1
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Fu Z, Jiang S, Sun Y, Zheng S, Zong L, Li P. Cut&tag: a powerful epigenetic tool for chromatin profiling. Epigenetics 2024; 19:2293411. [PMID: 38105608 PMCID: PMC10730171 DOI: 10.1080/15592294.2023.2293411] [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: 09/07/2023] [Accepted: 12/05/2023] [Indexed: 12/19/2023] Open
Abstract
Analysis of transcription factors and chromatin modifications at the genome-wide level provides insights into gene regulatory processes, such as transcription, cell differentiation and cellular response. Chromatin immunoprecipitation is the most popular and powerful approach for mapping chromatin, and other enzyme-tethering techniques have recently become available for living cells. Among these, Cleavage Under Targets and Tagmentation (CUT&Tag) is a relatively novel chromatin profiling method that has rapidly gained popularity in the field of epigenetics since 2019. It has also been widely adapted to map chromatin modifications and TFs in different species, illustrating the association of these chromatin epitopes with various physiological and pathological processes. Scalable single-cell CUT&Tag can be combined with distinct platforms to distinguish cellular identity, epigenetic features and even spatial chromatin profiling. In addition, CUT&Tag has been developed as a strategy for joint profiling of the epigenome, transcriptome or proteome on the same sample. In this review, we will mainly consolidate the applications of CUT&Tag and its derivatives on different platforms, give a detailed explanation of the pros and cons of this technique as well as the potential development trends and applications in the future.
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Affiliation(s)
- Zhijun Fu
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Sanjie Jiang
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Yiwen Sun
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Shanqiao Zheng
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
| | - Liang Zong
- BGI Tech Solutions Co, Ltd. BGI-Wuhan, Wuhan, China
| | - Peipei Li
- BGI Tech Solutions Co, Ltd. BGI-Shenzhen, Shenzhen, China
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2
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Li M, Na X, Lin F, Liang S, Huang Y, Song J, Xu X, Yang C. DMF-ChIP-seq for Highly Sensitive and Integrated Epigenomic Profiling of Low-Input Cells. ACS APPLIED MATERIALS & INTERFACES 2024. [PMID: 39303213 DOI: 10.1021/acsami.4c11280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
Abstract
Mapping genome-wide DNA-protein interactions (DPIs) provides insights into the epigenetic landscape of complex biological systems and elucidates the mechanisms of epigenetic regulation in biological progress. However, current technologies in DPI profiling still suffer from high cell demands, low detection sensitivity, and large reagent consumption. To address these problems, we developed DMF-ChIP-seq that builds on digital microfluidic (DMF) technology to profile genome-wide DPIs in a highly efficient, cost-effective, and user-friendly way. The entire workflow including cell pretreatment, antibody recognition, pA-Tn5 tagmentation, fragment enrichment, and PCR amplification is programmatically manipulated on a single chip. Leveraging closed submicroliter reaction volumes and a superhydrophobic interface, DMF-ChIP-seq presented higher sensitivity in peak enrichment than other current methods, with high accuracy (Pearson Correlation Coefficient (PCC) > 0.86) and high repeatability (PCC > 0.92). Furthermore, DMF-ChIP-seq was capable of processing the samples with as few as 8 cells while maintaining a high signal-to-noise ratio. By applying DMF-ChIP-seq, H3K27ac histone modification of early embryonic cells during differentiation was profiled for the investigation of epigenomic landscape dynamics. With the benefits of high efficiency and sensitivity in DPI analysis, the system provides great promise in studying epigenetic regulation during various biological processes.
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Affiliation(s)
- Mingyin Li
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Na
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Fanghe Lin
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Shanshan Liang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yuehan Huang
- School of International Education, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jia Song
- Institute for Developmental and Regenerative Cardiovascular Medicine, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200092, China
| | - Xing Xu
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
- Department of Laboratory Medicine, Key Laboratory of Clinical Laboratory Technology for Precision Medicine, School of Medical Technology and Engineering, Fujian Medical University, Fuzhou 350005, China
| | - Chaoyong Yang
- The MOE Key Laboratory of Spectrochemical Analysis & Instrumentation, the Key Laboratory of Chemical Biology of Fujian Province, State Key Laboratory of Physical Chemistry of Solid Surfaces, Collaborative Innovation Center of Chemistry for Energy Materials, Department of Chemical Biology, Department of Chemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
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3
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Dong C, Meng X, Zhang T, Guo Z, Liu Y, Wu P, Chen S, Zhou F, Ma Y, Xiong H, Shu S, He A. Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. Nat Methods 2024; 21:1624-1633. [PMID: 39025969 PMCID: PMC11399096 DOI: 10.1038/s41592-024-02360-0] [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: 08/13/2023] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
Studies of molecular and cellular functions of small-molecule inhibitors in cancer treatment, eliciting effects by targeting genome and epigenome associated proteins, requires measurement of drug-target engagement in single-cell resolution. Here we present EpiChem for in situ single-cell joint mapping of small molecules and multimodal epigenomic landscape. We demonstrate single-cell co-assays of three small molecules together with histone modifications, chromatin accessibility or target proteins in human colorectal cancer (CRC) organoids. Integrated multimodal analysis reveals diverse drug interactions in the context of chromatin states within heterogeneous CRC organoids. We further reveal drug genomic binding dynamics and adaptive epigenome across cell types after small-molecule drug treatment in CRC organoids. This method provides a unique tool to exploit the mechanisms of cell type-specific drug actions.
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Affiliation(s)
- Chao Dong
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xiaoxuan Meng
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Tong Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Zhifang Guo
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Yaxi Liu
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Peihuang Wu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China
| | - Shiwei Chen
- Peking University International Cancer Institute, Beijing, China
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China
| | - Fanqi Zhou
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Yanni Ma
- State Key Laboratory of Medical Molecular Biology, Haihe laboratory of Cell Ecosystem, Key Laboratory of RNA and Hematopoietic Regulation, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Haiqing Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China
- Tianjin Institutes of Health Science, Tianjin, China
| | - Shaokun Shu
- State Key Laboratory of Molecular Oncology, Beijing Key Laboratory of Carcinogenesis and Translational Research, Department of Lymphoma, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University International Cancer Institute, Beijing, China.
- Peking University-Yunnan Baiyao International Medical Research Center, Beijing, China.
| | - Aibin He
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Key laboratory of Carcinogenesis and Translational Research of Ministry of Education of China, Peking University Cancer Hospital & Institute, Beijing, China.
- Peking University Chengdu Academy for Advanced Interdisciplinary Biotechnologies, Chengdu, China.
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4
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Stuart T. Progress in multifactorial single-cell chromatin profiling methods. Biochem Soc Trans 2024; 52:1827-1839. [PMID: 39023855 DOI: 10.1042/bst20231471] [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: 06/30/2024] [Revised: 07/01/2024] [Accepted: 07/08/2024] [Indexed: 07/20/2024]
Abstract
Chromatin states play a key role in shaping overall cellular states and fates. Building a complete picture of the functional state of chromatin in cells requires the co-detection of several distinct biochemical aspects. These span DNA methylation, chromatin accessibility, chromosomal conformation, histone posttranslational modifications, and more. While this certainly presents a challenging task, over the past few years many new and creative methods have been developed that now enable co-assay of these different aspects of chromatin at single cell resolution. This field is entering an exciting phase, where a confluence of technological improvements, decreased sequencing costs, and computational innovation are presenting new opportunities to dissect the diversity of chromatin states present in tissues, and how these states may influence gene regulation. In this review, I discuss the spectrum of current experimental approaches for multifactorial chromatin profiling, highlight some of the experimental and analytical challenges, as well as some areas for further innovation.
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Affiliation(s)
- Tim Stuart
- Genome Institute of Singapore (GIS), Agency for Science, Technology and Research (A*STAR), 60 Biopolis Street, Genome, Singapore 138672, Republic of Singapore
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5
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Pepin AS, Schneider R. Emerging toolkits for decoding the co-occurrence of modified histones and chromatin proteins. EMBO Rep 2024; 25:3202-3220. [PMID: 39095610 PMCID: PMC11316037 DOI: 10.1038/s44319-024-00199-2] [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: 02/28/2024] [Revised: 05/10/2024] [Accepted: 06/10/2024] [Indexed: 08/04/2024] Open
Abstract
In eukaryotes, DNA is packaged into chromatin with the help of highly conserved histone proteins. Together with DNA-binding proteins, posttranslational modifications (PTMs) on these histones play crucial roles in regulating genome function, cell fate determination, inheritance of acquired traits, cellular states, and diseases. While most studies have focused on individual DNA-binding proteins, chromatin proteins, or histone PTMs in bulk cell populations, such chromatin features co-occur and potentially act cooperatively to accomplish specific functions in a given cell. This review discusses state-of-the-art techniques for the simultaneous profiling of multiple chromatin features in low-input samples and single cells, focusing on histone PTMs, DNA-binding, and chromatin proteins. We cover the origins of the currently available toolkits, compare and contrast their characteristic features, and discuss challenges and perspectives for future applications. Studying the co-occurrence of histone PTMs, DNA-binding proteins, and chromatin proteins in single cells will be central for a better understanding of the biological relevance of combinatorial chromatin features, their impact on genomic output, and cellular heterogeneity.
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Affiliation(s)
- Anne-Sophie Pepin
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany
| | - Robert Schneider
- Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
- Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
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Sun F, Li H, Sun D, Fu S, Gu L, Shao X, Wang Q, Dong X, Duan B, Xing F, Wu J, Xiao M, Zhao F, Han JDJ, Liu Q, Fan X, Li C, Wang C, Shi T. Single-cell omics: experimental workflow, data analyses and applications. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-023-2561-0. [PMID: 39060615 DOI: 10.1007/s11427-023-2561-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/18/2024] [Indexed: 07/28/2024]
Abstract
Cells are the fundamental units of biological systems and exhibit unique development trajectories and molecular features. Our exploration of how the genomes orchestrate the formation and maintenance of each cell, and control the cellular phenotypes of various organismsis, is both captivating and intricate. Since the inception of the first single-cell RNA technology, technologies related to single-cell sequencing have experienced rapid advancements in recent years. These technologies have expanded horizontally to include single-cell genome, epigenome, proteome, and metabolome, while vertically, they have progressed to integrate multiple omics data and incorporate additional information such as spatial scRNA-seq and CRISPR screening. Single-cell omics represent a groundbreaking advancement in the biomedical field, offering profound insights into the understanding of complex diseases, including cancers. Here, we comprehensively summarize recent advances in single-cell omics technologies, with a specific focus on the methodology section. This overview aims to guide researchers in selecting appropriate methods for single-cell sequencing and related data analysis.
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Affiliation(s)
- Fengying Sun
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China
| | - Haoyan Li
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dongqing Sun
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Shaliu Fu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Lei Gu
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Shao
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China
| | - Qinqin Wang
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Xin Dong
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Bin Duan
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China
| | - Feiyang Xing
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jun Wu
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Minmin Xiao
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
| | - Fangqing Zhao
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, 100871, China.
| | - Qi Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Shanghai East Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, 311121, China.
- Shanghai Research Institute for Intelligent Autonomous Systems, Shanghai, 201210, China.
| | - Xiaohui Fan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
- National Key Laboratory of Chinese Medicine Modernization, Innovation Center of Yangtze River Delta, Zhejiang University, Jiaxing, 314103, China.
- Zhejiang Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, 310006, China.
| | - Chen Li
- Center for Single-cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Chenfei Wang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Orthopaedic Department, Tongji Hospital, Bioinformatics Department, School of Life Sciences and Technology, Tongji University, Shanghai, 200082, China.
- Frontier Science Center for Stem Cells, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Tieliu Shi
- Department of Clinical Laboratory, the Affiliated Wuhu Hospital of East China Normal University (The Second People's Hospital of Wuhu City), Wuhu, 241000, China.
- Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, the Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, 200241, China.
- Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE, School of Statistics, East China Normal University, Shanghai, 200062, China.
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7
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Rhaman MS, Ali M, Ye W, Li B. Opportunities and Challenges in Advancing Plant Research with Single-cell Omics. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae026. [PMID: 38996445 PMCID: PMC11423859 DOI: 10.1093/gpbjnl/qzae026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 07/14/2024]
Abstract
Plants possess diverse cell types and intricate regulatory mechanisms to adapt to the ever-changing environment of nature. Various strategies have been employed to study cell types and their developmental progressions, including single-cell sequencing methods which provide high-dimensional catalogs to address biological concerns. In recent years, single-cell sequencing technologies in transcriptomics, epigenomics, proteomics, metabolomics, and spatial transcriptomics have been increasingly used in plant science to reveal intricate biological relationships at the single-cell level. However, the application of single-cell technologies to plants is more limited due to the challenges posed by cell structure. This review outlines the advancements in single-cell omics technologies, their implications in plant systems, future research applications, and the challenges of single-cell omics in plant systems.
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Affiliation(s)
- Mohammad Saidur Rhaman
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Muhammad Ali
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Wenxiu Ye
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
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8
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Chen Y, Ye X, Zhong Y, Kang X, Tang Y, Zhu H, Pang C, Ning S, Liang S, Zhang F, Li C, Li J, Gu C, Cheng Y, Kuang Z, Qiu J, Jin J, Luo H, Fu M, Hui HX, Li L, Ruan D, Liu P, Chen X, Sun L, Ai S, Gao X. SP6 controls human cytotrophoblast fate decisions and trophoblast stem cell establishment by targeting MSX2 regulatory elements. Dev Cell 2024; 59:1506-1522.e11. [PMID: 38582082 DOI: 10.1016/j.devcel.2024.03.025] [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: 07/27/2023] [Revised: 12/14/2023] [Accepted: 03/12/2024] [Indexed: 04/08/2024]
Abstract
The commitment and differentiation of human placental progenitor cytotrophoblast (CT) cells are crucial for a successful pregnancy, but the underlying mechanism remains poorly understood. Here, we identified the transcription factor (TF), specificity protein 6 (SP6), as a human species-specific trophoblast lineage TF expressed in human placental CT cells. Using pluripotent stem cells as a model, we demonstrated that SP6 controls CT generation and the establishment of trophoblast stem cells (TSCs) and identified msh homeobox 2 (MSX2) as the downstream effector in these events. Mechanistically, we showed that SP6 interacts with histone acetyltransferase P300 to alter the landscape of H3K27ac at targeted regulatory elements, thereby favoring transcriptional activation and facilitating CT cell fate decisions and TSC maintenance. Our results established SP6 as a regulator of the human trophoblast lineage and implied its role in placental development and the pathogenies of placental diseases.
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Affiliation(s)
- Yanglin Chen
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xianhua Ye
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yulong Zhong
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Xiangjin Kang
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China
| | - Yanqing Tang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Haoyun Zhu
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Changmiao Pang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shaoqiang Ning
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Shiqing Liang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Feifan Zhang
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chao Li
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jie Li
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Chengtao Gu
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Yuanxiong Cheng
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital, Southern Medical University, Guangzhou 510630, Guangdong, China
| | - Zhanpeng Kuang
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Jingyang Qiu
- Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Jin Jin
- Department of Gynaecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Haisi Luo
- Department of Gynaecology and Obstetrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China
| | - Mingyu Fu
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hannah Xiaoyan Hui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong 999077, China
| | - Lei Li
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510150, China; Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou 510515, China
| | - Degong Ruan
- School of Biomedical Sciences, Stem Cell, and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Pentao Liu
- School of Biomedical Sciences, Stem Cell, and Regenerative Medicine Consortium, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Liangzhong Sun
- Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
| | - Shanshan Ai
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China.
| | - Xuefei Gao
- Guangdong Provincial Key Laboratory of Bone and Joint Degenerative Diseases, Department of Physiology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China; Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital, Southern Medical University, Guangzhou 510630, Guangdong, China; Department of Pediatrics, Nanfang Hospital, Southern Medical University, Guangzhou 510515, China.
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9
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Xu Q, Zhang Y, Xu W, Liu D, Jin W, Chen X, Hong N. The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. Nucleic Acids Res 2024; 52:3106-3120. [PMID: 38364856 PMCID: PMC11014328 DOI: 10.1093/nar/gkae095] [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: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024] Open
Abstract
Chromatin accessibility plays a critical role in the regulation of cell fate decisions. Although gene expression changes have been extensively profiled at the single-cell level during early embryogenesis, the dynamics of chromatin accessibility at cis-regulatory elements remain poorly studied. Here, we used a plate-based single-cell ATAC-seq method to profile the chromatin accessibility dynamics of over 10 000 nuclei from zebrafish embryos. We investigated several important time points immediately after zygotic genome activation (ZGA), covering key developmental stages up to dome. The results revealed key chromatin signatures in the first cell fate specifications when cells start to differentiate into enveloping layer (EVL) and yolk syncytial layer (YSL) cells. Finally, we uncovered many potential cell-type specific enhancers and transcription factor motifs that are important for the cell fate specifications.
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Affiliation(s)
- Qiushi Xu
- Harbin Institute of Technology, Harbin, China
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Yunlong Zhang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wei Xu
- GMU-GIBH Joint School of Life Sciences, The Guangdong-Hong Kong-Macau Joint Laboratory for Cell Fate Regulation and Diseases, Guangzhou Medical University, Guangdong, China
| | - Dong Liu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
| | - Ni Hong
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055 Guangdong, China
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10
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Bárcenas-Walls JR, Ansaloni F, Hervé B, Strandback E, Nyman T, Castelo-Branco G, Bartošovič M. Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution. Nat Protoc 2024; 19:791-830. [PMID: 38129675 DOI: 10.1038/s41596-023-00932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/19/2023] [Indexed: 12/23/2023]
Abstract
The ability to comprehensively analyze the chromatin state with single-cell resolution is crucial for understanding gene regulatory principles in heterogenous tissues or during development. Recently, we developed a nanobody-based single-cell CUT&Tag (nano-CT) protocol to simultaneously profile three epigenetic modalities-two histone marks and open chromatin state-from the same single cell. Nano-CT implements a new set of secondary nanobody-Tn5 fusion proteins to direct barcoded tagmentation by Tn5 transposase to genomic targets labeled by primary antibodies raised in different species. Such nanobody-Tn5 fusion proteins are currently not commercially available, and their in-house production and purification can be completed in 3-4 d by following our detailed protocol. The single-cell indexing in nano-CT is performed on a commercially available platform, making it widely accessible to the community. In comparison to other multimodal methods, nano-CT stands out in data complexity, low sample requirements and the flexibility to choose two of the three modalities. In addition, nano-CT works efficiently with fresh brain samples, generating multimodal epigenomic profiles for thousands of brain cells at single-cell resolution. The nano-CT protocol can be completed in just 3 d by users with basic skills in standard molecular biology and bioinformatics, although previous experience with single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) is beneficial for more in-depth data analysis. As a multimodal assay, nano-CT holds immense potential to reveal interactions of various chromatin modalities, to explore epigenetic heterogeneity and to increase our understanding of the role and interplay that chromatin dynamics has in cellular development.
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Affiliation(s)
| | - Federico Ansaloni
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Bastien Hervé
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Emilia Strandback
- Protein Science Facility, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Nyman
- Protein Science Facility, Department of Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Gonçalo Castelo-Branco
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
- Ming Wai Lau Centre for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Marek Bartošovič
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
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11
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Bai D, Zhang X, Xiang H, Guo Z, Zhu C, Yi C. Simultaneous single-cell analysis of 5mC and 5hmC with SIMPLE-seq. Nat Biotechnol 2024:10.1038/s41587-024-02148-9. [PMID: 38336903 DOI: 10.1038/s41587-024-02148-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/18/2024] [Indexed: 02/12/2024]
Abstract
Dynamic 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) modifications to DNA regulate gene expression in a cell-type-specific manner and are associated with various biological processes, but the two modalities have not yet been measured simultaneously from the same genome at the single-cell level. Here we present SIMPLE-seq, a scalable, base resolution method for joint analysis of 5mC and 5hmC from thousands of single cells. Based on orthogonal labeling and recording of 'C-to-T' mutational signals from 5mC and 5hmC sites, SIMPLE-seq detects these two modifications from the same molecules in single cells and enables unbiased DNA methylation dynamics analysis of heterogeneous biological samples. We applied this method to mouse embryonic stem cells, human peripheral blood mononuclear cells and mouse brain to give joint epigenome maps at single-cell and single-molecule resolution. Integrated analysis of these two cytosine modifications reveals distinct epigenetic patterns associated with divergent regulatory programs in different cell types as well as cell states.
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Affiliation(s)
- Dongsheng Bai
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaoting Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Huifen Xiang
- Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Anhui, China
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, Coordination Chemistry Institute, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, China
| | - Chenxu Zhu
- New York Genome Center, New York, NY, USA.
- Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
- Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.
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12
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Sichani AS, Khoddam S, Shakeri S, Tavakkoli Z, Jafroodi AR, Dabbaghipour R, Sisakht M, Fallahi J. Partial Reprogramming as a Method for Regenerating Neural Tissues in Aged Organisms. Cell Reprogram 2024; 26:10-23. [PMID: 38381402 DOI: 10.1089/cell.2023.0123] [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: 02/22/2024] Open
Abstract
Aging causes numerous age-related diseases, leading the human species to death. Nevertheless, rejuvenating strategies based on cell epigenetic modifications are a possible approach to counteract disease progression while getting old. Cell reprogramming of adult somatic cells toward pluripotency ought to be a promising tool for age-related diseases. However, researchers do not have control over this process as cells lose their fate, and cause potential cancerous cells or unexpected cell phenotypes. Direct and partial reprogramming were introduced in recent years with distinctive applications. Although direct reprogramming makes cells lose their identity, it has various applications in regeneration medicine. Temporary and regulated in vivo overexpression of Yamanaka factors has been shown in several experimental contexts to be achievable and is used to rejuvenate mice models. This regeneration can be accomplished by altering the epigenetic adult cell signature to the signature of a younger cell. The greatest advantage of partial reprogramming is that this method does not allow cells to lose their identity when they are resetting their epigenetic clock. It is a regimen of short-term Oct3/4, Sox2, Klf4, and c-Myc expression in vivo that prevents full reprogramming to the pluripotent state and avoids both tumorigenesis and the presence of unwanted undifferentiated cells. We know that many neurological age-related diseases, such as Alzheimer's disease, stroke, dementia, and Parkinson's disease, are the main cause of death in the last decades of life. Therefore, scientists have a special tendency regarding neuroregeneration methods to increase human life expectancy.
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Affiliation(s)
- Ali Saber Sichani
- Department of Biology, Texas A&M University, College Station, Texas, USA
| | - Somayeh Khoddam
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shayan Shakeri
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Tavakkoli
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Arad Ranji Jafroodi
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Dabbaghipour
- Department of Medical Genetics, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohsen Sisakht
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Jafar Fallahi
- Department of Molecular Medicine, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences, Shiraz, Iran
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13
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Xiong H, Wang Q, Li CC, He A. Single-cell joint profiling of multiple epigenetic proteins and gene transcription. SCIENCE ADVANCES 2024; 10:eadi3664. [PMID: 38170774 PMCID: PMC10796078 DOI: 10.1126/sciadv.adi3664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/01/2023] [Indexed: 01/05/2024]
Abstract
Sculpting the epigenome with a combination of histone modifications and transcription factor occupancy determines gene transcription and cell fate specification. Here, we first develop uCoTarget, utilizing a split-pool barcoding strategy for realizing ultrahigh-throughput single-cell joint profiling of multiple epigenetic proteins. Through extensive optimization for sensitivity and multimodality resolution, we demonstrate that uCoTarget enables simultaneous detection of five histone modifications (H3K27ac, H3K4me3, H3K4me1, H3K36me3, and H3K27me3) in 19,860 single cells. We applied uCoTarget to the in vitro generation of hematopoietic stem/progenitor cells (HSPCs) from human embryonic stem cells, presenting multimodal epigenomic profiles in 26,418 single cells. uCoTarget reveals establishment of pairing of HSPC enhancers (H3K27ac) and promoters (H3K4me3) and RUNX1 engagement priming for H3K27ac activation along the HSPC path. We then develop uCoTargetX, an expansion of uCoTarget to simultaneously measure transcriptome and multiple epigenome targets. Together, our methods enable generalizable, versatile multimodal profiles for reconstructing comprehensive epigenome and transcriptome landscapes and analyzing the regulatory interplay at single-cell level.
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Affiliation(s)
- Haiqing Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Qianhao Wang
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chen C. Li
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Aibin He
- Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Key laboratory of Carcinogenesis and Translational Research of Ministry of Education of China, Peking University Cancer Hospital & Institute, Peking University, Beijing 100142, China
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14
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Han Y, Huang C, Pan Y, Gu X. Single Cell Sequencing Technology and Its Application in Alzheimer's Disease. J Alzheimers Dis 2024; 97:1033-1050. [PMID: 38217599 DOI: 10.3233/jad-230861] [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: 01/15/2024]
Abstract
Alzheimer's disease (AD) involves degeneration of cells in the brain. Due to insidious onset and slow progression, AD is often not diagnosed until it gets progressed to a more severe stage. The diagnosis and treatment of AD has been a challenge. In recent years, high-throughput sequencing technologies have exhibited advantages in exploring the pathogenesis of diseases. However, the types of cells of the central nervous system are complex and traditional bulk sequencing cannot reflect their heterogeneity. Single-cell sequencing technology enables study at the individual cell level and has an irreplaceable advantage in the study of complex diseases. In recent years, this field has expanded rapidly and several types of single-cell sequencing technologies have emerged, including transcriptomics, epigenomics, genomics and proteomics. This review article provides an overview of these single-cell sequencing technologies and their application in AD.
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Affiliation(s)
- Yuru Han
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Congying Huang
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yuhui Pan
- Center for Disease Control and Prevention of Harbin, Harbin, China
| | - Xuefeng Gu
- Shanghai Key Laboratory of Molecular Imaging, Zhoupu Hospital, Shanghai University of Medicine and Health Sciences, Shanghai, China
- School of Pharmacy, Shanghai University of Medicine & Health Sciences, Shanghai, China
- School of Health Sciences and Engineering, University of Shanghai for Science and Technology, Shanghai, China
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15
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Janssens DH, Greene JE, Wu SJ, Codomo CA, Minot SS, Furlan SN, Ahmad K, Henikoff S. Scalable single-cell profiling of chromatin modifications with sciCUT&Tag. Nat Protoc 2024; 19:83-112. [PMID: 37935964 PMCID: PMC11229882 DOI: 10.1038/s41596-023-00905-9] [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: 02/06/2023] [Accepted: 08/18/2023] [Indexed: 11/09/2023]
Abstract
Cleavage under targets and tagmentation (CUT&Tag) is an antibody-directed in situ chromatin profiling strategy that is rapidly replacing immune precipitation-based methods, such as chromatin immunoprecipitation-sequencing. The efficiency of the method enables chromatin profiling in single cells but is limited by the numbers of cells that can be profiled. Here, we describe a combinatorial barcoding strategy for CUT&Tag that harnesses a nanowell dispenser for simple, high-resolution, high-throughput, single-cell chromatin profiling. In this single-cell combinatorial indexing CUT&Tag (sciCUT&Tag) protocol, lightly cross-linked nuclei are bound to magnetic beads and incubated with primary and secondary antibodies in bulk and then arrayed in a 96-well plate for a first round of cellular indexing by antibody-directed Tn5 tagmentation. The sample is then repooled, mixed and arrayed across 5,184 nanowells at a density of 12-24 nuclei per well for a second round of cellular indexing during PCR amplification of the sequencing-ready library. This protocol can be completed in 1.5 days by a research technician, and we illustrate the optimized protocol by profiling histone modifications associated with developmental gene repression (H3K27me3) as well as transcriptional activation (H3K4me1-2-3) in human peripheral blood mononuclear cells and use single-nucleotide polymorphisms to facilitate collision removal. We have also used sciCUT&Tag for simultaneous profiling of multiple chromatin epitopes in single cells. The reduced cost, improved resolution and scalability of sciCUT&Tag make it an attractive platform to profile chromatin features in single cells.
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Affiliation(s)
- Derek H Janssens
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob E Greene
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Medicine and Mechanisms of Disease (M3D) PhD Program, University of Washington, Seattle, WA, USA
| | - Steven J Wu
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Molecular Engineering & Sciences Institute, University of Washington, Seattle, WA, USA
| | - Christine A Codomo
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Samuel S Minot
- Data Core, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Scott N Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
- Department of Pediatrics, University of Washington, Seattle, WA, USA
- Brotman-Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA
| | - Kami Ahmad
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
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16
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Gaza HV, Bhardwaj V, Zeller P. Single-Cell Histone Modification Profiling with Cell Enrichment Using sortChIC. Methods Mol Biol 2024; 2846:215-241. [PMID: 39141239 DOI: 10.1007/978-1-0716-4071-5_14] [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: 08/15/2024]
Abstract
Histone post-translational modifications (PTMs) influence the overall structure of the chromatin and gene expression. Over the course of cell differentiation, the distribution of histone modifications is remodeled, resulting in cell type-specific patterns. In the past, their study was limited to abundant cell types that could be purified in necessary numbers. However, studying these cell type-specific dynamic changes in heterogeneous in vivo settings requires sensitive single-cell methods. Current advances in single-cell sequencing methods remove these limitations, allowing the study of nonpurifiable cell types. One complicating factor is that some of the most biologically interesting cell types, including stem and progenitor cells that undergo differentiation, only make up a small fraction of cells in a tissue. This makes whole-tissue analysis rather inefficient. In this chapter, we present a sort-assisted single-cell Chromatin ImmunoCleavage sequencing technique (sortChIC) to map histone PTMs in single cells. This technique combines the mapping of histone PTM location in combination with surface staining-based enrichment, to allow the integration of established strategies for rare cell type enrichment. In general terms, this will enable researchers to quantify local and global chromatin changes in dynamic complex biological systems and can provide additional information on their contribution to lineage and cell-type specification in physiological conditions and disease.
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Affiliation(s)
- Helena Viñas Gaza
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Vivek Bhardwaj
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Peter Zeller
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Oncode Institute, Utrecht, The Netherlands.
- University Medical Center Utrecht, Utrecht, The Netherlands.
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17
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Wang K, Zhang X, Cheng H, Ma W, Bao G, Dong L, Gou Y, Yang J, Cai H. SingleScan: a comprehensive resource for single-cell sequencing data processing and mining. BMC Bioinformatics 2023; 24:463. [PMID: 38062357 PMCID: PMC10704760 DOI: 10.1186/s12859-023-05590-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023] Open
Abstract
Single-cell sequencing has shed light on previously inaccessible biological questions from different fields of research, including organism development, immune function, and disease progression. The number of single-cell-based studies increased dramatically over the past decade. Several new methods and tools have been continuously developed, making it extremely tricky to navigate this research landscape and develop an up-to-date workflow to analyze single-cell sequencing data, particularly for researchers seeking to enter this field without computational experience. Moreover, choosing appropriate tools and optimal parameters to meet the demands of researchers represents a major challenge in processing single-cell sequencing data. However, a specific resource for easy access to detailed information on single-cell sequencing methods and data processing pipelines is still lacking. In the present study, an online resource called SingleScan was developed to curate all up-to-date single-cell transcriptome/genome analyzing tools and pipelines. All the available tools were categorized according to their main tasks, and several typical workflows for single-cell data analysis were summarized. In addition, spatial transcriptomics, which is a breakthrough molecular analysis method that enables researchers to measure all gene activity in tissue samples and map the site of activity, was included along with a portion of single-cell and spatial analysis solutions. For each processing step, the available tools and specific parameters used in published articles are provided and how these parameters affect the results is shown in the resource. All information used in the resource was manually extracted from related literature. An interactive website was designed for data retrieval, visualization, and download. By analyzing the included tools and literature, users can gain insights into the trends of single-cell studies and easily grasp the specific usage of a specific tool. SingleScan will facilitate the analysis of single-cell sequencing data and promote the development of new tools to meet the growing and diverse needs of the research community. The SingleScan database is publicly accessible via the website at http://cailab.labshare.cn/SingleScan .
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Affiliation(s)
- Kun Wang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Xiao Zhang
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, 611731, China
- Chinese Academy of Sciences Sichuan Translational Medicine Research Hospital, Chengdu, 610072, China
| | - Hansen Cheng
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Wenhao Ma
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Guangchao Bao
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Liting Dong
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yixiong Gou
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Jian Yang
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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18
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Hu Y, Shen F, Yang X, Han T, Long Z, Wen J, Huang J, Shen J, Guo Q. Single-cell sequencing technology applied to epigenetics for the study of tumor heterogeneity. Clin Epigenetics 2023; 15:161. [PMID: 37821906 PMCID: PMC10568863 DOI: 10.1186/s13148-023-01574-x] [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: 07/16/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023] Open
Abstract
BACKGROUND Previous studies have traditionally attributed the initiation of cancer cells to genetic mutations, considering them as the fundamental drivers of carcinogenesis. However, recent research has shed light on the crucial role of epigenomic alterations in various cell types present within the tumor microenvironment, suggesting their potential contribution to tumor formation and progression. Despite these significant findings, the progress in understanding the epigenetic mechanisms regulating tumor heterogeneity has been impeded over the past few years due to the lack of appropriate technical tools and methodologies. RESULTS The emergence of single-cell sequencing has enhanced our understanding of the epigenetic mechanisms governing tumor heterogeneity by revealing the distinct epigenetic layers of individual cells (chromatin accessibility, DNA/RNA methylation, histone modifications, nucleosome localization) and the diverse omics (transcriptomics, genomics, multi-omics) at the single-cell level. These technologies provide us with new insights into the molecular basis of intratumoral heterogeneity and help uncover key molecular events and driving mechanisms in tumor development. CONCLUSION This paper provides a comprehensive review of the emerging analytical and experimental approaches of single-cell sequencing in various omics, focusing specifically on epigenomics. These approaches have the potential to capture and integrate multiple dimensions of individual cancer cells, thereby revealing tumor heterogeneity and epigenetic features. Additionally, this paper outlines the future trends of these technologies and their current technical limitations.
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Affiliation(s)
- Yuhua Hu
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Feng Shen
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Department of Neurosurgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Xi Yang
- Department of Radiation Oncology, Cancer Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Tingting Han
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
| | - Zhuowen Long
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Jiale Wen
- Graduate School, Dalian Medical University, Dalian, 116044, Liaoning, China
- Department of Cardiology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China
| | - Junxing Huang
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Jiangfeng Shen
- Department of Thoracic Surgery, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
| | - Qing Guo
- Department of Oncology, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou School of Clinical Medicine, Nanjing Medical University, Taizhou, 225300, Jiangsu, China.
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19
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Shi Q, Chen X, Zhang Z. Decoding Human Biology and Disease Using Single-cell Omics Technologies. GENOMICS, PROTEOMICS & BIOINFORMATICS 2023; 21:926-949. [PMID: 37739168 PMCID: PMC10928380 DOI: 10.1016/j.gpb.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 05/22/2023] [Accepted: 06/08/2023] [Indexed: 09/24/2023]
Abstract
Over the past decade, advances in single-cell omics (SCO) technologies have enabled the investigation of cellular heterogeneity at an unprecedented resolution and scale, opening a new avenue for understanding human biology and disease. In this review, we summarize the developments of sequencing-based SCO technologies and computational methods, and focus on considerable insights acquired from SCO sequencing studies to understand normal and diseased properties, with a particular emphasis on cancer research. We also discuss the technological improvements of SCO and its possible contribution to fundamental research of the human, as well as its great potential in clinical diagnoses and personalized therapies of human disease.
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Affiliation(s)
- Qiang Shi
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xueyan Chen
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zemin Zhang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing 100871, China; Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China; Changping Laboratory, Beijing 102206, China.
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20
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Zhang Y, Li X, Gao S, Liao Y, Luo Y, Liu M, Bian Y, Xiong H, Yue Y, He A. Genetic reporter for live tracing fluid flow forces during cell fate segregation in mouse blastocyst development. Cell Stem Cell 2023; 30:1110-1123.e9. [PMID: 37541214 DOI: 10.1016/j.stem.2023.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/02/2023] [Accepted: 07/10/2023] [Indexed: 08/06/2023]
Abstract
Mechanical forces are known to be important in mammalian blastocyst formation; however, due to limited tools, specific force inputs and how they relay to first cell fate control of inner cell mass (ICM) and/or trophectoderm (TE) remain elusive. Combining in toto live imaging and various perturbation experiments, we demonstrate and measure fluid flow forces existing in the mouse blastocyst cavity and identify Klf2(Krüppel-like factor 2) as a fluid force reporter with force-responsive enhancers. Long-term live imaging and lineage reconstructions reveal that blastomeres subject to higher fluid flow forces adopt ICM cell fates. These are reinforced by internal ferrofluid-induced flow force assays. We also utilize ex vivo fluid flow force mimicking and pharmacological perturbations to confirm mechanosensing specificity. Together, we report a genetically encoded reporter for continuously monitoring fluid flow forces and cell fate decisions and provide a live imaging framework to infer force information enriched lineage landscape during development. VIDEO ABSTRACT.
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Affiliation(s)
- Youdong Zhang
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xin Li
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Shu Gao
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuanhui Liao
- School of Software and Microelectronics, Peking University, Beijing 100871, China
| | - Yingjie Luo
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Min Liu
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yunkun Bian
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haiqing Xiong
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yanzhu Yue
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Department of Cell Fate and Diseases, Jilin Provincial Key Laboratory of Women's Reproductive Health, the First Hospital of Jilin University, Changchun, Jilin 130061, China.
| | - Aibin He
- Institute of Molecular Medicine, National Biomedical Imaging Center, College of Future Technology, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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21
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Chang L, Deng E, Wang J, Zhou W, Ao J, Liu R, Su D, Fan X. Single-cell third-generation sequencing-based multi-omics uncovers gene expression changes governed by ecDNA and structural variants in cancer cells. Clin Transl Med 2023; 13:e1351. [PMID: 37517066 PMCID: PMC10387328 DOI: 10.1002/ctm2.1351] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 07/17/2023] [Accepted: 07/21/2023] [Indexed: 08/01/2023] Open
Abstract
BACKGROUND Cancer cells often exhibit large-scale genomic variations, such as circular extrachromosomal DNA (ecDNA) and structural variants (SVs), which have been highly correlated with the initiation and progression of cancer. Currently, no adequate method exists to unveil how these variations regulate gene expression in heterogeneous cancer cell populations at a single-cell resolution. METHODS Here, we developed a single-cell multi-omics sequencing method, scGTP-seq, to analyse ecDNA and SVs using long-read sequencing technologies. RESULTS AND CONCLUSIONS We demonstrated that our method can efficiently detect ecDNA and SVs and illustrated how these variations affect transcriptomic changes in various cell lines. Finally, we applied and validated this method in a clinical sample of hepatocellular carcinoma (HCC), demonstrating a feasible way to monitor the evolution of ecDNA and SVs during cancer progression.
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Affiliation(s)
- Lei Chang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- Present address:
Department of Cellular and Molecular MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Enze Deng
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jun Wang
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Wei Zhou
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Jian Ao
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
| | - Rong Liu
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
| | - Dan Su
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
| | - Xiaoying Fan
- GMU‐GIBH Joint School of Life SciencesGuangdong‐Hong Kong‐Macau Joint Laboratory for Cell Fate Regulation and DiseasesGuangzhou National LaboratoryGuangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Innovation centre for Advanced Interdisciplinary MedicineThe Fifth Affiliated Hospital of Guangzhou Medical UniversityGuangzhouGuangdong ProvinceP. R. China
- Department of Biomedical DevicesThe Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory)GuangzhouGuangdong ProvinceP. R. China
- The Guangzhou Institutes of Biomedicine and HealthChinese Academy of SciencesGuangzhouGuangdong ProvinceP. R. China
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22
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Stuart T, Hao S, Zhang B, Mekerishvili L, Landau DA, Maniatis S, Satija R, Raimondi I. Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution. Nat Biotechnol 2023; 41:806-812. [PMID: 36536150 PMCID: PMC10272075 DOI: 10.1038/s41587-022-01588-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 10/24/2022] [Indexed: 12/24/2022]
Abstract
Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility and other factors. Current methods for defining chromatin states cannot measure more than one aspect in a single experiment at single-cell resolution. Here we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), an assay capable of measuring the genome-wide presence of up to three histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq uses recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk-cell and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and in human immune cells. We also extend NTT-seq to enable simultaneous profiling of cell surface protein expression and multimodal chromatin states to study cells of the immune system.
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Affiliation(s)
- Tim Stuart
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Stephanie Hao
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Bingjie Zhang
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Levan Mekerishvili
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Dan A Landau
- New York Genome Center, New York, NY, USA
- Weill Cornell Medicine, New York, NY, USA
| | - Silas Maniatis
- Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Rahul Satija
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Ivan Raimondi
- Technology Innovation Lab, New York Genome Center, New York, NY, USA.
- Weill Cornell Medicine, New York, NY, USA.
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23
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Yu W, Wang HL, Zhang J, Yin C. The effects of epigenetic modifications on bone remodeling in age-related osteoporosis. Connect Tissue Res 2023; 64:105-116. [PMID: 36271658 DOI: 10.1080/03008207.2022.2120392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE As the population ages, there is an increased risk of fracture and morbidity diseases associated with aging, such as age-related osteoporosis and other bone diseases linked to aging skeletons. RESULTS Several bone-related cells, including multipotent bone mesenchymal stem cells, osteoblasts that form bone tissue, and osteoclasts that break it down, are in symbiotic relationships throughout life. Growing evidence indicates that epigenetic modifications of cells caused by aging contribute to compromised bone remodeling and lead to osteoporosis. A number of epigenetic mechanisms are at play, including DNA/RNA modifications, histone modifications, microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), as well as chromatin remodeling. CONCLUSION In this review, we summarized the epigenetic modifications of different bone-related cells during the development and progression of osteoporosis associated with aging. Additionally, we described a compensatory recovery mechanism under epigenetic regulation that may lead to new strategies for regulating bone remodeling in age-related osteoporosis.
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Affiliation(s)
- Wenyue Yu
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
| | - He-Ling Wang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
| | - Jianying Zhang
- Xiangya School of Stomatology, Central South University, Changsha, China
| | - Chengcheng Yin
- School and Hospital of Stomatology, Liaoning Provincial Key Laboratory of Oral Diseases, China Medical University, Shenyang, China
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24
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Single-cell proteomics enabled by next-generation sequencing or mass spectrometry. Nat Methods 2023; 20:363-374. [PMID: 36864196 DOI: 10.1038/s41592-023-01791-5] [Citation(s) in RCA: 84] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/24/2023] [Indexed: 03/04/2023]
Abstract
In the last decade, single-cell RNA sequencing routinely performed on large numbers of single cells has greatly advanced our understanding of the underlying heterogeneity of complex biological systems. Technological advances have also enabled protein measurements, further contributing to the elucidation of cell types and states present in complex tissues. Recently, there have been independent advances in mass spectrometric techniques bringing us one step closer to characterizing single-cell proteomes. Here we discuss the challenges of detecting proteins in single cells by both mass spectrometry and sequencing-based methods. We review the state of the art for these techniques and propose that there is a space for technological advancements and complementary approaches that maximize the advantages of both classes of technologies.
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25
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Penkov D, Zubkova E, Parfyonova Y. Tn5 DNA Transposase in Multi-Omics Research. Methods Protoc 2023; 6:mps6020024. [PMID: 36961044 PMCID: PMC10037646 DOI: 10.3390/mps6020024] [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] [Received: 12/15/2022] [Revised: 02/21/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Tn5 transposase use in biotechnology has substantially advanced the sequencing applications of genome-wide analysis of cells. This is mainly due to the ability of Tn5 transposase to efficiently transpose DNA essentially randomly into any target DNA without the aid of other factors. This concise review is focused on the advances in Tn5 applications in multi-omics technologies, genome-wide profiling, and Tn5 hybrid molecule creation. The possibilities of other transposase uses are also discussed.
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Affiliation(s)
- Dmitry Penkov
- IRCCS San Raffaele Hospital, 20132 Milan, Italy
- National Medical Research Centre of Cardiology Named after E. I. Chazov, 121552 Moscow, Russia
| | - Ekaterina Zubkova
- National Medical Research Centre of Cardiology Named after E. I. Chazov, 121552 Moscow, Russia
| | - Yelena Parfyonova
- National Medical Research Centre of Cardiology Named after E. I. Chazov, 121552 Moscow, Russia
- Faculty of Medicine, Lomonosov Moscow State University, 119991 Moscow, Russia
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26
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Wang M, Li Q, Liu L. Factors and Methods for the Detection of Gene Expression Regulation. Biomolecules 2023; 13:biom13020304. [PMID: 36830673 PMCID: PMC9953580 DOI: 10.3390/biom13020304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 02/01/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Gene-expression regulation involves multiple processes and a range of regulatory factors. In this review, we describe the key factors that regulate gene expression, including transcription factors (TFs), chromatin accessibility, histone modifications, DNA methylation, and RNA modifications. In addition, we also describe methods that can be used to detect these regulatory factors.
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27
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Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nat Genet 2023; 55:333-345. [PMID: 36539617 PMCID: PMC9925381 DOI: 10.1038/s41588-022-01260-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 11/01/2022] [Indexed: 12/24/2022]
Abstract
Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages.
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28
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Wooten M, Takushi B, Ahmad K, Henikoff S. Aclarubicin stimulates RNA polymerase II elongation at closely spaced divergent promoters. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.09.523323. [PMID: 36712130 PMCID: PMC9882078 DOI: 10.1101/2023.01.09.523323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Anthracyclines are a class of widely prescribed anti-cancer drugs that disrupt chromatin by intercalating into DNA and enhancing nucleosome turnover. To understand the molecular consequences of anthracycline-mediated chromatin disruption, we utilized CUT&Tag to profile RNA polymerase II during anthracycline treatment in Drosophila cells. We observed that treatment with the anthracycline aclarubicin leads to elevated levels of elongating RNA polymerase II and changes in chromatin accessibility. We found that promoter proximity and orientation impacts chromatin changes during aclarubicin treatment, as closely spaced divergent promoter pairs show greater chromatin changes when compared to codirectionally-oriented tandem promoters. We also found that aclarubicin treatment changes the distribution of non-canonical DNA G-quadruplex structures both at promoters and at G-rich pericentromeric repeats. Our work suggests that the anti-cancer activity of aclarubicin is driven by the effects of nucleosome disruption on RNA polymerase II, chromatin accessibility and DNA structures.
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Affiliation(s)
- Matthew Wooten
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
| | | | - Kami Ahmad
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
| | - Steven Henikoff
- Fred Hutchinson Cancer Center, Seattle, WA 98109-1024, USA
- Howard Hughes Medical Institute
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29
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scChIX-seq infers dynamic relationships between histone modifications in single cells. Nat Biotechnol 2023:10.1038/s41587-022-01560-3. [PMID: 36593403 DOI: 10.1038/s41587-022-01560-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/12/2022] [Indexed: 01/03/2023]
Abstract
Regulation of chromatin states involves the dynamic interplay between different histone modifications to control gene expression. Recent advances have enabled mapping of histone marks in single cells, but most methods are constrained to profile only one histone mark per cell. Here, we present an integrated experimental and computational framework, scChIX-seq (single-cell chromatin immunocleavage and unmixing sequencing), to map several histone marks in single cells. scChIX-seq multiplexes two histone marks together in single cells, then computationally deconvolves the signal using training data from respective histone mark profiles. This framework learns the cell-type-specific correlation structure between histone marks, and therefore does not require a priori assumptions of their genomic distributions. Using scChIX-seq, we demonstrate multimodal analysis of histone marks in single cells across a range of mark combinations. Modeling dynamics of in vitro macrophage differentiation enables integrated analysis of chromatin velocity. Overall, scChIX-seq unlocks systematic interrogation of the interplay between histone modifications in single cells.
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30
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Ouyang W, Li X. CUT&Tag for Mapping In Vivo Protein-DNA Interactions in Plants. Methods Mol Biol 2023; 2698:109-117. [PMID: 37682472 DOI: 10.1007/978-1-0716-3354-0_8] [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: 09/09/2023]
Abstract
Histone post-translational modifications and transcription factors (TFs) play vital roles in regulating gene expression. A comprehensive understanding of transcriptional regulation requires genome-wide mapping of chromatin features such as histone modifications and TF binding sites. Here, we describe a detailed nucleus CUT&Tag (Cleavage Under Targets and Tagmentation) protocol, which is an antibody-guided in situ protein-DNA interaction mapping method using protein A/G fused Tn5 transposase. Compared with regular ChIP-seq in plants, nucleus CUT&Tag (nCUT&Tag) omits many steps such as sonication and immunoprecipitation, thus saving much time and making it possible to efficiently profile chromatin features from low-input and even single cells with higher signal-to-noise ratio.
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Affiliation(s)
- Weizhi Ouyang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
| | - Xingwang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China.
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31
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Martin BK, Qiu C, Nichols E, Phung M, Green-Gladden R, Srivatsan S, Blecher-Gonen R, Beliveau BJ, Trapnell C, Cao J, Shendure J. Optimized single-nucleus transcriptional profiling by combinatorial indexing. Nat Protoc 2023; 18:188-207. [PMID: 36261634 PMCID: PMC9839601 DOI: 10.1038/s41596-022-00752-0] [Citation(s) in RCA: 40] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 06/30/2022] [Indexed: 01/17/2023]
Abstract
Single-cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that has historically exhibited variable performance on different tissues, as well as lower sensitivity than alternative methods. Here, we report a simplified, optimized version of the sci-RNA-seq protocol with three rounds of split-pool indexing that is faster, more robust and more sensitive and has a higher yield than the original protocol, with reagent costs on the order of 1 cent per cell or less. The total hands-on time from nuclei isolation to final library preparation takes 2-3 d, depending on the number of samples sharing the experiment. The improvements also allow RNA profiling from tissues rich in RNases like older mouse embryos or adult tissues that were problematic for the original method. We showcase the optimized protocol via whole-organism analysis of an E16.5 mouse embryo, profiling ~380,000 nuclei in a single experiment. Finally, we introduce a 'Tiny-Sci' protocol for experiments in which input material is very limited.
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Affiliation(s)
- Beth K. Martin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Chengxiang Qiu
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Eva Nichols
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Melissa Phung
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Department of Biology, Case Western Reserve University, Cleveland, OH, USA
| | - Rula Green-Gladden
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Division of Hematology/Oncology, Seattle Children’s Hospital, Seattle, WA, USA
| | - Sanjay Srivatsan
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Medical Scientist Training Program, University of Washington, Seattle, WA, USA
| | - Ronnie Blecher-Gonen
- The Crown Genomics Institute of the Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Israel
| | - Brian J. Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Cole Trapnell
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA
| | - Junyue Cao
- Laboratory of Single-Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA. .,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA. .,Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA. .,Howard Hughes Medical Institute, Seattle, WA, USA.
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32
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Preissl S, Gaulton KJ, Ren B. Characterizing cis-regulatory elements using single-cell epigenomics. Nat Rev Genet 2023; 24:21-43. [PMID: 35840754 PMCID: PMC9771884 DOI: 10.1038/s41576-022-00509-1] [Citation(s) in RCA: 65] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2022] [Indexed: 12/24/2022]
Abstract
Cell type-specific gene expression patterns and dynamics during development or in disease are controlled by cis-regulatory elements (CREs), such as promoters and enhancers. Distinct classes of CREs can be characterized by their epigenomic features, including DNA methylation, chromatin accessibility, combinations of histone modifications and conformation of local chromatin. Tremendous progress has been made in cataloguing CREs in the human genome using bulk transcriptomic and epigenomic methods. However, single-cell epigenomic and multi-omic technologies have the potential to provide deeper insight into cell type-specific gene regulatory programmes as well as into how they change during development, in response to environmental cues and through disease pathogenesis. Here, we highlight recent advances in single-cell epigenomic methods and analytical tools and discuss their readiness for human tissue profiling.
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Affiliation(s)
- Sebastian Preissl
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Institute of Experimental and Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
| | - Kyle J Gaulton
- Department of Paediatrics, Paediatric Diabetes Research Center, University of California San Diego, La Jolla, CA, USA.
| | - Bing Ren
- Center for Epigenomics, University of California San Diego, La Jolla, CA, USA.
- Department of Cellular and Molecular Medicine, University of California San Diego, School of Medicine, La Jolla, CA, USA.
- Ludwig Institute for Cancer Research, La Jolla, CA, USA.
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33
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Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag. Nat Biotechnol 2022:10.1038/s41587-022-01535-4. [DOI: 10.1038/s41587-022-01535-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 09/28/2022] [Indexed: 12/24/2022]
Abstract
AbstractProbing histone modifications at a single-cell level in thousands of cells has been enabled by technologies such as single-cell CUT&Tag. Here we describe nano-CUT&Tag (nano-CT), which allows simultaneous mapping of up to three epigenomic modalities at single-cell resolution using nanobody-Tn5 fusion proteins. Multimodal nano-CT is compatible with starting materials as low as 25,000–200,000 cells and has significantly higher sensitivity and number of fragments per cell than single-cell CUT&Tag. We use nano-CT to simultaneously profile chromatin accessibility, H3K27ac, and H3K27me3 in juvenile mouse brain, allowing for discrimination of more cell types and states than unimodal single-cell CUT&Tag. We also infer chromatin velocity between assay for transposase-accessible chromatin (ATAC) and H3K27ac in the oligodendrocyte lineage and deconvolute H3K27me3 repressive states, finding two sequential waves of H3K27me3 repression at distinct gene modules during oligodendrocyte lineage progression. Given its high resolution, versatility, and multimodal features, nano-CT allows unique insights in epigenetic landscapes in complex biological systems at the single-cell level.
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Li C, Yin Z, Xiao R, Huang B, Cui Y, Wang H, Xiang Y, Wang L, Lei L, Ye J, Li T, Zhong Y, Guo F, Xia Y, Fang P, Liang K. G-quadruplexes sense natural porphyrin metabolites for regulation of gene transcription and chromatin landscapes. Genome Biol 2022; 23:259. [PMID: 36522639 PMCID: PMC9753424 DOI: 10.1186/s13059-022-02830-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 12/02/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND G-quadruplexes (G4s) are unique noncanonical nucleic acid secondary structures, which have been proposed to physically interact with transcription factors and chromatin remodelers to regulate cell type-specific transcriptome and shape chromatin landscapes. RESULTS Based on the direct interaction between G4 and natural porphyrins, we establish genome-wide approaches to profile where the iron-liganded porphyrin hemin can bind in the chromatin. Hemin promotes genome-wide G4 formation, impairs transcription initiation, and alters chromatin landscapes, including decreased H3K27ac and H3K4me3 modifications at promoters. Interestingly, G4 status is not involved in the canonical hemin-BACH1-NRF2-mediated enhancer activation process, highlighting an unprecedented G4-dependent mechanism for metabolic regulation of transcription. Furthermore, hemin treatment induces specific gene expression profiles in hepatocytes, underscoring the in vivo potential for metabolic control of gene transcription by porphyrins. CONCLUSIONS These studies demonstrate that G4 functions as a sensor for natural porphyrin metabolites in cells, revealing a G4-dependent mechanism for metabolic regulation of gene transcription and chromatin landscapes, which will deepen our knowledge of G4 biology and the contribution of cellular metabolites to gene regulation.
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Affiliation(s)
- Conghui Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Zhinang Yin
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ruijing Xiao
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Beili Huang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yali Cui
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Honghong Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Ying Xiang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lingrui Wang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Lingyu Lei
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Jiaqin Ye
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Tianyu Li
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Youquan Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Fangteng Guo
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
| | - Yuchen Xia
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan, 430071, China
- TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071, China
| | - Pingping Fang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
| | - Kaiwei Liang
- School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
- TaiKang Center for Life and Medical Sciences, TaiKang Medical School, Wuhan University, Wuhan, 430071, China.
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, 430071, China.
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Zeng L, Yang K, Zhang T, Zhu X, Hao W, Chen H, Ge J. Research progress of single-cell transcriptome sequencing in autoimmune diseases and autoinflammatory disease: A review. J Autoimmun 2022; 133:102919. [PMID: 36242821 DOI: 10.1016/j.jaut.2022.102919] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 12/07/2022]
Abstract
Autoimmunity refers to the phenomenon that the body's immune system produces antibodies or sensitized lymphocytes to its own tissues to cause an immune response. Immune disorders caused by autoimmunity can mediate autoimmune diseases. Autoimmune diseases have complicated pathogenesis due to the many types of cells involved, and the mechanism is still unclear. The emergence of single-cell research technology can solve the problem that ordinary transcriptome technology cannot be accurate to cell type. It provides unbiased results through independent analysis of cells in tissues and provides more mRNA information for identifying cell subpopulations, which provides a novel approach to study disruption of immune tolerance and disturbance of pro-inflammatory pathways on a cellular basis. It may fundamentally change the understanding of molecular pathways in the pathogenesis of autoimmune diseases and develop targeted drugs. Single-cell transcriptome sequencing (scRNA-seq) has been widely applied in autoimmune diseases, which provides a powerful tool for demonstrating the cellular heterogeneity of tissues involved in various immune inflammations, identifying pathogenic cell populations, and revealing the mechanism of disease occurrence and development. This review describes the principles of scRNA-seq, introduces common sequencing platforms and practical procedures, and focuses on the progress of scRNA-seq in 41 autoimmune diseases, which include 9 systemic autoimmune diseases and autoinflammatory diseases (rheumatoid arthritis, systemic lupus erythematosus, etc.) and 32 organ-specific autoimmune diseases (5 Skin diseases, 3 Nervous system diseases, 4 Eye diseases, 2 Respiratory system diseases, 2 Circulatory system diseases, 6 Liver, Gallbladder and Pancreas diseases, 2 Gastrointestinal system diseases, 3 Muscle, Bones and joint diseases, 3 Urinary system diseases, 2 Reproductive system diseases). This review also prospects the molecular mechanism targets of autoimmune diseases from the multi-molecular level and multi-dimensional analysis combined with single-cell multi-omics sequencing technology (such as scRNA-seq, Single cell ATAC-seq and single cell immune group library sequencing), which provides a reference for further exploring the pathogenesis and marker screening of autoimmune diseases and autoimmune inflammatory diseases in the future.
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Affiliation(s)
- Liuting Zeng
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Kailin Yang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Tianqing Zhang
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China
| | - Xiaofei Zhu
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China.
| | - Wensa Hao
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hua Chen
- Department of Rheumatology, Peking Union Medical College Hospital, Chinese Academy of Medical Science & Peking Union Medical College, National Clinical Research Center for Dermatologic and Immunologic Diseases, State Key Laboratory of Complex Severe and Rare Diseases, Beijing, China.
| | - Jinwen Ge
- Key Laboratory of Hunan Province for Integrated Traditional Chinese and Western Medicine on Prevention and Treatment of Cardio-Cerebral Diseases, Hunan University of Chinese Medicine, Changsha, China; Hunan Academy of Chinese Medicine, Changsha, China.
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Liu Y, Liang S, Wang B, Zhao J, Zi X, Yan S, Dou T, Jia J, Wang K, Ge C. Advances in Single-Cell Sequencing Technology and Its Application in Poultry Science. Genes (Basel) 2022; 13:genes13122211. [PMID: 36553479 PMCID: PMC9778011 DOI: 10.3390/genes13122211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Revised: 11/20/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
Single-cell sequencing (SCS) uses a single cell as the research material and involves three dimensions: genes, phenotypes and cell biological mechanisms. This type of research can locate target cells, analyze the dynamic changes in the target cells and the relationships between the cells, and pinpoint the molecular mechanism of cell formation. Currently, a common problem faced by animal husbandry scientists is how to apply existing science and technology to promote the production of high-quality livestock and poultry products and to breed livestock for disease resistance; this is also a bottleneck for the sustainable development of animal husbandry. In recent years, although SCS technology has been successfully applied in the fields of medicine and bioscience, its application in poultry science has been rarely reported. With the sustainable development of science and technology and the poultry industry, SCS technology has great potential in the application of poultry science (or animal husbandry). Therefore, it is necessary to review the innovation of SCS technology and its application in poultry science. This article summarizes the current main technical methods of SCS and its application in poultry, which can provide potential references for its future applications in precision breeding, disease prevention and control, immunity, and cell identification.
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Affiliation(s)
- Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Shuangmin Liang
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Bo Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jinbo Zhao
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xiannian Zi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Shixiong Yan
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tengfei Dou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Junjing Jia
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Correspondence:
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2cChIP-seq and 2cMeDIP-seq: The Carrier-Assisted Methods for Epigenomic Profiling of Small Cell Numbers or Single Cells. Int J Mol Sci 2022; 23:ijms232213984. [PMID: 36430462 PMCID: PMC9692998 DOI: 10.3390/ijms232213984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/15/2022] [Indexed: 11/16/2022] Open
Abstract
Chromatin immunoprecipitation coupled with high-throughput sequencing (ChIP-seq) can profile genome-wide epigenetic marks associated with regulatory genomic elements. However, conventional ChIP-seq is challenging when examining limited numbers of cells. Here, we developed a new technique by supplementing carrier materials of both chemically modified mimics with epigenetic marks and dUTP-containing DNA fragments during conventional ChIP procedures (hereafter referred to as 2cChIP-seq), thus dramatically improving immunoprecipitation efficiency and reducing DNA loss of low-input ChIP-seq samples. Using this strategy, we generated high-quality epigenomic profiles of histone modifications or DNA methylation in 10-1000 cells. By introducing Tn5 transposase-assisted fragmentation, 2cChIP-seq reliably captured genomic regions with histone modification at the single-cell level in about 100 cells. Moreover, we characterized the methylome of 100 differentiated female germline stem cells (FGSCs) and observed a particular DNA methylation signature potentially involved in the differentiation of mouse germline stem cells. Hence, we provided a reliable and robust epigenomic profiling approach for small cell numbers and single cells.
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Lu T, Ang CE, Zhuang X. Spatially resolved epigenomic profiling of single cells in complex tissues. Cell 2022; 185:4448-4464.e17. [PMID: 36272405 PMCID: PMC9691621 DOI: 10.1016/j.cell.2022.09.035] [Citation(s) in RCA: 59] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 08/22/2022] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
The recent development of spatial omics methods has enabled single-cell profiling of the transcriptome and 3D genome organization with high spatial resolution. Expanding the repertoire of spatial omics tools, a spatially resolved single-cell epigenomics method will accelerate understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved epigenomic profiling of single cells using in situ tagmentation and transcription followed by multiplexed imaging. We demonstrated the ability to profile histone modifications marking active promoters, putative enhancers, and silent promoters in individual cells, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results suggested putative promoter-enhancer pairs and enhancer hubs regulating developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
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Affiliation(s)
- Tian Lu
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Cheen Euong Ang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02138, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Department of Physics, Harvard University, Cambridge, MA 02138, USA.
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Henikoff S, Ahmad K. In situ tools for chromatin structural epigenomics. Protein Sci 2022; 31:e4458. [PMID: 36170035 PMCID: PMC9601787 DOI: 10.1002/pro.4458] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/19/2022] [Accepted: 09/22/2022] [Indexed: 12/14/2022]
Abstract
Technological progress over the past 15 years has fueled an explosion in genome-wide chromatin profiling tools that take advantage of low-cost short-read sequencing technologies to map particular chromatin features. Here, we survey the recent development of epigenomic tools that provide precise positions of chromatin proteins genome-wide in intact cells or nuclei. Some profiling tools are based on tethering Micrococcal Nuclease to chromatin proteins of interest in situ, whereas others similarly tether Tn5 transposase to integrate DNA sequencing adapters (tagmentation) and so eliminate the need for library preparation. These in situ cleavage and tagmentation tools have gained in popularity over the past few years, with many protocol enhancements and adaptations for single-cell and spatial chromatin profiling. The application of experimental and computational tools to address problems in gene regulation, eukaryotic development, and human disease are helping to define the emerging field of chromatin structural epigenomics.
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Affiliation(s)
- Steven Henikoff
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
- Howard Hughes Medical InstituteChevy ChaseMarylandUSA
| | - Kami Ahmad
- Fred Hutchinson Cancer CenterSeattleWashingtonUSA
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40
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Nam AS, Dusaj N, Izzo F, Murali R, Myers RM, Mouhieddine TH, Sotelo J, Benbarche S, Waarts M, Gaiti F, Tahri S, Levine R, Abdel-Wahab O, Godley LA, Chaligne R, Ghobrial I, Landau DA. Single-cell multi-omics of human clonal hematopoiesis reveals that DNMT3A R882 mutations perturb early progenitor states through selective hypomethylation. Nat Genet 2022; 54:1514-1526. [PMID: 36138229 PMCID: PMC10068894 DOI: 10.1038/s41588-022-01179-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Somatic mutations in cancer genes have been detected in clonal expansions across healthy human tissue, including in clonal hematopoiesis. However, because mutated and wild-type cells are admixed, we have limited ability to link genotypes with phenotypes. To overcome this limitation, we leveraged multi-modality single-cell sequencing, capturing genotype, transcriptomes and methylomes in progenitors from individuals with DNMT3A R882 mutated clonal hematopoiesis. DNMT3A mutations result in myeloid over lymphoid bias, and an expansion of immature myeloid progenitors primed toward megakaryocytic-erythroid fate, with dysregulated expression of lineage and leukemia stem cell markers. Mutated DNMT3A leads to preferential hypomethylation of polycomb repressive complex 2 targets and a specific CpG flanking motif. Notably, the hypomethylation motif is enriched in binding motifs of key hematopoietic transcription factors, serving as a potential mechanistic link between DNMT3A mutations and aberrant transcriptional phenotypes. Thus, single-cell multi-omics paves the road to defining the downstream consequences of mutations that drive clonal mosaicism.
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Affiliation(s)
- Anna S Nam
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- New York Genome Center, New York, NY, USA
| | - Neville Dusaj
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Franco Izzo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Rekha Murali
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Tri-Institutional MD-PhD Program, Weill Cornell Medicine, Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tarek H Mouhieddine
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jesus Sotelo
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Salima Benbarche
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Michael Waarts
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Federico Gaiti
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Sabrin Tahri
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Ross Levine
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lucy A Godley
- Section of Hematology/Oncology, Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Ronan Chaligne
- New York Genome Center, New York, NY, USA
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Irene Ghobrial
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dan A Landau
- New York Genome Center, New York, NY, USA.
- Division of Hematology and Medical Oncology, Department of Medicine and Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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Sreenivasan VKA, Balachandran S, Spielmann M. The role of single-cell genomics in human genetics. J Med Genet 2022; 59:827-839. [PMID: 35790352 PMCID: PMC9411920 DOI: 10.1136/jmedgenet-2022-108588] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022]
Abstract
Single-cell sequencing is a powerful approach that can detect genetic alterations and their phenotypic consequences in the context of human development, with cellular resolution. Humans start out as single-cell zygotes and undergo fission and differentiation to develop into multicellular organisms. Before fertilisation and during development, the cellular genome acquires hundreds of mutations that propagate down the cell lineage. Whether germline or somatic in nature, some of these mutations may have significant genotypic impact and lead to diseased cellular phenotypes, either systemically or confined to a tissue. Single-cell sequencing enables the detection and monitoring of the genotype and the consequent molecular phenotypes at a cellular resolution. It offers powerful tools to compare the cellular lineage between 'normal' and 'diseased' conditions and to establish genotype-phenotype relationships. By preserving cellular heterogeneity, single-cell sequencing, unlike bulk-sequencing, allows the detection of even small, diseased subpopulations of cells within an otherwise normal tissue. Indeed, the characterisation of biopsies with cellular resolution can provide a mechanistic view of the disease. While single-cell approaches are currently used mainly in basic research, it can be expected that applications of these technologies in the clinic may aid the detection, diagnosis and eventually the treatment of rare genetic diseases as well as cancer. This review article provides an overview of the single-cell sequencing technologies in the context of human genetics, with an aim to empower clinicians to understand and interpret the single-cell sequencing data and analyses. We discuss the state-of-the-art experimental and analytical workflows and highlight current challenges/limitations. Notably, we focus on two prospective applications of the technology in human genetics, namely the annotation of the non-coding genome using single-cell functional genomics and the use of single-cell sequencing data for in silico variant prioritisation.
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Affiliation(s)
- Varun K A Sreenivasan
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
| | - Saranya Balachandran
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
| | - Malte Spielmann
- Institute of Human Genetics, University Hospital Schleswig-Holstein, University of Lübeck and Kiel University, Lübeck and Kiel, Germany
- Human Molecular Genetics Group, Max Planck Institute for Molecular Genetics, Berlin, Germany
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Yadav RP, Polavarapu VK, Xing P, Chen X. FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded Samples. Curr Protoc 2022; 2:e535. [PMID: 35994571 DOI: 10.1002/cpz1.535] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In basic and translational cancer research, the majority of biopsies are stored in formalin-fixed paraffin-embedded (FFPE) samples. Chromatin accessibility reflects the degree to which nuclear macromolecules can physically interact with chromatinized DNA and plays a key role in gene regulation in different physiological conditions. As such, the profiling of chromatin accessibility in archived FFPE tissue can be critical to understanding gene regulation in health and disease. Due to the high degree of DNA damage in FFPE samples, accurate mapping of chromatin accessibility in these specimens is extremely difficult. To address this issue, we recently established FFPE-ATAC, a highly sensitive method based on T7-Tn5-mediated transposition followed by in vitro transcription (IVT), to generate high-quality chromatin accessibility profiles with 500-50,000 nuclei from a single FFPE tissue section. In FFPE-ATAC, which we describe here, the T7-Tn5 adaptors are inserted into the genome after FFPE sample preparation and are unlikely to sustain the DNA breakage that occurs during reverse cross-linking of these samples. It should, therefore, remain at the ends of broken accessible chromatin sites after reverse cross-linking. IVT is then used to convert the two ends of the broken DNA fragments to RNA molecules before making sequencing libraries from the IVT RNAs and further decoding Tn5 adaptor insertion sites in the genome. Through this strategy, users can decode the flanking sequences of the accessible chromatin even if there are breaks between adjacent pairs of T7-T5 adaptor insertion sites. This method is applicable to dissecting chromatin profiles of a small section of the tissue sample, characterizing stage and region-specific gene regulation and disease-associated chromatin regulation in FFPE tissues. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation from FFPE tissue samples Basic Protocol 2: T7-Tn5 transposase tagmentation, reverse-crosslinking, and in vitro transcription Basic Protocol 3: Preparation of libraries for high-throughput sequencing.
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Affiliation(s)
- Ram Prakash Yadav
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | | | - Pengwei Xing
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Abstract
The single-cell revolution in the field of genomics is in full bloom, with clever new molecular biology tricks appearing regularly that allow researchers to explore new modalities or scale up their projects to millions of cells and beyond. Techniques abound to measure RNA expression, DNA alterations, protein abundance, chromatin accessibility, and more, all with single-cell resolution and often in combination. Despite such a rapidly changing technology landscape, there are several fundamental principles that are applicable to the majority of experimental workflows to help users avoid pitfalls and exploit the advantages of the chosen platform. In this overview article, we describe a variety of popular single-cell genomics technologies and address some common questions pertaining to study design, sample preparation, quality control, and sequencing strategy. As the majority of relevant publications currently revolve around single-cell RNA-seq, we will prioritize this genomics modality in our discussion. © 2022 Wiley Periodicals LLC.
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Affiliation(s)
- Claire Regan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
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Casado-Pelaez M, Bueno-Costa A, Esteller M. Single cell cancer epigenetics. Trends Cancer 2022; 8:820-838. [PMID: 35821003 DOI: 10.1016/j.trecan.2022.06.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 05/02/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Bulk sequencing methodologies have allowed us to make great progress in cancer research. Unfortunately, these techniques lack the resolution to fully unravel the epigenetic mechanisms that govern tumor heterogeneity. Consequently, many novel single cell-sequencing methodologies have been developed over the past decade, allowing us to explore the epigenetic components that regulate different aspects of cancer heterogeneity, namely: clonal heterogeneity, tumor microenvironment (TME), spatial organization, intratumoral differentiation programs, metastasis, and resistance mechanisms. In this review, we explore the different sequencing techniques that enable researchers to study different aspects of epigenetics (DNA methylation, chromatin accessibility, histone modifications, DNA-protein interactions, and chromatin 3D architecture) at the single cell level, their potential applications in cancer, and their current technical limitations.
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Affiliation(s)
- Marta Casado-Pelaez
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Alberto Bueno-Costa
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain
| | - Manel Esteller
- Josep Carreras Leukaemia Research Institute (IJC), Badalona, Barcelona, Catalonia, Spain; Centro de Investigacion Biomedica en Red Cancer (CIBERONC), 28029 Madrid, Spain; Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia, Spain; Physiological Sciences Department, School of Medicine and Health Sciences, University of Barcelona (UB), Barcelona, Catalonia, Spain.
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45
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Pan L, Ku WL, Tang Q, Cao Y, Zhao K. scPCOR-seq enables co-profiling of chromatin occupancy and RNAs in single cells. Commun Biol 2022; 5:678. [PMID: 35804086 PMCID: PMC9270334 DOI: 10.1038/s42003-022-03584-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/30/2022] Open
Abstract
Cell-to-cell variation in gene expression is a widespread phenomenon, which may play important roles in cellular differentiation, function, and disease development1–9. Chromatin is implicated in contributing to the cellular heterogeneity in gene expression10–16. Fully understanding the mechanisms of cellular heterogeneity requires simultaneous measurement of RNA and occupancy of histone modifications and transcription factors on chromatin due to their critical roles in transcriptional regulation17,18. We generally term the occupancy of histone modifications and transcription factors as Chromatin occupancy. Here, we report a technique, termed scPCOR-seq (single-cell Profiling of Chromatin Occupancy and RNAs Sequencing), for simultaneously profiling genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell. We demonstrated that scPCOR-seq can profile either H3K4me3 or RNAPII and RNAs in a mixture of human H1, GM12878 and 293 T cells at a single-cell resolution and either H3K4me3, RNAPII, or RNA profile can correctly separate the cells. Application of scPCOR-seq to the in vitro differentiation of the erythrocyte precursor CD36 cells from human CD34 stem or progenitor cells revealed that H3K4me3 and RNA exhibit distinct properties in clustering cells during differentiation. Overall, our work provides a promising approach to understand the relationships among different omics layers. scPCOR-seq is a single-cell sequencing technique that enables simultaneous profiling of genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell.
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Affiliation(s)
- Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Wai Lim Ku
- 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
| | - Yaqiang Cao
- 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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He J, Lin L, Chen J. Practical bioinformatics pipelines for single-cell RNA-seq data analysis. BIOPHYSICS REPORTS 2022; 8:158-169. [PMID: 37288243 PMCID: PMC10189648 DOI: 10.52601/bpr.2022.210041] [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: 08/19/2021] [Accepted: 03/01/2022] [Indexed: 11/05/2022] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool to explore cells. With an increasing number of scRNA-seq data analysis tools that have been developed, it is challenging for users to choose and compare their performance. Here, we present an overview of the workflow for computational analysis of scRNA-seq data. We detail the steps of a typical scRNA-seq analysis, including experimental design, pre-processing and quality control, feature selection, dimensionality reduction, cell clustering and annotation, and downstream analysis including batch correction, trajectory inference and cell-cell communication. We provide guidelines according to our best practice. This review will be helpful for the experimentalists interested in analyzing their data, and will aid the users seeking to update their analysis pipelines.
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Affiliation(s)
- Jiangping He
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
| | - Lihui Lin
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jiekai Chen
- Center for Cell Lineage and Atlas (CCLA), Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510320, China
- Key Laboratory of Regenerative Biology of the Chinese Academy of Sciences and Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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47
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Wang C, Fan X. Single-cell multi-omics sequencing and its applications in studying the nervous system. BIOPHYSICS REPORTS 2022; 8:136-149. [PMID: 37288245 PMCID: PMC10189649 DOI: 10.52601/bpr.2021.210031] [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: 07/30/2021] [Accepted: 09/04/2021] [Indexed: 11/05/2022] Open
Abstract
Single-cell sequencing has become one of the most powerful and popular techniques in dissecting molecular heterogeneity and modeling the cellular architecture of a biological system. During the past twenty years, the throughput of single-cell sequencing has increased from hundreds of cells to over tens of thousands of cells in parallel. Moreover, this technology has been developed from sequencing transcriptome to measure different omics such as DNA methylome, chromatin accessibility, and so on. Currently, multi-omics which can analyze different omics in the same cell is rapidly advancing. This work advances the study of many biosystems, including the nervous system. Here, we review current single-cell multi-omics sequencing techniques and describe how they improve our understanding of the nervous system. Finally, we discuss the open scientific questions in neural research that may be answered through further improvement of single-cell multi-omics sequencing technology.
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Affiliation(s)
- Chaoyang Wang
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
| | - Xiaoying Fan
- Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou 510005, China
- The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou 510700, China
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48
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Abstract
Dramatic nuclear reorganization occurs during early development to convert terminally differentiated gametes to a totipotent zygote, which then gives rise to an embryo. Aberrant epigenome resetting severely impairs embryo development and even leads to lethality. How the epigenomes are inherited, reprogrammed, and reestablished in this critical developmental period has gradually been unveiled through the rapid development of technologies including ultrasensitive chromatin analysis methods. In this review, we summarize the latest findings on epigenetic reprogramming in gametogenesis and embryogenesis, and how it contributes to gamete maturation and parental-to-zygotic transition. Finally, we highlight the key questions that remain to be answered to fully understand chromatin regulation and nuclear reprogramming in early development.
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Affiliation(s)
- Zhenhai Du
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Ke Zhang
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Wei Xie
- Center for Stem Cell Biology and Regenerative Medicine, MOE Key Laboratory of Bioinformatics, Tsinghua University, Beijing 100084, China
- Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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49
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Mo Y, Jiao Y. Advances and applications of single-cell omics technologies in plant research. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1551-1563. [PMID: 35426954 DOI: 10.1111/tpj.15772] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 06/14/2023]
Abstract
Single-cell sequencing approaches reveal the intracellular dynamics of individual cells and answer biological questions with high-dimensional catalogs of millions of cells, including genomics, transcriptomics, chromatin accessibility, epigenomics, and proteomics data across species. These emerging yet thriving technologies have been fully embraced by the field of plant biology, with a constantly expanding portfolio of applications. Here, we introduce the current technical advances used for single-cell omics, especially single-cell genome and transcriptome sequencing. Firstly, we overview methods for protoplast and nucleus isolation and genome and transcriptome amplification. Subsequently, we use well-executed benchmarking studies to highlight advances made through the application of single-cell omics techniques. Looking forward, we offer a glimpse of additional hurdles and future opportunities that will introduce broad adoption of single-cell sequencing with revolutionary perspectives in plant biology.
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Affiliation(s)
- Yajin Mo
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuling Jiao
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, School of Life Sciences, Peking University, Beijing, 100871, China
- State Key Laboratory of Plant Genomics and National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
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50
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Xu X, Zhang M, Zhang X, Liu Y, Cai L, Zhang Q, Chen Q, Lin L, Lin S, Song Y, Zhu Z, Yang C. Decoding Expression Dynamics of Protein and Transcriptome at the Single-Cell Level in Paired Picoliter Chambers. Anal Chem 2022; 94:8164-8173. [PMID: 35650660 DOI: 10.1021/acs.analchem.1c05312] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simultaneous analysis of mRNAs and proteins at the single-cell level provides information about the dynamics and correlations of gene and protein expressions in individual cells, enabling a comprehensive study of cellular heterogeneity and expression patterns. Here, we present a platform for about 1000 cellular indexing of mRNAs and membrane proteins, named multi-Paired-seq, with high cell utilization, accurate molecular measurement, and low cost. Based on hydrodynamic differential flow resistance, multi-Paired-seq largely improves cell utilization in the percentage of cells measured in population (>95%). Combined with the pump/valve structure, cell-free antibodies and mRNAs can be removed completely for highly accurate detection (R = 0.96) of protein copies. The picoliter reaction chambers allow high detection sensitivity for both mRNA transcripts and protein copies and low sequencing cost. Using multi-Paired-seq, three clusters of known breast cancer cell types are identified according to multimodal measurements, and the expression correlations between mRNAs and proteins under altered conditions are quantified. Multi-Paired-seq provides multimodal measurements at the single-cell level, which offers a new tool for cell biology, developmental biology, drug discovery, and precision medicine.
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Affiliation(s)
- Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Xuebing Zhang
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Linfeng Cai
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qianqian Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Qin Chen
- Suzhou Dynamic Biosystems Co., Ltd., Suzhou, Jiangsu 215000, China
| | - Li Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Shichao Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Yanling Song
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Zhi Zhu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China
| | - Chaoyong Yang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian 361005, China.,Institute of Molecular Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
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