emerged as a defining feature of the activation of quiescent basal stem cells. This work provides a comprehensive resource for understanding the role of higher-order chromatin interactions in cell-fate specification and differentiation in the adult mouse mammary gland.
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Affiliation(s)
- Michael J.G. Milevskiy
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Hannah D. Coughlan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Serena R. Kane
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Timothy M. Johanson
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Somayeh Kordafshari
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Wing Fuk Chan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Minhsuang Tsai
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Elliot Surgenor
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Stephen Wilcox
- Advanced Technology and Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Rhys S. Allan
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Immunology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Yunshun Chen
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Geoffrey J. Lindeman
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia
- Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Gordon K. Smyth
- Bioinformatics Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- School of Mathematics and Statistics, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E. Visvader
- ACRF Cancer Biology and Stem Cells Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
- Department of Medical Biology, The University of Melbourne, Parkville, VIC 3010, Australia
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21
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Lee H, Seo P. Accessible gene borders establish a core structural unit for chromatin architecture in Arabidopsis. Nucleic Acids Res 2023; 51:10261-10277. [PMID: 37884483 PMCID: PMC10602878 DOI: 10.1093/nar/gkad710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 08/08/2023] [Accepted: 08/16/2023] [Indexed: 10/28/2023] Open
Abstract
Three-dimensional (3D) chromatin structure is linked to transcriptional regulation in multicellular eukaryotes including plants. Taking advantage of high-resolution Hi-C (high-throughput chromatin conformation capture), we detected a small structural unit with 3D chromatin architecture in the Arabidopsis genome, which lacks topologically associating domains, and also in the genomes of tomato, maize, and Marchantia polymorpha. The 3D folding domain unit was usually established around an individual gene and was dependent on chromatin accessibility at the transcription start site (TSS) and transcription end site (TES). We also observed larger contact domains containing two or more neighboring genes, which were dependent on accessible border regions. Binding of transcription factors to accessible TSS/TES regions formed these gene domains. We successfully simulated these Hi-C contact maps via computational modeling using chromatin accessibility as input. Our results demonstrate that gene domains establish basic 3D chromatin architecture units that likely contribute to higher-order 3D genome folding in plants.
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Affiliation(s)
- Hongwoo Lee
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Pil Joon Seo
- Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul 08826, Korea
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22
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Kai Y, Liu N, Orkin SH, Yuan GC. Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC. BMC Genomics 2023; 24:614. [PMID: 37833630 PMCID: PMC10571287 DOI: 10.1186/s12864-023-09675-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Accepted: 09/12/2023] [Indexed: 10/15/2023] Open
Abstract
BACKGROUND Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments. RESULTS To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments. CONCLUSIONS DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.
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Affiliation(s)
- Yan Kai
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nan Liu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Stuart H Orkin
- Cancer and Blood Disorders Center, Boston Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Howards Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, Charles Bronfman Institute for Precision Medicine, New York, NY, 10029, USA.
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23
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Feng Y, Guo L, Yang C, Zheng H, Xiao X, Ma H. The local density of H3K9me3 dictates the stability of HP1α condensates-mediated genomic interactions. J Genet Genomics 2023; 50:776-785. [PMID: 37116579 DOI: 10.1016/j.jgg.2023.04.006] [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: 01/01/2023] [Revised: 04/10/2023] [Accepted: 04/13/2023] [Indexed: 04/30/2023]
Abstract
The human genome can be demarcated into domains based on distinct epigenetic states. The trimethylation of histone H3 lysine 9 (H3K9me3) is essential for the formation of constitutive heterochromatin nanodomains. However, the extent to which genomic regions require specific densities or degrees of H3K9me3 for stable interactions remains unclear. Here, we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions. We select three loci (IDR3, TCF3, and PR1) with distinct levels of H3K9me3 to examine the genomic interactions and association with endogenous Heterochromatin Protein 1 (HP1α) condensates. Our results demonstrate a positive correlation between the levels of H3K9me3 at the loci and their association with HP1α condensates. By dual-color labeling and long-term tracking of IDR3 and PR1 loci, we find a periodical association between the two ranging from one to three hours. Epigenetic perturbation-induced Genome organization (EpiGo)-KRAB introduces ∼20 kilobases of H3K9me3 at the TCF3 locus, which is sufficient to establish a stable association between TCF3 and HP1α condensates. In addition, EpiGo-mediated H3K9me3 also leads to stable genomic interaction between IDR3 and TCF3. Briefly, these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1α condensates.
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Affiliation(s)
- Ying Feng
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China; Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Li Guo
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Chen Yang
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
| | - Hui Zheng
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Xiao Xiao
- School of Biotechnology, East China University of Science and Technology, Shanghai 200237, China.
| | - Hanhui Ma
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China.
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24
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Qiu X, Liang G, Zhou W, Sen R, Atchison ML. Multiple lineage-specific epigenetic landscapes at the antigen receptor loci. AGING RESEARCH (HONG KONG, CHINA) 2023; 1:9340010. [PMID: 38770228 PMCID: PMC11103674 DOI: 10.26599/agr.2023.9340010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Antigen receptors (AgRs) expressed on B and T cells provide the adaptive immune system with ability to detect numerous foreign antigens. Epigenetic features of B cell receptor (BCR) and T cell receptor (TCR) genes were previously studied in lymphocytes, but little is known about their epigenetic features in other cells. Here, we explored histone modifications and transcription markers at the BCR and TCR loci in lymphocytes (pro-B, DP T cells, and mature CD4+ T cells), compared to embryonic stem (ES) cells and neurons. In B cells, the BCR loci exhibited active histone modifications and transcriptional markers indicative of active loci. Similar results were observed at the TCR loci in T cells. All loci were largely inactive in neurons. Surprisingly, in ES cells all AgR loci displayed a high degree of active histone modifications and markers of active transcription. Locations of these active histone modifications in ES cells were largely distinct from those in pro-B cells, and co-localized at numerous binding locations for transcription factors Oct4, Sox2, and Nanog. ES and pro-B cells also showed distinct binding patterns for the ubiquitous transcription factor YY1 and chromatin remodeler Brg1. On the contrary, there were many overlapping CCCTC-binding factor (CTCF) binding patterns when comparing ES cells, pro-B cells, and neurons. Our study identifies epigenetic features in ES cells and lymphocytes that may be related to ES cell pluripotency and lymphocyte tissue-specific activation at the AgR loci.
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Affiliation(s)
- Xiang Qiu
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Guanxiang Liang
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland 21205, USA
| | - Ranjan Sen
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, Baltimore, Maryland 21224, USA
| | - Michael L. Atchison
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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25
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Zhang Z, Li F, Zhao J, Zheng C. CapsNetYY1: identifying YY1-mediated chromatin loops based on a capsule network architecture. BMC Genomics 2023; 24:448. [PMID: 37559017 PMCID: PMC10410878 DOI: 10.1186/s12864-023-09217-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/28/2023] [Indexed: 08/11/2023] Open
Abstract
BACKGROUND Previous studies have identified that chromosome structure plays a very important role in gene control. The transcription factor Yin Yang 1 (YY1), a multifunctional DNA binding protein, could form a dimer to mediate chromatin loops and active enhancer-promoter interactions. The deletion of YY1 or point mutations at the YY1 binding sites significantly inhibit the enhancer-promoter interactions and affect gene expression. To date, only a few computational methods are available for identifying YY1-mediated chromatin loops. RESULTS We proposed a novel model named CapsNetYY1, which was based on capsule network architecture to identify whether a pair of YY1 motifs can form a chromatin loop. Firstly, we encode the DNA sequence using one-hot encoding method. Secondly, multi-scale convolution layer is used to extract local features of the sequence, and bidirectional gated recurrent unit is used to learn the features across time steps. Finally, capsule networks (convolution capsule layer and digital capsule layer) used to extract higher level features and recognize YY1-mediated chromatin loops. Compared with DeepYY1, the only prediction for YY1-mediated chromatin loops, our model CapsNetYY1 achieved the better performance on the independent datasets (AUC [Formula: see text]). CONCLUSION The results indicate that CapsNetYY1 is an excellent method for identifying YY1-mediated chromatin loops. We believe that the CapsNetYY1 method will be used for predictive classification of other DNA sequences.
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Affiliation(s)
- Zhimin Zhang
- College of Mathematics and System Sciences, Xinjiang University, Urumqi, China
| | - Fenglin Li
- College of Mathematics and System Sciences, Xinjiang University, Urumqi, China
| | - Jianping Zhao
- College of Mathematics and System Sciences, Xinjiang University, Urumqi, China.
| | - Chunhou Zheng
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, Information Materials and Intelligent Sensing Laboratory of Anhui Province, and School of Artificial Intelligence, Anhui University, Hefei, China.
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26
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Syed SA, Shqillo K, Nand A, Zhan Y, Dekker J, Imbalzano AN. Protein arginine methyltransferase 5 (Prmt5) localizes to chromatin loop anchors and modulates expression of genes at TAD boundaries during early adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.13.544859. [PMID: 37398486 PMCID: PMC10312757 DOI: 10.1101/2023.06.13.544859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Protein arginine methyltransferase 5 (Prmt5) is an essential regulator of embryonic development and adult progenitor cell functions. Prmt5 expression is mis-regulated in many cancers, and the development of Prmt5 inhibitors as cancer therapeutics is an active area of research. Prmt5 functions via effects on gene expression, splicing, DNA repair, and other critical cellular processes. We examined whether Prmt5 functions broadly as a genome-wide regulator of gene transcription and higher-order chromatin interactions during the initial stages of adipogenesis using ChIP-Seq, RNA-seq, and Hi-C using 3T3-L1 cells, a frequently utilized model for adipogenesis. We observed robust genome-wide Prmt5 chromatin-binding at the onset of differentiation. Prmt5 localized to transcriptionally active genomic regions, acting as both a positive and a negative regulator. A subset of Prmt5 binding sites co-localized with mediators of chromatin organization at chromatin loop anchors. Prmt5 knockdown decreased insulation strength at the boundaries of topologically associating domains (TADs) adjacent to sites with Prmt5 and CTCF co-localization. Genes overlapping such weakened TAD boundaries showed transcriptional dysregulation. This study identifies Prmt5 as a broad regulator of gene expression, including regulation of early adipogenic factors, and reveals an unappreciated requirement for Prmt5 in maintaining strong insulation at TAD boundaries and overall chromatin organization.
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Affiliation(s)
- Sabriya A Syed
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Kristina Shqillo
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ankita Nand
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Ye Zhan
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
| | - Job Dekker
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, MA USA
- Howard Hughes Medical Institute, Chevy Chase, MD USA
| | - Anthony N Imbalzano
- Department of Biochemistry and Molecular Biotechnology, University of Massachusetts Chan Medical School, Worcester, MA USA
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27
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Li S, Shen X. Long interspersed nuclear element 1 and B1/Alu repeats blueprint genome compartmentalization. Curr Opin Genet Dev 2023; 80:102049. [PMID: 37229928 DOI: 10.1016/j.gde.2023.102049] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/14/2023] [Accepted: 04/15/2023] [Indexed: 05/27/2023]
Abstract
The organization of the genome into euchromatin and heterochromatin has been known for almost 100 years [1]. More than 50% of mammalian genomes contain repetitive sequences [2,3]. Recently, a functional link between the genome and its folding has been identified [4,5]. Homotypic clustering of long interspersed nuclear element 1 (LINE1 or L1) and B1/Alu retrotransposons forms grossly exclusive nuclear domains that characterize and predict heterochromatin and euchromatin, respectively. The spatial segregation of L1 and B1/Alu-rich compartments is conserved in mammalian cells and can be rebuilt during the cell cycle and established de novo in early embryogenesis. Inhibition of L1 RNA drastically weakened homotypic repeat contacts and compartmental segregation, indicating that L1 plays a more significant role than just being a compartmental marker. This simple and inclusive genetic coding model of L1 and B1/Alu in shaping the macroscopic structure of the genome provides a plausible explanation for the remarkable conservation and robustness of its folding in mammalian cells. It also proposes a conserved core structure on which subsequent dynamic regulation takes place.
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Affiliation(s)
- Siyang Li
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xiaohua Shen
- Department of Basic Medical Sciences, School of Medicine, Center for Life Sciences, Tsinghua University, Beijing 100084, China.
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28
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Hamba Y, Kamatani T, Miya F, Boroevich KA, Tsunoda T. Topologically associating domain underlies tissue specific expression of long intergenic non-coding RNAs. iScience 2023; 26:106640. [PMID: 37250307 PMCID: PMC10214471 DOI: 10.1016/j.isci.2023.106640] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/15/2022] [Accepted: 04/05/2023] [Indexed: 05/31/2023] Open
Abstract
Accumulating evidence indicates that long intergenic non-coding RNAs (lincRNAs) show more tissue-specific expression patterns than protein-coding genes (PCGs). However, although lincRNAs are subject to canonical transcriptional regulation like PCGs, the molecular basis for the specificity of their expression patterns remains unclear. Here, using expression data and coordinates of topologically associating domains (TADs) in human tissues, we show that lincRNA loci are significantly enriched in the more internal region of TADs compared to PCGs and that lincRNAs within TADs have higher tissue specificity than those outside TADs. Based on these, we propose an analytical framework to interpret transcriptional status using lincRNA as an indicator. We applied it to hypertrophic cardiomyopathy data and found disease-specific transcriptional regulation: ectopic expression of keratin at the TAD level and derepression of myocyte differentiation-related genes by E2F1 with down-regulation of LINC00881. Our results provide understanding of the function and regulation of lincRNAs according to genomic structure.
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Affiliation(s)
- Yu Hamba
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Takashi Kamatani
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Department of AI Technology Development, M&D Data Science Center, Tokyo Medical and Dental University, Tokyo 101-0062, Japan
- Division of Precision Cancer Medicine, Tokyo Medical and Dental University Hospital, Tokyo 113-8519, Japan
- Division of Pulmonary Medicine, Department of Medicine, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Fuyuki Miya
- Center for Medical Genetics, Keio University School of Medicine, Tokyo 160-8582, Japan
| | - Keith A. Boroevich
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Tatsuhiko Tsunoda
- Laboratory for Medical Science Mathematics, Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
- Laboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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29
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Amin A, Kadam S, Mieczkowski J, Ahmed I, Bhat YA, Shah F, Tolstorukov MY, Kingston RE, Padinhateeri R, Wani AH. Disruption of polyhomeotic polymerization decreases nucleosome occupancy and alters genome accessibility. Life Sci Alliance 2023; 6:e202201768. [PMID: 36849253 PMCID: PMC9973501 DOI: 10.26508/lsa.202201768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 02/16/2023] [Accepted: 02/16/2023] [Indexed: 03/01/2023] Open
Abstract
Chromatin attains its three-dimensional (3D) conformation by establishing contacts between different noncontiguous regions. Sterile Alpha Motif (SAM)-mediated polymerization of the polyhomeotic (PH) protein regulates subnuclear clustering of Polycomb Repressive Complex 1 (PRC1) and chromatin topology. The mutations that perturb the ability of the PH to polymerize, disrupt long-range chromatin contacts, alter Hox gene expression, and lead to developmental defects. To understand the underlying mechanism, we combined the experiments and theory to investigate the effect of this SAM domain mutation on nucleosome occupancy and accessibility on a genome wide scale. Our data show that disruption of PH polymerization because of SAM domain mutation decreases nucleosome occupancy and alters accessibility. Polymer simulations investigating the interplay between distant chromatin contacts and nucleosome occupancy, both of which are regulated by PH polymerization, suggest that nucleosome density increases when contacts between different regions of chromatin are established. Taken together, it appears that SAM domain-mediated PH polymerization biomechanically regulates the organization of chromatin at multiple scales from nucleosomes to chromosomes and we suggest that higher order organization can have a top-down causation effect on nucleosome occupancy.
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Affiliation(s)
- Adfar Amin
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Sangram Kadam
- Department of Biosciences and Bioengineering, IIT, Bombay, India
| | - Jakub Mieczkowski
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Ikhlak Ahmed
- CIRI, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A Bhat
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Fouziya Shah
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | | | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | | | - Ajazul H Wani
- Department of Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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30
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Gavrilov AA, Evko GS, Galitsyna AA, Ulianov SV, Kochetkova TV, Merkel AY, Tyakht AV, Razin SV. RNA-DNA interactomes of three prokaryotes uncovered by proximity ligation. Commun Biol 2023; 6:473. [PMID: 37120653 PMCID: PMC10148824 DOI: 10.1038/s42003-023-04853-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 04/19/2023] [Indexed: 05/01/2023] Open
Abstract
Proximity ligation approaches, which are widely used to study the spatial organization of the genome, also make it possible to reveal patterns of RNA-DNA interactions. Here, we use RedC, an RNA-DNA proximity ligation approach, to assess the distribution of major RNA types along the genomes of E. coli, B. subtilis, and thermophilic archaeon T. adornatum. We find that (i) messenger RNAs preferentially interact with their cognate genes and the genes located downstream in the same operon, which is consistent with polycistronic transcription; (ii) ribosomal RNAs preferentially interact with active protein-coding genes in both bacteria and archaea, indicating co-transcriptional translation; and (iii) 6S noncoding RNA, a negative regulator of bacterial transcription, is depleted from active genes in E. coli and B. subtilis. We conclude that the RedC data provide a rich resource for studying both transcription dynamics and the function of noncoding RNAs in microbial organisms.
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Affiliation(s)
- Alexey A Gavrilov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Grigory S Evko
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | | | - Sergey V Ulianov
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia
| | - Tatiana V Kochetkova
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander Y Merkel
- Winogradsky Institute of Microbiology, Federal Research Center of Biotechnology, Russian Academy of Sciences, 117312, Moscow, Russia
| | - Alexander V Tyakht
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Sergey V Razin
- Institute of Gene Biology, Russian Academy of Sciences, 119334, Moscow, Russia.
- Faculty of Biology, Lomonosov Moscow State University, 119991, Moscow, Russia.
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31
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Kai Y, Liu N, Orkin SH, Yuan GC. Identifying Quantitatively Differential Chromosomal Compartmentalization Changes and Their Biological Significance from Hi-C data using DARIC. RESEARCH SQUARE 2023:rs.3.rs-2814806. [PMID: 37162846 PMCID: PMC10168473 DOI: 10.21203/rs.3.rs-2814806/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Background Chromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and oncogenesis. However, currently the prevalent method for comparative analysis of compartmentalization landscapes between different cell types is limited to the qualitative switched compartments. Results To identify genomic regions with quantitatively differential compartmentalization changes from genome-wide chromatin conformation data like Hi-C, we developed a computational framework named DARIC. DARIC includes three modules: compartmentalization quantification, normalization, and differential analysis. Comparing DARIC with the conventional compartment switching analysis reveals substantial regions characterized by quantitatively significant compartmentalization changes without switching. These changes are accompanied by changes in gene expression, chromatin accessibility, H3K27ac intensity, as well as the interactions with nuclear lamina proteins and nuclear positioning, highlighting the functional importance of such quantitative changes in gene regulation. We applied DARIC to dissect the quantitative compartmentalization changes during human cardiomyocyte differentiation and identified two distinct mechanisms for gene activation based on the association with compartmentalization changes. Using the quantitative compartmentalization measurement module from DARIC, we further dissected the compartment variability landscape in the human genome by analyzing a compendium of 32 Hi-C datasets from 4DN. We discovered an interesting correlation between compartmentalization variability and sub-compartments. Conclusions DARIC is a useful tool for analyzing quantitative compartmentalization changes and mining novel biological insights from increasing Hi-C data. Our results demonstrate the functional significance of quantitative compartmentalization changes in gene regulation, and provide new insights into the relationship between compartmentalization variability and sub-compartments in the human genome.
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Affiliation(s)
| | - Nan Liu
- Bone Marrow Transplantation Center of the First Affiliated Hospital, Zhejiang University School of Medicine, 310003 Hangzhou, China
- Liangzhu Laboratory, Zhejiang University Medical Center, Hangzhou, 311121, China
| | - Stuart H Orkin
- Howards Hughes Medical Institute, Boston MA 02115, USA
- Lead contact
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Charles Bronfman Institute for Precision Medicine, Icahn School of Medicine at Mount Sinai, New York NY 10029, USA
- Lead contact
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32
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Romero IG. Seeing humans through an evolutionary lens. Science 2023; 380:360-361. [PMID: 37104588 DOI: 10.1126/science.adh0745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
A collection of mammalian genomes provides insights into human biology and evolution.
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Affiliation(s)
- Irene Gallego Romero
- Melbourne Integrative Genomics, University of Melbourne, Parkville, VIC, Australia
- School of BioSciences, University of Melbourne, Parkville, VIC, Australia
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33
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Ni L, Tian Z. Toward cis-regulation in soybean: a 3D genome scope. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:28. [PMID: 37313524 PMCID: PMC10248674 DOI: 10.1007/s11032-023-01374-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/25/2023] [Indexed: 06/15/2023]
Abstract
In eukaryotic cells, 3D genome plays an important role in the regulation of gene spatiotemporal expression, which is essential for the biological and developmental processes in a life cycle. In the past decade, the development of high-throughput technologies greatly enhances our ability to map the 3D genome organization, identifies multiple 3D genome structures, and investigates the functional role of 3D genome organization in gene regulation, which facilitates our understandings of cis-regulatory landscape and biological development. Comparing with the comprehensive analyses of 3D genome in mammals and model plants, the progress in soybean is much less. Future development and application of tools to precisely manipulate 3D genome structure at different levels will significantly strengthen the functional genome study and molecular breeding in soybean. Here, we review the recent progresses in 3D genome study and discuss future directions, which may help to improve soybean 3D functional genome study and molecular breeding.
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Affiliation(s)
- Lingbin Ni
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101 China
- College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing, 100049 China
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34
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Zhuo B, Zhang Q, Xie T, Wang Y, Chen Z, Zuo D, Guo B. Integrative epigenetic analysis reveals AP-1 promotes activation of tumor-infiltrating regulatory T cells in HCC. Cell Mol Life Sci 2023; 80:103. [PMID: 36941472 PMCID: PMC11071886 DOI: 10.1007/s00018-023-04746-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 02/06/2023] [Accepted: 03/02/2023] [Indexed: 03/23/2023]
Abstract
Regulatory T (Treg) cells that infiltrate human tumors exhibit stronger immunosuppressive activity compared to peripheral blood Treg cells (PBTRs), thus hindering the induction of effective antitumor immunity. Previous transcriptome studies have identified a set of genes that are conserved in tumor-infiltrating Treg cells (TITRs). However, epigenetic profiles of TITRs have not yet been completely deciphered. Here, we employed ATAC-seq and CUT&Tag assays to integrate transcriptome profiles and identify functional regulatory elements in TITRs. We observed a global difference in chromatin accessibility and enhancer landscapes between TITRs and PBTRs. We identified two types of active enhancer formation in TITRs. The H3K4me1-predetermined enhancers are poised to be activated in response to tumor microenvironmental stimuli. We found that AP-1 family motifs are enriched at the enhancer regions of TITRs. Finally, we validated that c-Jun binds at regulatory regions to regulate signature genes of TITRs and AP-1 is required for Treg cells activation in vitro. High c-Jun expression is correlated with poor survival in human HCC. Overall, our results provide insights into the mechanism of AP-1-mediated activation of TITRs and can hopefully be used to develop new therapeutic strategies targeting TITRs in liver cancer treatment.
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Affiliation(s)
- Baowen Zhuo
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
- Medical Research Institute, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, Guangdong, China
| | - Qifan Zhang
- Department of General Surgery, Division of Hepatobiliopancreatic Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Tingyan Xie
- Medical Research Institute, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, Guangdong, China
| | - Yidan Wang
- Department of Laboratory Medicine, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, Guangdong, China
| | - Zhengliang Chen
- Department of Immunology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Daming Zuo
- Department of Medical Laboratory, School of Laboratory Medicine and Biotechnology, Southern Medical University, Guangzhou, 510515, Guangdong, China.
| | - Bo Guo
- Medical Research Institute, Shenzhen Baoan Women's and Children's Hospital, Jinan University, Shenzhen, 518102, Guangdong, China.
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35
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Liu S, Tang Q, Zhao K. Analysis of Chromatin Interaction and Accessibility by Trac-Looping. Methods Mol Biol 2023; 2611:85-97. [PMID: 36807066 DOI: 10.1007/978-1-0716-2899-7_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Spatial organization of the genome modulates pivotal biological processes. The emerging new technologies have provided novel insights into genome structure and its role in regulating cell activities. To examine the genome-wide chromatin interactions at accessible chromatin regions, we developed a DNA transposase-mediated analysis of chromatin looping (Trac-looping) method for simultaneously detecting chromatin interactions and chromatin accessibility. Here, we describe a detailed protocol of generating Trac-looping libraries.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Qingsong Tang
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA.
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36
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Low-affinity CTCF binding drives transcriptional regulation whereas high-affinity binding encompasses architectural functions. iScience 2023; 26:106106. [PMID: 36852270 PMCID: PMC9958374 DOI: 10.1016/j.isci.2023.106106] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 10/14/2022] [Accepted: 01/27/2023] [Indexed: 02/05/2023] Open
Abstract
CTCF is a DNA-binding protein which plays critical roles in chromatin structure organization and transcriptional regulation; however, little is known about the functional determinants of different CTCF-binding sites (CBS). Using a conditional mouse model, we have identified one set of CBSs that are lost upon CTCF depletion (lost CBSs) and another set that persists (retained CBSs). Retained CBSs are more similar to the consensus CTCF-binding sequence and usually span tandem CTCF peaks. Lost CBSs are enriched at enhancers and promoters and associate with active chromatin marks and higher transcriptional activity. In contrast, retained CBSs are enriched at TAD and loop boundaries. Integration of ChIP-seq and RNA-seq data has revealed that retained CBSs are located at the boundaries between distinct chromatin states, acting as chromatin barriers. Our results provide evidence that transient, lost CBSs are involved in transcriptional regulation, whereas retained CBSs are critical for establishing higher-order chromatin architecture.
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37
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Zhao M, Feng D, Hu L, Liu L, Wu J, Hu Z, Long H, Kuang Q, Ouyang L, Lu Q. 3D genome alterations in T cells associated with disease activity of systemic lupus erythematosus. Ann Rheum Dis 2023; 82:226-234. [PMID: 36690410 PMCID: PMC9887402 DOI: 10.1136/ard-2022-222653] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/17/2022] [Indexed: 02/03/2023]
Abstract
OBJECTIVES Three-dimensional (3D) genome alterations can dysregulate gene expression by rewiring physical interactions within chromosomes in a tissue-specific or cell-specific manner and lead to diseases. We aimed to elucidate the 3D genome structure and its role in gene expression networks dysregulated in systemic lupus erythematosus (SLE). METHODS We performed Hi-C experiments using CD4+ T cells from 7 patients with SLE and 5 age-matched and sex-matched healthy controls (HCs) combined with RNA sequencing analysis. Further integrative analyses, including transcription factor motif enrichment, SPI1 knockdown and histone modifications (H3K27ac, H3K4me1, H3K4me3), were performed for altered loop-associated gene loci in SLE. RESULTS We deciphered the 3D chromosome organisation in T cells of patients with SLE and found it was clearly distinct from that of HCs and closely associated with the disease activity of SLE. Importantly, we identified loops within chromosomes associated with the disease activity of SLE and differentially expressed genes and found some key histone modifications close to these loops. Moreover, we demonstrated the contribution of the transcription factor SPI1, whose motif is located in the altered loop in SLE, to the overexpression of interferon pathway gene. In addition, we identified the potential influences of genetic variations in 3D genome alterations in SLE. CONCLUSIONS Our results highlight the 3D genome structure alterations associated with SLE development and provide a foundation for future interrogation of the relationships between chromosome structure and gene expression control in SLE.
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Affiliation(s)
- Ming Zhao
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
| | - Delong Feng
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Longyuan Hu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lin Liu
- Epigenetic Group, Frasergen Bioinformatics Co, Ltd, Wuhan, China
| | - Jiali Wu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Zhi Hu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Haojun Long
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qiqi Kuang
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Lianlian Ouyang
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
| | - Qianjin Lu
- Department of Dermatology, The Second Xiangya Hospital of Central South University, Changsha, China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Institute of Dermatology, Chinese Academy of Medical Sciences, Nanjing, China
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38
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Pan-3D genome analysis reveals structural and functional differentiation of soybean genomes. Genome Biol 2023; 24:12. [PMID: 36658660 PMCID: PMC9850592 DOI: 10.1186/s13059-023-02854-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND High-order chromatin structure plays important roles in gene regulation. However, the diversity of the three-dimensional (3D) genome across plant accessions are seldom reported. RESULTS Here, we perform the pan-3D genome analysis using Hi-C sequencing data from 27 soybean accessions and comprehensively investigate the relationships between 3D genomic variations and structural variations (SVs) as well as gene expression. We find that intersection regions between A/B compartments largely contribute to compartment divergence. Topologically associating domain (TAD) boundaries in A compartments exhibit significantly higher density compared to those in B compartments. Pan-3D genome analysis shows that core TAD boundaries have the highest transcription start site (TSS) density and lowest GC content and repeat percentage. Further investigation shows that non-long terminal repeat (non-LTR) retrotransposons play important roles in maintaining TAD boundaries, while Gypsy elements and satellite repeats are associated with private TAD boundaries. Moreover, presence and absence variation (PAV) is found to be the major contributor to 3D genome variations. Nevertheless, approximately 55% of 3D genome variations are not associated with obvious genetic variations, and half of them affect the flanking gene expression. In addition, we find that the 3D genome may also undergo selection during soybean domestication. CONCLUSION Our study sheds light on the role of 3D genomes in plant genetic diversity and provides a valuable resource for studying gene regulation and genome evolution.
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Okabe A, Kaneda A. Hi-C Analysis to Identify Genome-Wide Chromatin Structural Aberration in Cancer. Methods Mol Biol 2023; 2519:127-140. [PMID: 36066718 DOI: 10.1007/978-1-0716-2433-3_15] [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] [Indexed: 06/15/2023]
Abstract
Hi-C is a method that analyzes genome-wide chromatin structure using next-generation sequencer. Chromatin structure is crucial for regulating transcription or replication, and Hi-C has revealed the hierarchical chromatin structures, such as loop, domain , and compartment structures. Aberrant alteration of these structures causes disease, and a number of structural aberrations in cancer cells have been reported recently. Besides, Hi-C can identify chromosome rearrangements that frequently occurred in cancer. Therefore, Hi-C is a powerful technique to analyze epigenomic and genomic aberrations in tumorigenesis. Here we will introduce the basic protocol of Hi-C in experimental and analytical aspects.
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Affiliation(s)
- Atsushi Okabe
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba, Japan.
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40
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Michieletto MF, Tello-Cajiao JJ, Mowel WK, Chandra A, Yoon S, Joannas L, Clark ML, Jimenez MT, Wright JM, Lundgren P, Williams A, Thaiss CA, Vahedi G, Henao-Mejia J. Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation. Nat Immunol 2023; 24:42-54. [PMID: 36050414 PMCID: PMC10134076 DOI: 10.1038/s41590-022-01295-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 07/18/2022] [Indexed: 01/06/2023]
Abstract
Innate lymphoid cells (ILCs) are well-characterized immune cells that play key roles in host defense and tissue homeostasis. Yet, how the three-dimensional (3D) genome organization underlies the development and functions of ILCs is unknown. Herein, we carried out an integrative analysis of the 3D genome structure, chromatin accessibility and gene expression in mature ILCs. Our results revealed that the local 3D configuration of the genome is rewired specifically at loci associated with ILC biology to promote their development and functional differentiation. Importantly, we demonstrated that the ontogenesis of ILC2s and the progression of allergic airway inflammation are determined by a unique local 3D configuration of the region containing the ILC-lineage-defining factor Id2, which is characterized by multiple interactions between the Id2 promoter and distal regulatory elements bound by the transcription factors GATA-3 and RORα, unveiling the mechanism whereby the Id2 expression is specifically controlled in group 2 ILCs.
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Affiliation(s)
- Michaël F Michieletto
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John J Tello-Cajiao
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Walter K Mowel
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Aditi Chandra
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sora Yoon
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Leonel Joannas
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Megan L Clark
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Monica T Jimenez
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jasmine M Wright
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Patrick Lundgren
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Adam Williams
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Christoph A Thaiss
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.,Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Golnaz Vahedi
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Jorge Henao-Mejia
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA. .,Division of Protective Immunity, Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
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41
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Fritz AJ, Ghule PN, Toor R, Dillac L, Perelman J, Boyd J, Lian JB, Gordon JA, Frietze S, Van Wijnen A, Stein JL, Stein GS. Spatiotemporal Epigenetic Control of the Histone Gene Chromatin Landscape during the Cell Cycle. Crit Rev Eukaryot Gene Expr 2023; 33:85-97. [PMID: 37017672 PMCID: PMC10826887 DOI: 10.1615/critreveukaryotgeneexpr.2022046190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Higher-order genomic organization supports the activation of histone genes in response to cell cycle regulatory cues that epigenetically mediates stringent control of transcription at the G1/S-phase transition. Histone locus bodies (HLBs) are dynamic, non-membranous, phase-separated nuclear domains where the regulatory machinery for histone gene expression is organized and assembled to support spatiotemporal epigenetic control of histone genes. HLBs provide molecular hubs that support synthesis and processing of DNA replication-dependent histone mRNAs. These regulatory microenvironments support long-range genomic interactions among non-contiguous histone genes within a single topologically associating domain (TAD). HLBs respond to activation of the cyclin E/CDK2/NPAT/HINFP pathway at the G1/S transition. HINFP and its coactivator NPAT form a complex within HLBs that controls histone mRNA transcription to support histone protein synthesis and packaging of newly replicated DNA. Loss of HINFP compromises H4 gene expression and chromatin formation, which may result in DNA damage and impede cell cycle progression. HLBs provide a paradigm for higher-order genomic organization of a subnuclear domain that executes an obligatory cell cycle-controlled function in response to cyclin E/CDK2 signaling. Understanding the coordinately and spatiotemporally organized regulatory programs in focally defined nuclear domains provides insight into molecular infrastructure for responsiveness to cell signaling pathways that mediate biological control of growth, differentiation phenotype, and are compromised in cancer.
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Affiliation(s)
- Andrew J. Fritz
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Prachi N. Ghule
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Rabail Toor
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Louis Dillac
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Jonah Perelman
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Joseph Boyd
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Jane B. Lian
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Johnathan A.R. Gordon
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Seth Frietze
- University of Vermont Cancer Center, Burlington, Vermont, USA
- College of Nursing and Health Sciences, University of Vermont, Burlington, Vermont, USA
| | - Andre Van Wijnen
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
| | - Janet L. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
| | - Gary S. Stein
- Department of Biochemistry, University of Vermont, Burlington, Vermont, USA
- University of Vermont Cancer Center, Burlington, Vermont, USA
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42
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Ding T, Zhang H. Novel biological insights revealed from the investigation of multiscale genome architecture. Comput Struct Biotechnol J 2022; 21:312-325. [PMID: 36582436 PMCID: PMC9791078 DOI: 10.1016/j.csbj.2022.12.009] [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: 08/12/2022] [Revised: 12/06/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
Gene expression and cell fate determination require precise and coordinated epigenetic regulation. The complex three-dimensional (3D) genome organization plays a critical role in transcription in myriad biological processes. A wide range of architectural features of the 3D genome, including chromatin loops, topologically associated domains (TADs), chromatin compartments, and phase separation, together regulate the chromatin state and transcriptional activity at multiple levels. With the help of 3D genome informatics, recent biochemistry and imaging approaches based on different strategies have revealed functional interactions among biomacromolecules, even at the single-cell level. Here, we review the occurrence, mechanistic basis, and functional implications of dynamic genome organization, and outline recent experimental and computational approaches for profiling multiscale genome architecture to provide robust tools for studying the 3D genome.
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Affiliation(s)
| | - He Zhang
- Corresponding author at: School of Life Science and Technology, Tongji University, Shanghai 200092, PR China.
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43
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Liang W, Wang S, Wang H, Li X, Meng Q, Zhao Y, Zheng C. When 3D genome technology meets viral infection, including SARS-CoV-2. J Med Virol 2022; 94:5627-5639. [PMID: 35916043 PMCID: PMC9538846 DOI: 10.1002/jmv.28040] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/09/2022] [Accepted: 07/30/2022] [Indexed: 01/06/2023]
Abstract
Mammalian chromosomes undergo varying degrees of compression to form three-dimensional genome structures. These three-dimensional structures undergo dynamic and precise chromatin interactions to achieve precise spatial and temporal regulation of gene expression. Most eukaryotic DNA viruses can invade their genomes into the nucleus. However, it is still poorly understood how the viral genome is precisely positioned after entering the host cell nucleus to find the most suitable location and whether it can specifically interact with the host genome to hijack the host transcriptional factories or even integrate into the host genome to complete its transcription and replication rapidly. Chromosome conformation capture technology can reveal long-range chromatin interactions between different chromosomal sites in the nucleus, potentially providing a reference for viral DNA-host chromatin interactions. This review summarized the research progress on the three-dimensional interaction between virus and host genome and the impact of virus integration into the host genome on gene transcription regulation, aiming to provide new insights into chromatin interaction and viral gene transcription regulation, laying the foundation for the treatment of infectious diseases.
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Affiliation(s)
- Weizheng Liang
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
| | - Shuangqing Wang
- Department of NeurologyShenzhen University General Hospital, Shenzhen UniversityShenzhen, Guangdong ProvinceChina
| | - Hao Wang
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
| | - Xiushen Li
- Department of Obstetrics and GynecologyShenzhen University General HospitalShenzhen, GuangdongChina
- Guangdong Key Laboratory for Biomedical Measurements and Ultrasound Imaging, School of Biomedical EngineeringShenzhen University Health Science CenterShenzhen, GuangdongChina
- Shenzhen Key LaboratoryShenzhen University General HospitalShenzhen, GuangdongChina
| | - Qingxue Meng
- Central LaboratoryThe First Affiliated Hospital of Hebei North UniversityZhangjiakouChina
| | - Yan Zhao
- Department of Mathematics and Computer ScienceFree University BerlinBerlinGermany
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical SciencesFujian Medical UniversityFuzhouChina
- Department of Microbiology, Immunology and Infectious DiseasesUniversity of CalgaryCalgaryAlbertaCanada
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life SciencesInner Mongolia UniversityHohhotChina
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44
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Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M. Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. Cell Rep 2022; 41:111730. [PMID: 36450242 PMCID: PMC9793828 DOI: 10.1016/j.celrep.2022.111730] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Revised: 09/14/2022] [Accepted: 11/04/2022] [Indexed: 12/02/2022] Open
Abstract
Mammalian genomes are organized into three-dimensional DNA structures called A/B compartments that are associated with transcriptional activity/inactivity. However, whether these structures are simply correlated with gene expression or are permissive/impermissible to transcription has remained largely unknown because we lack methods to measure DNA organization and transcription simultaneously. Recently, we developed RNA & DNA (RD)-SPRITE, which enables genome-wide measurements of the spatial organization of RNA and DNA. Here we show that RD-SPRITE measures genomic structure surrounding nascent pre-mRNAs and maps their spatial contacts. We find that transcription occurs within B compartments-with multiple active genes simultaneously colocalizing within the same B compartment-and at genes proximal to nucleoli. These results suggest that localization near or within nuclear structures thought to be inactive does not preclude transcription and that active transcription can occur throughout the nucleus. In general, we anticipate RD-SPRITE will be a powerful tool for exploring relationships between genome structure and transcription.
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Affiliation(s)
- Isabel N. Goronzy
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA,Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA,These authors contributed equally
| | - Sofia A. Quinodoz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,Present address: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA,These authors contributed equally,Correspondence: (S.A.Q.), (M.G.)
| | - Joanna W. Jachowicz
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,Present address: Institute of Molecular Biotechnology of the Austrian Academy of Science (IMBA), 1030 Vienna, Austria,These authors contributed equally
| | - Noah Ollikainen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,These authors contributed equally
| | - Prashant Bhat
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mitchell Guttman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA,Lead contact,Correspondence: (S.A.Q.), (M.G.)
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45
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Liu S, Cao Y, Cui K, Tang Q, Zhao K. Hi-TrAC reveals division of labor of transcription factors in organizing chromatin loops. Nat Commun 2022; 13:6679. [PMID: 36335136 PMCID: PMC9637178 DOI: 10.1038/s41467-022-34276-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 10/20/2022] [Indexed: 11/08/2022] Open
Abstract
The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation-free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among regulatory elements. Hi-TrAC detects chromatin looping among accessible regions at single nucleosome resolution. With almost half-million identified loops, we reveal a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discover that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we introduce a methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of transcription factors in organizing chromatin loops for genome organization and gene expression.
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Affiliation(s)
- Shuai Liu
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Yaqiang Cao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Kairong Cui
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Qingsong Tang
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
| | - Keji Zhao
- grid.94365.3d0000 0001 2297 5165Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD USA
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Top(ological-operon) secret behind the long-range transcriptional coupling. Signal Transduct Target Ther 2022; 7:366. [PMID: 36243717 PMCID: PMC9569333 DOI: 10.1038/s41392-022-01195-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/04/2022] [Accepted: 09/11/2022] [Indexed: 11/08/2022] Open
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Giacoman-Lozano M, Meléndez-Ramírez C, Martinez-Ledesma E, Cuevas-Diaz Duran R, Velasco I. Epigenetics of neural differentiation: Spotlight on enhancers. Front Cell Dev Biol 2022; 10:1001701. [PMID: 36313573 PMCID: PMC9606577 DOI: 10.3389/fcell.2022.1001701] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 10/03/2022] [Indexed: 11/28/2022] Open
Abstract
Neural induction, both in vivo and in vitro, includes cellular and molecular changes that result in phenotypic specialization related to specific transcriptional patterns. These changes are achieved through the implementation of complex gene regulatory networks. Furthermore, these regulatory networks are influenced by epigenetic mechanisms that drive cell heterogeneity and cell-type specificity, in a controlled and complex manner. Epigenetic marks, such as DNA methylation and histone residue modifications, are highly dynamic and stage-specific during neurogenesis. Genome-wide assessment of these modifications has allowed the identification of distinct non-coding regulatory regions involved in neural cell differentiation, maturation, and plasticity. Enhancers are short DNA regulatory regions that bind transcription factors (TFs) and interact with gene promoters to increase transcriptional activity. They are of special interest in neuroscience because they are enriched in neurons and underlie the cell-type-specificity and dynamic gene expression profiles. Classification of the full epigenomic landscape of neural subtypes is important to better understand gene regulation in brain health and during diseases. Advances in novel next-generation high-throughput sequencing technologies, genome editing, Genome-wide association studies (GWAS), stem cell differentiation, and brain organoids are allowing researchers to study brain development and neurodegenerative diseases with an unprecedented resolution. Herein, we describe important epigenetic mechanisms related to neurogenesis in mammals. We focus on the potential roles of neural enhancers in neurogenesis, cell-fate commitment, and neuronal plasticity. We review recent findings on epigenetic regulatory mechanisms involved in neurogenesis and discuss how sequence variations within enhancers may be associated with genetic risk for neurological and psychiatric disorders.
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Affiliation(s)
- Mayela Giacoman-Lozano
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
| | - César Meléndez-Ramírez
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
| | - Emmanuel Martinez-Ledesma
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- Tecnologico de Monterrey, The Institute for Obesity Research, Monterrey, NL, Mexico
| | - Raquel Cuevas-Diaz Duran
- Tecnologico de Monterrey, Escuela de Medicina y Ciencias de la Salud, Monterrey, NL, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
| | - Iván Velasco
- Instituto de Fisiología Celular—Neurociencias, Universidad Nacional Autónoma de Mexico, Mexico City, Mexico
- Laboratorio de Reprogramación Celular, Instituto Nacional de Neurología y Neurocirugía “Manuel Velasco Suárez”, Mexico City, Mexico
- *Correspondence: Raquel Cuevas-Diaz Duran, ; Iván Velasco,
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Zhang P, Wu Y, Zhou H, Zhou B, Zhang H, Wu H. CLNN-loop: a deep learning model to predict CTCF-mediated chromatin loops in the different cell lines and CTCF-binding sites (CBS) pair types. Bioinformatics 2022; 38:4497-4504. [PMID: 35997565 DOI: 10.1093/bioinformatics/btac575] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/28/2022] [Accepted: 08/22/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Three-dimensional (3D) genome organization is of vital importance in gene regulation and disease mechanisms. Previous studies have shown that CTCF-mediated chromatin loops are crucial to studying the 3D structure of cells. Although various experimental techniques have been developed to detect chromatin loops, they have been found to be time-consuming and costly. Nowadays, various sequence-based computational methods can capture significant features of 3D genome organization and help predict chromatin loops. However, these methods have low performance and poor generalization ability in predicting chromatin loops. RESULTS Here, we propose a novel deep learning model, called CLNN-loop, to predict chromatin loops in different cell lines and CTCF-binding sites (CBS) pair types by fusing multiple sequence-based features. The analysis of a series of examinations based on the datasets in the previous study shows that CLNN-loop has satisfactory performance and is superior to the existing methods in terms of predicting chromatin loops. In addition, we apply the SHAP framework to interpret the predictions of different models, and find that CTCF motif and sequence conservation are important signs of chromatin loops in different cell lines and CBS pair types. AVAILABILITY AND IMPLEMENTATION The source code of CLNN-loop is freely available at https://github.com/HaoWuLab-Bioinformatics/CLNN-loop and the webserver of CLNN-loop is freely available at http://hwclnn.sdu.edu.cn. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pengyu Zhang
- School of Software, Shandong University, Jinan, Shandong 250101, China.,College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yingfu Wu
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Haoru Zhou
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Bing Zhou
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hongming Zhang
- College of Information Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Wu
- School of Software, Shandong University, Jinan, Shandong 250101, China
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Comparison of the somatic TADs and lampbrush chromomere-loop complexes in transcriptionally active prophase I oocytes. Chromosoma 2022; 131:207-223. [PMID: 36031655 DOI: 10.1007/s00412-022-00780-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 11/03/2022]
Abstract
In diplotene oocyte nuclei of all vertebrate species, except mammals, chromosomes lack interchromosomal contacts and chromatin is linearly compartmentalized into distinct chromomere-loop complexes forming lampbrush chromosomes. However, the mechanisms underlying the formation of chromomere-loop complexes remain unexplored. Here we aimed to compare somatic topologically associating domains (TADs), recently identified in chicken embryonic fibroblasts, with chromomere-loop complexes in lampbrush meiotic chromosomes. By measuring 3D-distances and colocalization between linear equidistantly located genomic loci, positioned within one TAD or separated by a TAD border, we confirmed the presence of predicted TADs in chicken embryonic fibroblast nuclei. Using three-colored FISH with BAC probes, we mapped equidistant genomic regions included in several sequential somatic TADs on isolated chicken lampbrush chromosomes. Eight genomic regions, each comprising two or three somatic TADs, were mapped to non-overlapping neighboring lampbrush chromatin domains - lateral loops, chromomeres, or chromomere-loop complexes. Genomic loci from the neighboring somatic TADs could localize in one lampbrush chromomere-loop complex, while genomic loci belonging to the same somatic TAD could be localized in neighboring lampbrush chromomere-loop domains. In addition, FISH-mapping of BAC probes to the nascent transcripts on the lateral loops indicates transcription of at least 17 protein-coding genes and 2 non-coding RNA genes during the lampbrush stage of chicken oogenesis, including genes involved in oocyte maturation and early embryo development.
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Gamliel A, Meluzzi D, Oh S, Jiang N, Destici E, Rosenfeld MG, Nair SJ. Long-distance association of topological boundaries through nuclear condensates. Proc Natl Acad Sci U S A 2022; 119:e2206216119. [PMID: 35914133 PMCID: PMC9371644 DOI: 10.1073/pnas.2206216119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/24/2022] [Indexed: 01/09/2023] Open
Abstract
The eukaryotic genome is partitioned into distinct topological domains separated by boundary elements. Emerging data support the concept that several well-established nuclear compartments are ribonucleoprotein condensates assembled through the physical process of phase separation. Here, based on our demonstration that chemical disruption of nuclear condensate assembly weakens the insulation properties of a specific subset (∼20%) of topologically associated domain (TAD) boundaries, we report that the disrupted boundaries are characterized by a high level of transcription and striking spatial clustering. These topological boundary regions tend to be spatially associated, even interchromosomally, segregate with nuclear speckles, and harbor a specific subset of "housekeeping" genes widely expressed in diverse cell types. These observations reveal a previously unappreciated mode of genome organization mediated by conserved boundary elements harboring highly and widely expressed transcription units and associated transcriptional condensates.
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Affiliation(s)
- Amir Gamliel
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Dario Meluzzi
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Soohwan Oh
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Nan Jiang
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Eugin Destici
- Department of Neurosciences, University of California San Diego, La Jolla, CA 92093
| | - Michael G Rosenfeld
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
| | - Sreejith J Nair
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
- HHMI, University of California San Diego, La Jolla, CA 92093
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