1
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Wernersson E, Gelali E, Girelli G, Wang S, Castillo D, Mattsson Langseth C, Verron Q, Nguyen HQ, Chattoraj S, Martinez Casals A, Blom H, Lundberg E, Nilsson M, Marti-Renom MA, Wu CT, Crosetto N, Bienko M. Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images. Nat Methods 2024; 21:1245-1256. [PMID: 38844629 PMCID: PMC11239506 DOI: 10.1038/s41592-024-02294-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Accepted: 04/25/2024] [Indexed: 07/13/2024]
Abstract
Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of extractable biological information. To overcome these limitations, here we develop Deconwolf, an open-source, user-friendly software for high-performance deconvolution of widefield fluorescence microscopy images, which efficiently runs on laptop computers. Deconwolf enables accurate quantification of crowded diffraction limited fluorescence dots in DNA and RNA fluorescence in situ hybridization images and allows robust detection of individual transcripts in tissue sections imaged with ×20 air objectives. Deconvolution of in situ spatial transcriptomics images with Deconwolf increased the number of transcripts identified more than threefold, while the application of Deconwolf to images obtained by fluorescence in situ sequencing of barcoded Oligopaint probes drastically improved chromosome tracing. Deconwolf greatly facilitates the use of deconvolution in many bioimaging applications.
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Affiliation(s)
- Erik Wernersson
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Eleni Gelali
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Gabriele Girelli
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Su Wang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - David Castillo
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Christoffer Mattsson Langseth
- Science for Life Laboratory, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Quentin Verron
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Huy Q Nguyen
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Acuity Spatial Genomics, Newton, MA, USA
| | - Shyamtanu Chattoraj
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Acuity Spatial Genomics, Newton, MA, USA
| | - Anna Martinez Casals
- Science for Life Laboratory, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Hans Blom
- Science for Life Laboratory, Stockholm, Sweden
- Department of Applied Physics, Royal Institute of Technology, Solna, Sweden
| | - Emma Lundberg
- Science for Life Laboratory, Stockholm, Sweden
- School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden
- Department of Bioengineering, Stanford University, Stanford, CA, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Mats Nilsson
- Science for Life Laboratory, Stockholm, Sweden
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Marc A Marti-Renom
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
- Pompeu Fabra University, Barcelona, Spain
- ICREA, Barcelona, Spain
| | - Chao-Ting Wu
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute, Harvard Medical School, Boston, MA, USA
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
- Human Technopole, Milan, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.
- Science for Life Laboratory, Stockholm, Sweden.
- Human Technopole, Milan, Italy.
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2
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Zhang N, Harbers L, Simonetti M, Diekmann C, Verron Q, Berrino E, Bellomo SE, Longo GMC, Ratz M, Schultz N, Tarish F, Su P, Han B, Wang W, Onorato S, Grassini D, Ballarino R, Giordano S, Yang Q, Sapino A, Frisén J, Alkass K, Druid H, Roukos V, Helleday T, Marchiò C, Bienko M, Crosetto N. High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue. Nat Commun 2024; 15:3475. [PMID: 38658552 PMCID: PMC11043350 DOI: 10.1038/s41467-024-47664-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024] Open
Abstract
Somatic copy number alterations (SCNAs) are pervasive in advanced human cancers, but their prevalence and spatial distribution in early-stage, localized tumors and their surrounding normal tissues are poorly characterized. Here, we perform multi-region, single-cell DNA sequencing to characterize the SCNA landscape across tumor-rich and normal tissue in two male patients with localized prostate cancer. We identify two distinct karyotypes: 'pseudo-diploid' cells harboring few SCNAs and highly aneuploid cells. Pseudo-diploid cells form numerous small-sized subclones ranging from highly spatially localized to broadly spread subclones. In contrast, aneuploid cells do not form subclones and are detected throughout the prostate, including normal tissue regions. Highly localized pseudo-diploid subclones are confined within tumor-rich regions and carry deletions in multiple tumor-suppressor genes. Our study reveals that SCNAs are widespread in normal and tumor regions across the prostate in localized prostate cancer patients and suggests that a subset of pseudo-diploid cells drive tumorigenesis in the aging prostate.
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Affiliation(s)
- Ning Zhang
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Michele Simonetti
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Quentin Verron
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Sara E Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Oncology, University of Turin, Turin, Italy
| | | | - Michael Ratz
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
| | - Niklas Schultz
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | | | - Peng Su
- Department of Pathology, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Bo Han
- Department of Pathology, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Wanzhong Wang
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Sofia Onorato
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Dora Grassini
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Roberto Ballarino
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
| | - Silvia Giordano
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Oncology, University of Turin, Turin, Italy
| | - Qifeng Yang
- Department of Breast Surgery, General Surgery, Qilu Hospital of Shandong University, Ji'nan, 250012, China
| | - Anna Sapino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Jonas Frisén
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
| | - Kanar Alkass
- Department of Cell and Molecular Biology, Karolinska Institute, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Henrik Druid
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Vassilis Roukos
- Institute of Molecular Biology (IMB), Mainz, 55128, Germany
- Department of General Biology, Medical School, University of Patras, Patras, Greece
| | - Thomas Helleday
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Stockholm, 17177, Sweden
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Stockholm, 17177, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 20157, Milan, Italy.
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3
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Chen JP, Diekmann C, Wu H, Chen C, Della Chiara G, Berrino E, Georgiadis KL, Bouwman BAM, Virdi M, Harbers L, Bellomo SE, Marchiò C, Bienko M, Crosetto N. scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells. Nat Commun 2024; 15:1768. [PMID: 38409079 PMCID: PMC10897160 DOI: 10.1038/s41467-024-45972-y] [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: 03/07/2023] [Accepted: 02/08/2024] [Indexed: 02/28/2024] Open
Abstract
Extrachromosomal circular DNAs (eccDNAs) have emerged as important intra-cellular mobile genetic elements that affect gene copy number and exert in trans regulatory roles within the cell nucleus. Here, we describe scCircle-seq, a method for profiling eccDNAs and unraveling their diversity and complexity in single cells. We implement and validate scCircle-seq in normal and cancer cell lines, demonstrating that most eccDNAs vary largely between cells and are stochastically inherited during cell division, although their genomic landscape is cell type-specific and can be used to accurately cluster cells of the same origin. eccDNAs are preferentially produced from chromatin regions enriched in H3K9me3 and H3K27me3 histone marks and are induced during replication stress conditions. Concomitant sequencing of eccDNAs and RNA from the same cell uncovers the absence of correlation between eccDNA copy number and gene expression levels, except for a few oncogenes, including MYC, contained within a large eccDNA in colorectal cancer cells. Lastly, we apply scCircle-seq to one prostate cancer and two breast cancer specimens, revealing cancer-specific eccDNA landscapes and a higher propensity of eccDNAs to form in amplified genomic regions. scCircle-seq is a scalable tool that can be used to dissect the complexity of eccDNAs across different cell and tissue types, and further expands the potential of eccDNAs for cancer diagnostics.
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Affiliation(s)
- Jinxin Phaedo Chen
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
| | - Constantin Diekmann
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Honggui Wu
- Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, PR China
- School of Life Sciences, Peking University, Beijing, PR China
| | - Chong Chen
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, PR China
| | | | - Enrico Berrino
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Konstantinos L Georgiadis
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
- Department of Oncology and Pathology, Karolinska Institutet, Stockholm, 17177, Sweden
| | - Britta A M Bouwman
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Mohit Virdi
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy
| | - Luuk Harbers
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden
| | - Sara Erika Bellomo
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
| | - Caterina Marchiò
- Candiolo Cancer Institute, FPO - IRCCS, Candiolo, SP142, km 3,95, 10060, Turin, Italy
- Department of Medical Sciences, University of Turin, Turin, Italy
| | - Magda Bienko
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
| | - Nicola Crosetto
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, 17177, Sweden.
- Science for Life Laboratory, Tomtebodavägen 23A, Solna, 17165, Sweden.
- Human Technopole, Viale Rita Levi-Montalcini 1, 22157, Milan, Italy.
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4
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Bialy N, Alber F, Andrews B, Angelo M, Beliveau B, Bintu L, Boettiger A, Boehm U, Brown CM, Maina MB, Chambers JJ, Cimini BA, Eliceiri K, Errington R, Faklaris O, Gaudreault N, Germain RN, Goscinski W, Grunwald D, Halter M, Hanein D, Hickey JW, Lacoste J, Laude A, Lundberg E, Ma J, Malacrida L, Moore J, Nelson G, Neumann EK, Nitschke R, Onami S, Pimentel JA, Plant AL, Radtke AJ, Sabata B, Schapiro D, Schöneberg J, Spraggins JM, Sudar D, Adrien Maria Vierdag WM, Volkmann N, Wählby C, Wang SS, Yaniv Z, Strambio-De-Castillia C. Harmonizing the Generation and Pre-publication Stewardship of FAIR Image data. ARXIV 2024:arXiv:2401.13022v4. [PMID: 38351940 PMCID: PMC10862930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Together with the molecular knowledge of genes and proteins, biological images promise to significantly enhance the scientific understanding of complex cellular systems and to advance predictive and personalized therapeutic products for human health. For this potential to be realized, quality-assured image data must be shared among labs at a global scale to be compared, pooled, and reanalyzed, thus unleashing untold potential beyond the original purpose for which the data was generated. There are two broad sets of requirements to enable image data sharing in the life sciences. One set of requirements is articulated in the companion White Paper entitled "Enabling Global Image Data Sharing in the Life Sciences," which is published in parallel and addresses the need to build the cyberinfrastructure for sharing the digital array data (arXiv:2401.13023 [q-bio.OT], https://doi.org/10.48550/arXiv.2401.13023). In this White Paper, we detail a broad set of requirements, which involves collecting, managing, presenting, and propagating contextual information essential to assess the quality, understand the content, interpret the scientific implications, and reuse image data in the context of the experimental details. We start by providing an overview of the main lessons learned to date through international community activities, which have recently made considerable progress toward generating community standard practices for imaging Quality Control (QC) and metadata. We then provide a clear set of recommendations for amplifying this work. The driving goal is to address remaining challenges, and democratize access to common practices and tools for a spectrum of biomedical researchers, regardless of their expertise, access to resources, and geographical location.
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Affiliation(s)
- Nikki Bialy
- Morgridge Institute for Research, Madison, USA
| | | | | | | | | | | | | | | | | | | | | | - Beth A Cimini
- Broad Institute of MIT and Harvard, Imaging Platform, Cambridge, USA
| | - Kevin Eliceiri
- Morgridge Institute for Research, Madison, USA
- University of Wisconsin-Madison, Madison, USA
| | | | | | | | - Ronald N Germain
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | - Michael Halter
- National Institute of Standards and Technology, Gaithersburg, USA
| | | | | | | | - Alex Laude
- Newcastle University, Newcastle upon Tyne, UK
| | - Emma Lundberg
- Stanford University, Palo Alto, USA
- SciLifeLab, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, USA
| | - Leonel Malacrida
- Institut Pasteur de Montevideo, & Universidad de la República, Montevideo, Uruguay
| | - Josh Moore
- German BioImaging-Gesellschaft für Mikroskopie und Bildanalyse e.V., Constance, Germany
| | - Glyn Nelson
- Newcastle University, Newcastle upon Tyne, UK
| | | | | | - Shuichi Onami
- RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | | | - Anne L Plant
- National Institute of Standards and Technology, Gaithersburg, USA
| | - Andrea J Radtke
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
| | | | | | | | | | - Damir Sudar
- Quantitative Imaging Systems LLC, Portland, USA
| | | | | | | | | | - Ziv Yaniv
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, USA
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5
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Aguilar R, Camplisson CK, Lin Q, Miga KH, Noble WS, Beliveau BJ. Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. Nat Commun 2024; 15:1027. [PMID: 38310092 PMCID: PMC10838309 DOI: 10.1038/s41467-024-45385-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 01/22/2024] [Indexed: 02/05/2024] Open
Abstract
Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate > 100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.
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Affiliation(s)
- Robin Aguilar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Qiaoyi Lin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Karen H Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, CA, USA
| | - William S Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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6
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Perez MW, Camplisson CK, Beliveau BJ. Designing Oligonucleotide-Based FISH Probe Sets with PaintSHOP. Methods Mol Biol 2024; 2784:177-189. [PMID: 38502486 DOI: 10.1007/978-1-0716-3766-1_12] [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: 03/21/2024]
Abstract
Fluorescent in situ hybridization (FISH) enables the visualization of the position and abundance of nucleic acid molecules in fixed cell and tissue samples. Many FISH-based methods employ sets of synthetic, computationally designed DNA oligonucleotide (oligo) FISH probes, including massively multiplexed imaging spatial transcriptomics and spatial genomics technologies. Oligo probes can either be designed de novo or accessed from an existing database of pre-discovered probe sequences. This chapter describes the use of PaintSHOP, a user-friendly, web-based platform for the design of sets of oligo-based FISH probes. PaintSHOP hosts large collections of pre-discovered probes from many model organisms and also provides collections of functional sequences such as primers and readout domains and interactive tools to add these functional sequences to selected probes. Detailed examples are provided for three common experimental scenarios.
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Affiliation(s)
- Monika W Perez
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Conor K Camplisson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Brian J Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, USA.
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7
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Shen J, Liu Y, Teng X, Jin L, Feng L, Sun X, Zhao F, Huang B, Zhong J, Chen Y, Wang L. Spatial Transcriptomics of Aging Rat Ovaries Reveals Unexplored Cell Subpopulations with Reduced Antioxidative Defense. Gerontology 2023; 69:1315-1329. [PMID: 37717573 DOI: 10.1159/000533922] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Accepted: 08/29/2023] [Indexed: 09/19/2023] Open
Abstract
INTRODUCTION Ovarian aging is characterized by a gradual decline in quantity and quality of oocytes and lower chance of fertility. Better understanding the genetic modulation during ovarian aging can further address available treatment options for aging-related ovarian diseases and fertility preservation. METHODS A novel technique spatial transcriptomics (ST) was used to investigate the spatial transcriptome features of rat ovaries. Transcriptomes from ST spots in the young and aged ovaries were clustered using differentially expressed genes. These data were analyzed to determine the spatial organization of age-induced heterogeneity and potential mechanisms underlying ovarian aging. RESULTS In this study, ST technology was applied to profile the comprehensive spatial imaging in young and aged rat ovary. Fifteen ovarian cell clusters with distinct gene-expression signatures were identified. The gene expression dynamics of granulosa cell clusters revealed three sub-types with sequential developmental stages. Aged ovary showed a significant decrease in the number of granulosa cells from the antral follicle. Besides, a remarkable rearrangement of interstitial gland cells was detected in aging ovary. Further analysis of aging-associated transcriptional changes revealed that the disturbance of oxidative pathway was a crucial factor in ovarian aging. CONCLUSIONS This study firstly described an aging-related spatial transcriptome changes in ovary and identified the potential targets for prevention of ovarian aging. These data may provide the basis for further investigations of the diagnosis and treatment of aging-related ovarian disorders.
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Affiliation(s)
- Jiayu Shen
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China,
| | - Yuanyuan Liu
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xinyuan Teng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Ligui Jin
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Lin Feng
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiwen Sun
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Fengdong Zhao
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bao Huang
- Department of Orthopaedic Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinjie Zhong
- Department of Basic Medicine Sciences, and Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yingying Chen
- Department of Basic Medicine Sciences, and Department of Obstetrics of the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liquan Wang
- Department of Obstetrics and Gynecology, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
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8
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Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S. Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. Mol Cell 2023; 83:2624-2640. [PMID: 37419111 PMCID: PMC10528254 DOI: 10.1016/j.molcel.2023.06.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 07/09/2023]
Abstract
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome and the nucleus in space and time. We summarize progress by the consortium and highlight the development of technologies for (1) mapping genome folding and identifying roles of nuclear components and bodies, proteins, and RNA, (2) characterizing nuclear organization with time or single-cell resolution, and (3) imaging of nuclear organization. With these tools, the consortium has provided over 2,000 public datasets. Integrative computational models based on these data are starting to reveal connections between genome structure and function. We then present a forward-looking perspective and outline current aims to (1) delineate dynamics of nuclear architecture at different timescales, from minutes to weeks as cells differentiate, in populations and in single cells, (2) characterize cis-determinants and trans-modulators of genome organization, (3) test functional consequences of changes in cis- and trans-regulators, and (4) develop predictive models of genome structure and function.
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Affiliation(s)
- Job Dekker
- University of Massachusetts Chan Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Frank Alber
- University of California, Los Angeles, Los Angeles, CA, USA
| | | | | | - Benoit G Bruneau
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | | | | | | | | | | | - Bo Huang
- University of California, San Francisco, San Francisco, CA, USA
| | - Danwei Huangfu
- Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Reza Kalhor
- Johns Hopkins University, Baltimore, MD, USA
| | | | - Wenbo Li
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Yun Li
- University of North Carolina, Gillings School of Global Public Health, Chapel Hill, NC, USA
| | - Jian Ma
- Carnegie Mellon University, Pittsburgh, PA, USA
| | | | | | | | - Katherine S Pollard
- Gladstone Institutes, San Francisco, CA, USA; University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA, USA
| | | | - Bing Ren
- University of California, San Diego, La Jolla, CA, USA
| | - Yijun Ruan
- Zhejiang University, Hangzhou, Zhejiang, China
| | | | - Yin Shen
- University of California, San Francisco, San Francisco, CA, USA
| | | | - Xiaokun Shu
- University of California, San Francisco, San Francisco, CA, USA
| | | | | | | | - Sheng Zhong
- University of California, San Diego, La Jolla, CA, USA.
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9
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Harun A, Liu H, Song S, Asghar S, Wen X, Fang Z, Chen C. Oligonucleotide Fluorescence In Situ Hybridization: An Efficient Chromosome Painting Method in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:2816. [PMID: 37570972 PMCID: PMC10420648 DOI: 10.3390/plants12152816] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Fluorescence in situ hybridization (FISH) is an indispensable technique for studying chromosomes in plants. However, traditional FISH methods, such as BAC, rDNA, tandem repeats, and distributed repetitive sequence probe-based FISH, have certain limitations, including difficulties in probe synthesis, low sensitivity, cross-hybridization, and limited resolution. In contrast, oligo-based FISH represents a more efficient method for chromosomal studies in plants. Oligo probes are computationally designed and synthesized for any plant species with a sequenced genome and are suitable for single and repetitive DNA sequences, entire chromosomes, or chromosomal segments. Furthermore, oligo probes used in the FISH experiment provide high specificity, resolution, and multiplexing. Moreover, oligo probes made from one species are applicable for studying other genetically and taxonomically related species whose genome has not been sequenced yet, facilitating molecular cytogenetic studies of non-model plants. However, there are some limitations of oligo probes that should be considered, such as requiring prior knowledge of the probe design process and FISH signal issues with shorter probes of background noises during oligo-FISH experiments. This review comprehensively discusses de novo oligo probe synthesis with more focus on single-copy DNA sequences, preparation, improvement, and factors that affect oligo-FISH efficiency. Furthermore, this review highlights recent applications of oligo-FISH in a wide range of plant chromosomal studies.
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Affiliation(s)
- Arrashid Harun
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Hui Liu
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Shipeng Song
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Sumeera Asghar
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
| | - Xiaopeng Wen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
| | - Zhongming Fang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
| | - Chunli Chen
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Rice Industry Technology Research, College of Agricultural Sciences, Guizhou University, Guiyang 550025, China;
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Institute of Agro-Bioengineering, College of Life Science, Guizhou University, Guiyang 550025, China; (S.A.); (X.W.)
- National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Hubei Hongshan Laboratory, Wuhan 430070, China; (H.L.); (S.S.)
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10
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Poisson W, Bastien A, Gilbert I, Carrier A, Prunier J, Robert C. Cytogenetic screening of a Canadian swine breeding nucleus using a newly developed karyotyping method named oligo-banding. Genet Sel Evol 2023; 55:47. [PMID: 37430194 DOI: 10.1186/s12711-023-00819-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND The frequency of chromosomal rearrangements in Canadian breeding boars has been estimated at 0.91 to 1.64%. These abnormalities are widely recognized as a potential cause of subfertility in livestock production. Since artificial insemination is practiced in almost all intensive pig production systems, the use of elite boars carrying cytogenetic defects that have an impact on fertility can lead to major economic losses. To avoid keeping subfertile boars in artificial insemination centres and spreading chromosomal defects within populations, cytogenetic screening of boars is crucial. Different techniques are used for this purpose, but several issues are frequently encountered, i.e. environmental factors can influence the quality of results, the lack of genomic information outputted by these techniques, and the need for prior cytogenetic skills. The aim of this study was to develop a new pig karyotyping method based on fluorescent banding patterns. RESULTS The use of 207,847 specific oligonucleotides generated 96 fluorescent bands that are distributed across the 18 autosomes and the sex chromosomes. Tested alongside conventional G-banding, this oligo-banding method allowed us to identify four chromosomal translocations and a rare unbalanced chromosomal rearrangement that was not detected by conventional banding. In addition, this method allowed us to investigate chromosomal imbalance in spermatozoa. CONCLUSIONS The use of oligo-banding was found to be appropriate for detecting chromosomal aberrations in a Canadian pig nucleus and its convenient design and use make it an interesting tool for livestock karyotyping and cytogenetic studies.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandre Bastien
- Plateforme d'imagerie et microscopie, Institut de biologie intégrative et des systèmes, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Québec, QC, Canada.
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11
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Joo J, Cho S, Hong S, Min S, Kim K, Kumar R, Choi JM, Shin Y, Jung I. Probabilistic establishment of speckle-associated inter-chromosomal interactions. Nucleic Acids Res 2023; 51:5377-5395. [PMID: 37013988 PMCID: PMC10287923 DOI: 10.1093/nar/gkad211] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 03/08/2023] [Accepted: 03/25/2023] [Indexed: 04/05/2023] Open
Abstract
Inter-chromosomal interactions play a crucial role in genome organization, yet the organizational principles remain elusive. Here, we introduce a novel computational method to systematically characterize inter-chromosomal interactions using in situ Hi-C results from various cell types. Our method successfully identifies two apparently hub-like inter-chromosomal contacts associated with nuclear speckles and nucleoli, respectively. Interestingly, we discover that nuclear speckle-associated inter-chromosomal interactions are highly cell-type invariant with a marked enrichment of cell-type common super-enhancers (CSEs). Validation using DNA Oligopaint fluorescence in situ hybridization (FISH) shows a strong but probabilistic interaction behavior between nuclear speckles and CSE-harboring genomic regions. Strikingly, we find that the likelihood of speckle-CSE associations can accurately predict two experimentally measured inter-chromosomal contacts from Hi-C and Oligopaint DNA FISH. Our probabilistic establishment model well describes the hub-like structure observed at the population level as a cumulative effect of summing individual stochastic chromatin-speckle interactions. Lastly, we observe that CSEs are highly co-occupied by MAZ binding and MAZ depletion leads to significant disorganization of speckle-associated inter-chromosomal contacts. Taken together, our results propose a simple organizational principle of inter-chromosomal interactions mediated by MAZ-occupied CSEs.
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Affiliation(s)
- Jaegeon Joo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Sunghyun Cho
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sukbum Hong
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sunwoo Min
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Kyukwang Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
| | - Rajeev Kumar
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Jeong-Mo Choi
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University, Busan 46241, Republic of Korea
| | - Yongdae Shin
- Department of Mechanical Engineering, Seoul National University, Seoul 08826, Republic of Korea
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Inkyung Jung
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea
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12
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Salataj E, Spilianakis CG, Chaumeil J. Single-cell detection of primary transcripts, their genomic loci and nuclear factors by 3D immuno-RNA/DNA FISH in T cells. Front Immunol 2023; 14:1156077. [PMID: 37215121 PMCID: PMC10193148 DOI: 10.3389/fimmu.2023.1156077] [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: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 05/24/2023] Open
Abstract
Over the past decades, it has become increasingly clear that higher order chromatin folding and organization within the nucleus is involved in the regulation of genome activity and serves as an additional epigenetic mechanism that modulates cellular functions and gene expression programs in diverse biological processes. In particular, dynamic allelic interactions and nuclear locations can be of functional importance during the process of lymphoid differentiation and the regulation of immune responses. Analyses of the proximity between chromatin and/or nuclear regions can be performed on populations of cells with high-throughput sequencing approaches such as chromatin conformation capture ("3C"-based) or DNA adenine methyltransferase identification (DamID) methods, or, in individual cells, by the simultaneous visualization of genomic loci, their primary transcripts and nuclear compartments within the 3-dimensional nuclear space using Fluorescence In Situ Hybridization (FISH) and immunostaining. Here, we present a detailed protocol to simultaneously detect nascent RNA transcripts (3D RNA FISH), their genomic loci (3D DNA FISH) and/or their chromosome territories (CT paint DNA FISH) combined with the antibody-based detection of various nuclear factors (immunofluorescence). We delineate the application and effectiveness of this robust and reproducible protocol in several murine T lymphocyte subtypes (from differentiating thymic T cells, to activated splenic and peripheral T cells) as well as other murine cells, including embryonic stem cells, B cells, megakaryocytes and macrophages.
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Affiliation(s)
- Eralda Salataj
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Charalampos G. Spilianakis
- Institute of Molecular Biology and Biotechnology-Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Julie Chaumeil
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
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13
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Poisson W, Prunier J, Carrier A, Gilbert I, Mastromonaco G, Albert V, Taillon J, Bourret V, Droit A, Côté SD, Robert C. Chromosome-level assembly of the Rangifer tarandus genome and validation of cervid and bovid evolution insights. BMC Genomics 2023; 24:142. [PMID: 36959567 PMCID: PMC10037892 DOI: 10.1186/s12864-023-09189-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/14/2023] [Indexed: 03/25/2023] Open
Abstract
BACKGROUND Genome assembly into chromosomes facilitates several analyses including cytogenetics, genomics and phylogenetics. Despite rapid development in bioinformatics, however, assembly beyond scaffolds remains challenging, especially in species without closely related well-assembled and available reference genomes. So far, four draft genomes of Rangifer tarandus (caribou or reindeer, a circumpolar distributed cervid species) have been published, but none with chromosome-level assembly. This emblematic northern species is of high interest in ecological studies and conservation since most populations are declining. RESULTS We have designed specific probes based on Oligopaint FISH technology to upgrade the latest published reindeer and caribou chromosome-level genomes. Using this oligonucleotide-based method, we found six mis-assembled scaffolds and physically mapped 68 of the largest scaffolds representing 78% of the most recent R. tarandus genome assembly. Combining physical mapping and comparative genomics, it was possible to document chromosomal evolution among Cervidae and closely related bovids. CONCLUSIONS Our results provide validation for the current chromosome-level genome assembly as well as resources to use chromosome banding in studies of Rangifer tarandus.
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Affiliation(s)
- William Poisson
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Julien Prunier
- Département de biochimie, microbiologie et bio-informatique, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Alexandra Carrier
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | - Isabelle Gilbert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada
| | | | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Québec, QC, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Québec, QC, Canada
| | - Steeve D Côté
- Caribou Ungava, Département de biologie and Centre d'études nordiques, Faculté des sciences et de génie, Université Laval, Québec, QC, Canada
| | - Claude Robert
- Département des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle, Québec, QC, Canada.
- Réseau Québécois en reproduction, QC, Saint-Hyacinthe, Canada.
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14
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Aguilar R, Camplisson CK, Lin Q, Miga KH, Noble WS, Beliveau BJ. Tigerfish designs oligonucleotide-based in situ hybridization probes targeting intervals of highly repetitive DNA at the scale of genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.530899. [PMID: 36945528 PMCID: PMC10028787 DOI: 10.1101/2023.03.06.530899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Fluorescent in situ hybridization (FISH) is a powerful method for the targeted visualization of nucleic acids in their native contexts. Recent technological advances have leveraged computationally designed oligonucleotide (oligo) probes to interrogate >100 distinct targets in the same sample, pushing the boundaries of FISH-based assays. However, even in the most highly multiplexed experiments, repetitive DNA regions are typically not included as targets, as the computational design of specific probes against such regions presents significant technical challenges. Consequently, many open questions remain about the organization and function of highly repetitive sequences. Here, we introduce Tigerfish, a software tool for the genome-scale design of oligo probes against repetitive DNA intervals. We showcase Tigerfish by designing a panel of 24 interval-specific repeat probes specific to each of the 24 human chromosomes and imaging this panel on metaphase spreads and in interphase nuclei. Tigerfish extends the powerful toolkit of oligo-based FISH to highly repetitive DNA.
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Affiliation(s)
- Robin Aguilar
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Qiaoyi Lin
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Karen H. Miga
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, CA, USA
| | - William S. Noble
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA
| | - Brian J. Beliveau
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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15
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Li Y, Huang D, Pei Y, Wu Y, Xu R, Quan F, Gao H, Zhang J, Hou H, Zhang K, Li J. CasSABER for Programmable In Situ Visualization of Low and Nonrepetitive Gene Loci. Anal Chem 2023; 95:2992-3001. [PMID: 36703533 DOI: 10.1021/acs.analchem.2c04867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Site-specific imaging of target genes using CRISPR probes is essential for understanding the molecular mechanisms of gene function and engineering tools to modulate its downstream pathways. Herein, we develop CRISPR/Cas9-mediated signal amplification by exchange reaction (CasSABER) for programmable in situ imaging of low and nonrepetitive regions of the target gene in the cell nucleus. The presynthesized primer-exchange reaction (PER) probe is able to hybridize multiple fluorophore-bearing imager strands to specifically light up dCas9/sgRNA target-bound gene loci, enabling in situ imaging of fixed cellular gene loci with high specificity and signal-to-noise ratio. In combination with a multiround branching strategy, we successfully detected nonrepetitive gene regions using a single sgRNA. As an intensity-codable and orthogonal probe system, CasSABER enables the adjustable amplification of local signals in fixed cells, resulting in the simultaneous visualization of multicopy and single-copy gene loci with similar fluorescence intensity. Owing to avoiding the complexity of controlling in situ mutistep enzymatic reactions, CasSABER shows good reliability, sensitivity, and ease of implementation, providing a rapid and cost-effective molecular toolkit for studying multigene interaction in fundamental research and gene diagnosis.
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Affiliation(s)
- Yanan Li
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Di Huang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yiran Pei
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Yonghua Wu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Ru Xu
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Fenglei Quan
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hua Gao
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Junli Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Hongwei Hou
- China National Tobacco Quality Supervision & Test Center, Zhengzhou450001, China
- Beijing Institute of Life Science and Technology, Beijing100083, China
| | - Kaixiang Zhang
- School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, Collaborative Innovation Center of New Drug Research and Safety Evaluation, State Key Laboratory of Esophageal Cancer Prevention & Treatment, Zhengzhou University, Zhengzhou450001, China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing100084, China
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16
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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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17
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The era of 3D and spatial genomics. Trends Genet 2022; 38:1062-1075. [PMID: 35680466 DOI: 10.1016/j.tig.2022.05.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 12/28/2022]
Abstract
Over a decade ago the advent of high-throughput chromosome conformation capture (Hi-C) sparked a new era of 3D genomics. Since then the number of methods for mapping the 3D genome has flourished, enabling an ever-increasing understanding of how DNA is packaged in the nucleus and how the spatiotemporal organization of the genome orchestrates its vital functions. More recently, the next generation of spatial genomics technologies has begun to reveal how genome sequence and 3D genome organization vary between cells in their tissue context. We summarize how the toolkit for charting genome topology has evolved over the past decade and discuss how new technological developments are advancing the field of 3D and spatial genomics.
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18
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Vaknin I, Amit R. Molecular and experimental tools to design synthetic enhancers. Curr Opin Biotechnol 2022; 76:102728. [PMID: 35525178 DOI: 10.1016/j.copbio.2022.102728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/03/2022]
Abstract
Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously. This review includes the latest commercial DNA OL synthesis technology and its capabilities, and a general 'know-how' guide for the design, construction, and analysis of OL-based synthetic enhancer characterization experiments. Specifically, we focus on synthetic-enhancer-based massively parallel reporter assay, Sort-seq methodologies (e.g. flow cytometry, deep sequencing), and a brief description of machine learning-based attempts for OL-analysis and follow-up validation experiments.
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Affiliation(s)
- Inbal Vaknin
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel; The Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 3200000, Israel.
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19
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Nakayama K, Shachar S, Finn EH, Sato H, Hirakawa A, Misteli T. Large-scale mapping of positional changes of hypoxia-responsive genes upon activation. Mol Biol Cell 2022; 33:ar72. [PMID: 35476603 PMCID: PMC9635277 DOI: 10.1091/mbc.e21-11-0593] [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] [Indexed: 12/02/2022] Open
Abstract
Chromosome structure and nuclear organization are important factors in the regulation of gene expression. Transcription of a gene is influenced by local and global chromosome features such as chromatin condensation status. The relationship between the 3D position of a gene in the nucleus and its activity is less clear. Here we used high-throughput imaging to perform a large-scale analysis of the spatial location of nearly 100 hypoxia-responsive genes to determine whether their location and activity state are correlated. Radial distance analysis demonstrated that the majority of Hypoxia-Inducible Factor (HIF)- and CREB-dependent hypoxia-responsive genes are located in the intermediate region of the nucleus, and some of them changed their radial position in hypoxia. Analysis of the relative distances among a subset of HIF target genes revealed that some gene pairs altered their relative location to each other on hypoxic treatment, suggesting higher-order chromatin rearrangements. While these changes in location occurred in response to hypoxic activation of the target genes, they did not correlate with the extent of their activation. These results suggest that induction of the hypoxia-responsive gene expression program is accompanied by spatial alterations of the genome, but that radial and relative gene positions are not directly related to gene activity.
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Affiliation(s)
- Koh Nakayama
- Oxygen Biology Laboratory, Medical Research Institute, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan.,Department of Pharmacology, School of Medicine, Asahikawa Medical University, Asahikawa, Hokkaido 078-8510, Japan.,Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Sigal Shachar
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Elizabeth H Finn
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
| | - Hiroyuki Sato
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Akihiro Hirakawa
- Department of Clinical Biostatistics, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University (TMDU), Bunkyo-ku, Tokyo 113-8510, Japan
| | - Tom Misteli
- Cell Biology of Genomes Group, Center for Cancer Research, National Cancer Institute NIH, Bethesda, 20892
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20
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Yang L, Wang B, Ma L, Fu P. An Update of Long-Noncoding RNAs in Acute Kidney Injury. Front Physiol 2022; 13:849403. [PMID: 35350698 PMCID: PMC8957988 DOI: 10.3389/fphys.2022.849403] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/15/2022] [Indexed: 02/05/2023] Open
Abstract
Acute kidney injury (AKI) is a global public health concern with high morbidity, mortality, and medical costs. Despite advances in medicine, effective therapeutic regimens for AKI remain limited. Long non-coding RNAs (lncRNAs) are a subtype of non-coding RNAs, which longer than 200 nucleotides and perform extremely diverse functions in biological processes. Recently, lncRNAs have emerged as promising biomarkers and key mediators to AKI. Meanwhile, existing research reveals that the aberrant expression of lncRNAs has been linked to major pathological processes in AKI, including the inflammatory response, cell proliferation, and apoptosis, via forming the lncRNA/microRNA/target gene regulatory axis. Following a comprehensive and systematic search of the available literature, 87 relevant papers spanning the years 2005 to 2021 were identified. This review aims to provide and update an overview of lncRNAs in AKI, and further shed light on their potential utility as AKI biomarkers and therapeutic targets.
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Affiliation(s)
- Lina Yang
- Kidney Research Institute, Division of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Bo Wang
- Kidney Research Institute, Division of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Liang Ma
- Kidney Research Institute, Division of Nephrology, West China Hospital of Sichuan University, Chengdu, China
| | - Ping Fu
- Kidney Research Institute, Division of Nephrology, West China Hospital of Sichuan University, Chengdu, China
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21
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Brandstetter K, Zülske T, Ragoczy T, Hörl D, Guirao-Ortiz M, Steinek C, Barnes T, Stumberger G, Schwach J, Haugen E, Rynes E, Korber P, Stamatoyannopoulos JA, Leonhardt H, Wedemann G, Harz H. Differences in nanoscale organization of regulatory active and inactive human chromatin. Biophys J 2022; 121:977-990. [PMID: 35150617 PMCID: PMC8943813 DOI: 10.1016/j.bpj.2022.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 12/11/2021] [Accepted: 02/07/2022] [Indexed: 11/25/2022] Open
Abstract
Methodological advances in conformation capture techniques have fundamentally changed our understanding of chromatin architecture. However, the nanoscale organization of chromatin and its cell-to-cell variance are less studied. Analyzing genome-wide data from 733 human cell and tissue samples, we identified 2 prototypical regions that exhibit high or absent hypersensitivity to deoxyribonuclease I, respectively. These regulatory active or inactive regions were examined in the lymphoblast cell line K562 by using high-throughput super-resolution microscopy. In both regions, we systematically measured the physical distance of 2 fluorescence in situ hybridization spots spaced by only 5 kb of DNA. Unexpectedly, the resulting distance distributions range from very compact to almost elongated configurations of more than 200-nm length for both the active and inactive regions. Monte Carlo simulations of a coarse-grained model of these chromatin regions based on published data of nucleosome occupancy in K562 cells were performed to understand the underlying mechanisms. There was no parameter set for the simulation model that can explain the microscopically measured distance distributions. Obviously, the chromatin state given by the strength of internucleosomal interaction, nucleosome occupancy, or amount of histone H1 differs from cell to cell, which results in the observed broad distance distributions. This large variability was not expected, especially in inactive regions. The results for the mechanisms for different distance distributions on this scale are important for understanding the contacts that mediate gene regulation. Microscopic measurements show that the inactive region investigated here is expected to be embedded in a more compact chromatin environment. The simulation results of this region require an increase in the strength of internucleosomal interactions. It may be speculated that the higher density of chromatin is caused by the increased internucleosomal interaction strength.
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Affiliation(s)
- Katharina Brandstetter
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tilo Zülske
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany
| | - Tobias Ragoczy
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - David Hörl
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Miguel Guirao-Ortiz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Clemens Steinek
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Toby Barnes
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Gabriela Stumberger
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jonathan Schwach
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Eric Haugen
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Eric Rynes
- Altius Institute for Biomedical Sciences, Seattle, Washington
| | - Philipp Korber
- Biomedical Center (BMC), Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - John A Stamatoyannopoulos
- Altius Institute for Biomedical Sciences, Seattle, Washington; Department of Genome Sciences, University of Washington, Seattle, Washington; Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington
| | - Heinrich Leonhardt
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gero Wedemann
- Competence Center Bioinformatics, Institute for Applied Computer Science, Hochschule Stralsund, Stralsund, Germany.
| | - Hartmann Harz
- Human Biology & BioImaging, Faculty of Biology, Ludwig-Maximilians-Universität München, Munich, Germany.
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22
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Simultaneous visualization of DNA loci in single cells by combinatorial multi-color iFISH. Sci Data 2022; 9:47. [PMID: 35145120 PMCID: PMC8831585 DOI: 10.1038/s41597-022-01139-2] [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: 08/02/2021] [Accepted: 12/23/2021] [Indexed: 11/22/2022] Open
Abstract
Single-molecule DNA fluorescence in situ hybridization (FISH) techniques enable studying the three-dimensional (3D) organization of the genome at the single cell level. However, there is a major unmet need for open access, high quality, curated and reproducible DNA FISH datasets. Here, we describe a dataset obtained by applying our recently developed iFISH method to simultaneously visualize 16 small (size range: 62–73 kilobases, kb) DNA loci evenly spaced on chromosome 2 in human cells, in a single round of hybridization. We show how combinatorial color coding can be used to precisely localize multiple loci in 3D within single cells, and how inter-locus distances scale inversely with chromosome contact frequencies determined by high-throughput chromosome conformation capture (Hi-C). We provide raw images and 3D coordinates for nearly 10,000 FISH dots. Our dataset provides a free resource that can facilitate studies of 3D genome organization in single cells and can be used to develop automatic FISH analysis algorithms. Measurement(s) | DNA loci 3D coordinates | Technology Type(s) | Fluorescence In Situ Hybridization | Factor Type(s) | DNA FISH probe target (locus) | Sample Characteristic - Organism | Homo sapiens |
Machine-accessible metadata file describing the reported data: 10.6084/m9.figshare.17281358
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23
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Roy S, Ganguly N, Banerjee S. Exploring clinical implications and role of non-coding RNAs in lung carcinogenesis. Mol Biol Rep 2022; 49:6871-6883. [PMID: 35076850 DOI: 10.1007/s11033-022-07159-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/18/2022] [Indexed: 12/12/2022]
Abstract
Lung cancer is the utmost familiar category of cancer with greatest fatality rate worldwide and several regulatory mechanisms exercise cellular control on critical oncogenic trails implicated in lung associated carcinogenesis. The non-coding RNAs (ncRNAs) are shown to play a variety of regulatory roles, including stimulating cell proliferation, inhibiting programmed cell death, enhancing cancer cell metastatic ability and acquiring resistance to drugs. Furthermore, ncRNAs exhibit tissue-specific expression as well as great stability in bodily fluids. As a consequence, they are strong contenders for cancer based theragnostics. microRNA (miRNA) alters gene expression primarily by either degrading or interfering with the translation of targeted mRNA and long non-coding RNAs (lncRNAs) can influence gene expression by targeting transcriptional activators or repressors, RNA polymers and even DNA-duplex. lncRNAs are typically found to be dysregulated in lung cancer and hence targeting ncRNAs could be a viable strategy for developing potential therapies as well as for overcoming chemoresistance in lung cancer. The purpose of this review is to elucidate the role of ncRNAs, revisiting the recent studies in lung cancer.
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Affiliation(s)
- Swagata Roy
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India
| | - Neeldeep Ganguly
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India
| | - Satarupa Banerjee
- School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, 632 014, India.
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24
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Chebrout M, Koné MC, Jan HU, Cournut M, Letheule M, Fleurot R, Aguirre-Lavin T, Peynot N, Jouneau A, Beaujean N, Bonnet-Garnier A. Transcription of rRNA in early mouse embryos promotes chromatin reorganization and expression of major satellite repeats. J Cell Sci 2022; 135:274059. [DOI: 10.1242/jcs.258798] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/09/2022] [Indexed: 11/20/2022] Open
Abstract
During the first cell cycles of the early development, the chromatin of the embryo is highly reprogrammed alongside that embryonic genome starts its own transcription. The spatial organization of the genome is a major process that contributes to regulating gene transcription in time and space, however, it is poorly studied in the context of early embryos. To study the cause and effect link between transcription and spatial organization in embryos, we focused on the ribosomal genes, that are first silent and begin to transcribe during the 2-cell stage in the mouse. We demonstrated that ribosomal sequences and early unprocessed rRNAs are spatially organized in a very peculiar manner from the 2-cell to the 16-cell. Using drugs interfering with ribosomal DNA transcription, we show that this organization, totally different from somatic cells, depends on an active transcription of ribosomal genes and induces a unique chromatin environment that favors transcription of major satellite sequences after the 4-cell stage.
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Affiliation(s)
- Martine Chebrout
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Maïmouna Coura Koné
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Habib U. Jan
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Marie Cournut
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Martine Letheule
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Renaud Fleurot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Tiphaine Aguirre-Lavin
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Peynot
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Alice Jouneau
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Nathalie Beaujean
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
| | - Amélie Bonnet-Garnier
- Université Paris-Saclay, UVSQ, INRAE, BREED, 78350, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d'Alfort, BREED, 94700, Maisons-Alfort, France
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25
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Maslova A, Krasikova A. FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains. Front Cell Dev Biol 2021; 9:753097. [PMID: 34805161 PMCID: PMC8597843 DOI: 10.3389/fcell.2021.753097] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/08/2021] [Indexed: 12/14/2022] Open
Abstract
The intimate relationships between genome structure and function direct efforts toward deciphering three-dimensional chromatin organization within the interphase nuclei at different genomic length scales. For decades, major insights into chromatin structure at the level of large-scale euchromatin and heterochromatin compartments, chromosome territories, and subchromosomal regions resulted from the evolution of light microscopy and fluorescence in situ hybridization. Studies of nanoscale nucleosomal chromatin organization benefited from a variety of electron microscopy techniques. Recent breakthroughs in the investigation of mesoscale chromatin structures have emerged from chromatin conformation capture methods (C-methods). Chromatin has been found to form hierarchical domains with high frequency of local interactions from loop domains to topologically associating domains and compartments. During the last decade, advances in super-resolution light microscopy made these levels of chromatin folding amenable for microscopic examination. Here we are reviewing recent developments in FISH-based approaches for detection, quantitative measurements, and validation of contact chromatin domains deduced from C-based data. We specifically focus on the design and application of Oligopaint probes, which marked the latest progress in the imaging of chromatin domains. Vivid examples of chromatin domain FISH-visualization by means of conventional, super-resolution light and electron microscopy in different model organisms are provided.
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Affiliation(s)
| | - Alla Krasikova
- Laboratory of Nuclear Structure and Dynamics, Cytology and Histology Department, Saint Petersburg State University, Saint Petersburg, Russia
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26
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Wang M, Gu M, Liu L, Liu Y, Tian L. Single-Cell RNA Sequencing (scRNA-seq) in Cardiac Tissue: Applications and Limitations. Vasc Health Risk Manag 2021; 17:641-657. [PMID: 34629873 PMCID: PMC8495612 DOI: 10.2147/vhrm.s288090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Cardiovascular diseases (CVDs) are a group of disorders of the blood vessels and heart, which are considered as the leading causes of death worldwide. The pathology of CVDs could be related to the functional abnormalities of multiple cell types in the heart. Single-cell RNA sequencing (scRNA-seq) technology is a powerful method for characterizing individual cells and elucidating the molecular mechanisms by providing a high resolution of transcriptomic changes at the single-cell level. Specifically, scRNA-seq has provided novel insights into CVDs by identifying rare cardiac cell types, inferring the trajectory tree, estimating RNA velocity, elucidating the cell-cell communication, and comparing healthy and pathological heart samples. In this review, we summarize the different scRNA-seq platforms and published single-cell datasets in the cardiovascular field, and describe the utilities and limitations of this technology. Lastly, we discuss the future perspective of the application of scRNA-seq technology into cardiovascular research.
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Affiliation(s)
- Mingqiang Wang
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Mingxia Gu
- Perinatal Institute, Division of Pulmonary Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
- Center for Stem Cell and Organoid Medicine, CuSTOM, Division of Developmental Biology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, 45229, USA
| | - Ling Liu
- Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Yu Liu
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Lei Tian
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA
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27
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PaintSHOP enables the interactive design of transcriptome- and genome-scale oligonucleotide FISH experiments. Nat Methods 2021; 18:937-944. [PMID: 34226720 PMCID: PMC8349872 DOI: 10.1038/s41592-021-01187-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 05/18/2021] [Indexed: 12/31/2022]
Abstract
Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments utilizing oligo FISH probes. Here, we introduce Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs, and to easily generate files documenting library design. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community. Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments, democratizes and standardizes the process of designing complex probe sets for the oligo FISH community.
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28
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Liu G, Zhang T. Single Copy Oligonucleotide Fluorescence In Situ Hybridization Probe Design Platforms: Development, Application and Evaluation. Int J Mol Sci 2021; 22:ijms22137124. [PMID: 34281175 PMCID: PMC8268824 DOI: 10.3390/ijms22137124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 12/30/2022] Open
Abstract
Oligonucleotides fluorescence in situ hybridization (Oligo-FISH) is an emerging technology and is an important tool in research areas such as detection of chromosome variation, identification of allopolyploid, and deciphering of three-dimensional (3D) genome structures. Based on the demand for highly efficient oligo probes for oligo-FISH experiments, increasing numbers of tools have been developed for probe design in recent years. Obsolete oligonucleotide design tools have been adapted for oligo-FISH probe design because of their similar considerations. With the development of DNA sequencing and large-scale synthesis, novel tools have been designed to increase the specificity of designed oligo probes and enable genome-scale oligo probe design, which has greatly improved the application of single copy oligo-FISH. Despite this, few studies have introduced the development of the oligo-FISH probe design tools and their application in FISH experiments systematically. Besides, a comprehensive comparison and evaluation is lacking for the available tools. In this review, we provide an overview of the oligo-FISH probe design process, summarize the development and application of the available tools, evaluate several state-of-art tools, and eventually provide guidance for single copy oligo-FISH probe design.
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Affiliation(s)
- Guanqing Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Institutes of Agricultural Science and Technology Development, Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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29
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Wang Y, Cottle WT, Wang H, Feng XA, Mallon J, Gavrilov M, Bailey S, Ha T. Genome oligopaint via local denaturation fluorescence in situ hybridization. Mol Cell 2021; 81:1566-1577.e8. [PMID: 33657402 PMCID: PMC8026568 DOI: 10.1016/j.molcel.2021.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 11/22/2020] [Accepted: 02/04/2021] [Indexed: 12/26/2022]
Abstract
Cas9 in complex with a programmable guide RNA targets specific double-stranded DNA for cleavage. By harnessing Cas9 as a programmable loader of superhelicase to genomic DNA, we report a physiological-temperature DNA fluorescence in situ hybridization (FISH) method termed genome oligopaint via local denaturation (GOLD) FISH. Instead of global denaturation as in conventional DNA FISH, loading a superhelicase at a Cas9-generated nick allows for local DNA denaturation, reducing nonspecific binding of probes and avoiding harsh treatments such as heat denaturation. GOLD FISH relies on Cas9 cleaving target DNA sequences and avoids the high nuclear background associated with other genome labeling methods that rely on Cas9 binding. The excellent signal brightness and specificity enable us to image nonrepetitive genomic DNA loci and analyze the conformational differences between active and inactive X chromosomes. Finally, GOLD FISH could be used for rapid identification of HER2 gene amplification in patient tissue.
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Affiliation(s)
- Yanbo Wang
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Wayne Taylor Cottle
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Haobo Wang
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Xinyu Ashlee Feng
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - John Mallon
- Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Momcilo Gavrilov
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Scott Bailey
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Bloomberg School of Public Health, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Taekjip Ha
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205, USA; Howard Hughes Medical Institute, Baltimore, MD 21205, USA.
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30
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Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 2021; 16:1647-1713. [PMID: 33619390 PMCID: PMC8525907 DOI: 10.1038/s41596-020-00478-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 11/26/2020] [Indexed: 01/31/2023]
Abstract
Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2-6 d for data collection and 2-7 d for the automated steps of image analysis.
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31
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Teixeira H, Sousa AL, Azevedo AS. Bioinformatic Tools and Guidelines for the Design of Fluorescence In Situ Hybridization Probes. Methods Mol Biol 2021; 2246:35-50. [PMID: 33576981 DOI: 10.1007/978-1-0716-1115-9_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Fluorescence in situ hybridization (FISH) is a well-established technique that allows the detection of microorganisms in diverse types of samples (e.g., clinical, food, environmental samples, and biofilm communities). The FISH probe design is an essential step in this technique. For this, two strategies can be used, the manual form based on multiple sequence alignment to identify conserved regions and programs/software specifically developed for the selection of the sequence of the probe. Additionally, databases/software for the theoretical evaluation of the probes in terms of specificity, sensitivity, and thermodynamic parameters (melting temperature and Gibbs free energy change) are used. The purpose of this chapter is to describe the essential steps and guidelines for the design of FISH probes (e.g., DNA and Nucleic Acid Mimic (NAM) probes), and its theoretical evaluation through the application of diverse bioinformatic tools.
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Affiliation(s)
- Helena Teixeira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Ana L Sousa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal.,INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal
| | - Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
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32
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Gao N, Li Y, Li J, Gao Z, Yang Z, Li Y, Liu H, Fan T. Long Non-Coding RNAs: The Regulatory Mechanisms, Research Strategies, and Future Directions in Cancers. Front Oncol 2020; 10:598817. [PMID: 33392092 PMCID: PMC7775490 DOI: 10.3389/fonc.2020.598817] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/18/2020] [Indexed: 12/12/2022] Open
Abstract
The development and application of whole genome sequencing technology has greatly broadened our horizons on the capabilities of long non-coding RNAs (lncRNAs). LncRNAs are more than 200 nucleotides in length and lack protein-coding potential. Increasing evidence indicates that lncRNAs exert an irreplaceable role in tumor initiation, progression, as well as metastasis, and are novel molecular biomarkers for diagnosis and prognosis of cancer patients. Furthermore, lncRNAs and the pathways they influence might represent promising therapeutic targets for a number of tumors. Here, we discuss the recent advances in understanding of the specific regulatory mechanisms of lncRNAs. We focused on the signal, decoy, guide, and scaffold functions of lncRNAs at the epigenetic, transcription, and post-transcription levels in cancer cells. Additionally, we summarize the research strategies used to investigate the roles of lncRNAs in tumors, including lncRNAs screening, lncRNAs characteristic analyses, functional studies, and molecular mechanisms of lncRNAs. This review will provide a short but comprehensive description of the lncRNA functions in tumor development and progression, thus accelerating the clinical implementation of lncRNAs as tumor biomarkers and therapeutic targets.
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Affiliation(s)
- Na Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Yueheng Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Jing Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhengfan Gao
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
| | - Zhenzhen Yang
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China.,Translational Medicine Research Center, People's Hospital of Zhengzhou, Zhengzhou, China
| | - Yong Li
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China.,Faculty of Medicine, St George and Sutherland Clinical School, St George Hospital, The University of New South Wales (UNSW) Sydney, Kensington, NSW, Australia
| | - Hongtao Liu
- Laboratory for Cell Biology, College of Life Sciences of Zhengzhou University, Zhengzhou, China
| | - Tianli Fan
- Department of Pharmacology, School of Basic Medicine, Zhengzhou University, Zhengzhou, China
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33
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Tarbier M, Mackowiak SD, Frade J, Catuara-Solarz S, Biryukova I, Gelali E, Menéndez DB, Zapata L, Ossowski S, Bienko M, Gallant CJ, Friedländer MR. Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells. Nat Commun 2020; 11:5445. [PMID: 33116115 PMCID: PMC7595044 DOI: 10.1038/s41467-020-19011-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 09/15/2020] [Indexed: 01/19/2023] Open
Abstract
Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply a tailored experimental design that eliminates these confounders, and report thousands of intrinsically covarying gene pairs in mouse embryonic stem cells. These covariations form a network with biological properties, outlining known and novel gene interactions. We provide the first evidence that miRNAs naturally induce transcriptome-wide covariations and compare the relative importance of nuclear organization, transcriptional and post-transcriptional regulation in defining covariations. We find that nuclear organization has the greatest impact, and that genes encoding for physically interacting proteins specifically tend to covary, suggesting importance for protein complex formation. Our results lend support to the concept of post-transcriptional RNA operons, but we further present evidence that nuclear proximity of genes may provide substantial functional regulation in mammalian single cells. Gene expression covariation can be studied by single-cell RNA sequencing. Here the authors analyze intrinsically covarying gene pairs by eliminating the confounding effects in single-cell experiments and observe covariation of proximal genes and miRNA-induced covariation of target mRNAs.
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Affiliation(s)
- Marcel Tarbier
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Sebastian D Mackowiak
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - João Frade
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Silvina Catuara-Solarz
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Inna Biryukova
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Eleni Gelali
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Diego Bárcena Menéndez
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain
| | - Luis Zapata
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Center for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Stephan Ossowski
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Barcelona, Spain.,Department of Experimental and Health Sciences, University Pompeu Fabra, Barcelona, Spain.,Institute of Medical Genetics and Applied Genomics, University of Tübingen, Tübingen, Germany
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Marc R Friedländer
- Science for Life Laboratory, Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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34
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Jayaraman P, Mosbruger T, Hu T, Tairis NG, Wu C, Clark PM, D’Arcy M, Ferriola D, Mackiewicz K, Gai X, Monos D, Sarmady M. AnthOligo: automating the design of oligonucleotides for capture/enrichment technologies. Bioinformatics 2020; 36:4353-4356. [PMID: 32484858 PMCID: PMC7520035 DOI: 10.1093/bioinformatics/btaa552] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 05/22/2020] [Accepted: 05/28/2020] [Indexed: 11/13/2022] Open
Abstract
SUMMARY A number of methods have been devised to address the need for targeted genomic resequencing. One of these methods, region-specific extraction (RSE) is characterized by the capture of long DNA fragments (15-20 kb) by magnetic beads, after enzymatic extension of oligonucleotides hybridized to selected genomic regions. Facilitating the selection of the most appropriate capture oligos for targeting a region of interest, satisfying the properties of temperature (Tm) and entropy (ΔG), while minimizing the formation of primer-dimers in a pooled experiment, is therefore necessary. Manual design and selection of oligos becomes very challenging, complicated by factors such as length of the target region and number of targeted regions. Here we describe, AnthOligo, a web-based application developed to optimally automate the process of generation of oligo sequences used to target and capture the continuum of large and complex genomic regions. Apart from generating oligos for RSE, this program may have wider applications in the design of customizable internal oligos to be used as baits for gene panel analysis or even probes for large-scale comparative genomic hybridization array processes. AnthOligo was tested by capturing the Major Histocompatibility Complex (MHC) of a random sample.The application provides users with a simple interface to upload an input file in BED format and customize parameters for each task. The task of probe design in AnthOligo commences when a user uploads an input file and concludes with the generation of a result-set containing an optimal set of region-specific oligos. AnthOligo is currently available as a public web application with URL: http://antholigo.chop.edu. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | | | - Taishan Hu
- Department of Pathology and Laboratory Medicine
| | | | - Chao Wu
- Department of Biomedical Health & Informatics, The Children's Hospitals of Philadelphia, Philadelphia, PA, USA
| | - Peter M Clark
- Department of Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Raritan, NJ, USA
| | - Monica D’Arcy
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | | | - Katarzyna Mackiewicz
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
| | - Xiaowu Gai
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Pathology and Laboratory Medicine, Center for Personalized Medicine, Children’s Hospital of Los Angeles, Los Angeles, CA, USA
| | - Dimitrios Monos
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Mahdi Sarmady
- Department of Pathology and Laboratory Medicine
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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35
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Asp M, Giacomello S, Larsson L, Wu C, Fürth D, Qian X, Wärdell E, Custodio J, Reimegård J, Salmén F, Österholm C, Ståhl PL, Sundström E, Åkesson E, Bergmann O, Bienko M, Månsson-Broberg A, Nilsson M, Sylvén C, Lundeberg J. A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart. Cell 2020; 179:1647-1660.e19. [PMID: 31835037 DOI: 10.1016/j.cell.2019.11.025] [Citation(s) in RCA: 345] [Impact Index Per Article: 86.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/06/2019] [Accepted: 11/14/2019] [Indexed: 10/25/2022]
Abstract
The process of cardiac morphogenesis in humans is incompletely understood. Its full characterization requires a deep exploration of the organ-wide orchestration of gene expression with a single-cell spatial resolution. Here, we present a molecular approach that reveals the comprehensive transcriptional landscape of cell types populating the embryonic heart at three developmental stages and that maps cell-type-specific gene expression to specific anatomical domains. Spatial transcriptomics identified unique gene profiles that correspond to distinct anatomical regions in each developmental stage. Human embryonic cardiac cell types identified by single-cell RNA sequencing confirmed and enriched the spatial annotation of embryonic cardiac gene expression. In situ sequencing was then used to refine these results and create a spatial subcellular map for the three developmental phases. Finally, we generated a publicly available web resource of the human developing heart to facilitate future studies on human cardiogenesis.
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Affiliation(s)
- Michaela Asp
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
| | - Stefania Giacomello
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden; Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
| | - Ludvig Larsson
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Chenglin Wu
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Daniel Fürth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Xiaoyan Qian
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Eva Wärdell
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joaquin Custodio
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Johan Reimegård
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Fredrik Salmén
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences) and University Medical Center Utrecht, Cancer Genomics Netherlands, Utrecht, the Netherlands
| | - Cecilia Österholm
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Patrik L Ståhl
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Erik Sundström
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Elisabet Åkesson
- Department of Neurobiology, Care Sciences and Society, Karolinska Institutet, R&D Unit, Stockholms Sjukhem, Stockholm, Sweden
| | - Olaf Bergmann
- Center for Regenerative Therapies Dresden, TU-Dresden, Dresden, Germany; Karolinska Institutet, Cell and Molecular Biology, Stockholm, Sweden
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | | | - Mats Nilsson
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Christer Sylvén
- Department of Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Joakim Lundeberg
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, Stockholm, Sweden.
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36
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GPSeq reveals the radial organization of chromatin in the cell nucleus. Nat Biotechnol 2020; 38:1184-1193. [PMID: 32451505 PMCID: PMC7610410 DOI: 10.1038/s41587-020-0519-y] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 04/09/2020] [Indexed: 12/18/2022]
Abstract
With the exception of lamina-associated domains, the radial organization of chromatin in mammalian cells remains largely unexplored. Here, we describe genomic loci positioning by sequencing (GPSeq), a genome-wide method for inferring distances to the nuclear lamina all along the nuclear radius. GPSeq relies on gradual restriction digestion of chromatin from the nuclear lamina towards the nucleus center, followed by sequencing of the generated cut sites. Using GPSeq, we mapped the radial organization of the human genome at 100 kb resolution, which revealed radial patterns of genomic and epigenomic features, gene expression, as well as A/B subcompartments. By combining radial information with chromosome contact frequencies measured by Hi-C, we substantially improved the accuracy of whole-genome structure modeling. Finally, we charted the radial topography of DNA double-strand breaks, germline variants and cancer mutations, and found that they have distinctive radial arrangements in A/B subcompartments. We conclude that GPSeq can reveal fundamental aspects of genome architecture.
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37
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Boettiger A, Murphy S. Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends Genet 2020; 36:273-287. [PMID: 32007290 PMCID: PMC7197267 DOI: 10.1016/j.tig.2019.12.010] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/12/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2022]
Abstract
It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.
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Affiliation(s)
- Alistair Boettiger
- Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| | - Sedona Murphy
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
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38
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Crosetto N, Bienko M. Radial Organization in the Mammalian Nucleus. Front Genet 2020; 11:33. [PMID: 32117447 PMCID: PMC7028756 DOI: 10.3389/fgene.2020.00033] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/10/2020] [Indexed: 11/13/2022] Open
Abstract
In eukaryotic cells, most of the genetic material is contained within a highly specialized organelle—the nucleus. A large body of evidence indicates that, within the nucleus, chromatinized DNA is spatially organized at multiple length scales. The higher-order organization of chromatin is crucial for proper execution of multiple genome functions, including DNA replication and transcription. Here, we review our current knowledge on the spatial organization of chromatin in the nucleus of mammalian cells, focusing in particular on how chromatin is radially arranged with respect to the nuclear lamina. We then discuss the possible mechanisms by which the radial organization of chromatin in the cell nucleus is established. Lastly, we propose a unifying model of nuclear spatial organization, and suggest novel approaches to test it.
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Affiliation(s)
- Nicola Crosetto
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Magda Bienko
- Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
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