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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. Genome Biol 2024; 25:115. [PMID: 38711126 PMCID: PMC11071213 DOI: 10.1186/s13059-024-03261-3] [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: 09/23/2023] [Accepted: 04/28/2024] [Indexed: 05/08/2024] Open
Abstract
BACKGROUND In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties are originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. RESULTS In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays. CONCLUSIONS Our results provide the first window into the 5-hmU and chromatin accessibility landscapes in dinoflagellates.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Matthew P Swaffer
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, CA, 94305, USA.
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA, 94305, USA.
- Department of Applied Physics, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, USA.
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2
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Li D, Qian X, Wang Y, Yin Y, Sun H, Zhao H, Wu J, Qiu L. Molecular characterization and functional roles of circulating cell-free extrachromosomal circular DNA. Clin Chim Acta 2024; 556:117822. [PMID: 38325714 DOI: 10.1016/j.cca.2024.117822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Circular DNA segments isolated from chromosomes are known as extrachromosomal circular DNA (eccDNA). Its distinct structure and characteristics, along with the variations observed in different disease states, makes it a promising biomarker. Recent studies have revealed the presence of eccDNAs in body fluids, indicating their involvement in various biological functions. This finding opens up avenues for utilizing eccDNAs as convenient and real-time biomarkers for disease diagnosis, treatment monitoring, and prognosis assessment through noninvasive analysis of body fluids. In this comprehensive review, we focused on elucidating the size profiles, potential mechanisms of formation and clearance, detection methods, and potential clinical applications of eccDNAs. We aimed to provide a valuable reference resource for future research in this field.
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Affiliation(s)
- Dandan Li
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Xia Qian
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yingjie Wang
- Department of Orthopedic Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Yicong Yin
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Huishan Sun
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China
| | - Haitao Zhao
- Department of Liver Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Jie Wu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
| | - Ling Qiu
- Department of Laboratory Medicine, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College (CAMS & PUMC), Beijing 100730, China.
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3
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Isaac RS, Tullius TW, Hansen KG, Dubocanin D, Couvillion M, Stergachis AB, Churchman LS. Single-nucleoid architecture reveals heterogeneous packaging of mitochondrial DNA. Nat Struct Mol Biol 2024; 31:568-577. [PMID: 38347148 DOI: 10.1038/s41594-024-01225-6] [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: 10/14/2022] [Accepted: 01/09/2024] [Indexed: 03/03/2024]
Abstract
Cellular metabolism relies on the regulation and maintenance of mitochondrial DNA (mtDNA). Hundreds to thousands of copies of mtDNA exist in each cell, yet because mitochondria lack histones or other machinery important for nuclear genome compaction, it remains unresolved how mtDNA is packaged into individual nucleoids. In this study, we used long-read single-molecule accessibility mapping to measure the compaction of individual full-length mtDNA molecules at near single-nucleotide resolution. We found that, unlike the nuclear genome, human mtDNA largely undergoes all-or-none global compaction, with most nucleoids existing in an inaccessible, inactive state. Highly accessible mitochondrial nucleoids are co-occupied by transcription and replication components and selectively form a triple-stranded displacement loop structure. In addition, we showed that the primary nucleoid-associated protein TFAM directly modulates the fraction of inaccessible nucleoids both in vivo and in vitro, acting consistently with a nucleation-and-spreading mechanism to coat and compact mitochondrial nucleoids. Together, these findings reveal the primary architecture of mtDNA packaging and regulation in human cells.
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Affiliation(s)
- R Stefan Isaac
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Thomas W Tullius
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Katja G Hansen
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danilo Dubocanin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Mary Couvillion
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
| | - L Stirling Churchman
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
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4
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Proteins shaping global chromatin accessibility. Nat Genet 2024; 56:367-368. [PMID: 38418745 DOI: 10.1038/s41588-024-01667-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
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5
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Ishii S, Kakizuka T, Park SJ, Tagawa A, Sanbo C, Tanabe H, Ohkawa Y, Nakanishi M, Nakai K, Miyanari Y. Genome-wide ATAC-see screening identifies TFDP1 as a modulator of global chromatin accessibility. Nat Genet 2024; 56:473-482. [PMID: 38361031 DOI: 10.1038/s41588-024-01658-1] [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: 02/05/2020] [Accepted: 01/08/2024] [Indexed: 02/17/2024]
Abstract
Chromatin accessibility is a hallmark of active regulatory regions and is functionally linked to transcriptional networks and cell identity. However, the molecular mechanisms and networks that govern chromatin accessibility have not been thoroughly studied. Here we conducted a genome-wide CRISPR screening combined with an optimized ATAC-see protocol to identify genes that modulate global chromatin accessibility. In addition to known chromatin regulators like CREBBP and EP400, we discovered a number of previously unrecognized proteins that modulate chromatin accessibility, including TFDP1, HNRNPU, EIF3D and THAP11 belonging to diverse biological pathways. ATAC-seq analysis upon their knockouts revealed their distinct and specific effects on chromatin accessibility. Remarkably, we found that TFDP1, a transcription factor, modulates global chromatin accessibility through transcriptional regulation of canonical histones. In addition, our findings highlight the manipulation of chromatin accessibility as an approach to enhance various cell engineering applications, including genome editing and induced pluripotent stem cell reprogramming.
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Affiliation(s)
- Satoko Ishii
- The Graduate University for Advanced Studies, SOKENDAI, Okazaki, Japan
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Taishi Kakizuka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Sung-Joon Park
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Ayako Tagawa
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan
| | - Chiaki Sanbo
- National Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan
- Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Japan
| | - Hideyuki Tanabe
- Research Center for Integrative Evolutionary Science, SOKENDAI, Hayama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Kenta Nakai
- Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yusuke Miyanari
- WPI Nano Life Science Institute, Kanazawa University, Kanazawa, Japan.
- Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
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6
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Di Bona M, Bakhoum SF. Micronuclei and Cancer. Cancer Discov 2024; 14:214-226. [PMID: 38197599 DOI: 10.1158/2159-8290.cd-23-1073] [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: 09/18/2023] [Revised: 11/20/2023] [Accepted: 12/18/2023] [Indexed: 01/11/2024]
Abstract
Chromosome-containing micronuclei are a feature of human cancer. Micronuclei arise from chromosome mis-segregation and characterize tumors with elevated rates of chromosomal instability. Although their association with cancer has been long recognized, only recently have we broadened our understanding of the mechanisms that govern micronuclei formation and their role in tumor progression. In this review, we provide a brief historical account of micronuclei, depict the mechanisms underpinning their creation, and illuminate their capacity to propel tumor evolution through genetic, epigenetic, and transcriptional transformations. We also posit the prospect of leveraging micronuclei as biomarkers and therapeutic targets in chromosomally unstable cancers. SIGNIFICANCE Micronuclei in chromosomally unstable cancer cells serve as pivotal catalysts for cancer progression, instigating transformative genomic, epigenetic, and transcriptional alterations. This comprehensive review not only synthesizes our present comprehension but also outlines a framework for translating this knowledge into pioneering biomarkers and therapeutics, thereby illuminating novel paths for personalized cancer management.
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Affiliation(s)
- Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, New York
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, New York
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7
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Wu N, Wei L, Zhu Z, Liu Q, Li K, Mao F, Qiao J, Zhao X. Innovative insights into extrachromosomal circular DNAs in gynecologic tumors and reproduction. Protein Cell 2024; 15:6-20. [PMID: 37233789 PMCID: PMC10762679 DOI: 10.1093/procel/pwad032] [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: 03/20/2023] [Accepted: 05/03/2023] [Indexed: 05/27/2023] Open
Abstract
Originating but free from chromosomal DNA, extrachromosomal circular DNAs (eccDNAs) are organized in circular form and have long been found in unicellular and multicellular eukaryotes. Their biogenesis and function are poorly understood as they are characterized by sequence homology with linear DNA, for which few detection methods are available. Recent advances in high-throughput sequencing technologies have revealed that eccDNAs play crucial roles in tumor formation, evolution, and drug resistance as well as aging, genomic diversity, and other biological processes, bringing it back to the research hotspot. Several mechanisms of eccDNA formation have been proposed, including the breakage-fusion-bridge (BFB) and translocation-deletion-amplification models. Gynecologic tumors and disorders of embryonic and fetal development are major threats to human reproductive health. The roles of eccDNAs in these pathological processes have been partially elucidated since the first discovery of eccDNA in pig sperm and the double minutes in ovarian cancer ascites. The present review summarized the research history, biogenesis, and currently available detection and analytical methods for eccDNAs and clarified their functions in gynecologic tumors and reproduction. We also proposed the application of eccDNAs as drug targets and liquid biopsy markers for prenatal diagnosis and the early detection, prognosis, and treatment of gynecologic tumors. This review lays theoretical foundations for future investigations into the complex regulatory networks of eccDNAs in vital physiological and pathological processes.
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Affiliation(s)
- Ning Wu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Ling Wei
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Zhipeng Zhu
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Qiang Liu
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
| | - Kailong Li
- Department of Biochemistry and Biophysics, Beijing Key Laboratory of Protein Posttranslational Modifications and Cell Function, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Fengbiao Mao
- Institute of Medical Innovation and Research, Peking University Third Hospital, Beijing 100191, China
- Cancer Center, Peking University Third Hospital, Beijing 100191, China
| | - Jie Qiao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
- Beijing Advanced Innovation Center for Genomics, Beijing 100191, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100191, China
| | - Xiaolu Zhao
- State Key Laboratory of Female Fertility Promotion, Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Peking University Third Hospital, Beijing 100191, China
- National Clinical Research Center for Obstetrics and Gynecology, Peking University Third Hospital, Beijing 100191, China
- Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing 100191, China
- Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing 100191, China
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8
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Zhu YP, Speir M, Tan Z, Lee JC, Nowell CJ, Chen AA, Amatullah H, Salinger AJ, Huang CJ, Wu G, Peng W, Askari K, Griffis E, Ghassemian M, Santini J, Gerlic M, Kiosses WB, Catz SD, Hoffman HM, Greco KF, Weller E, Thompson PR, Wong LP, Sadreyev R, Jeffrey KL, Croker BA. NET formation is a default epigenetic program controlled by PAD4 in apoptotic neutrophils. SCIENCE ADVANCES 2023; 9:eadj1397. [PMID: 38117877 PMCID: PMC10732518 DOI: 10.1126/sciadv.adj1397] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 12/04/2023] [Indexed: 12/22/2023]
Abstract
Neutrophil extracellular traps (NETs) not only counteract bacterial and fungal pathogens but can also promote thrombosis, autoimmunity, and sterile inflammation. The presence of citrullinated histones, generated by the peptidylarginine deiminase 4 (PAD4), is synonymous with NETosis and is considered independent of apoptosis. Mitochondrial- and death receptor-mediated apoptosis promote gasdermin E (GSDME)-dependent calcium mobilization and membrane permeabilization leading to histone H3 citrullination (H3Cit), nuclear DNA extrusion, and cytoplast formation. H3Cit is concentrated at the promoter in bone marrow neutrophils and redistributes in a coordinated process from promoter to intergenic and intronic regions during apoptosis. Loss of GSDME prevents nuclear and plasma membrane disruption of apoptotic neutrophils but prolongs early apoptosis-induced cellular changes to the chromatin and cytoplasmic granules. Apoptotic signaling engages PAD4 in neutrophils, establishing a cellular state that is primed for NETosis, but that occurs only upon membrane disruption by GSDME, thereby redefining the end of life for neutrophils.
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Affiliation(s)
- Yanfang Peipei Zhu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Immunology Center of Georgia, Augusta University, Augusta, GA 30912, USA
| | - Mary Speir
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - ZheHao Tan
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Jamie Casey Lee
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Cameron J. Nowell
- Monash Institute of Pharmaceutical Sciences, Parkville, Victoria 3052, Australia
| | - Alyce A. Chen
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ari J. Salinger
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Carolyn J. Huang
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Gio Wu
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Weiqi Peng
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kasra Askari
- Scripps Research Institute, La Jolla, CA 92037, USA
| | - Eric Griffis
- Nikon Imaging Center, University of California San Diego, La Jolla, CA 92093, USA
| | - Majid Ghassemian
- Biomolecular and Proteomics Mass Spectrometry Facility, University of California San Diego, La Jolla, CA 92093, USA
| | - Jennifer Santini
- UCSD School of Medicine Microscopy Core, University of California San Diego, La Jolla 92093, CA, USA
| | - Motti Gerlic
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | | | | | - Hal M. Hoffman
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Kimberly F. Greco
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Edie Weller
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Biostatistics and Research Design Center, Institutional Centers for Clinical and Translational Research, Boston Children’s Hospital, Boston, 02115, USA
| | - Paul R. Thompson
- Program in Chemical Biology and Department of Biochemistry and Molecular Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lai Ping Wong
- Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Ruslan Sadreyev
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Kate L. Jeffrey
- Department of Medicine, Division of Gastroenterology and the Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston MA 02114, USA
- Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ben A. Croker
- Department of Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
- Division of Hematology/Oncology, Boston Children’s Hospital, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
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Li J, Chen Z, Bai Y, Wei Y, Guo D, Liu Z, Niu Y, Shi B, Zhang X, Cai Y, Zhao Z, Hu J, Wang J, Liu X, Li S, Zhao F. Integration of ATAC-Seq and RNA-Seq Analysis to Identify Key Genes in the Longissimus Dorsi Muscle Development of the Tianzhu White Yak. Int J Mol Sci 2023; 25:158. [PMID: 38203329 PMCID: PMC10779322 DOI: 10.3390/ijms25010158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 12/18/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
During the postnatal stages, skeletal muscle development undergoes a series of meticulously regulated alterations in gene expression. However, limited studies have employed chromatin accessibility to unravel the underlying molecular mechanisms governing muscle development in yak species. Therefore, we conducted an analysis of both gene expression levels and chromatin accessibility to comprehensively characterize the dynamic genome-wide chromatin accessibility during muscle growth and development in the Tianzhu white yak, thereby elucidating the features of accessible chromatin regions throughout this process. Initially, we compared the differences in chromatin accessibility between two groups and observed that calves exhibited higher levels of chromatin accessibility compared to adult cattle, particularly within ±2 kb of the transcription start site (TSS). In order to investigate the correlation between alterations in chromatin accessible regions and variations in gene expression levels, we employed a combination of ATAC-seq and RNA-seq techniques, leading to the identification of 18 central transcriptional factors (TFs) and 110 key genes with significant effects. Through further analysis, we successfully identified several TFs, including Sp1, YY1, MyoG, MEF2A and MEF2C, as well as a number of candidate genes (ANKRD2, ANKRD1, BTG2 and LMOD3) which may be closely associated with muscle growth and development. Moreover, we constructed an interactive network program encompassing hub TFs and key genes related to muscle growth and development. This innovative approach provided valuable insights into the molecular mechanism underlying skeletal muscle development in the postnatal stages of Tianzhu white yaks while also establishing a solid theoretical foundation for future research on yak muscle development.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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10
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Han M, Perkins MH, Novaes LS, Xu T, Chang H. Advances in transposable elements: from mechanisms to applications in mammalian genomics. Front Genet 2023; 14:1290146. [PMID: 38098473 PMCID: PMC10719622 DOI: 10.3389/fgene.2023.1290146] [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: 09/07/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
It has been 70 years since Barbara McClintock discovered transposable elements (TE), and the mechanistic studies and functional applications of transposable elements have been at the forefront of life science research. As an essential part of the genome, TEs have been discovered in most species of prokaryotes and eukaryotes, and the relative proportion of the total genetic sequence they comprise gradually increases with the expansion of the genome. In humans, TEs account for about 40% of the genome and are deeply involved in gene regulation, chromosome structure maintenance, inflammatory response, and the etiology of genetic and non-genetic diseases. In-depth functional studies of TEs in mammalian cells and the human body have led to a greater understanding of these fundamental biological processes. At the same time, as a potent mutagen and efficient genome editing tool, TEs have been transformed into biological tools critical for developing new techniques. By controlling the random insertion of TEs into the genome to change the phenotype in cells and model organisms, critical proteins of many diseases have been systematically identified. Exploiting the TE's highly efficient in vitro insertion activity has driven the development of cutting-edge sequencing technologies. Recently, a new technology combining CRISPR with TEs was reported, which provides a novel targeted insertion system to both academia and industry. We suggest that interrogating biological processes that generally depend on the actions of TEs with TEs-derived genetic tools is a very efficient strategy. For example, excessive activation of TEs is an essential factor in the occurrence of cancer in humans. As potent mutagens, TEs have also been used to unravel the key regulatory elements and mechanisms of carcinogenesis. Through this review, we aim to effectively combine the traditional views of TEs with recent research progress, systematically link the mechanistic discoveries of TEs with the technological developments of TE-based tools, and provide a comprehensive approach and understanding for researchers in different fields.
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Affiliation(s)
- Mei Han
- Guangzhou National Laboratory, Guangzhou, China
| | - Matthew H. Perkins
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Leonardo Santana Novaes
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Tao Xu
- Guangzhou National Laboratory, Guangzhou, China
| | - Hao Chang
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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11
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Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J. CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. Nat Commun 2023; 14:7346. [PMID: 37963886 PMCID: PMC10645931 DOI: 10.1038/s41467-023-43158-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 11/16/2023] Open
Abstract
Genomic DNA (gDNA) undergoes structural interconversion between single- and double-stranded states during transcription, DNA repair and replication, which is critical for cellular homeostasis. We describe "CHEX-seq" which identifies the single-stranded DNA (ssDNA) in situ in individual cells. CHEX-seq uses 3'-terminal blocked, light-activatable probes to prime the copying of ssDNA into complementary DNA that is sequenced, thereby reporting the genome-wide single-stranded chromatin landscape. CHEX-seq is benchmarked in human K562 cells, and its utilities are demonstrated in cultures of mouse and human brain cells as well as immunostained spatially localized neurons in brain sections. The amount of ssDNA is dynamically regulated in response to perturbation. CHEX-seq also identifies single-stranded regions of mitochondrial DNA in single cells. Surprisingly, CHEX-seq identifies single-stranded loci in mouse and human gDNA that catalyze porphyrin metalation in vitro, suggesting a catalytic activity for genomic ssDNA. We posit that endogenous DNA enzymatic activity is a function of genomic ssDNA.
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Affiliation(s)
- Youtao Lu
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jaehee Lee
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jifen Li
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Srinivasa Rao Allu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jinhui Wang
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - HyunBum Kim
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kevin L Bullaughey
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stephen A Fisher
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Erik Nordgren
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Jean G Rosario
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Stewart A Anderson
- Department of Psychiatry, Children's Hospital of Philadelphia, ARC 517, 3615 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Alexandra V Ulyanova
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - H Isaac Chen
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - John A Wolf
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - M Sean Grady
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sergei A Vinogradov
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Junhyong Kim
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - James Eberwine
- Department of Systems Pharmacology and Translational Therapeutics Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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12
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Alexandrov T, Saez‐Rodriguez J, Saka SK. Enablers and challenges of spatial omics, a melting pot of technologies. Mol Syst Biol 2023; 19:e10571. [PMID: 37842805 PMCID: PMC10632737 DOI: 10.15252/msb.202110571] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 07/31/2023] [Accepted: 08/03/2023] [Indexed: 10/17/2023] Open
Abstract
Spatial omics has emerged as a rapidly growing and fruitful field with hundreds of publications presenting novel methods for obtaining spatially resolved information for any omics data type on spatial scales ranging from subcellular to organismal. From a technology development perspective, spatial omics is a highly interdisciplinary field that integrates imaging and omics, spatial and molecular analyses, sequencing and mass spectrometry, and image analysis and bioinformatics. The emergence of this field has not only opened a window into spatial biology, but also created multiple novel opportunities, questions, and challenges for method developers. Here, we provide the perspective of technology developers on what makes the spatial omics field unique. After providing a brief overview of the state of the art, we discuss technological enablers and challenges and present our vision about the future applications and impact of this melting pot.
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Affiliation(s)
- Theodore Alexandrov
- Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- BioInnovation InstituteCopenhagenDenmark
| | - Julio Saez‐Rodriguez
- Molecular Medicine Partnership UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
- Faculty of Medicine and Heidelberg University Hospital, Institute for Computational BiomedicineHeidelberg UniversityHeidelbergGermany
| | - Sinem K Saka
- Genome Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
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13
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Carraro C, Bonaguro L, Srinivasa R, van Uelft M, Isakzai V, Schulte-Schrepping J, Gambhir P, Elmzzahi T, Montgomery JV, Hayer H, Li Y, Theis H, Kraut M, Mahbubani KT, Aschenbrenner AC, König I, Fava E, Fried HU, De Domenico E, Beyer M, Saglam A, Schultze JL. Chromatin accessibility profiling of targeted cell populations with laser capture microdissection coupled to ATAC-seq. CELL REPORTS METHODS 2023; 3:100598. [PMID: 37776856 PMCID: PMC10626193 DOI: 10.1016/j.crmeth.2023.100598] [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: 03/27/2023] [Revised: 08/04/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
Spatially resolved omics technologies reveal context-dependent cellular regulatory networks in tissues of interest. Beyond transcriptome analysis, information on epigenetic traits and chromatin accessibility can provide further insights on gene regulation in health and disease. Nevertheless, compared to the enormous advancements in spatial transcriptomics technologies, the field of spatial epigenomics is much younger and still underexplored. In this study, we report laser capture microdissection coupled to ATAC-seq (LCM-ATAC-seq) applied to fresh frozen samples for the spatial characterization of chromatin accessibility. We first demonstrate the efficient use of LCM coupled to in situ tagmentation and evaluate its performance as a function of cell number, microdissected areas, and tissue type. Further, we demonstrate its use for the targeted chromatin accessibility analysis of discrete contiguous or scattered cell populations in tissues via single-nuclei capture based on immunostaining for specific cellular markers.
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Affiliation(s)
- Caterina Carraro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany.
| | - Lorenzo Bonaguro
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Rachana Srinivasa
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Martina van Uelft
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Victoria Isakzai
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Jonas Schulte-Schrepping
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Prerna Gambhir
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Tarek Elmzzahi
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Jessica V Montgomery
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hannah Hayer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany
| | - Yuanfang Li
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Heidi Theis
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Michael Kraut
- PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Krishnaa T Mahbubani
- Department of Surgery, University of Cambridge, and Cambridge NIHR Biomedical Research Centre, Cambridge, UK
| | - Anna C Aschenbrenner
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Ireen König
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Eugenio Fava
- Core Research Facilities and Services, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Hans-Ulrich Fried
- Core Research Facilities and Services, Light Microscope Facility (LMF), Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Elena De Domenico
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
| | - Marc Beyer
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany; Immunogenomics & Neurodegeneration, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany
| | - Adem Saglam
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany.
| | - Joachim L Schultze
- Systems Medicine, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V., Bonn, Germany; Genomics and Immunoregulation, Life & Medical Sciences (LIMES) Institute, University of Bonn, Bonn, Germany; PRECISE Platform for Genomics and Epigenomics, Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) e.V. and University of Bonn, Bonn, Germany
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14
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Feng L, Barrows D, Zhong L, Mätlik K, Porter EG, Djomo AM, Yau I, Soshnev AA, Carroll TS, Wen D, Hatten ME, Garcia BA, Allis CD. Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.29.560141. [PMID: 37808786 PMCID: PMC10557780 DOI: 10.1101/2023.09.29.560141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Chromatin is a crucial regulator of gene expression and tightly controls development across species. Mutations in only one copy of multiple histone genes were identified in children with developmental disorders characterized by microcephaly, but their mechanistic roles in development remain unclear. Here we focus on dominant mutations affecting histone H4 lysine 91. These H4K91 mutants form aberrant nuclear puncta at specific heterochromatin regions. Mechanistically, H4K91 mutants demonstrate enhanced binding to the histone variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminishes the mutant localization to chromatin. Our functional studies demonstrate that H4K91 mutant expression increases chromatin accessibility, alters developmental gene expression through accelerating pro-neural differentiation, and causes reduced mouse brain size in vivo, reminiscent of the microcephaly phenotypes of patients. Together, our studies unveil a distinct molecular pathogenic mechanism from other known histone mutants, where H4K91 mutants misregulate cell fate during development through abnormal genomic localization.
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Affiliation(s)
- Lijuan Feng
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Douglas Barrows
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Liangwen Zhong
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Kärt Mätlik
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Elizabeth G. Porter
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - Annaelle M. Djomo
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
| | - Iris Yau
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Hunter College of the City University of New York, Yalow Honors Scholar Program, New York, NY
| | - Alexey A. Soshnev
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
- Department of Neuroscience, Developmental and Regenerative Biology, The University of Texas at San Antonio, San Antonio, TX
| | - Thomas S. Carroll
- The Rockefeller University, Bioinformatics Resource Center, New York, NY
| | - Duancheng Wen
- Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medicine, New York, NY
| | - Mary E. Hatten
- The Rockefeller University, Laboratory of Developmental Neurobiology, New York, NY
| | - Benjamin A. Garcia
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO
| | - C. David Allis
- The Rockefeller University, Laboratory of Chromatin Biology and Epigenetics, New York, NY
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15
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Marinov GK, Chen X, Swaffer MP, Xiang T, Grossman AR, Greenleaf WJ. Genome-wide distribution of 5-hydroxymethyluracil and chromatin accessibility in the Breviolum minutum genome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558303. [PMID: 37781619 PMCID: PMC10541103 DOI: 10.1101/2023.09.18.558303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
In dinoflagellates, a unique and extremely divergent genomic and nuclear organization has evolved. The highly unusual features of dinoflagellate nuclei and genomes include permanently condensed liquid crystalline chromosomes, primarily packaged by proteins other than histones, genes organized in very long unidirectional gene arrays, a general absence of transcriptional regulation, high abundance of the otherwise very rare DNA modification 5-hydroxymethyluracil (5-hmU), and many others. While most of these fascinating properties were originally identified in the 1970s and 1980s, they have not yet been investigated using modern genomic tools. In this work, we address some of the outstanding questions regarding dinoflagellate genome organization by mapping the genome-wide distribution of 5-hmU (using both immunoprecipitation-based and basepair-resolution chemical mapping approaches) and of chromatin accessibility in the genome of the Symbiodiniaceae dinoflagellate Breviolum minutum. We find that the 5-hmU modification is preferentially enriched over certain classes of repetitive elements, often coincides with the boundaries between gene arrays, and is generally correlated with decreased chromatin accessibility, the latter otherwise being largely uniform along the genome. We discuss the potential roles of 5-hmU in the functional organization of dinoflagellate genomes and its relationship to the transcriptional landscape of gene arrays.
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Affiliation(s)
- Georgi K Marinov
- Department of Genetics, Stanford University, Stanford, California 94305, USA
| | - Xinyi Chen
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
| | | | - Tingting Xiang
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - Arthur R Grossman
- Department of Plant Biology, Carnegie Institution for Science, Stanford, California 94305, USA
| | - William J Greenleaf
- Department of Genetics, Stanford University, Stanford, California 94305, USA
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA
- Department of Applied Physics, Stanford University, Stanford, California 94305, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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16
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Catalán A, Merondun J, Knief U, Wolf JBW. Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows. PLoS Genet 2023; 19:e1010901. [PMID: 37747941 PMCID: PMC10575545 DOI: 10.1371/journal.pgen.1010901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 10/13/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
The evolution of genetic sex determination is often accompanied by degradation of the sex-limited chromosome. Male heterogametic systems have evolved convergent, epigenetic mechanisms restoring the resulting imbalance in gene dosage between diploid autosomes (AA) and the hemizygous sex chromosome (X). Female heterogametic systems (AAf Zf, AAm ZZm) tend to only show partial dosage compensation (0.5 < Zf:AAf < 1) and dosage balance (0.5
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Affiliation(s)
- Ana Catalán
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Justin Merondun
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
| | - Ulrich Knief
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
- Evolutionary Biology & Ecology,Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Jochen B. W. Wolf
- Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden
- Division of Evolutionary Biology, LMU Munich, Planegg-Martinsried, Germany
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17
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Penagos-Puig A, Claudio-Galeana S, Stephenson-Gussinye A, Jácome-López K, Aguilar-Lomas A, Chen X, Pérez-Molina R, Furlan-Magaril M. RNA polymerase II pausing regulates chromatin organization in erythrocytes. Nat Struct Mol Biol 2023; 30:1092-1104. [PMID: 37500929 DOI: 10.1038/s41594-023-01037-0] [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: 06/14/2022] [Accepted: 06/16/2023] [Indexed: 07/29/2023]
Abstract
Chicken erythrocytes are nucleated cells often considered to be transcriptionally inactive, although the epigenetic changes and chromatin remodeling that would mediate transcriptional repression and the extent of gene silencing during avian terminal erythroid differentiation are not fully understood. Here, we characterize the changes in gene expression, chromatin accessibility, genome organization and chromatin nuclear disposition during the terminal stages of erythropoiesis in chicken and uncover complex chromatin reorganization at different genomic scales. We observe a robust decrease in transcription in erythrocytes, but a set of genes maintains their expression, including genes involved in RNA polymerase II (Pol II) promoter-proximal pausing. Erythrocytes exhibit a reoriented nuclear architecture, with accessible chromatin positioned towards the nuclear periphery together with the paused RNA Pol II. In erythrocytes, chromatin domains are partially lost genome-wide, except at minidomains retained around paused promoters. Our results suggest that promoter-proximal pausing of RNA Pol II contributes to the transcriptional regulation of the erythroid genome and highlight the role of RNA polymerase in the maintenance of local chromatin organization.
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Affiliation(s)
- Andrés Penagos-Puig
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Aura Stephenson-Gussinye
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Karina Jácome-López
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Amaury Aguilar-Lomas
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Xingqi Chen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Rosario Pérez-Molina
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico.
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18
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Zou J, Li J, Zhong X, Tang D, Fan X, Chen R. Liver in infections: a single-cell and spatial transcriptomics perspective. J Biomed Sci 2023; 30:53. [PMID: 37430371 PMCID: PMC10332047 DOI: 10.1186/s12929-023-00945-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 06/27/2023] [Indexed: 07/12/2023] Open
Abstract
The liver is an immune organ that plays a vital role in the detection, capture, and clearance of pathogens and foreign antigens that invade the human body. During acute and chronic infections, the liver transforms from a tolerant to an active immune state. The defence mechanism of the liver mainly depends on a complicated network of intrahepatic and translocated immune cells and non-immune cells. Therefore, a comprehensive liver cell atlas in both healthy and diseased states is needed for new therapeutic target development and disease intervention improvement. With the development of high-throughput single-cell technology, we can now decipher heterogeneity, differentiation, and intercellular communication at the single-cell level in sophisticated organs and complicated diseases. In this concise review, we aimed to summarise the advancement of emerging high-throughput single-cell technologies and re-define our understanding of liver function towards infections, including hepatitis B virus, hepatitis C virus, Plasmodium, schistosomiasis, endotoxemia, and corona virus disease 2019 (COVID-19). We also unravel previously unknown pathogenic pathways and disease mechanisms for the development of new therapeutic targets. As high-throughput single-cell technologies mature, their integration into spatial transcriptomics, multiomics, and clinical data analysis will aid in patient stratification and in developing effective treatment plans for patients with or without liver injury due to infectious diseases.
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Affiliation(s)
- Ju Zou
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jie Li
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao Zhong
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Daolin Tang
- Department of Surgery, UT Southwestern Medical Center, Dallas, TX, USA
| | - Xuegong Fan
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ruochan Chen
- Hunan Key Laboratory of Viral Hepatitis, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
- Department of Infectious Diseases, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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19
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Zhang C, Hong X, Yu H, Xu H, Qiu X, Cai W, Hocher B, Dai W, Tang D, Liu D, Dai Y. Gene regulatory network study of rheumatoid arthritis in single-cell chromatin landscapes of peripheral blood mononuclear cells. Mod Rheumatol 2023; 33:739-750. [PMID: 35796437 DOI: 10.1093/mr/roac072] [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: 03/17/2022] [Revised: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Assays for transposase-accessible chromatin with single-cell sequencing (scATAC-seq) contribute to the progress in epigenetic studies. The purpose of our project was to discover the transcription factors (TFs) that were involved in the pathogenesis of rheumatoid arthritis (RA) at a single-cell resolution using epigenetic technology. METHODS Peripheral blood mononuclear cells of seven RA patients and seven natural controls were extracted nuclei suspensions for library construction. Subsequently, scATAC-seq was performed to generate a high-resolution map of active regulatory DNA for bioinformatics analysis. RESULTS We obtained 22 accessible chromatin patterns. Then, 10 key TFs were involved in RA pathogenesis by regulating the activity of mitogen-activated protein kinase. Consequently, two genes (PTPRC and SPAG9) regulated by 10 key TFs were found, which may be associated with RA disease pathogenesis, and these TFs were obviously enriched in RA patients (P < .05, fold change value > 1.2). With further quantitative polymerase chain reaction validation on PTPRC and SPAG9 in monocytes, we found differential expression of these two genes, which were regulated by eight TFs [ZNF384, HNF1B, DMRTA2, MEF2A, NFE2L1, CREB3L4 (var. 2), FOSL2::JUNB (var. 2), and MEF2B], showing highly accessible binding sites in RA patients. CONCLUSIONS These findings demonstrate the value of using scATAC-seq to reveal transcriptional regulatory variation in RA-derived peripheral blood mononuclear cells, providing insights into therapy from an epigenetic perspective.
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Affiliation(s)
- Cantong Zhang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Xiaoping Hong
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Haiyan Yu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Huixuan Xu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Xiaofen Qiu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Wanxia Cai
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Berthold Hocher
- Fifth Department of Medicine (Nephrology/Endocrinology/Rheumatology), University Medical Centre Mannheim, University of Heidelberg, Germany
| | - Weier Dai
- College of Natural Science, University of Texas at Austin, Austin, TX, USA
| | - Donge Tang
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Dongzhou Liu
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
| | - Yong Dai
- The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong, China
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20
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Agustinus AS, Al-Rawi D, Dameracharla B, Raviram R, Jones BSCL, Stransky S, Scipioni L, Luebeck J, Di Bona M, Norkunaite D, Myers RM, Duran M, Choi S, Weigelt B, Yomtoubian S, McPherson A, Toufektchan E, Keuper K, Mischel PS, Mittal V, Shah SP, Maciejowski J, Storchova Z, Gratton E, Ly P, Landau D, Bakhoum MF, Koche RP, Sidoli S, Bafna V, David Y, Bakhoum SF. Epigenetic dysregulation from chromosomal transit in micronuclei. Nature 2023; 619:176-183. [PMID: 37286593 PMCID: PMC10322720 DOI: 10.1038/s41586-023-06084-7] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 04/14/2023] [Indexed: 06/09/2023]
Abstract
Chromosomal instability (CIN) and epigenetic alterations are characteristics of advanced and metastatic cancers1-4, but whether they are mechanistically linked is unknown. Here we show that missegregation of mitotic chromosomes, their sequestration in micronuclei5,6 and subsequent rupture of the micronuclear envelope7 profoundly disrupt normal histone post-translational modifications (PTMs), a phenomenon conserved across humans and mice, as well as in cancer and non-transformed cells. Some of the changes in histone PTMs occur because of the rupture of the micronuclear envelope, whereas others are inherited from mitotic abnormalities before the micronucleus is formed. Using orthogonal approaches, we demonstrate that micronuclei exhibit extensive differences in chromatin accessibility, with a strong positional bias between promoters and distal or intergenic regions, in line with observed redistributions of histone PTMs. Inducing CIN causes widespread epigenetic dysregulation, and chromosomes that transit in micronuclei experience heritable abnormalities in their accessibility long after they have been reincorporated into the primary nucleus. Thus, as well as altering genomic copy number, CIN promotes epigenetic reprogramming and heterogeneity in cancer.
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Affiliation(s)
- Albert S Agustinus
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA
| | - Duaa Al-Rawi
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Bhargavi Dameracharla
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | | | - Bailey S C L Jones
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Stransky
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Lorenzo Scipioni
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Jens Luebeck
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Melody Di Bona
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Danguole Norkunaite
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Robert M Myers
- New York Genome Center, New York, NY, USA
- Tri-institutional MD-PhD Program, New York, NY, USA
| | - Mercedes Duran
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Seongmin Choi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shira Yomtoubian
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Eléonore Toufektchan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kristina Keuper
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Paul S Mischel
- Department of Pathology, School of Medicine, Stanford University, Stanford, CA, USA
| | - Vivek Mittal
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Cell and Developmental Biology, Weill Cornell Medicine, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - John Maciejowski
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Zuzana Storchova
- Department of Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Enrico Gratton
- School of Engineering, University of California, Irvine, Irvine, CA, USA
| | - Peter Ly
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dan Landau
- New York Genome Center, New York, NY, USA
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Mathieu F Bakhoum
- Department of Ophthalmology and Visual Science, Yale University School of Medicine, New Haven, CT, USA
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale University, New Haven, CT, USA
| | - Richard P Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Vineet Bafna
- Department of Computer Science, University of California, San Diego, La Jolla, CA, USA
| | - Yael David
- Pharmacology Graduate Program, Weill Cornell Medicine, New York, NY, USA.
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Tri-institutional PhD Program in Chemical Biology, New York, NY, USA.
| | - Samuel F Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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21
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Arshadi A, Tolomeo D, Venuto S, Storlazzi CT. Advancements in Focal Amplification Detection in Tumor/Liquid Biopsies and Emerging Clinical Applications. Genes (Basel) 2023; 14:1304. [PMID: 37372484 PMCID: PMC10298061 DOI: 10.3390/genes14061304] [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: 05/17/2023] [Revised: 06/14/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Focal amplifications (FAs) are crucial in cancer research due to their significant diagnostic, prognostic, and therapeutic implications. FAs manifest in various forms, such as episomes, double minute chromosomes, and homogeneously staining regions, arising through different mechanisms and mainly contributing to cancer cell heterogeneity, the leading cause of drug resistance in therapy. Numerous wet-lab, mainly FISH, PCR-based assays, next-generation sequencing, and bioinformatics approaches have been set up to detect FAs, unravel the internal structure of amplicons, assess their chromatin compaction status, and investigate the transcriptional landscape associated with their occurrence in cancer cells. Most of them are tailored for tumor samples, even at the single-cell level. Conversely, very limited approaches have been set up to detect FAs in liquid biopsies. This evidence suggests the need to improve these non-invasive investigations for early tumor detection, monitoring disease progression, and evaluating treatment response. Despite the potential therapeutic implications of FAs, such as, for example, the use of HER2-specific compounds for patients with ERBB2 amplification, challenges remain, including developing selective and effective FA-targeting agents and understanding the molecular mechanisms underlying FA maintenance and replication. This review details a state-of-the-art of FA investigation, with a particular focus on liquid biopsies and single-cell approaches in tumor samples, emphasizing their potential to revolutionize the future diagnosis, prognosis, and treatment of cancer patients.
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Affiliation(s)
| | | | | | - Clelia Tiziana Storlazzi
- Department of Biosciences, Biotechnology and Environment, University of Bari Aldo Moro, 70125 Bari, Italy; (A.A.); (D.T.); (S.V.)
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22
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Herrera-Uribe J, Lim KS, Byrne KA, Daharsh L, Liu H, Corbett RJ, Marco G, Schroyen M, Koltes JE, Loving CL, Tuggle CK. Integrative profiling of gene expression and chromatin accessibility elucidates specific transcriptional networks in porcine neutrophils. Front Genet 2023; 14:1107462. [PMID: 37287538 PMCID: PMC10242145 DOI: 10.3389/fgene.2023.1107462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023] Open
Abstract
Neutrophils are vital components of the immune system for limiting the invasion and proliferation of pathogens in the body. Surprisingly, the functional annotation of porcine neutrophils is still limited. The transcriptomic and epigenetic assessment of porcine neutrophils from healthy pigs was performed by bulk RNA sequencing and transposase accessible chromatin sequencing (ATAC-seq). First, we sequenced and compared the transcriptome of porcine neutrophils with eight other immune cell transcriptomes to identify a neutrophil-enriched gene list within a detected neutrophil co-expression module. Second, we used ATAC-seq analysis to report for the first time the genome-wide chromatin accessible regions of porcine neutrophils. A combined analysis using both transcriptomic and chromatin accessibility data further defined the neutrophil co-expression network controlled by transcription factors likely important for neutrophil lineage commitment and function. We identified chromatin accessible regions around promoters of neutrophil-specific genes that were predicted to be bound by neutrophil-specific transcription factors. Additionally, published DNA methylation data from porcine immune cells including neutrophils were used to link low DNA methylation patterns to accessible chromatin regions and genes with highly enriched expression in porcine neutrophils. In summary, our data provides the first integrative analysis of the accessible chromatin regions and transcriptional status of porcine neutrophils, contributing to the Functional Annotation of Animal Genomes (FAANG) project, and demonstrates the utility of chromatin accessible regions to identify and enrich our understanding of transcriptional networks in a cell type such as neutrophils.
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Affiliation(s)
- Juber Herrera-Uribe
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Kyu-Sang Lim
- Department of Animal Science, Iowa State University, Ames, IA, United States
- Department of Animal Resource Science, Kongju National University, Yesan, Republic of Korea
| | - Kristen A. Byrne
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
| | - Lance Daharsh
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Haibo Liu
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Ryan J. Corbett
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Gianna Marco
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Martine Schroyen
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - James E. Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Crystal L. Loving
- USDA-Agriculture Research Service, National Animal Disease Center, Food Safety and Enteric Pathogens Research Unit, Ames, IA, United States
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23
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Hu N, Wang J, Ju B, Li Y, Fan P, Jin X, Kang X, Wu S. Recent advances of osteoimmunology research in rheumatoid arthritis: From single-cell omics approach. Chin Med J (Engl) 2023:00029330-990000000-00608. [PMID: 37166215 DOI: 10.1097/cm9.0000000000002678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Indexed: 05/12/2023] Open
Abstract
ABSTRACT Cellular immune responses as well as generalized and periarticular bone loss are the key pathogenic features of rheumatoid arthritis (RA). Under the pathological conditions of RA, dysregulated inflammation and immune processes tightly interact with skeletal system, resulting in pathological bone damage via inhibition of bone formation or induction of bone resorption. Single-cell omics technologies are revolutionary tools in the field of modern biological research.They enable the display of the state and function of cells in various environments from a single-cell resolution, thus making it conducive to identify the dysregulated molecular mechanisms of bone destruction in RA as well as the discovery of potential therapeutic targets and biomarkers. Here, we summarize the latest findings of single-cell omics technologies in osteoimmunology research in RA. These results suggest that single-cell omics have made significant contributions to transcriptomics and dynamics of specific cells involved in bone remodeling, providing a new direction for our understanding of cellular heterogeneity in the study of osteoimmunology in RA.
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Affiliation(s)
- Nan Hu
- Department of Rheumatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Jing Wang
- Department of Rheumatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Bomiao Ju
- Department of Rheumatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Yuanyuan Li
- Department of Rheumatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Ping Fan
- Department of Rheumatology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Xinxin Jin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Xiaomin Kang
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Shufang Wu
- Center for Translational Medicine, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
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24
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Lareau CA, Liu V, Muus C, Praktiknjo SD, Nitsch L, Kautz P, Sandor K, Yin Y, Gutierrez JC, Pelka K, Satpathy AT, Regev A, Sankaran VG, Ludwig LS. Mitochondrial single-cell ATAC-seq for high-throughput multi-omic detection of mitochondrial genotypes and chromatin accessibility. Nat Protoc 2023; 18:1416-1440. [PMID: 36792778 PMCID: PMC10317201 DOI: 10.1038/s41596-022-00795-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 11/11/2022] [Indexed: 02/17/2023]
Abstract
Natural sequence variation within mitochondrial DNA (mtDNA) contributes to human phenotypes and may serve as natural genetic markers in human cells for clonal and lineage tracing. We recently developed a single-cell multi-omic approach, called 'mitochondrial single-cell assay for transposase-accessible chromatin with sequencing' (mtscATAC-seq), enabling concomitant high-throughput mtDNA genotyping and accessible chromatin profiling. Specifically, our technique allows the mitochondrial genome-wide inference of mtDNA variant heteroplasmy along with information on cell state and accessible chromatin variation in individual cells. Leveraging somatic mtDNA mutations, our method further enables inference of clonal relationships among native ex vivo-derived human cells not amenable to genetic engineering-based clonal tracing approaches. Here, we provide a step-by-step protocol for the use of mtscATAC-seq, including various cell-processing and flow cytometry workflows, by using primary hematopoietic cells, subsequent single-cell genomic library preparation and sequencing that collectively take ~3-4 days to complete. We discuss experimental and computational data quality control metrics and considerations for the extension to other mammalian tissues. Overall, mtscATAC-seq provides a broadly applicable platform to map clonal relationships between cells in human tissues, investigate fundamental aspects of mitochondrial genetics and enable additional modes of multi-omic discovery.
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Affiliation(s)
- Caleb A Lareau
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA.
| | - Vincent Liu
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Christoph Muus
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Samantha D Praktiknjo
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
| | - Lena Nitsch
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Pauline Kautz
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Katalin Sandor
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Yajie Yin
- Department of Pathology, Stanford University, Stanford, CA, USA
| | | | - Karin Pelka
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University, Stanford, CA, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, USA
- Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA
| | - Aviv Regev
- Genentech, South San Francisco, CA, USA.
| | - Vijay G Sankaran
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Leif S Ludwig
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association (MDC), Berlin Institute for Medical Systems Biology (BIMSB), Berlin, Germany.
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25
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Mangiameli SM, Chen H, Earl AS, Dobkin JA, Lesman D, Buenrostro JD, Chen F. Photoselective sequencing: microscopically guided genomic measurements with subcellular resolution. Nat Methods 2023; 20:686-694. [PMID: 37106232 DOI: 10.1038/s41592-023-01845-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 03/13/2023] [Indexed: 04/29/2023]
Abstract
In biological systems, spatial organization and function are interconnected. Here we present photoselective sequencing, a new method for genomic and epigenomic profiling within morphologically distinct regions. Starting with an intact biological specimen, photoselective sequencing uses targeted illumination to selectively unblock a photocaged fragment library, restricting the sequencing-based readout to microscopically identified spatial regions. We validate photoselective sequencing by measuring the chromatin accessibility profiles of fluorescently labeled cell types within the mouse brain and comparing with published data. Furthermore, by combining photoselective sequencing with a computational strategy for decomposing bulk accessibility profiles, we find that the oligodendrocyte-lineage-cell population is relatively enriched for oligodendrocyte-progenitor cells in the cortex versus the corpus callosum. Finally, we leverage photoselective sequencing at the subcellular scale to identify features of chromatin that are correlated with positioning at the nuclear periphery. These results collectively demonstrate that photoselective sequencing is a flexible and generalizable platform for exploring the interplay of spatial structures with genomic and epigenomic properties.
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Affiliation(s)
- Sarah M Mangiameli
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Haiqi Chen
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cecil H. and Ida Green Center for Reproductive Biology Sciences, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Obstetrics and Gynecology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew S Earl
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Julie A Dobkin
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Daniel Lesman
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jason D Buenrostro
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
| | - Fei Chen
- Gene Regulation Observatory, The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
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26
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Heparanase Modulates Chromatin Accessibility. Cells 2023; 12:cells12060891. [PMID: 36980232 PMCID: PMC10047235 DOI: 10.3390/cells12060891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/04/2023] [Accepted: 03/11/2023] [Indexed: 03/18/2023] Open
Abstract
Heparanase is the sole endoglucuronidase that degrades heparan sulfate in the cell surface and extracellular matrix (ECM). Several studies have reported the localization of heparanase in the cell nucleus, but the functional role of the nuclear enzyme is still obscure. Subjecting mouse embryonic fibroblasts (MEFs) derived from heparanase knockout (Hpse-KO) mice and applying transposase-accessible chromatin with sequencing (ATAC-seq), we revealed that heparanase is involved in the regulation of chromatin accessibility. Integrating with genome-wide analysis of chromatin states revealed an overall low activity in the enhancer and promoter regions of Hpse-KO MEFs compared with wild-type (WT) MEFs. Western blot analysis of MEFs and tissues derived from Hpse-KO vs. WT mice confirmed reduced expression of H3K27ac (acetylated lysine at N-terminal position 27 of the histone H3 protein). Our results offer a mechanistic explanation for the well-documented attenuation of inflammatory responses and tumor growth in Hpse-KO mice.
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27
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Chen M, Liu X, Liu Q, Shi D, Li H. 3D genomics and its applications in precision medicine. Cell Mol Biol Lett 2023; 28:19. [PMID: 36879202 PMCID: PMC9987123 DOI: 10.1186/s11658-023-00428-x] [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: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 03/08/2023] Open
Abstract
Three-dimensional (3D) genomics is an emerging discipline that studies the three-dimensional structure of chromatin and the three-dimensional and functions of genomes. It mainly studies the three-dimensional conformation and functional regulation of intranuclear genomes, such as DNA replication, DNA recombination, genome folding, gene expression regulation, transcription factor regulation mechanism, and the maintenance of three-dimensional conformation of genomes. Self-chromosomal conformation capture (3C) technology has been developed, and 3D genomics and related fields have developed rapidly. In addition, chromatin interaction analysis techniques developed by 3C technologies, such as paired-end tag sequencing (ChIA-PET) and whole-genome chromosome conformation capture (Hi-C), enable scientists to further study the relationship between chromatin conformation and gene regulation in different species. Thus, the spatial conformation of plant, animal, and microbial genomes, transcriptional regulation mechanisms, interaction patterns of chromosomes, and the formation mechanism of spatiotemporal specificity of genomes are revealed. With the help of new experimental technologies, the identification of key genes and signal pathways related to life activities and diseases is sustaining the rapid development of life science, agriculture, and medicine. In this paper, the concept and development of 3D genomics and its application in agricultural science, life science, and medicine are introduced, which provides a theoretical basis for the study of biological life processes.
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Affiliation(s)
- Mengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Xingyu Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.,Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, 528225, China
| | - Deshun Shi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
| | - Hui Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning, 530004, Guangxi Province, China.
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28
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ATAC-See: A Tn5 Transposase-Mediated Assay for Detection of Chromatin Accessibility with Imaging. Methods Mol Biol 2023; 2611:285-291. [PMID: 36807074 DOI: 10.1007/978-1-0716-2899-7_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Assay of transposase-accessible chromatin with visualization (ATAC-see), a transposase-mediated imaging technology that enables direct imaging of the accessible genome in situ and deep sequencing to reveal the identity of the imaged elements. Here we image spatial organization of the accessible genome in HT1080 cells with this method.
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29
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Estève PO, Vishnu US, Chin HG, Pradhan S. NicE-viewSeq: An Integrative Visualization and Genomics Method to Detect Accessible Chromatin in Fixed Cells. Methods Mol Biol 2023; 2611:293-302. [PMID: 36807075 DOI: 10.1007/978-1-0716-2899-7_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
A novel genome-wide accessible chromatin visualization, quantitation, and sequencing method is described, which allows in situ fluorescence visualization and sequencing of the accessible chromatin in the mammalian cell. The cells are fixed by formaldehyde crosslinking, and processed using a modified nick translation method, where a nicking enzyme nicks one strand of DNA, and DNA polymerase incorporates biotin-conjugated dCTP, 5-methyl-dCTP, Fluorescein-12-dATP or Texas Red-5-dATP, dGTP, and dTTP. This allows accessible chromatin DNA to be labeled for visualization and on bead NGS library preparation. This technology allows cellular level chromatin accessibility quantification and genomic analysis of the epigenetic information in the chromatin, particularly accessible promoter, enhancers, nucleosome positioning, transcription factor occupancy, and other chromosomal protein binding.
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Affiliation(s)
| | | | - Hang Gyeong Chin
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA
| | - Sriharsa Pradhan
- Genome Biology Division, New England Biolabs, Inc., Ipswich, MA, USA.
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30
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Yu Q, Liu X, Fang J, Wu H, Guo C, Zhang W, Liu N, Jiang C, Sha Q, Yuan X, Wang Z, Qu K. Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution. SCIENCE ADVANCES 2023; 9:eadd2175. [PMID: 36696508 PMCID: PMC9876548 DOI: 10.1126/sciadv.add2175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Although mitotic chromosomes are highly compacted and transcriptionally inert, some active chromatin features are retained during mitosis to ensure the proper postmitotic reestablishment of maternal transcriptional programs, a phenomenon termed "mitotic bookmarking." However, the dynamics and regulation of mitotic bookmarking have not been systemically surveyed. Using single-cell transposase-accessible chromatin sequencing (scATAC-seq), we examined 6538 mitotic L02 human liver cells of variable stages and found that chromatin accessibility remained changing throughout cell division, with a constant decrease until metaphase and a gradual increase as chromosomes segregated. In particular, a subset of chromatin regions were identified to remain open throughout mitosis, and genes associated with these bookmarked regions are primarily linked to rapid reactivation upon mitotic exit. We also demonstrated that nuclear transcription factor Y subunit α (NF-YA) preferentially occupied bookmarked regions and contributed to transcriptional reactivation after mitosis. Our study uncovers the dynamic and regulatory blueprint of mitotic bookmarking.
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Affiliation(s)
- Qiaoni Yu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
| | - Xu Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Jingwen Fang
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
- HanGene Biotech, Xiaoshan Innovation Polis, Hangzhou, Zhejiang 311200, China
| | - Huihui Wu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Chuang Guo
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Wen Zhang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Nianping Liu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Chen Jiang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Qing Sha
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xiao Yuan
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
| | - Zhikai Wang
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Keck Center for Organoids Plasticity, Morehouse School of Medicine, Atlanta, GA, USA
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
| | - Kun Qu
- MOE Key Laboratory for Cellular Dynamics, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Institute of Artificial Intelligence, Hefei Comprehensive National Science Center, Hefei 230088, China
- Department of Oncology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230021, China
- Hefei National Research Center for Physical Sciences at the Microscale, University of Science and Technology of China, Hefei 230026, China
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31
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Miyanari Y. Imaging Chromatin Accessibility by Assay of Transposase-Accessible Chromatin with Visualization. Methods Mol Biol 2023; 2577:93-101. [PMID: 36173568 DOI: 10.1007/978-1-0716-2724-2_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Chromatin accessibility is one of the fundamental structures regulating genome functions including transcription and DNA repair. Recent technological advantages to analyze chromatin accessibility begun to explore the dynamics of local chromatin structures. Here I describe protocols for Assay of Transposase-Accessible Chromatin with Visualization (ATAC-see), which allows us to analyze subnuclear localization of accessible chromatin and quantify accessible chromatin at single-cell level.
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Affiliation(s)
- Yusuke Miyanari
- NanoLSI, Cancer Research Institute, Kanazawa University, Kanazawa, Japan.
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32
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Ayala-Guerrero L, Claudio-Galeana S, Furlan-Magaril M, Castro-Obregón S. Chromatin Structure from Development to Ageing. Subcell Biochem 2023; 102:7-51. [PMID: 36600128 DOI: 10.1007/978-3-031-21410-3_2] [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: 01/06/2023]
Abstract
Nuclear structure influences genome architecture, which contributes to determine patterns of gene expression. Global changes in chromatin dynamics are essential during development and differentiation, and are one of the hallmarks of ageing. This chapter describes the molecular dynamics of chromatin structure that occur during development and ageing. In the first part, we introduce general information about the nuclear lamina, the chromatin structure, and the 3D organization of the genome. Next, we detail the molecular hallmarks found during development and ageing, including the role of DNA and histone modifications, 3D genome dynamics, and changes in the nuclear lamina. Within the chapter we discuss the implications that genome structure has on the mechanisms that drive development and ageing, and the physiological consequences when these mechanisms fail.
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Affiliation(s)
- Lorelei Ayala-Guerrero
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Sherlyn Claudio-Galeana
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico
| | - Mayra Furlan-Magaril
- Departamento de Genética Molecular, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
| | - Susana Castro-Obregón
- Departamento de Neurodesarrollo y Fisiología, Instituto de Fisiología Celular, UNAM, Mexico City, Mexico.
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33
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Gassler J, Kobayashi W, Gáspár I, Ruangroengkulrith S, Mohanan A, Gómez Hernández L, Kravchenko P, Kümmecke M, Lalic A, Rifel N, Ashburn RJ, Zaczek M, Vallot A, Cuenca Rico L, Ladstätter S, Tachibana K. Zygotic genome activation by the totipotency pioneer factor Nr5a2. Science 2022; 378:1305-1315. [PMID: 36423263 DOI: 10.1126/science.abn7478] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Life begins with a switch in genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA). Despite its importance, the essential regulators of ZGA remain largely unknown in mammals. On the basis of de novo motif searches, we identified the orphan nuclear receptor Nr5a2 as a key activator of major ZGA in mouse two-cell embryos. Nr5a2 is required for progression beyond the two-cell stage. It binds to its motif within SINE B1/Alu retrotransposable elements found in cis-regulatory regions of ZGA genes. Chemical inhibition suggests that 72% of ZGA genes are regulated by Nr5a2 and potentially other orphan nuclear receptors. Nr5a2 promotes chromatin accessibility during ZGA and binds nucleosomal DNA in vitro. We conclude that Nr5a2 is an essential pioneer factor that regulates ZGA.
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Affiliation(s)
- Johanna Gassler
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Wataru Kobayashi
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Imre Gáspár
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | | | - Adarsh Mohanan
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Laura Gómez Hernández
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Pavel Kravchenko
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Maximilian Kümmecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Aleksandar Lalic
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Nikita Rifel
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Robert John Ashburn
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany
| | - Maciej Zaczek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Antoine Vallot
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Laura Cuenca Rico
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Sabrina Ladstätter
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
| | - Kikuë Tachibana
- Department of Totipotency, Max Planck Institute of Biochemistry (MPIB), Munich, Germany.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Vienna, Austria
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34
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Borgenvik A, Holmberg KO, Bolin S, Zhao M, Savov V, Rosén G, Hutter S, Garancher A, Rahmanto AS, Bergström T, Olsen TK, Mainwaring OJ, Sattanino D, Verbaan AD, Rusert JM, Sundström A, Bravo MB, Dang Y, Wenz AS, Richardson S, Fotaki G, Hill RM, Dubuc AM, Kalushkova A, Remke M, Čančer M, Jernberg-Wiklund H, Giraud G, Chen X, Taylor MD, Sangfelt O, Clifford SC, Schüller U, Wechsler-Reya RJ, Weishaupt H, Swartling FJ. Dormant SOX9-Positive Cells Facilitate MYC-Driven Recurrence of Medulloblastoma. Cancer Res 2022; 82:4586-4603. [PMID: 36219398 PMCID: PMC9755969 DOI: 10.1158/0008-5472.can-22-2108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 09/01/2022] [Accepted: 10/07/2022] [Indexed: 01/24/2023]
Abstract
Relapse is the leading cause of death in patients with medulloblastoma, the most common malignant pediatric brain tumor. A better understanding of the mechanisms underlying recurrence could lead to more effective therapies for targeting tumor relapses. Here, we observed that SOX9, a transcription factor and stem cell/glial fate marker, is limited to rare, quiescent cells in high-risk medulloblastoma with MYC amplification. In paired primary-recurrent patient samples, SOX9-positive cells accumulated in medulloblastoma relapses. SOX9 expression anti-correlated with MYC expression in murine and human medulloblastoma cells. However, SOX9-positive cells were plastic and could give rise to a MYC high state. To follow relapse at the single-cell level, an inducible dual Tet model of medulloblastoma was developed, in which MYC expression was redirected in vivo from treatment-sensitive bulk cells to dormant SOX9-positive cells using doxycycline treatment. SOX9 was essential for relapse initiation and depended on suppression of MYC activity to promote therapy resistance, epithelial-mesenchymal transition, and immune escape. p53 and DNA repair pathways were downregulated in recurrent tumors, whereas MGMT was upregulated. Recurrent tumor cells were found to be sensitive to treatment with an MGMT inhibitor and doxorubicin. These findings suggest that recurrence-specific targeting coupled with DNA repair inhibition comprises a potential therapeutic strategy in patients affected by medulloblastoma relapse. SIGNIFICANCE SOX9 facilitates therapy escape and recurrence in medulloblastoma via temporal inhibition of MYC/MYCN genes, revealing a strategy to specifically target SOX9-positive cells to prevent tumor relapse.
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Affiliation(s)
- Anna Borgenvik
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Karl O. Holmberg
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sara Bolin
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Miao Zhao
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Vasil Savov
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Gabriela Rosén
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Sonja Hutter
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Alexandra Garancher
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, San Diego, California
| | | | - Tobias Bergström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Thale Kristin Olsen
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Oliver J. Mainwaring
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Damiana Sattanino
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Annemieke D. Verbaan
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica M. Rusert
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, San Diego, California
| | - Anders Sundström
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mar Ballester Bravo
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Yonglong Dang
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Amelie S. Wenz
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Stacey Richardson
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Grammatiki Fotaki
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Rebecca M. Hill
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Adrian M. Dubuc
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Antonia Kalushkova
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Marc Remke
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matko Čančer
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Jernberg-Wiklund
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Géraldine Giraud
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Biomedical Centre, Uppsala University, Uppsala, Sweden
| | - Michael D. Taylor
- The Arthur and Sonia Labatt Brain Tumor Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olle Sangfelt
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Steven C. Clifford
- Wolfson Childhood Cancer Research Centre, Translational and Clinical Research Institute, Newcastle University Centre for Cancer, Newcastle upon Tyne, United Kingdom
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Paediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Robert J. Wechsler-Reya
- Tumor Initiation & Maintenance Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, San Diego, California
| | - Holger Weishaupt
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik J. Swartling
- Department of Immunology, Genetics, and Pathology, Science for Life Laboratory, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden.,Corresponding Author: Fredrik J. Swartling, Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala 751 85, Sweden. E-mail:
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35
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Ranjan R, Chen X. Quantitative imaging of chromatin inheritance using a dual-color histone in Drosophila germinal stem cells. STAR Protoc 2022; 3:101811. [PMID: 36386868 PMCID: PMC9640340 DOI: 10.1016/j.xpro.2022.101811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
We detail a stepwise protocol for the investigation and quantification of chromatin features during asymmetric cell division (ACD) of Drosophila germline stem cells (GSCs). We describe the use of a dual-color histone to study the inheritance of new and old histones. We detail steps for imaging and analysis of sister chromatid condensation dynamics and nucleosome density changes. In addition, this protocol could be applied to identify stem cells, which can be challenging to identify in intact tissues. For complete details on the use and execution of this protocol, please refer to Tran et al. (2012), Ranjan et al. (2019), and Ranjan et al. (2022).
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Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA; Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA.
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA; Department of Biology, The Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218-2685, USA.
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36
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Kato H, Tateishi K, Iwadate D, Yamamoto K, Fujiwara H, Nakatsuka T, Kudo Y, Hayakawa Y, Ijichi H, Otsuka M, Kishikawa T, Takahashi R, Miyabayashi K, Nakai Y, Hirata Y, Toyoda A, Morishita S, Fujishiro M. HNF1B-driven three-dimensional chromatin structure for molecular classification in pancreatic cancers. Cancer Sci 2022; 114:1672-1685. [PMID: 36511816 PMCID: PMC10067390 DOI: 10.1111/cas.15690] [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: 07/18/2022] [Revised: 10/09/2022] [Accepted: 11/22/2022] [Indexed: 12/15/2022] Open
Abstract
The molecular subtypes of pancreatic cancer (PC), either classical/progenitor-like or basal/squamous-like, are currently a major topic of research because of their direct association with clinical outcomes. Some transcription factors (TFs) have been reported to be associated with these subtypes. However, the mechanisms by which these molecular signatures of PCs are established remain unknown. Epigenetic regulatory processes, supported by dynamic changes in the chromatin structure, are essential for transcriptional profiles. Previously, we reported the importance of open chromatin profiles in the biological features and transcriptional status of PCs. Here, we aimed to analyze the relationships between three-dimensional (3D) genome structures and the molecular subtypes of human PCs using Hi-C analysis. We observed a correlation of the specific elements of 3D genome modules, including compartments, topologically associating domains, and enhancer-promoter loops, with the expression of related genes. We focused on HNF1B, a TF that is implicated in the progenitor subtype. Forced expression of HNF1B in squamous-type PC organoids induced the upregulation and downregulation of genes associated with progenitor and squamous subtypes, respectively. Long-range genomic interactions induced by HNF1B were accompanied by compartment modulation and H3K27ac redistribution. We also found that these HNF1B-induced changes in subtype-related gene expression required an intrinsically disordered region, suggesting a possible involvement of phase separation in compartment modulation. Thus, mapping of 3D structural changes induced by TFs, such as HNF1B, may become a useful resource for further understanding the molecular features of PCs.
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Affiliation(s)
- Hiroyuki Kato
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Tateishi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Gastroenterology, Department of Internal Medicine, St Marianna University School of Medicine, Kawasaki, Japan
| | - Dosuke Iwadate
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Keisuke Yamamoto
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Fujiwara
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Division of Gastroenterology, The Institute of Medical Science, Asahi Life Foundation, Tokyo, Japan
| | - Takuma Nakatsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yotaro Kudo
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoku Hayakawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Hideaki Ijichi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Motoyuki Otsuka
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Takahiro Kishikawa
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryota Takahashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Koji Miyabayashi
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yousuke Nakai
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,Department of Endoscopy and Endoscopic Surgery, The University of Tokyo Hospital, Tokyo, Japan
| | - Yoshihiro Hirata
- Division of Advanced Genome Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Shizuoka, Japan
| | - Shinichi Morishita
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Mitsuhiro Fujishiro
- Department of Gastroenterology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
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37
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Li W, Long Q, Wu H, Zhou Y, Duan L, Yuan H, Ding Y, Huang Y, Wu Y, Huang J, Liu D, Chen B, Zhang J, Qi J, Du S, Li L, Liu Y, Ruan Z, Liu Z, Liu Z, Zhao Y, Lu J, Wang J, Chan WY, Liu X. Nuclear localization of mitochondrial TCA cycle enzymes modulates pluripotency via histone acetylation. Nat Commun 2022; 13:7414. [PMID: 36460681 PMCID: PMC9718843 DOI: 10.1038/s41467-022-35199-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 11/22/2022] [Indexed: 12/03/2022] Open
Abstract
Pluripotent stem cells hold great promise in regenerative medicine and developmental biology studies. Mitochondrial metabolites, including tricarboxylic acid (TCA) cycle intermediates, have been reported to play critical roles in pluripotency. Here we show that TCA cycle enzymes including Pdha1, Pcb, Aco2, Cs, Idh3a, Ogdh, Sdha and Mdh2 are translocated to the nucleus during somatic cell reprogramming, primed-to-naive transition and totipotency acquisition. The nuclear-localized TCA cycle enzymes Pdha1, Pcb, Aco2, Cs, Idh3a promote somatic cell reprogramming and primed-to-naive transition. In addition, nuclear-localized TCA cycle enzymes, particularly nuclear-targeted Pdha1, facilitate the 2-cell program in pluripotent stem cells. Mechanistically, nuclear Pdha1 increases the acetyl-CoA and metabolite pool in the nucleus, leading to chromatin remodeling at pluripotency genes by enhancing histone H3 acetylation. Our results reveal an important role of mitochondrial TCA cycle enzymes in the epigenetic regulation of pluripotency that constitutes a mitochondria-to-nucleus retrograde signaling mode in different states of pluripotent acquisition.
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Affiliation(s)
- Wei Li
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Qi Long
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Hao Wu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Yanshuang Zhou
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Lifan Duan
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Hao Yuan
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Yingzhe Ding
- grid.9227.e0000000119573309Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Yile Huang
- grid.9227.e0000000119573309Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
| | - Yi Wu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Jinyu Huang
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Delong Liu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Baodan Chen
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Jian Zhang
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China
| | - Juntao Qi
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Shiwei Du
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Linpeng Li
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Yang Liu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zifeng Ruan
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zihuang Liu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Zichao Liu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yifan Zhao
- grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Jianghuan Lu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Junwei Wang
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China
| | - Wai-Yee Chan
- grid.10784.3a0000 0004 1937 0482CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Key Laboratory for Regenerative Medicine, Ministry of Education, School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Xingguo Liu
- grid.410737.60000 0000 8653 1072GMU-GIBH Joint School of Life Sciences, CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences; Guangzhou Medical University, Guangzhou, 510530 China ,grid.9227.e0000000119573309Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, China-New Zealand Joint Laboratory on Biomedicine and Health, CUHK-GIBH Joint Research Laboratory on Stem Cells and Regenerative Medicine, Institute for Stem Cell and Regeneration, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530 China ,grid.9227.e0000000119573309Centre for Regenerative Medicine and Health, Hong Kong Institute of Science & Innovation, Chinese Academy of Sciences, Hong Kong SAR, China
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38
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Mansisidor AR, Risca VI. Chromatin accessibility: methods, mechanisms, and biological insights. Nucleus 2022; 13:236-276. [PMID: 36404679 PMCID: PMC9683059 DOI: 10.1080/19491034.2022.2143106] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/23/2022] [Accepted: 10/30/2022] [Indexed: 11/22/2022] Open
Abstract
Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility in vivo include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.
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Affiliation(s)
- Andrés R. Mansisidor
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
| | - Viviana I. Risca
- Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY
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39
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Urban JA, Ranjan R, Chen X. Asymmetric Histone Inheritance: Establishment, Recognition, and Execution. Annu Rev Genet 2022; 56:113-143. [PMID: 35905975 PMCID: PMC10054593 DOI: 10.1146/annurev-genet-072920-125226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The discovery of biased histone inheritance in asymmetrically dividing Drosophila melanogaster male germline stem cells demonstrates one means to produce two distinct daughter cells with identical genetic material. This inspired further studies in different systems, which revealed that this phenomenon may be a widespread mechanism to introduce cellular diversity. While the extent of asymmetric histone inheritance could vary among systems, this phenomenon is proposed to occur in three steps: first, establishment of histone asymmetry between sister chromatids during DNA replication; second, recognition of sister chromatids carrying asymmetric histone information during mitosis; and third, execution of this asymmetry in the resulting daughter cells. By compiling the current knowledge from diverse eukaryotic systems, this review comprehensively details and compares known chromatin factors, mitotic machinery components, and cell cycle regulators that may contribute to each of these three steps. Also discussed are potential mechanisms that introduce and regulate variable histone inheritance modes and how these different modes may contribute to cell fate decisions in multicellular organisms.
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Affiliation(s)
- Jennifer A Urban
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA;
| | - Rajesh Ranjan
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
| | - Xin Chen
- Department of Biology, The Johns Hopkins University, Baltimore, Maryland, USA; .,Howard Hughes Medical Institute, The Johns Hopkins University, Baltimore, Maryland, USA; ,
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40
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Mota A, Berezicki S, Wernersson E, Harbers L, Li-Wang X, Gradin K, Peuckert C, Crosetto N, Bienko M. FRET-FISH probes chromatin compaction at individual genomic loci in single cells. Nat Commun 2022; 13:6680. [PMID: 36335096 PMCID: PMC9637210 DOI: 10.1038/s41467-022-34183-y] [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: 12/01/2021] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Chromatin compaction is a key biophysical property that influences multiple DNA transactions. Lack of chromatin accessibility is frequently used as proxy for chromatin compaction. However, we currently lack tools for directly probing chromatin compaction at individual genomic loci. To fill this gap, here we present FRET-FISH, a method combining fluorescence resonance energy transfer (FRET) with DNA fluorescence in situ hybridization (FISH) to probe chromatin compaction at select loci in single cells. We first validate FRET-FISH by comparing it with ATAC-seq, demonstrating that local compaction and accessibility are strongly correlated. FRET-FISH also detects expected differences in compaction upon treatment with drugs perturbing global chromatin condensation. We then leverage FRET-FISH to study local chromatin compaction on the active and inactive X chromosome, along the nuclear radius, in different cell cycle phases, and during increasing passage number. FRET-FISH is a robust tool for probing local chromatin compaction in single cells.
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Affiliation(s)
- Ana Mota
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Szymon Berezicki
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Erik Wernersson
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Luuk Harbers
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Xiaoze Li-Wang
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Katarina Gradin
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden
| | - Christiane Peuckert
- grid.10548.380000 0004 1936 9377Stockholm University, The Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm, Sweden
| | - Nicola Crosetto
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden ,grid.510779.d0000 0004 9414 6915Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
| | - Magda Bienko
- grid.4714.60000 0004 1937 0626Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, SE-17165 Sweden ,grid.452834.c0000 0004 5911 2402Science for Life Laboratory, Tomtebodavägen 23A, Solna, SE-17165 Sweden ,grid.510779.d0000 0004 9414 6915Human Technopole, Viale Rita Levi-Montalcini 1, 20157 Milan, Italy
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41
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Kervella M, Jahier M, Meli AC, Muchir A. Genome organization in cardiomyocytes expressing mutated A-type lamins. Front Cell Dev Biol 2022; 10:1030950. [PMID: 36274847 PMCID: PMC9585167 DOI: 10.3389/fcell.2022.1030950] [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: 08/29/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Cardiomyopathy is a myocardial disorder, in which the heart muscle is structurally and functionally abnormal, often leading to heart failure. Dilated cardiomyopathy is characterized by a compromised left ventricular function and contributes significantly to the heart failure epidemic, which represents a staggering clinical and public health problem worldwide. Gene mutations have been identified in 35% of patients with dilated cardiomyopathy. Pathogenic variants in LMNA, encoding nuclear A-type lamins, are one of the major causative causes of dilated cardiomyopathy (i.e. CardioLaminopathy). A-type lamins are type V intermediate filament proteins, which are the main components of the nuclear lamina. The nuclear lamina is connected to the cytoskeleton on one side, and to the chromatin on the other side. Among the models proposed to explain how CardioLaminopathy arises, the “chromatin model” posits an effect of mutated A-type lamins on the 3D genome organization and thus on the transcription activity of tissue-specific genes. Chromatin contacts with the nuclear lamina via specific genomic regions called lamina-associated domains lamina-associated domains. These LADs play a role in the chromatin organization and gene expression regulation. This review focuses on the identification of LADs and chromatin remodeling in cardiac muscle cells expressing mutated A-type lamins and discusses the methods and relevance of these findings in disease.
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Affiliation(s)
- Marie Kervella
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Maureen Jahier
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
| | - Albano C. Meli
- PhyMedExp, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Antoine Muchir
- Sorbonne Université, INSERM U974, Institute of Myology, Center of Research in Myology, Paris, France
- *Correspondence: Antoine Muchir,
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42
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A serotonergic axon-cilium synapse drives nuclear signaling to alter chromatin accessibility. Cell 2022; 185:3390-3407.e18. [PMID: 36055200 PMCID: PMC9789380 DOI: 10.1016/j.cell.2022.07.026] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 05/16/2022] [Accepted: 07/25/2022] [Indexed: 12/27/2022]
Abstract
Chemical synapses between axons and dendrites mediate neuronal intercellular communication. Here, we describe a synapse between axons and primary cilia: the axo-ciliary synapse. Using enhanced focused ion beam-scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between brainstem serotonergic axons and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, the 5-hydroxytryptamine receptor 6 (5-HTR6). Using a cilia-targeted serotonin sensor, we show that opto- and chemogenetic stimulation of serotonergic axons releases serotonin onto cilia. Ciliary 5-HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway, which modulates nuclear actin and increases histone acetylation and chromatin accessibility. Ablation of this pathway reduces chromatin accessibility in CA1 pyramidal neurons. As a signaling apparatus with proximity to the nucleus, axo-ciliary synapses short circuit neurotransmission to alter the postsynaptic neuron's epigenetic state.
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43
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Shi P, Nie Y, Yang J, Zhang W, Tang Z, Xu J. Fundamental and practical approaches for single-cell ATAC-seq analysis. ABIOTECH 2022; 3:212-223. [PMID: 36313930 PMCID: PMC9590475 DOI: 10.1007/s42994-022-00082-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 09/07/2022] [Indexed: 11/28/2022]
Abstract
Assays for transposase-accessible chromatin through high-throughput sequencing (ATAC-seq) are effective tools in the study of genome-wide chromatin accessibility landscapes. With the rapid development of single-cell technology, open chromatin regions that play essential roles in epigenetic regulation have been measured at the single-cell level using single-cell ATAC-seq approaches. The application of scATAC-seq has become as popular as that of scRNA-seq. However, owing to the nature of scATAC-seq data, which are sparse and noisy, processing the data requires different methodologies and empirical experience. This review presents a practical guide for processing scATAC-seq data, from quality evaluation to downstream analysis, for various applications. In addition to the epigenomic profiling from scATAC-seq, we also discuss recent studies in which the function of non-coding variants has been investigated based on cell type-specific cis-regulatory elements and how to use the by-product genetic information obtained from scATAC-seq to infer single-cell copy number variants and trace cell lineage. We anticipate that this review will assist researchers in designing and implementing scATAC-seq assays to facilitate research in diverse fields.
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Affiliation(s)
- Peiyu Shi
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Yage Nie
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jiawen Yang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Weixing Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Zhongjie Tang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
| | - Jin Xu
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275 China
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44
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Dong A, Liu J, Lin K, Zeng W, So WK, Hu S, Cheung TH. Global chromatin accessibility profiling analysis reveals a chronic activation state in aged muscle stem cells. iScience 2022; 25:104954. [PMID: 36093058 PMCID: PMC9459695 DOI: 10.1016/j.isci.2022.104954] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 06/30/2022] [Accepted: 08/12/2022] [Indexed: 11/26/2022] Open
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45
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Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 2022; 609:375-383. [PMID: 35978191 PMCID: PMC9452302 DOI: 10.1038/s41586-022-05094-1] [Citation(s) in RCA: 105] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 07/08/2022] [Indexed: 12/12/2022]
Abstract
Cellular function in tissue is dependent on the local environment, requiring new methods for spatial mapping of biomolecules and cells in the tissue context1. The emergence of spatial transcriptomics has enabled genome-scale gene expression mapping2-5, but the ability to capture spatial epigenetic information of tissue at the cellular level and genome scale is lacking. Here we describe a method for spatially resolved chromatin accessibility profiling of tissue sections using next-generation sequencing (spatial-ATAC-seq) by combining in situ Tn5 transposition chemistry6 and microfluidic deterministic barcoding5. Profiling mouse embryos using spatial-ATAC-seq delineated tissue-region-specific epigenetic landscapes and identified gene regulators involved in the development of the central nervous system. Mapping the accessible genome in the mouse and human brain revealed the intricate arealization of brain regions. Applying spatial-ATAC-seq to tonsil tissue resolved the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones. This technology progresses spatial biology by enabling spatially resolved chromatin accessibility profiling to improve our understanding of cell identity, cell state and cell fate decision in relation to epigenetic underpinnings in development and disease.
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Affiliation(s)
- Yanxiang Deng
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Marek Bartosovic
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Sai Ma
- Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Di Zhang
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
| | - Petra Kukanja
- Laboratory of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Yang Xiao
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | - Graham Su
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Yang Liu
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Xiaoyu Qin
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Gorazd B Rosoklija
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
| | - Andrew J Dwork
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Macedonian Academy of Sciences & Arts, Skopje, Republic of Macedonia
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - J John Mann
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
- Department of Radiology, Columbia University, New York, NY, USA
| | - Mina L Xu
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - Stephanie Halene
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Joseph E Craft
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT, USA
| | - Kam W Leong
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Maura Boldrini
- Department of Psychiatry, Columbia University, New York, NY, USA
- Division of Molecular Imaging and Neuropathology, New York State Psychiatric Institute, New York, NY, USA
| | - 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.
| | - Rong Fan
- Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
- Yale Stem Cell Center and Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA.
- Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
- Human and Translational Immunology Program, Yale School of Medicine, New Haven, CT, USA.
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Abstract
In cancer, complex genome rearrangements and other structural alterations, including the amplification of oncogenes on circular extrachromosomal DNA (ecDNA) elements, drive the formation and progression of tumors. ecDNA is a particularly challenging structural alteration. By untethering oncogenes from chromosomal constraints, it elevates oncogene copy number, drives intratumoral genetic heterogeneity, promotes rapid tumor evolution, and results in treatment resistance. The profound changes in DNA shape and nuclear architecture generated by ecDNA alter the transcriptional landscape of tumors by catalyzing new types of regulatory interactions that do not occur on chromosomes. The current suite of tools for interrogating cancer genomes is well suited for deciphering sequence but has limited ability to resolve the complex changes in DNA structure and dynamics that ecDNA generates. Here, we review the challenges of resolving ecDNA form and function and discuss the emerging tool kit for deciphering ecDNA architecture and spatial organization, including what has been learned to date about how this dramatic change in shape alters tumor development, progression, and drug resistance.
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Affiliation(s)
- Vineet Bafna
- Department of Computer Science and Engineering and Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, California, USA;
| | - Paul S Mischel
- Department of Pathology and ChEM-H, Stanford University School of Medicine, Stanford, California, USA;
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47
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Chen F, Xue J, Bai M, Fan C, Zhao Y. Lighting Up Nucleic Acid Modifications in Single Cells with DNA-Encoded Amplification. Acc Chem Res 2022; 55:2248-2259. [PMID: 35904502 DOI: 10.1021/acs.accounts.2c00269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Nucleic acids are naturally decorated with various chemical modifications at nucleobases. Most nucleic acid modifications (NAMs) do not alter Watson-Crick base pairing but can regulate gene expression known as "epigenetics". Their abundances present a very wide range, approximately 10-2 to 10-6 of total bases. Different NAMs may coexist in spatial proximity (e.g., <20 nm) in the crowded intracellular environment. Considering the highly dynamic chromatin accessibility (physical access to DNA), the NAMs in inaccessible DNA probably plays different roles. These multilayered features of NAMs vary from cell to cell. Our understanding of the function and mechanism of NAMs in biological processes and disease states has largely been driven by the expanding array of sequencing-based methodologies. However, an underexplored aspect is the measurement of the subcellular distribution, spatial proximity, and inaccessibility of NAMs in single cells. In recent years, we have developed new approaches that light up single-cell NAMs with single-site sensitivity. These methods are mainly based on the integration of chemical or chemoenzymatic tools, DNA amplification and nanotechnology, and/or microfluidics. An overview of these methods together with conventional methods such as immunofluorescence (IF) and fluorescence in situ hybridization (FISH) is provided in this Account.Our laboratory has proposed DNA-encoded amplification (DEA) as the main strategy for developing a set of single-cell NAM imaging methods. In brief, DEA transforms the different features of NAMs into unique DNA primers for rolling circle amplification (RCA) followed by FISH imaging. The first method is base-encoded amplifying FISH (BEA-FISH), in which we convert individual NAMs into RCA primers via chemoselective labeling and click bioconjugation. It enables the in situ visualization of low-abundance NAMs (e.g., 5hmU), which is impracticable by conventional methods. We subsequently developed pairwise proximity-differentiated amplifying FISH (PPDA-FISH), which integrates BEA-FISH with DNA nanotechnology. PPDA-FISH utilizes proximity ligation and toehold strand displacement to label the adjacent site of two different NAMs (one-to-one proximity) and their respective residual sites with three unique RCA probes. It achieves simultaneous counting of the above-mentioned three types of modified sites in the same cells. The third method is cellular macromolecule-tethered DNA walking indexing (Cell-TALKING) to probe more than two NAMs within the same nanoenvironments. Cell-TALKING uses dynamic DNA proximity cleavage to continuously activate different preblocked RCA primers (for each NAM) near one walking probe (for one target molecule). We have explored three NAMs around one histone (one-to-many proximity) in different cancer cell lines and clinical specimens. Then, we describe a single-cell hydrogel encoding amplification (scHEA) method by integrating droplet microfluidics with BEA-FISH. This method generates hydrogel beads that encapsulate single cells and their genomic DNA after cell lysis. It realizes the analysis of global (accessible and inaccessible) DNA from the same cells. We find that the global levels of both 5hmC and 5hmU in single cells can distinguish different breast cancer cells. Finally, the current limitations of these strategies and the future development directions are also discussed. We hope that this Account can spark new ideas and invite new efforts from different disciplines for single-cell NAM analysis.
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Affiliation(s)
- Feng Chen
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Jing Xue
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Min Bai
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi 710049, P. R. China
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48
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Tu X, Marand AP, Schmitz RJ, Zhong S. A combinatorial indexing strategy for low-cost epigenomic profiling of plant single cells. PLANT COMMUNICATIONS 2022; 3:100308. [PMID: 35605196 PMCID: PMC9284282 DOI: 10.1016/j.xplc.2022.100308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 02/22/2022] [Accepted: 02/28/2022] [Indexed: 06/15/2023]
Abstract
Understanding how cis-regulatory elements facilitate gene expression is a key question in biology. Recent advances in single-cell genomics have led to the discovery of cell-specific chromatin landscapes that underlie transcription programs in animal models. However, the high equipment and reagent costs of commercial systems limit their applications for many laboratories. In this study, we developed a combinatorial index and dual PCR barcode strategy to profile the Arabidopsis thaliana root single-cell epigenome without any specialized equipment. We generated chromatin accessibility profiles for 13 576 root nuclei with an average of 12 784 unique Tn5 integrations per cell. Integration of the single-cell assay for transposase-accessible chromatin sequencing and RNA sequencing data sets enabled the identification of 24 cell clusters with unique transcription, chromatin, and cis-regulatory signatures. Comparison with single-cell data generated using the commercial microfluidic platform from 10X Genomics revealed that this low-cost combinatorial index method is capable of unbiased identification of cell-type-specific chromatin accessibility. We anticipate that, by removing cost, instrumentation, and other technical obstacles, this method will be a valuable tool for routine investigation of single-cell epigenomes and provide new insights into plant growth and development and plant interactions with the environment.
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Affiliation(s)
- Xiaoyu Tu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; Shanghai Collaborative Innovation Center of Agri-Seeds, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | | | - Robert J Schmitz
- Department of Genetics, University of Georgia, Athens, GA 30602, USA.
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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49
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Guo A, Huang H, Zhu Z, Chen MJ, Shi H, Yuan S, Sharma P, Connelly JP, Liedmann S, Dhungana Y, Li Z, Haydar D, Yang M, Beere H, Yustein JT, DeRenzo C, Pruett-Miller SM, Crawford JC, Krenciute G, Roberts CWM, Chi H, Green DR. cBAF complex components and MYC cooperate early in CD8 + T cell fate. Nature 2022; 607:135-141. [PMID: 35732731 PMCID: PMC9623036 DOI: 10.1038/s41586-022-04849-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 05/10/2022] [Indexed: 01/03/2023]
Abstract
The identification of mechanisms to promote memory T (Tmem) cells has important implications for vaccination and anti-cancer immunotherapy1-4. Using a CRISPR-based screen for negative regulators of Tmem cell generation in vivo5, here we identify multiple components of the mammalian canonical BRG1/BRM-associated factor (cBAF)6,7. Several components of the cBAF complex are essential for the differentiation of activated CD8+ T cells into T effector (Teff) cells, and their loss promotes Tmem cell formation in vivo. During the first division of activated CD8+ T cells, cBAF and MYC8 frequently co-assort asymmetrically to the two daughter cells. Daughter cells with high MYC and high cBAF display a cell fate trajectory towards Teff cells, whereas those with low MYC and low cBAF preferentially differentiate towards Tmem cells. The cBAF complex and MYC physically interact to establish the chromatin landscape in activated CD8+ T cells. Treatment of naive CD8+ T cells with a putative cBAF inhibitor during the first 48 h of activation, before the generation of chimeric antigen receptor T (CAR-T) cells, markedly improves efficacy in a mouse solid tumour model. Our results establish cBAF as a negative determinant of Tmem cell fate and suggest that manipulation of cBAF early in T cell differentiation can improve cancer immunotherapy.
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Affiliation(s)
- Ao Guo
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongling Huang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhexin Zhu
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mark J Chen
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hao Shi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Sujing Yuan
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Piyush Sharma
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jon P Connelly
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Swantje Liedmann
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Yogesh Dhungana
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Zhenrui Li
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Dalia Haydar
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Mao Yang
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Helen Beere
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jason T Yustein
- Baylor Texas Children's Cancer and Hematology Centers, Texas Children's Hospital, Baylor College of Medicine, Houston, TX, USA
| | - Christopher DeRenzo
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Giedre Krenciute
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Comprehensive Cancer Center and Department of Oncology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Hongbo Chi
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
| | - Douglas R Green
- Department of Immunology, St Jude Children's Research Hospital, Memphis, TN, USA.
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50
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Christophorou MA. The virtues and vices of protein citrullination. ROYAL SOCIETY OPEN SCIENCE 2022; 9:220125. [PMID: 35706669 PMCID: PMC9174705 DOI: 10.1098/rsos.220125] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/16/2022] [Indexed: 05/03/2023]
Abstract
The post-translational modification of proteins expands the regulatory scope of the proteome far beyond what is achievable through genome regulation. The field of protein citrullination has seen significant progress in the last two decades. The small family of peptidylarginine deiminase (PADI or PAD) enzymes, which catalyse citrullination, have been implicated in virtually all facets of molecular and cell biology, from gene transcription and epigenetics to cell signalling and metabolism. We have learned about their association with a remarkable array of disease states and we are beginning to understand how they mediate normal physiological functions. However, while the biochemistry of PADI activation has been worked out in exquisite detail in vitro, we still lack a clear mechanistic understanding of the processes that regulate PADIs within cells, under physiological and pathophysiological conditions. This review summarizes and discusses the current knowledge, highlights some of the unanswered questions of immediate importance and gives a perspective on the outlook of the citrullination field.
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