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Bedree JK, Bourgeois J, Balani P, Cen L, Hendrickson EL, Kerns KA, Camilli A, McLean JS, Shi W, He X. Identifying essential genes in Schaalia odontolytica using a highly-saturated transposon library. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.604004. [PMID: 39071323 PMCID: PMC11275721 DOI: 10.1101/2024.07.17.604004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
The unique epibiotic-parasitic relationship between Nanosynbacter lyticus type strain TM7x, a member of the newly identified Candidate Phyla Radiation, now referred to as Patescibacteria, and its basibiont, Schaalia odontolytica strain XH001 (formerly Actinomyces odontolyticus), require more powerful genetic tools for deeper understanding of the genetic underpinnings that mediate their obligate relationship. Previous studies have mainly characterized the genomic landscape of XH001 during or post TM7x infection through comparative genomic or transcriptomic analyses followed by phenotypic analysis. Comprehensive genetic dissection of the pair is currently cumbersome due to the lack of robust genetic tools in TM7x. However, basic genetic tools are available for XH001 and this study expands the current genetic toolset by developing high-throughput transposon insertion sequencing (Tn-seq). Tn-seq was employed to screen for essential genes in XH001 under laboratory conditions. A highly saturated Tn-seq library was generated with nearly 660,000 unique insertion mutations, averaging one insertion every 2-3 nucleotides. 203 genes, 10.5% of the XH001 genome, were identified as putatively essential.
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Affiliation(s)
- Joseph K Bedree
- Section of Oral Biology, Division of Oral Biology and Medicine, School of Dentistry, University of California-Los Angeles, Los Angeles, CA, 90095
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Jacob Bourgeois
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Pooja Balani
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA 02115
| | - Lujia Cen
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Erik L Hendrickson
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Kristopher A Kerns
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Andrew Camilli
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Jeffrey S McLean
- Department of Periodontics, School of Dentistry, University of Washington, Seattle, WA, 98195
| | - Wenyuan Shi
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
| | - Xuesong He
- Department of Microbiology, The ADA Forsyth Institute; Cambridge, MA, 02142
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2
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Jia H, Tan S, Cai Y, Guo Y, Shen J, Zhang Y, Ma H, Zhang Q, Chen J, Qiao G, Ruan J, Zhang YE. Low-input PacBio sequencing generates high-quality individual fly genomes and characterizes mutational processes. Nat Commun 2024; 15:5644. [PMID: 38969648 PMCID: PMC11226609 DOI: 10.1038/s41467-024-49992-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Long-read sequencing, exemplified by PacBio, revolutionizes genomics, overcoming challenges like repetitive sequences. However, the high DNA requirement ( > 1 µg) is prohibitive for small organisms. We develop a low-input (100 ng), low-cost, and amplification-free library-generation method for PacBio sequencing (LILAP) using Tn5-based tagmentation and DNA circularization within one tube. We test LILAP with two Drosophila melanogaster individuals, and generate near-complete genomes, surpassing preexisting single-fly genomes. By analyzing variations in these two genomes, we characterize mutational processes: complex transpositions (transposon insertions together with extra duplications and/or deletions) prefer regions characterized by non-B DNA structures, and gene conversion of transposons occurs on both DNA and RNA levels. Concurrently, we generate two complete assemblies for the endosymbiotic bacterium Wolbachia in these flies and similarly detect transposon conversion. Thus, LILAP promises a broad PacBio sequencing adoption for not only mutational studies of flies and their symbionts but also explorations of other small organisms or precious samples.
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Affiliation(s)
- Hangxing Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Shengjun Tan
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Yingao Cai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yanyan Guo
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jieyu Shen
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiong Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Huijing Ma
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Qingzhu Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinfeng Chen
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Management of Pest Insects and Rodents, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gexia Qiao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jue Ruan
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
- University of Chinese Academy of Sciences, Beijing, China.
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3
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Pike A, Pietryski C, Deighan P, Kuehner J, Lau D, Seshan A, March PE. A simple, robust, broadly applicable insertion mutagenesis method to create random fluorescent protein: target protein fusions. G3 (BETHESDA, MD.) 2024; 14:jkae036. [PMID: 38366837 PMCID: PMC11075570 DOI: 10.1093/g3journal/jkae036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/18/2023] [Accepted: 02/05/2024] [Indexed: 02/18/2024]
Abstract
A simple, broadly applicable method was developed using an in vitro transposition reaction followed by transformation into Escherichia coli and screening plates for fluorescent colonies. The transposition reaction catalyzes the random insertion of a fluorescent protein open reading frame into a target gene on a plasmid. The transposition reaction is employed directly in an E. coli transformation with no further procedures. Plating at high colony density yields fluorescent colonies. Plasmids purified from fluorescent colonies contain random, in-frame fusion proteins into the target gene. The plate screen also results in expressed, stable proteins. A large library of chimeric proteins was produced, which was useful for downstream research. The effect of using different fluorescent proteins was investigated as well as the dependence of the linker sequence between the target and fluorescent protein open reading frames. The utility and simplicity of the method were demonstrated by the fact that it has been employed in an undergraduate biology laboratory class without failure over dozens of class sections. This suggests that the method will be useful in high-impact research at small liberal arts colleges with limited resources. However, in-frame fusion proteins were obtained from 8 different targets suggesting that the method is broadly applicable in any research setting.
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Affiliation(s)
- Andrew Pike
- Department of Biology, Oberlin College and Conservatory, 173 W. Lorain St, Oberlin, OH 44074, USA
| | - Cassandra Pietryski
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
| | - Padraig Deighan
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
| | - Jason Kuehner
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
| | - Derek Lau
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
| | - Anupama Seshan
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
| | - Paul E March
- Department of Biology, Emmanuel College, 400 The Fenway, Boston, MA 02115, USA
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Kutnowski N, Ghanim GE, Lee Y, Rio DC. Activity of zebrafish THAP9 transposase and zebrafish P element-like transposons. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.22.586318. [PMID: 38562726 PMCID: PMC10983969 DOI: 10.1101/2024.03.22.586318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Transposable elements are mobile DNA segments that are found ubiquitously across the three domains of life. One family of transposons, called P elements, were discovered in the fruit fly Drosophila melanogaster. Since their discovery, P element transposase-homologous genes (called THAP-domain containing 9 or THAP9) have been discovered in other animal genomes. Here, we show that the zebrafish (Danio rerio) genome contains both an active THAP9 transposase (zfTHAP9) and mobile P-like transposable elements (called Pdre). zfTHAP9 transposase can excise one of its own elements (Pdre2) and Drosophila P elements. Drosophila P element transposase (DmTNP) is also able to excise the zebrafish Pdre2 element, even though it's distinct from the Drosophila P element. However, zfTHAP9 cannot transpose Pdre2 or Drosophila P elements, indicating partial transposase activity. Characterization of the N-terminal THAP DNA binding domain of zfTHAP9 shows distinct DNA binding site preferences from DmTNP and mutation of the zfTHAP9, based on known mutations in DmTNP, generated a hyperactive protein,. These results define an active vertebrate THAP9 transposase that can act on the endogenous zebrafish Pdre and Drosophila P elements.
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Affiliation(s)
- Nitzan Kutnowski
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - George E Ghanim
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Yeon Lee
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Donald C Rio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
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5
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Laub V, Devraj K, Elias L, Schulte D. Bioinformatics for wet-lab scientists: practical application in sequencing analysis. BMC Genomics 2023; 24:382. [PMID: 37420172 DOI: 10.1186/s12864-023-09454-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/15/2023] [Indexed: 07/09/2023] Open
Abstract
BACKGROUND Genomics data is available to the scientific community after publication of research projects and can be investigated for a multitude of research questions. However, in many cases deposited data is only assessed and used for the initial publication, resulting in valuable resources not being exploited to their full depth. MAIN: A likely reason for this is that many wetlab-based researchers are not formally trained to apply bioinformatic tools and may therefore assume that they lack the necessary experience to do so themselves. In this article, we present a series of freely available, predominantly web-based platforms and bioinformatic tools that can be combined in analysis pipelines to interrogate different types of next-generation sequencing data. Additionally to the presented exemplary route, we also list a number of alternative tools that can be combined in a mix-and-match fashion. We place special emphasis on tools that can be followed and used correctly without extensive prior knowledge in programming. Such analysis pipelines can be applied to existing data downloaded from the public domain or be compared to the results of own experiments. CONCLUSION Integrating transcription factor binding to chromatin (ChIP-seq) with transcriptional output (RNA-seq) and chromatin accessibility (ATAC-seq) can not only assist to form a deeper understanding of the molecular interactions underlying transcriptional regulation but will also help establishing new hypotheses and pre-testing them in silico.
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Affiliation(s)
- Vera Laub
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany.
| | - Kavi Devraj
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, Telangana, India
| | - Lena Elias
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
| | - Dorothea Schulte
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Goethe University, Frankfurt, Germany
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6
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Chen N, Vohra M, Saladi SV. Protocol for Bulk-ATAC sequencing in head and neck squamous cell carcinoma. STAR Protoc 2023; 4:102233. [PMID: 37071527 DOI: 10.1016/j.xpro.2023.102233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 02/21/2023] [Accepted: 03/21/2023] [Indexed: 04/19/2023] Open
Abstract
The transposase-accessible chromatin using sequencing (ATAC-seq) offers a simplified approach to detect chromatin changes in cancer cells after genetic intervention and drug treatment. Here, we present an optimized ATAC-seq protocol to elucidate chromatin accessibility changes at the epigenetic level in head and neck squamous cell carcinoma cells. We describe steps for cell lysate preparation, transposition, and tagmentation, followed by library amplification and purification. We then detail next-generation sequencing and data analysis. For complete details on the use and execution of this protocol, please refer to Buenrostro et al.,1 Chen et al.,2.
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Affiliation(s)
- Nana Chen
- Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA.
| | - Manik Vohra
- Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Srinivas Vinod Saladi
- Department of Otolaryngology, Head and Neck Surgery, Massachusetts Eye and Ear Infirmary, Harvard Medical School, Head and Neck Lab, 20 Staniford Street 2W, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
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7
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Zhang Y, Tang Y, Sun Z, Jia J, Fang Y, Wan X, Fang D. Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing. Genome Res 2023; 33:412-426. [PMID: 36958795 PMCID: PMC10078286 DOI: 10.1101/gr.277213.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 02/01/2023] [Indexed: 03/25/2023]
Abstract
Tn5 transposon tagments double-stranded DNA and RNA/DNA hybrids to generate nucleic acids that are ready to be amplified for high-throughput sequencing. The nucleic acid substrates for the Tn5 transposon must be explored to increase the applications of Tn5. Here, we found that the Tn5 transposon can transpose oligos into the 5' end of single-stranded DNA longer than 140 nucleotides. Based on this property of Tn5, we developed a tagmentation-based and ligation-enabled single-stranded DNA sequencing method called TABLE-seq. Through a series of reaction temperature, time, and enzyme concentration tests, we applied TABLE-seq to strand-specific RNA sequencing, starting with as little as 30 pg of total RNA. Moreover, compared with traditional dUTP-based strand-specific RNA sequencing, this method detects more genes, has a higher strand specificity, and shows more evenly distributed reads across genes. Together, our results provide insights into the properties of Tn5 transposons and expand the applications of Tn5 in cutting-edge sequencing techniques.
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Affiliation(s)
- Yanjun Zhang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yin Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Zhongxing Sun
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Junqi Jia
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yuan Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Xinyi Wan
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Dong Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China;
- Department of Medical Oncology, Key Laboratory of Cancer Prevention and Intervention, Ministry of Education, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China
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8
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McKenzie AM, Henry C, Myers KS, Place MM, Keck JL. Identification of genetic interactions with priB links the PriA/PriB DNA replication restart pathway to double-strand DNA break repair in Escherichia coli. G3 (BETHESDA, MD.) 2022; 12:jkac295. [PMID: 36326440 PMCID: PMC9713433 DOI: 10.1093/g3journal/jkac295] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/20/2022] [Indexed: 11/30/2023]
Abstract
Collisions between DNA replication complexes (replisomes) and impediments such as damaged DNA or proteins tightly bound to the chromosome lead to premature dissociation of replisomes at least once per cell cycle in Escherichia coli. Left unrepaired, these events produce incompletely replicated chromosomes that cannot be properly partitioned into daughter cells. DNA replication restart, the process that reloads replisomes at prematurely terminated sites, is therefore essential in E. coli and other bacteria. Three replication restart pathways have been identified in E. coli: PriA/PriB, PriA/PriC, and PriC/Rep. A limited number of genetic interactions between replication restart and other genome maintenance pathways have been defined, but a systematic study placing replication restart reactions in a broader cellular context has not been performed. We have utilized transposon-insertion sequencing to identify new genetic interactions between DNA replication restart pathways and other cellular systems. Known genetic interactors with the priB replication restart gene (uniquely involved in the PriA/PriB pathway) were confirmed and several novel priB interactions were discovered. Targeted genetic and imaging-based experiments with priB and its genetic partners revealed significant double-strand DNA break accumulation in strains with mutations in dam, rep, rdgC, lexA, or polA. Modulating the activity of the RecA recombinase partially suppressed the detrimental effects of rdgC or lexA mutations in ΔpriB cells. Taken together, our results highlight roles for several genes in double-strand DNA break homeostasis and define a genetic network that facilitates DNA repair/processing upstream of PriA/PriB-mediated DNA replication restart in E. coli.
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Affiliation(s)
- Aidan M McKenzie
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
| | - Camille Henry
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kevin S Myers
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - Michael M Place
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI 53726, USA
| | - James L Keck
- Department of Biomolecular Chemistry, University of Wisconsin School of Medicine and Public Health, Madison, WI 53706, USA
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9
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Li Z, Zhao B, Qin C, Wang Y, Li T, Wang W. Chromatin Dynamics in Digestive System Cancer: Commander and Regulator. Front Oncol 2022; 12:935877. [PMID: 35965507 PMCID: PMC9372441 DOI: 10.3389/fonc.2022.935877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 06/23/2022] [Indexed: 11/30/2022] Open
Abstract
Digestive system tumors have a poor prognosis due to complex anatomy, insidious onset, challenges in early diagnosis, and chemoresistance. Epidemiological statistics has verified that digestive system tumors rank first in tumor-related death. Although a great number of studies are devoted to the molecular biological mechanism, early diagnostic markers, and application of new targeted drugs in digestive system tumors, the therapeutic effect is still not satisfactory. Epigenomic alterations including histone modification and chromatin remodeling are present in human cancers and are now known to cooperate with genetic changes to drive the cancer phenotype. Chromatin is the carrier of genetic information and consists of DNA, histones, non-histone proteins, and a small amount of RNA. Chromatin and nucleosomes control the stability of the eukaryotic genome and regulate DNA processes such as transcription, replication, and repair. The dynamic structure of chromatin plays a key role in this regulatory function. Structural fluctuations expose internal DNA and thus provide access to the nuclear machinery. The dynamic changes are affected by various complexes and epigenetic modifications. Variation of chromatin dynamics produces early and superior regulation of the expression of related genes and downstream pathways, thereby controlling tumor development. Intervention at the chromatin level can change the process of cancer earlier and is a feasible option for future tumor diagnosis and treatment. In this review, we introduced chromatin dynamics including chromatin remodeling, histone modifications, and chromatin accessibility, and current research on chromatin regulation in digestive system tumors was also summarized.
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10
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Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022; 17:1518-1552. [PMID: 35478247 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 112] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
Abstract
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) provides a simple and scalable way to detect the unique chromatin landscape associated with a cell type and how it may be altered by perturbation or disease. ATAC-seq requires a relatively small number of input cells and does not require a priori knowledge of the epigenetic marks or transcription factors governing the dynamics of the system. Here we describe an updated and optimized protocol for ATAC-seq, called Omni-ATAC, that is applicable across a broad range of cell and tissue types. The ATAC-seq workflow has five main steps: sample preparation, transposition, library preparation, sequencing and data analysis. This protocol details the steps to generate and sequence ATAC-seq libraries, with recommendations for sample preparation and downstream bioinformatic analysis. ATAC-seq libraries for roughly 12 samples can be generated in 10 h by someone familiar with basic molecular biology, and downstream sequencing analysis can be implemented using benchmarked pipelines by someone with basic bioinformatics skills and with access to a high-performance computing environment.
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Affiliation(s)
- Fiorella C Grandi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Hailey Modi
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - Lucas Kampman
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA.,Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA.,Department of Neurology, University of California San Francisco, San Francisco, CA, USA
| | - M Ryan Corces
- Gladstone Institute of Neurological Disease, San Francisco, CA, USA. .,Gladstone Institute of Data Science and Biotechnology, San Francisco, CA, USA. .,Department of Neurology, University of California San Francisco, San Francisco, CA, USA.
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11
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Nothof SA, Magdinier F, Van-Gils J. Chromatin Structure and Dynamics: Focus on Neuronal Differentiation and Pathological Implication. Genes (Basel) 2022; 13:genes13040639. [PMID: 35456445 PMCID: PMC9029427 DOI: 10.3390/genes13040639] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 03/28/2022] [Accepted: 03/31/2022] [Indexed: 02/07/2023] Open
Abstract
Chromatin structure is an essential regulator of gene expression. Its state of compaction contributes to the regulation of genetic programs, in particular during differentiation. Epigenetic processes, which include post-translational modifications of histones, DNA methylation and implication of non-coding RNA, are powerful regulators of gene expression. Neurogenesis and neuronal differentiation are spatio-temporally regulated events that allow the formation of the central nervous system components. Here, we review the chromatin structure and post-translational histone modifications associated with neuronal differentiation. Studying the impact of histone modifications on neuronal differentiation improves our understanding of the pathophysiological mechanisms of chromatinopathies and opens up new therapeutic avenues. In addition, we will discuss techniques for the analysis of histone modifications on a genome-wide scale and the pathologies associated with the dysregulation of the epigenetic machinery.
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Affiliation(s)
- Sophie A. Nothof
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Frédérique Magdinier
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
| | - Julien Van-Gils
- Marseille Medical Genetics, Aix Marseille University, Inserm, CEDEX 05, 13385 Marseille, France; (S.A.N.); (F.M.)
- Reference Center AD SOOR, AnDDI-RARE, Inserm U 1211, Medical Genetics Department, Bordeaux University, Center Hospitalier Universitaire de Bordeaux, 33076 Bordeaux, France
- Correspondence:
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12
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Optimization of the Omni-ATAC protocol to chromatin accessibility profiling in snap-frozen rat adipose and muscle tissues. MethodsX 2022; 9:101681. [PMID: 35464805 PMCID: PMC9027329 DOI: 10.1016/j.mex.2022.101681] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 03/22/2022] [Indexed: 01/11/2023] Open
Abstract
ATAC-seq is a fast and sensitive method for the epigenomic profiling of open chromatin and for mapping of transcription factor binding sites [1]. Despite the development of the Omni-ATAC protocol for the profiling of chromatin accessibility in frozen tissues [2], studies in adipose tissue have been restricted due to technical challenges including the high lipid content of adipocytes and reproducibility issues between replicates. Here, we provide a modified Omni-ATAC protocol that achieves high data reproducibility in various tissue types from rat, including adipose and muscle tissues [3].•This protocol describes a methodology that enables chromatin accessibility profiling from snap-frozen rat adipose and muscle tissues.•The technique comprises an optimized bead-based tissue homogenization process that substitutes to Dounce homogenization, reduces variability in the experimental procedure, and is adaptable to various tissue types.•In comparison with the Omni-ATAC protocol, the method described here results in improved ATAC-seq data quality that complies with ENCODE quality standards.
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13
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Riggs P, Blundell-Hunter G, Hagelberger J, Ren G, Ettwiller L, Berkmen M. Insertion Specificity of the hATx-6 Transposase of Hydra magnipapillata. Front Mol Biosci 2022; 8:734154. [PMID: 34988112 DOI: 10.3389/fmolb.2021.734154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 11/10/2021] [Indexed: 01/22/2023] Open
Abstract
Transposable elements (TE) are mobile genetic elements, present in all domains of life. They commonly encode a single transposase enzyme, that performs the excision and reintegration reactions, and these enzymes have been used in mutagenesis and creation of next-generation sequencing libraries. All transposases have some bias in the DNA sequence they bind to when reintegrating the TE DNA. We sought to identify a transposase that showed minimal sequence bias and could be produced recombinantly, using information from the literature and a novel bioinformatic analysis, resulting in the selection of the hATx-6 transposase from Hydra vulgaris (aka Hydra magnipapillata) for further study. This transposase was tested and shown to be active both in vitro and in vivo, and we were able to demonstrate very low sequence bias in its integration preference. This transposase could be an excellent candidate for use in biotechnology, such as the creation of next-generation sequencing libraries.
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Affiliation(s)
- Paul Riggs
- New England Biolabs, Ipswich, MA, United States
| | | | | | - Guoping Ren
- New England Biolabs, Ipswich, MA, United States
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14
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Wang X, Chen C, He C, Chen D, Yan W. Mapping open chromatin by ATAC-seq in bread wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:1074873. [PMID: 36466281 PMCID: PMC9709403 DOI: 10.3389/fpls.2022.1074873] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 10/31/2022] [Indexed: 05/14/2023]
Abstract
Gene transcription is largely regulated by cis-regulatory elements. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) is an emerging technology that can accurately map cis-regulatory elements in animals and plants. However, the presence of cell walls and chloroplasts in plants hinders the extraction of high-quality nuclei, thereby affects the quality of ATAC-seq data. Meanwhile, it is tricky to perform ATAC-seq with different tissue types, especially for those with limited size and amount. Moreover, with rapid growth of ATAC-seq datasets from plants, powerful and easy-to-use data analysis pipelines for ATAC-seq, especially for wheat is lacking. Here, we provided an all-in-one solution for mapping open chromatin in wheat including both experimental and data analysis procedure. We efficiently obtained nuclei with less cell debris from various wheat tissues. High-quality ATAC-seq data from young spike and ovary, which are hard to harvest were generated. We determined that the saturation sequencing depth of wheat ATAC-seq is about 16 Gb. Particularly, we developed a powerful and easy-to-use online pipeline to analyze the wheat ATAC-seq data and this pipeline can be easily extended to other plant species. The method developed here will facilitate plant regulatory genome study not only for wheat but also for other plant species.
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Affiliation(s)
- Xin Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chuanye Chen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
| | - Chao He
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Chao He, ; Wenhao Yan,
| | - Dijun Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, China
| | - Wenhao Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, China
- *Correspondence: Chao He, ; Wenhao Yan,
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15
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Zhang H, Lu T, Liu S, Yang J, Sun G, Cheng T, Xu J, Chen F, Yen K. Comprehensive understanding of Tn5 insertion preference improves transcription regulatory element identification. NAR Genom Bioinform 2021; 3:lqab094. [PMID: 34729473 PMCID: PMC8557372 DOI: 10.1093/nargab/lqab094] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 09/20/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Tn5 transposase, which can efficiently tagment the genome, has been widely adopted as a molecular tool in next-generation sequencing, from short-read sequencing to more complex methods such as assay for transposase-accessible chromatin using sequencing (ATAC-seq). Here, we systematically map Tn5 insertion characteristics across several model organisms, finding critical parameters that affect its insertion. On naked genomic DNA, we found that Tn5 insertion is not uniformly distributed or random. To uncover drivers of these biases, we used a machine learning framework, which revealed that DNA shape cooperatively works with DNA motif to affect Tn5 insertion preference. These intrinsic insertion preferences can be modeled using nucleotide dependence information from DNA sequences, and we developed a computational pipeline to correct for these biases in ATAC-seq data. Using our pipeline, we show that bias correction improves the overall performance of ATAC-seq peak detection, recovering many potential false-negative peaks. Furthermore, we found that these peaks are bound by transcription factors, underscoring the biological relevance of capturing this additional information. These findings highlight the benefits of an improved understanding and precise correction of Tn5 insertion preference.
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Affiliation(s)
- Houyu Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Shan Liu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jianyu Yang
- Department of Developmental Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Guohuan Sun
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jin Xu
- Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology, Guangzhou 510006, China
| | - Fangyao Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China
| | - Kuangyu Yen
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
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16
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Choudhery S, Brown AJ, Akusobi C, Rubin EJ, Sassetti CM, Ioerger TR. Modeling Site-Specific Nucleotide Biases Affecting Himar1 Transposon Insertion Frequencies in TnSeq Data Sets. mSystems 2021; 6:e0087621. [PMID: 34665010 PMCID: PMC8525568 DOI: 10.1128/msystems.00876-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 09/27/2021] [Indexed: 11/20/2022] Open
Abstract
TnSeq is a widely used methodology for determining gene essentiality, conditional fitness, and genetic interactions in bacteria. The Himar1 transposon is restricted to insertions at TA dinucleotides, but otherwise, few site-specific biases have been identified. As a result, most analytical approaches assume that insertions are expected to be randomly distributed among TA sites in nonessential regions. However, through analysis of Himar1 transposon libraries in Mycobacterium tuberculosis, we demonstrate that there are site-specific biases that affect the frequency of insertion of the Himar1 transposon at different TA sites. We use machine learning and statistical models to characterize patterns in the nucleotides surrounding TA sites that correlate with high or low insertion counts. We then develop a quantitative model based on these patterns that can be used to predict the expected counts at each TA site based on nucleotide context, which can explain up to half of the variance in insertion counts. We show that these insertion preferences exist in Himar1 TnSeq data sets from other mycobacterial and nonmycobacterial species. We present an improved method for identification of essential genes, called TTN-Fitness, that can better distinguish true biological fitness effects by comparing observed counts to expected counts based on our site-specific model of insertion preferences. Compared to previous essentiality methods, TTN-Fitness can make finer distinctions among genes whose disruption causes a fitness defect (or advantage), separating them out from the large pool of nonessentials, and is able to classify many smaller genes (with few TA sites) that were previously characterized as uncertain. IMPORTANCE When using the Himar1 transposon to create transposon insertion mutant libraries, it is known that the transposon is restricted to insertions at TA dinucleotide sites throughout the genome, and the absence of insertions is used to infer which genes are essential (or conditionally essential) in a bacterial organism. It is widely assumed that insertions in nonessential regions are otherwise random, and this assumption is used as the basis of several methods for statistical analysis of TnSeq data. In this paper, we show that the nucleotide sequence surrounding TA sites influences the magnitude of insertions, and these Himar1 insertion preferences (sequence biases) can partially explain why some sites have higher counts than others. We use this predictive model to make improved estimates of the fitness effects of genes, which help make finer distinctions of the phenotype and biological consequences of disruption of nonessential genes.
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Affiliation(s)
- Sanjeevani Choudhery
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - A. Jacob Brown
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
| | - Chidiebere Akusobi
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Eric J. Rubin
- Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, Massachusetts, USA
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, Texas, USA
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17
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Abstract
It has been just over 10 years since the initial description of transposase-based methods to prepare high-throughput sequencing libraries, or "tagmentation," in which a hyperactive transposase is used to simultaneously fragment target DNA and append universal adapter sequences. Tagmentation effectively replaced a series of processing steps in traditional workflows with one single reaction. It is the simplicity, coupled with the high efficiency of tagmentation, that has made it a favored means of sequencing library construction and fueled a diverse range of adaptations to assay a variety of molecular properties. In recent years, this has been centered in the single-cell space with a catalog of tagmentation-based assays that have been developed, covering a substantial swath of the regulatory landscape. To date, there have been a number of excellent reviews on single-cell technologies structured around the molecular properties that can be profiled. This review is instead framed around the central components and properties of tagmentation and how they have enabled the development of innovative molecular tools to probe the regulatory landscape of single cells. Furthermore, the granular specifics on cell throughput or richness of data provided by the extensive list of individual technologies are not discussed. Such metrics are rapidly changing and highly sample specific and are better left to studies that directly compare technologies for assays against one another in a rigorously controlled framework. The hope for this review is that, in laying out the diversity of molecular techniques at each stage of these assay platforms, new ideas may arise for others to pursue that will further advance the field of single-cell genomics.
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Affiliation(s)
- Andrew C Adey
- Department of Molecular & Medical Genetics, Knight Cancer Institute, Knight Cardiovascular Institute, Cancer Early Detection Advanced Research Center, Oregon Health and Science University, Portland, Oregon 97239, USA
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18
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In vitro amplification of whole large plasmids via transposon-mediated oriC insertion. Biotechniques 2021; 71:528-533. [PMID: 34463121 DOI: 10.2144/btn-2021-0068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
DNA amplification is a fundamental technique in molecular biology. The replication cycle reaction is a new method for amplification of large circular DNA having oriC sequences, which is a replication initiation site of the Escherichia coli chromosome. We here developed a replication cycle reaction-based method useful for amplification of various circular DNAs lacking oriC, even in the absence of any sequence information, via transposon-mediated oriC insertion to the circular DNA template. A 15-kb non-oriC plasmid was amplified from a very small amount of starting DNA (50 fg, 1 fM). The method was also applicable to GC-rich plasmid (69%) or large F-plasmid (230 kb). This method thus provides a powerful tool to amplify various environmental circular DNAs.
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19
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Xu W, Wen Y, Liang Y, Xu Q, Wang X, Jin W, Chen X. A plate-based single-cell ATAC-seq workflow for fast and robust profiling of chromatin accessibility. Nat Protoc 2021; 16:4084-4107. [PMID: 34282334 DOI: 10.1038/s41596-021-00583-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 06/04/2021] [Indexed: 02/06/2023]
Abstract
Profiling chromatin accessibility at the single-cell level provides critical information about cell type composition and cell-to-cell variation within a complex tissue. Emerging techniques for the interrogation of chromatin accessibility in individual cells allow investigation of the fundamental mechanisms that lead to the variability of different cells. This protocol describes a fast and robust method for single-cell chromatin accessibility profiling based on the assay for transposase-accessible chromatin using sequencing (ATAC-seq). The method combines up-front bulk Tn5 tagging of chromatin with flow cytometry to isolate single nuclei or cells. Reagents required to generate sequencing libraries are added to the same well in the plate where cells are sorted. The protocol described here generates data of high complexity and excellent signal-to-noise ratio and can be combined with index sorting for in-depth characterization of cell types. The whole experimental procedure can be finished within 1 or 2 d with a throughput of hundreds to thousands of nuclei, and the data can be processed by the provided computational pipeline. The execution of the protocol only requires basic techniques and equipment in a molecular biology laboratory with flow cytometry support.
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Affiliation(s)
- Wei Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yi Wen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yingying Liang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Qiushi Xu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xuefei Wang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenfei Jin
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xi Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China.
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20
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Bode D, Cull AH, Rubio-Lara JA, Kent DG. Exploiting Single-Cell Tools in Gene and Cell Therapy. Front Immunol 2021; 12:702636. [PMID: 34322133 PMCID: PMC8312222 DOI: 10.3389/fimmu.2021.702636] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
Single-cell molecular tools have been developed at an incredible pace over the last five years as sequencing costs continue to drop and numerous molecular assays have been coupled to sequencing readouts. This rapid period of technological development has facilitated the delineation of individual molecular characteristics including the genome, transcriptome, epigenome, and proteome of individual cells, leading to an unprecedented resolution of the molecular networks governing complex biological systems. The immense power of single-cell molecular screens has been particularly highlighted through work in systems where cellular heterogeneity is a key feature, such as stem cell biology, immunology, and tumor cell biology. Single-cell-omics technologies have already contributed to the identification of novel disease biomarkers, cellular subsets, therapeutic targets and diagnostics, many of which would have been undetectable by bulk sequencing approaches. More recently, efforts to integrate single-cell multi-omics with single cell functional output and/or physical location have been challenging but have led to substantial advances. Perhaps most excitingly, there are emerging opportunities to reach beyond the description of static cellular states with recent advances in modulation of cells through CRISPR technology, in particular with the development of base editors which greatly raises the prospect of cell and gene therapies. In this review, we provide a brief overview of emerging single-cell technologies and discuss current developments in integrating single-cell molecular screens and performing single-cell multi-omics for clinical applications. We also discuss how single-cell molecular assays can be usefully combined with functional data to unpick the mechanism of cellular decision-making. Finally, we reflect upon the introduction of spatial transcriptomics and proteomics, its complementary role with single-cell RNA sequencing (scRNA-seq) and potential application in cellular and gene therapy.
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Affiliation(s)
- Daniel Bode
- Wellcome Medical Research Council (MRC) Cambridge Stem Cell Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Alyssa H. Cull
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - Juan A. Rubio-Lara
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
| | - David G. Kent
- York Biomedical Research Institute, Department of Biology, University of York, York, United Kingdom
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21
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Rapid ordering of barcoded transposon insertion libraries of anaerobic bacteria. Nat Protoc 2021; 16:3049-3071. [PMID: 34021295 DOI: 10.1038/s41596-021-00531-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2019] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Commensal bacteria from the human intestinal microbiota play important roles in health and disease. Research into the mechanisms by which these bacteria exert their effects is hampered by the complexity of the microbiota, the strict growth requirements of the individual species and a lack of genetic tools and resources. The assembly of ordered transposon insertion libraries, in which nearly all nonessential genes have been disrupted and the strains stored as independent monocultures, would be a transformative resource for research into many microbiota members. However, assembly of these libraries must be fast and inexpensive in order to empower investigation of the large number of species that typically compose gut communities. The methods used to generate ordered libraries must also be adapted to the anaerobic growth requirements of most intestinal bacteria. We have developed a protocol to assemble ordered libraries of transposon insertion mutants that is fast, cheap and effective for even strict anaerobes. The protocol differs from currently available methods by making use of cell sorting to order the library and barcoded transposons to facilitate the localization of ordered mutations in the library. By tracking transposon insertions using barcode sequencing, our approach increases the accuracy and reduces the time and effort required to locate mutants in the library. Ordered libraries can be sorted and characterized over the course of 2 weeks using this approach. We expect this protocol will lower the barrier to generating comprehensive, ordered mutant libraries for many species in the human microbiota, allowing for new investigations into genotype-phenotype relationships within this important microbial ecosystem.
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22
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Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
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Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
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23
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Liscovitch-Brauer N, Montalbano A, Deng J, Méndez-Mancilla A, Wessels HH, Moss NG, Kung CY, Sookdeo A, Guo X, Geller E, Jaini S, Smibert P, Sanjana NE. Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens. Nat Biotechnol 2021; 39:1270-1277. [PMID: 33927415 DOI: 10.1038/s41587-021-00902-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 03/13/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]
Abstract
CRISPR screens have been used to connect genetic perturbations with changes in gene expression and phenotypes. Here we describe a CRISPR-based, single-cell combinatorial indexing assay for transposase-accessible chromatin (CRISPR-sciATAC) to link genetic perturbations to genome-wide chromatin accessibility in a large number of cells. In human myelogenous leukemia cells, we apply CRISPR-sciATAC to target 105 chromatin-related genes, generating chromatin accessibility data for ~30,000 single cells. We correlate the loss of specific chromatin remodelers with changes in accessibility globally and at the binding sites of individual transcription factors (TFs). For example, we show that loss of the H3K27 methyltransferase EZH2 increases accessibility at heterochromatic regions involved in embryonic development and triggers expression of genes in the HOXA and HOXD clusters. At a subset of regulatory sites, we also analyze changes in nucleosome spacing following the loss of chromatin remodelers. CRISPR-sciATAC is a high-throughput, single-cell method for studying the effect of genetic perturbations on chromatin in normal and disease states.
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Affiliation(s)
- Noa Liscovitch-Brauer
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Antonino Montalbano
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Jiale Deng
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Alejandro Méndez-Mancilla
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Hans-Hermann Wessels
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Nicholas G Moss
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Chia-Yu Kung
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Akash Sookdeo
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Xinyi Guo
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Evan Geller
- New York Genome Center, New York, NY, USA.,Department of Biology, New York University, New York, NY, USA
| | - Suma Jaini
- New York Genome Center, New York, NY, USA.,Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Peter Smibert
- New York Genome Center, New York, NY, USA.,Technology Innovation Lab, New York Genome Center, New York, NY, USA
| | - Neville E Sanjana
- New York Genome Center, New York, NY, USA. .,Department of Biology, New York University, New York, NY, USA.
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24
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Sinha S, Satpathy AT, Zhou W, Ji H, Stratton JA, Jaffer A, Bahlis N, Morrissy S, Biernaskie JA. Profiling Chromatin Accessibility at Single-cell Resolution. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:172-190. [PMID: 33581341 PMCID: PMC8602754 DOI: 10.1016/j.gpb.2020.06.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 03/04/2020] [Accepted: 08/15/2020] [Indexed: 01/22/2023]
Abstract
How distinct transcriptional programs are enacted to generate cellular heterogeneity and plasticity, and enable complex fate decisions are important open questions. One key regulator is the cell’s epigenome state that drives distinct transcriptional programs by regulating chromatin accessibility. Genome-wide chromatin accessibility measurements can impart insights into regulatory sequences (in)accessible to DNA-binding proteins at a single-cell resolution. This review outlines molecular methods and bioinformatic tools for capturing cell-to-cell chromatin variation using single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) in a scalable fashion. It also covers joint profiling of chromatin with transcriptome/proteome measurements, computational strategies to integrate multi-omic measurements, and predictive bioinformatic tools to infer chromatin accessibility from single-cell transcriptomic datasets. Methodological refinements that increase power for cell discovery through robust chromatin coverage and integrate measurements from multiple modalities will further expand our understanding of gene regulation during homeostasis and disease.
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Affiliation(s)
- Sarthak Sinha
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada.
| | - Ansuman T Satpathy
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Weiqiang Zhou
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Hongkai Ji
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Jo A Stratton
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Arzina Jaffer
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Nizar Bahlis
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada
| | - Sorana Morrissy
- Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 4Z6, Canada; Department of Biochemistry and Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Jeff A Biernaskie
- Department of Comparative Biology & Experimental Medicine, Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; Alberta Children's Hospital Research Institute, University of Calgary, Calgary, AB T2N 4N1, Canada; Hotchkiss Brain Institute, University of Calgary, Calgary, AB T2N 4N1, Canada.
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25
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Minnoye L, Marinov GK, Krausgruber T, Pan L, Marand AP, Secchia S, Greenleaf WJ, Furlong EEM, Zhao K, Schmitz RJ, Bock C, Aerts S. Chromatin accessibility profiling methods. NATURE REVIEWS. METHODS PRIMERS 2021; 1:10. [PMID: 38410680 PMCID: PMC10895463 DOI: 10.1038/s43586-020-00008-9] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/01/2020] [Indexed: 02/06/2023]
Abstract
Chromatin accessibility, or the physical access to chromatinized DNA, is a widely studied characteristic of the eukaryotic genome. As active regulatory DNA elements are generally 'accessible', the genome-wide profiling of chromatin accessibility can be used to identify candidate regulatory genomic regions in a tissue or cell type. Multiple biochemical methods have been developed to profile chromatin accessibility, both in bulk and at the single-cell level. Depending on the method, enzymatic cleavage, transposition or DNA methyltransferases are used, followed by high-throughput sequencing, providing a view of genome-wide chromatin accessibility. In this Primer, we discuss these biochemical methods, as well as bioinformatics tools for analysing and interpreting the generated data, and insights into the key regulators underlying developmental, evolutionary and disease processes. We outline standards for data quality, reproducibility and deposition used by the genomics community. Although chromatin accessibility profiling is invaluable to study gene regulation, alone it provides only a partial view of this complex process. Orthogonal assays facilitate the interpretation of accessible regions with respect to enhancer-promoter proximity, functional transcription factor binding and regulatory function. We envision that technological improvements including single-molecule, multi-omics and spatial methods will bring further insight into the secrets of genome regulation.
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Affiliation(s)
- Liesbeth Minnoye
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Thomas Krausgruber
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lixia Pan
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Stefano Secchia
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | | | - Eileen E M Furlong
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, Division of Intramural Research, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA
| | | | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- Institute of Artificial Intelligence and Decision Support, Center for Medical Statistics, Informatics, and Intelligent Systems, Medical University of Vienna, Vienna, Austria
| | - Stein Aerts
- Center for Brain & Disease Research, VIB-KU Leuven, Leuven, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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26
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Abstract
Recent studies have renewed interest in developing novel antiviral therapeutics and vaccines based on defective interfering particles (DIPs)—a subset of viral deletion mutants that conditionally replicate. Identifying and engineering DIPs require that viral cis- and trans-acting elements be accurately mapped. It has long been known that noncoding genomic regions can be obligate cis elements acted upon in trans by gene products. In viruses, cis elements regulate gene expression, encapsidation, and other maturation processes, but mapping these elements relies on targeted iterative deletion or laborious prospecting for rare spontaneously occurring mutants. Here, we introduce a method to comprehensively map viral cis and trans elements at single-nucleotide resolution by high-throughput random deletion. Variable-size deletions are randomly generated by transposon integration, excision, and exonuclease chewback and then barcoded for tracking via sequencing (i.e., random deletion library sequencing [RanDeL-seq]). Using RanDeL-seq, we generated and screened >23,000 HIV-1 variants to generate a single-base resolution map of HIV-1’s cis and trans elements. The resulting landscape recapitulated HIV-1’s known cis-acting elements (i.e., long terminal repeat [LTR], Ψ, and Rev response element [RRE]) and, surprisingly, indicated that HIV-1’s central DNA flap (i.e., central polypurine tract [cPPT] to central termination sequence [CTS]) is as critical as the LTR, Ψ, and RRE for long-term passage. Strikingly, RanDeL-seq identified a previously unreported ∼300-bp region downstream of RRE extending to splice acceptor 7 that is equally critical for sustained viral passage. RanDeL-seq was also used to construct and screen a library of >90,000 variants of Zika virus (ZIKV). Unexpectedly, RanDeL-seq indicated that ZIKV’s cis-acting regions are larger than the untranscribed (UTR) termini, encompassing a large fraction of the nonstructural genes. Collectively, RanDeL-seq provides a versatile framework for generating viral deletion mutants, enabling discovery of replication mechanisms and development of novel antiviral therapeutics, particularly for emerging viral infections.
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Zachariadis V, Cheng H, Andrews N, Enge M. A Highly Scalable Method for Joint Whole-Genome Sequencing and Gene-Expression Profiling of Single Cells. Mol Cell 2020; 80:541-553.e5. [PMID: 33068522 DOI: 10.1016/j.molcel.2020.09.025] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/17/2020] [Accepted: 09/21/2020] [Indexed: 12/18/2022]
Abstract
To address how genetic variation alters gene expression in complex cell mixtures, we developed direct nuclear tagmentation and RNA sequencing (DNTR-seq), which enables whole-genome and mRNA sequencing jointly in single cells. DNTR-seq readily identified minor subclones within leukemia patients. In a large-scale DNA damage screen, DNTR-seq was used to detect regions under purifying selection and identified genes where mRNA abundance was resistant to copy-number alteration, suggesting strong genetic compensation. mRNA sequencing (mRNA-seq) quality equals RNA-only methods, and the low positional bias of genomic libraries allowed detection of sub-megabase aberrations at ultra-low coverage. Each cell library is individually addressable and can be re-sequenced at increased depth, allowing multi-tiered study designs. Additionally, the direct tagmentation protocol enables coverage-independent estimation of ploidy, which can be used to identify cell singlets. Thus, DNTR-seq directly links each cell's state to its corresponding genome at scale, enabling routine analysis of heterogeneous tumors and other complex tissues.
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Affiliation(s)
- Vasilios Zachariadis
- Department of Oncology-Pathology Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Huaitao Cheng
- Department of Oncology-Pathology Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Nathanael Andrews
- Department of Oncology-Pathology Karolinska Institutet, 171 64 Stockholm, Sweden
| | - Martin Enge
- Department of Oncology-Pathology Karolinska Institutet, 171 64 Stockholm, Sweden.
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28
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Yoshimura A, Covington BC, Gallant É, Zhang C, Li A, Seyedsayamdost MR. Unlocking Cryptic Metabolites with Mass Spectrometry-Guided Transposon Mutant Selection. ACS Chem Biol 2020; 15:2766-2774. [PMID: 32808751 DOI: 10.1021/acschembio.0c00558] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The products of most secondary metabolite biosynthetic gene clusters (BGCs) have yet to be discovered, in part due to low expression levels in laboratory cultures. Reporter-guided mutant selection (RGMS) has recently been developed for this purpose: a mutant library is generated and screened, using genetic reporters to a chosen BGC, to select transcriptionally active mutants that then enable the characterization of the "cryptic" metabolite. The requirement for genetic reporters limits the approach to a single pathway within genetically tractable microorganisms. Herein, we utilize untargeted metabolomics in conjunction with transposon mutagenesis to provide a global read-out of secondary metabolism across large numbers of mutants. We employ self-organizing map analytics and imaging mass spectrometry to identify and characterize seven cryptic metabolites from mutant libraries of two different Burkholderia species. Applications of the methodologies reported can expand our understanding of the products and regulation of cryptic BGCs across phylogenetically diverse bacteria.
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Affiliation(s)
- Aya Yoshimura
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Brett C. Covington
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Étienne Gallant
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Chen Zhang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Anran Li
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
| | - Mohammad R. Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
- Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544, United States
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29
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Ma S, Zhang Y. Profiling chromatin regulatory landscape: insights into the development of ChIP-seq and ATAC-seq. MOLECULAR BIOMEDICINE 2020; 1:9. [PMID: 34765994 PMCID: PMC7546943 DOI: 10.1186/s43556-020-00009-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/04/2020] [Indexed: 12/16/2022] Open
Abstract
Chromatin regulatory landscape plays a critical role in many disease processes and embryo development. Epigenome sequencing technologies such as chromatin immunoprecipitation sequencing (ChIP-seq) and assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) have enabled us to dissect the pan-genomic regulatory landscape of cells and tissues in both time and space dimensions by detecting specific chromatin state and its corresponding transcription factors. Pioneered by the advancement of chromatin immunoprecipitation-chip (ChIP-chip) technology, abundant epigenome profiling technologies have become available such as ChIP-seq, DNase I hypersensitive site sequencing (DNase-seq), ATAC-seq and so on. The advent of single-cell sequencing has revolutionized the next-generation sequencing, applications in single-cell epigenetics are enriched rapidly. Epigenome sequencing technologies have evolved from low-throughput to high-throughput and from bulk sample to the single-cell scope, which unprecedentedly benefits scientists to interpret life from different angles. In this review, after briefly introducing the background knowledge of epigenome biology, we discuss the development of epigenome sequencing technologies, especially ChIP-seq & ATAC-seq and their current applications in scientific research. Finally, we provide insights into future applications and challenges.
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Affiliation(s)
- Shaoqian Ma
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
| | - Yongyou Zhang
- School of Life Sciences, Xiamen University, Xiamen, 361102 Fujian China
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30
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Cree SL, Chua EW, Crowther J, Dobson RCJ, Kennedy MA. G-quadruplex structures bind to EZ-Tn5 transposase. Biochimie 2020; 177:190-197. [PMID: 32805304 DOI: 10.1016/j.biochi.2020.07.022] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 07/31/2020] [Accepted: 07/31/2020] [Indexed: 11/17/2022]
Abstract
Next generation DNA sequencing and analysis of amplicons spanning the pharmacogene CYP2D6 suggested that the Nextera transposase used for fragmenting and providing sequencing priming sites displayed a targeting bias. This manifested as dramatically lower sequencing coverage at sites in the amplicon that appeared likely to form G-quadruplex structures. Since secondary DNA structures such as G-quadruplexes are abundant in the human genome, and are known to interact with many other proteins, we further investigated these sites of low coverage. Our investigation revealed that G-quadruplex structures are formed in vitro within the CYP2D6 pharmacogene at these sites, and G-quadruplexes can interact with the hyperactive Tn5 transposase (EZ-Tn5) with high affinity. These findings indicate that secondary DNA structures such as G-quadruplexes may represent preferential transposon integration sites and provide additional evidence for the role of G-quadruplex structures in transposition or viral integration processes.
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Affiliation(s)
- Simone L Cree
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Eng Wee Chua
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand
| | - Jennifer Crowther
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Renwick C J Dobson
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand; Bio21 Molecular Science and Biotechnology Institute, Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Martin A Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, 8140, New Zealand.
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31
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Lu B, Dong L, Yi D, Zhang M, Zhu C, Li X, Yi C. Transposase-assisted tagmentation of RNA/DNA hybrid duplexes. eLife 2020; 9:54919. [PMID: 32701057 PMCID: PMC7402673 DOI: 10.7554/elife.54919] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/22/2020] [Indexed: 12/22/2022] Open
Abstract
Tn5-mediated transposition of double-strand DNA has been widely utilized in various high-throughput sequencing applications. Here, we report that the Tn5 transposase is also capable of direct tagmentation of RNA/DNA hybrids in vitro. As a proof-of-concept application, we utilized this activity to replace the traditional library construction procedure of RNA sequencing, which contains many laborious and time-consuming processes. Results of Transposase-assisted RNA/DNA hybrids Co-tagmEntation (termed ‘TRACE-seq’) are compared to traditional RNA-seq methods in terms of detected gene number, gene body coverage, gene expression measurement, library complexity, and differential expression analysis. At the meantime, TRACE-seq enables a cost-effective one-tube library construction protocol and hence is more rapid (within 6 hr) and convenient. We expect this tagmentation activity on RNA/DNA hybrids to have broad potentials on RNA biology and chromatin research.
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Affiliation(s)
- Bo Lu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Liting Dong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Danyang Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chenxu Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Xiaoyu Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.,Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China
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32
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Kesselring L, Miskey C, Zuliani C, Querques I, Kapitonov V, Laukó A, Fehér A, Palazzo A, Diem T, Lustig J, Sebe A, Wang Y, Dinnyés A, Izsvák Z, Barabas O, Ivics Z. A single amino acid switch converts the Sleeping Beauty transposase into an efficient unidirectional excisionase with utility in stem cell reprogramming. Nucleic Acids Res 2020; 48:316-331. [PMID: 31777924 PMCID: PMC6943129 DOI: 10.1093/nar/gkz1119] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 11/07/2019] [Accepted: 11/22/2019] [Indexed: 12/26/2022] Open
Abstract
The Sleeping Beauty (SB) transposon is an advanced tool for genetic engineering and a useful model to investigate cut-and-paste DNA transposition in vertebrate cells. Here, we identify novel SB transposase mutants that display efficient and canonical excision but practically unmeasurable genomic re-integration. Based on phylogenetic analyses, we establish compensating amino acid replacements that fully rescue the integration defect of these mutants, suggesting epistasis between these amino acid residues. We further show that the transposons excised by the exc+/int− transposase mutants form extrachromosomal circles that cannot undergo a further round of transposition, thereby representing dead-end products of the excision reaction. Finally, we demonstrate the utility of the exc+/int− transposase in cassette removal for the generation of reprogramming factor-free induced pluripotent stem cells. Lack of genomic integration and formation of transposon circles following excision is reminiscent of signal sequence removal during V(D)J recombination, and implies that cut-and-paste DNA transposition can be converted to a unidirectional process by a single amino acid change.
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Affiliation(s)
- Lisa Kesselring
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Csaba Miskey
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Cecilia Zuliani
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Vladimir Kapitonov
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | | | - Anita Fehér
- BioTalentum Ltd, Gödöllő, 2100 Gödöllő, Hungary
| | - Antonio Palazzo
- Department of Biology, University of Bari 'Aldo Moro', Italy
| | - Tanja Diem
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Janna Lustig
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Attila Sebe
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
| | - Yongming Wang
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | | | - Zsuzsanna Izsvák
- Mobile DNA, Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Zoltán Ivics
- Transposition and Genome Engineering, Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany
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33
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Ryan GE, Farley EK. Functional genomic approaches to elucidate the role of enhancers during development. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2020; 12:e1467. [PMID: 31808313 PMCID: PMC7027484 DOI: 10.1002/wsbm.1467] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 10/02/2019] [Accepted: 10/11/2019] [Indexed: 12/22/2022]
Abstract
Successful development depends on the precise tissue-specific regulation of genes by enhancers, genetic elements that act as switches to control when and where genes are expressed. Because enhancers are critical for development, and the majority of disease-associated mutations reside within enhancers, it is essential to understand which sequences within enhancers are important for function. Advances in sequencing technology have enabled the rapid generation of genomic data that predict putative active enhancers, but functionally validating these sequences at scale remains a fundamental challenge. Herein, we discuss the power of genome-wide strategies used to identify candidate enhancers, and also highlight limitations and misconceptions that have arisen from these data. We discuss the use of massively parallel reporter assays to test enhancers for function at scale. We also review recent advances in our ability to study gene regulation during development, including CRISPR-based tools to manipulate genomes and single-cell transcriptomics to finely map gene expression. Finally, we look ahead to a synthesis of complementary genomic approaches that will advance our understanding of enhancer function during development. This article is categorized under: Physiology > Mammalian Physiology in Health and Disease Developmental Biology > Developmental Processes in Health and Disease Laboratory Methods and Technologies > Genetic/Genomic Methods.
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Affiliation(s)
- Genevieve E. Ryan
- Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
- Division of Biological Sciences, Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
| | - Emma K. Farley
- Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
- Division of Biological Sciences, Department of MedicineUniversity of CaliforniaSan DiegoCalifornia
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34
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Abstract
RNA sequencing is widely used to measure gene expression in biomedical research; therefore, improvements in the simplicity and accuracy of the technology are desirable. All existing RNA sequencing methods rely on the conversion of RNA into double-stranded DNA through reverse transcription followed by second-strand synthesis. The latter step requires additional enzymes and purification, and introduces sequence-dependent bias. Here, we show that Tn5 transposase, which randomly binds and cuts double-stranded DNA, can directly fragment and prime the RNA/DNA heteroduplexes generated by reverse transcription. The primed fragments are then subject to PCR amplification. This provides an approach for simple and accurate RNA characterization and quantification. Transcriptome profiling by RNA sequencing (RNA-seq) has been widely used to characterize cellular status, but it relies on second-strand complementary DNA (cDNA) synthesis to generate initial material for library preparation. Here we use bacterial transposase Tn5, which has been increasingly used in various high-throughput DNA analyses, to construct RNA-seq libraries without second-strand synthesis. We show that Tn5 transposome can randomly bind RNA/DNA heteroduplexes and add sequencing adapters onto RNA directly after reverse transcription. This method, Sequencing HEteRo RNA-DNA-hYbrid (SHERRY), is versatile and scalable. SHERRY accepts a wide range of starting materials, from bulk RNA to single cells. SHERRY offers a greatly simplified protocol and produces results with higher reproducibility and GC uniformity compared with prevailing RNA-seq methods.
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35
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Guynet C, Nicolas E, Ton-Hoang B, Bouet JY, Hallet B. First Biochemical Steps on Bacterial Transposition Pathways. Methods Mol Biol 2020; 2075:157-177. [PMID: 31584162 DOI: 10.1007/978-1-4939-9877-7_12] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Transposons are found in a wide variety of forms throughout the prokaryotic world where they actively contribute to the adaptive strategies of bacterial communities and hence, to the continuous emergence of new multiresistant pathogens. Contrasting with their biological and societal impact, only a few bacterial transposons have been the subject of detailed molecular studies. In this chapter, we propose a set of reliable biochemical methods as a primary route for studying new transposition mechanisms. These methods include (a) a straightforward approach termed "thermal shift induction" to produce the transposase in a soluble and properly folded configuration prior to its purification, (b) an adaptation of classical electrophoretic mobility shift assays (EMSA) combined to fluorescently labeled DNA substrates to determine the DNA content of different complexes assembled by the transposase, and (c) a highly sensitive "in-gel" DNA footprinting assay to further characterize these complexes at the base pair resolution level. A combination of these approaches was recently applied to decipher the molecular organization of key intermediates in the Tn3-family transposition pathway, a mechanism that has long been refractory to biochemical studies.
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Affiliation(s)
- Catherine Guynet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France.
| | - Emilien Nicolas
- Laboratory of Evolutionary Genetics and Ecology (LEGE), Department of Biology-URBE, University of Namur (UNamur), Namur, Belgium
| | - Bao Ton-Hoang
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Jean-Yves Bouet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre de Biologie Intégrative (CBI), Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, UPS, Toulouse, France
| | - Bernard Hallet
- Louvain Institute of Biomolecular Science and Technology (LIBST), Université Catholique de Louvain (UCLouvain), Louvain-la-Neuve, Belgium.
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36
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Klein DC, Hainer SJ. Genomic methods in profiling DNA accessibility and factor localization. Chromosome Res 2019; 28:69-85. [PMID: 31776829 PMCID: PMC7125251 DOI: 10.1007/s10577-019-09619-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 10/10/2019] [Accepted: 10/15/2019] [Indexed: 12/24/2022]
Abstract
Recent advancements in next-generation sequencing technologies and accompanying reductions in cost have led to an explosion of techniques to examine DNA accessibility and protein localization on chromatin genome-wide. Generally, accessible regions of chromatin are permissive for factor binding and are therefore hotspots for regulation of gene expression; conversely, genomic regions that are highly occupied by histone proteins are not permissive for factor binding and are less likely to be active regulatory regions. Identifying regions of differential accessibility can be useful to uncover putative gene regulatory regions, such as enhancers, promoters, and insulators. In addition, DNA-binding proteins, such as transcription factors that preferentially bind certain DNA sequences and histone proteins that form the core of the nucleosome, play essential roles in all DNA-templated processes. Determining the genomic localization of chromatin-bound proteins is therefore essential in determining functional roles, sequence motifs important for factor binding, and regulatory networks controlling gene expression. In this review, we discuss techniques for determining DNA accessibility and nucleosome positioning (DNase-seq, FAIRE-seq, MNase-seq, and ATAC-seq) and techniques for detecting and functionally characterizing chromatin-bound proteins (ChIP-seq, DamID, and CUT&RUN). These methods have been optimized to varying degrees of resolution, specificity, and ease of use. Here, we outline some advantages and disadvantages of these techniques, their general protocols, and a brief discussion of their development. Together, these complimentary approaches have provided an unparalleled view of chromatin architecture and functional gene regulation.
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Affiliation(s)
- David C Klein
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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37
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Orita I, Futatsuishi R, Adachi K, Ohira T, Kaneko A, Minowa K, Suzuki M, Tamura T, Nakamura S, Imanaka T, Suzuki T, Fukui T. Random mutagenesis of a hyperthermophilic archaeon identified tRNA modifications associated with cellular hyperthermotolerance. Nucleic Acids Res 2019; 47:1964-1976. [PMID: 30605516 PMCID: PMC6393311 DOI: 10.1093/nar/gky1313] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2018] [Revised: 12/05/2018] [Accepted: 12/22/2018] [Indexed: 12/20/2022] Open
Abstract
Random mutagenesis for the hyperthermophilic archaeon Thermococcus kodakarensis was established by the insertion of an artificial transposon designed to allow easy identification of the transposon-inserted locus. The phenotypic screening was applied for the isolation of thermosensitive mutants of T. kodakarensis, which resulted in the isolation of 16 mutants showing defective growth at the supraoptimal temperature 93°C. The high occurrence of the mutants suggested that the high thermotolerance of hyperthermophiles was achieved by a combination of diverse gene functions. The transposon insertion sites in two-thirds of the mutants were identified in a group of genes responsible for tRNA modifications including 7-formamidino-7-deaza-guanosine (archaeosine), N1-methyladenosine/N1-methylinosine, N4-acetylcytidine, and N2-dimethylguanosine/N2,N2-dimethylguanosine. LC–MS/MS analyses of tRNA nucleosides and fragments exhibited disappearance of the corresponding modifications in the mutants. The melting temperature of total tRNA fraction isolated from the mutants lacking archaeosine or N1-methyladenosine/N1-methylinosine decreased significantly, suggesting that the thermosensitive phenotype of these mutants was attributed to low stability of the hypomodified tRNAs. Genes for metabolism, transporters, and hypothetical proteins were also identified in the thermosensitive mutants. The present results demonstrated the usefulness of random mutagenesis for the studies on the hyperthermophile, as well as crucial roles of tRNA modifications in cellular thermotolerance.
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Affiliation(s)
- Izumi Orita
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Ryohei Futatsuishi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Kyoko Adachi
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takayuki Ohira
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Akira Kaneko
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Keiichi Minowa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Miho Suzuki
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Takeshi Tamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Satoshi Nakamura
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, 1-1-1 Noji-higashi, Kusatsu 525-8577, Japan
| | - Tsutomu Suzuki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Toshiaki Fukui
- School of Life Science and Technology, Tokyo Institute of Technology, Midori-ku, Yokohama 226-8501, Japan
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Sato S, Arimura Y, Kujirai T, Harada A, Maehara K, Nogami J, Ohkawa Y, Kurumizaka H. Biochemical analysis of nucleosome targeting by Tn5 transposase. Open Biol 2019; 9:190116. [PMID: 31409230 PMCID: PMC6731594 DOI: 10.1098/rsob.190116] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Tn5 transposase is a bacterial enzyme that integrates a DNA fragment into genomic DNA, and is used as a tool for detecting nucleosome-free regions of genomic DNA in eukaryotes. However, in chromatin, the DNA targeting by Tn5 transposase has remained unclear. In the present study, we reconstituted well-positioned 601 dinucleosomes, in which two nucleosomes are connected with a linker DNA, and studied the DNA integration sites in the dinucleosomes by Tn5 transposase in vitro. We found that Tn5 transposase preferentially targets near the entry-exit DNA regions within the nucleosome. Tn5 transposase minimally cleaved the dinucleosome without a linker DNA, indicating that the linker DNA between two nucleosomes is important for the Tn5 transposase activity. In the presence of a 30 base-pair linker DNA, Tn5 transposase targets the middle of the linker DNA, in addition to the entry-exit sites of the nucleosome. Intriguingly, this Tn5-targeting characteristic is conserved in a dinucleosome substrate with a different DNA sequence from the 601 sequence. Therefore, the Tn5-targeting preference in the nucleosomal templates reported here provides important information for the interpretation of Tn5 transposase-based genomics methods, such as ATAC-seq.
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Affiliation(s)
- Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Yasuhiro Arimura
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Jumpei Nogami
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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Montero-Blay A, Miravet-Verde S, Lluch-Senar M, Piñero-Lambea C, Serrano L. SynMyco transposon: engineering transposon vectors for efficient transformation of minimal genomes. DNA Res 2019; 26:327-339. [PMID: 31257417 PMCID: PMC6704405 DOI: 10.1093/dnares/dsz012] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Accepted: 05/16/2019] [Indexed: 11/17/2022] Open
Abstract
Mycoplasmas are important model organisms for Systems and Synthetic Biology, and are pathogenic to a wide variety of species. Despite their relevance, many of the tools established for genome editing in other microorganisms are not available for Mycoplasmas. The Tn4001 transposon is the reference tool to work with these bacteria, but the transformation efficiencies (TEs) reported for the different species vary substantially. Here, we explore the mechanisms underlying these differences in four Mycoplasma species, Mycoplasma agalactiae, Mycoplasma feriruminatoris, Mycoplasma gallisepticum and Mycoplasma pneumoniae, selected for being representative members of each cluster of the Mycoplasma genus. We found that regulatory regions (RRs) driving the expression of the transposase and the antibiotic resistance marker have a major impact on the TEs. We then designed a synthetic RR termed SynMyco RR to control the expression of the key transposon vector elements. Using this synthetic RR, we were able to increase the TE for M. gallisepticum, M. feriruminatoris and M. agalactiae by 30-, 980- and 1036-fold, respectively. Finally, to illustrate the potential of this new transposon, we performed the first essentiality study in M. agalactiae, basing our study on more than 199,000 genome insertions.
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Affiliation(s)
- Ariadna Montero-Blay
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Samuel Miravet-Verde
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Maria Lluch-Senar
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Carlos Piñero-Lambea
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain
| | - Luis Serrano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain.,ICREA, Pg. Lluis Companys 23, Barcelona, Spain
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Blundell-Hunter G, Tellier M, Chalmers R. Transposase subunit architecture and its relationship to genome size and the rate of transposition in prokaryotes and eukaryotes. Nucleic Acids Res 2019; 46:9637-9646. [PMID: 30184164 PMCID: PMC6182136 DOI: 10.1093/nar/gky794] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/01/2018] [Indexed: 12/17/2022] Open
Abstract
Cut-and-paste transposons are important tools for mutagenesis, gene-delivery and DNA sequencing applications. At the molecular level, the most thoroughly understood are Tn5 and Tn10 in bacteria, and mariner and hAT elements in eukaryotes. All bacterial cut-and-paste transposases characterized to date are monomeric prior to interacting with the transposon end, while all eukaryotic transposases are multimers. Although there is a limited sample size, we proposed that this defines two pathways for transpososome assembly which distinguishes the mechanism of the bacterial and eukaryotic transposons. We predicted that the respective pathways would dictate how the rate of transposition is related to transposase concentration and genome size. Here, we have tested these predictions by creating a single-chain dimer version of the bacterial Tn5 transposase. We show that artificial dimerization switches the transpososome assembly pathway from the bacterial-style to the eukaryotic-style. Although this had no effect in vitro, where the transposase does not have to search far to locate the transposon ends, it increased the rate of transposition in bacterial and HeLa cell assays. However, in contrast to the mariner elements, the Tn5 single-chain dimer remained unaffected by over-production inhibition, which is an emergent property of the transposase subunit structure in the mariner elements.
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Affiliation(s)
- George Blundell-Hunter
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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Osorio H, Jara C, Fuenzalida K, Rey-Jurado E, Vásquez M. High-efficiency nuclear transformation of the microalgae Nannochloropsis oceanica using Tn5 Transposome for the generation of altered lipid accumulation phenotypes. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:134. [PMID: 31168324 PMCID: PMC6545213 DOI: 10.1186/s13068-019-1475-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 05/23/2019] [Indexed: 06/09/2023]
Abstract
BACKGROUND One of the major problems in the production of lipids for biotechnological purposes using microalgae is maintaining a high productivity of these molecules without reducing cellular biomass. High production rates are usually obtained by cultivating microalgae under different stress conditions. However, many of these changes usually result in lower biomass productivity. Therefore, the optimization of the culture conditions and genetic modification techniques in these organisms is needed to generate robust new strains for profitable economic use. RESULTS In this work, we describe a new strategy for random mutation of genomic DNA in the microalgae Nannochloropsis oceanica by insertion of a Transposome complex Tn5. This complex contains an antibiotic-resistance cassette commanded by a CMV viral promoter that allows high efficiency of transformation and the generation of mutants. This strategy, complemented with a large-scale identification and selection system for mutants, such as flow cytometry with cell selection, allowed us to obtain clonal cultures of mutants with altered phenotypes in the accumulation of intracellular lipids. The characterization of some of these mutants uncovered new genes that are likely to be involved in the regulation of lipid synthesis, revealing possible cellular responses that influence the intracellular homeostasis of lipids. CONCLUSION The strategies proposed here are easy to implement in different types of microalgae and provide a promising scenario for improving biotechnological applications.
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Affiliation(s)
- Hector Osorio
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Carol Jara
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Karen Fuenzalida
- Departamento de Fisiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Emma Rey-Jurado
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
| | - Mónica Vásquez
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O´Higgins 340, Santiago, Chile
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Stubbs FE, Conway-Campbell BL, Lightman SL. Thirty years of neuroendocrinology: Technological advances pave the way for molecular discovery. J Neuroendocrinol 2019; 31:e12653. [PMID: 30362285 DOI: 10.1111/jne.12653] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/16/2018] [Accepted: 10/21/2018] [Indexed: 12/12/2022]
Abstract
Since the 1950s, the systems level interactions between the hypothalamus, pituitary and end organs such as the adrenal, thyroid and gonads have been well known; however, it is only over the last three decades that advances in molecular biology and information technology have provided a tremendous expansion of knowledge at the molecular level. Neuroendocrinology has benefitted from developments in molecular genetics, epigenetics and epigenomics, and most recently optogenetics and pharmacogenetics. This has enabled a new understanding of gene regulation, transcription, translation and post-translational regulation, which should help direct the development of drugs to treat neuroendocrine-related diseases.
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Affiliation(s)
- Felicity E Stubbs
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Becky L Conway-Campbell
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
| | - Stafford L Lightman
- Henry Wellcome Laboratories for Integrative Neuroscience and Endocrinology, University of Bristol, Bristol, UK
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Naorem SS, Han J, Zhang SY, Zhang J, Graham LB, Song A, Smith CV, Rashid F, Guo H. Efficient transposon mutagenesis mediated by an IPTG-controlled conditional suicide plasmid. BMC Microbiol 2018; 18:158. [PMID: 30355324 PMCID: PMC6201506 DOI: 10.1186/s12866-018-1319-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 10/16/2018] [Indexed: 11/17/2022] Open
Abstract
Background Transposon mutagenesis is highly valuable for bacterial genetic and genomic studies. The transposons are usually delivered into host cells through conjugation or electroporation of a suicide plasmid. However, many bacterial species cannot be efficiently conjugated or transformed for transposon saturation mutagenesis. For this reason, temperature-sensitive (ts) plasmids have also been developed for transposon mutagenesis, but prolonged incubation at high temperatures to induce ts plasmid loss can be harmful to the hosts and lead to enrichment of mutants with adaptive genetic changes. In addition, the ts phenotype of a plasmid is often strain- or species-specific, as it may become non-ts or suicidal in different bacterial species. Results We have engineered several conditional suicide plasmids that have a broad host range and whose loss is IPTG-controlled. One construct, which has the highest stability in the absence of IPTG induction, was then used as a curable vector to deliver hyperactive miniTn5 transposons for insertional mutagenesis. Our analyses show that these new tools can be used for efficient and regulatable transposon mutagenesis in Escherichia coli, Acinetobacter baylyi and Pseudomonas aeruginosa. In P. aeruginosa PAO1, we have used this method to generate a Tn5 insertion library with an estimated diversity of ~ 108, which is ~ 2 logs larger than the best transposon insertional library of PAO1 and related Pseudomonas strains previously reported. Conclusion We have developed a number of IPTG-controlled conditional suicide plasmids. By exploiting one of them for transposon delivery, a highly efficient and broadly useful mutagenesis system has been developed. As the assay condition is mild, we believe that our methodology will have broad applications in microbiology research. Electronic supplementary material The online version of this article (10.1186/s12866-018-1319-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Santa S Naorem
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Jin Han
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Stephanie Y Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Junyi Zhang
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Lindsey B Graham
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Angelou Song
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Cameron V Smith
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Fariha Rashid
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Huatao Guo
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.
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Transposase-Mediated Chromosomal Integration of Exogenous Genes in Acidithiobacillus ferrooxidans. Appl Environ Microbiol 2018; 84:AEM.01381-18. [PMID: 30143507 DOI: 10.1128/aem.01381-18] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 08/20/2018] [Indexed: 01/21/2023] Open
Abstract
The development of Acidithiobacillus ferrooxidans as a non-model host organism for synthetic biology is hampered by a lack of genetic tools and techniques. New plating and liquid-based selection methods were developed to improve the identification of transformed cell lines. Enabled by these methods, a hyperactive transposase was used to generate mutants with integrated genes for the expression of the superfolder green fluorescent protein (sfGFP) gene or a 2-keto decarboxylase (KDC) gene, which enabled the production and secretion of isobutyric acid (IBA). An inverse PCR method was used to identify the insertion sites of the KDC gene in several mutants, leading to the identification of a region on the chromosome that may be suitable for future genetic insertions. These results demonstrate that functional exogenous metabolic genes have been chromosomally integrated into A. ferrooxidans, and this advance will facilitate the future development of these cells for new biotechnology applications.IMPORTANCE Acidithiobacillus ferrooxidans is an iron- and sulfur-oxidizing chemolithoautotroph and is a key member of the microbial consortia used in industrial biomining applications. There is interest in exploiting these cells for other metal recovery applications as well as in developing them as unique nonmodel microbial cell factories. Plasmid-driven expression of exogenous genes has been reported, and homologous recombination has been used to knock out some gene expression. Here, new selection protocols facilitated the development of a transposition method for chromosomal integration of exogenous genes into A. ferrooxidans This greatly expands the available genetic toolbox, which will open the door to greater metabolic engineering efforts for these cells.
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45
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Trac-looping measures genome structure and chromatin accessibility. Nat Methods 2018; 15:741-747. [PMID: 30150754 DOI: 10.1038/s41592-018-0107-y] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 07/15/2018] [Indexed: 12/22/2022]
Abstract
Long-range chromatin interactions play critical roles in genome organization and regulation of transcription. We now report transposase-mediated analysis of chromatin looping (Trac-looping) for simultaneous detection of multiscale genome-wide chromatin interactions among regulatory elements and chromatin accessibility. With this technique, a bivalent oligonucleotide linker is inserted between two interacting regions such that the chromatin interactions are captured without prior chromatin fragmentation and proximity-based ligation. Application of Trac-looping to human CD4+ T cells revealed substantial reorganization of enhancer-promoter interactions associated with changes in gene expression after T cell receptor stimulation.
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Abstract
ChIP-seq and ChIP-exo identify where proteins bind along any genome in vivo. Although ChIP-seq is widely adopted in academic research, it has inherently high noise. In contrast, ChIP-exo has relatively low noise and achieves near-base pair resolution. Consequently, and unlike other genomic assays, ChIP-exo provides structural information on genome-wide binding proteins. Construction of ChIP-exo libraries is technically difficult. Here we describe greatly simplified ChIP-exo methods, each with use-specific advantages. This is achieved through assay optimization and use of Tn5 tagmentation and/or single-stranded DNA ligation. Greater library yields, lower processing time, and lower costs are achieved. In comparing assays, we reveal substantial limitations in other ChIP-based assays. Importantly, the new ChIP-exo assays allow high-resolution detection of some protein-DNA interactions in organs and in as few as 27,000 cells. It is suitable for high-throughput parallelization. The simplicity of ChIP-exo now makes it a highly appropriate substitute for ChIP-seq, and for broader adoption. While ChIP-exo is low noise and highly informative regarding genome-wide binding proteins, libraries are difficult to construct. Here the authors present a simplified ChIP-exo method for high-resolution detection of interactions.
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47
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Ponrathnam T, Mishra RK. From chromosomes to genomes: new insights with emerging techniques. THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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Mielich K, Shtifman-Segal E, Golz JC, Zeng G, Wang Y, Berman J, Kunze R. Maize Transposable Elements Ac/ Ds as Insertion Mutagenesis Tools in Candida albicans. G3 (BETHESDA, MD.) 2018; 8:1139-1145. [PMID: 29378819 PMCID: PMC5873905 DOI: 10.1534/g3.117.300388] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/26/2018] [Indexed: 12/23/2022]
Abstract
In nonmodel systems, genetic research is often limited by the lack of techniques for the generation and identification of gene mutations. One approach to overcome this bottleneck is the application of transposons for gene tagging. We have established a two-element transposon tagging system, based on the transposable elements Activator (Ac)/Dissociation (Ds) from maize, for in vivo insertion mutagenesis in the fungal human pathogen Candida albicans A nonautonomous Ds transposon carrying a selectable marker was constructed into the ADE2 promoter on chromosome 3 and a codon usage-adapted Ac transposase gene was inserted into the neutral NEUT5L locus on chromosome 5. In C. albicans cells expressing the transposase, the Ds element efficiently excised and reintegrated elsewhere in the genome, which makes the Ac/Ds transposons promising tools for saturating insertion mutagenesis in clinical strains of C. albicans.
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Affiliation(s)
- Kevin Mielich
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Ella Shtifman-Segal
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Julia C Golz
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
| | - Guisheng Zeng
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Yue Wang
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, 138673, Singapore
| | - Judith Berman
- Department of Molecular Microbiology and Biotechnology, George Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv 69978, Israel
| | - Reinhard Kunze
- Institute of Biology, Dahlem Centre of Plant Sciences, Free University pf Berlin, 14195, Germany
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Wu J, Dai W, Wu L, Wang J. SALP, a new single-stranded DNA library preparation method especially useful for the high-throughput characterization of chromatin openness states. BMC Genomics 2018; 19:143. [PMID: 29439663 PMCID: PMC5811972 DOI: 10.1186/s12864-018-4530-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 02/05/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Next-generation sequencing (NGS) is fundamental to the current biological and biomedical research. Construction of sequencing library is a key step of NGS. Therefore, various library construction methods have been explored. However, the current methods are still limited by some shortcomings. RESULTS This study developed a new NGS library construction method, Single strand Adaptor Library Preparation (SALP), by using a novel single strand adaptor (SSA). SSA is a double-stranded oligonucleotide with a 3' overhang of 3 random nucleotides, which can be efficiently ligated to the 3' end of single strand DNA by T4 DNA ligase. SALP can be started with any denatured DNA fragments such as those sheared by Tn5 tagmentation, enzyme digestion and sonication. When started with Tn5-tagmented chromatin, SALP can overcome a key limitation of ATAC-seq and become a high-throughput NGS library construction method, SALP-seq, which can be used to comparatively characterize the chromatin openness state of multiple cells unbiasly. In this way, this study successfully characterized the comparative chromatin openness states of four different cell lines, including GM12878, HepG2, HeLa and 293T, with SALP-seq. Similarly, this study also successfully characterized the chromatin openness states of HepG2 cells with SALP-seq by using 105 to 500 cells. CONCLUSIONS This study developed a new NGS library construction method, SALP, by using a novel kind of single strand adaptor (SSA), which should has wide applications in the future due to its unique performance.
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Affiliation(s)
- Jian Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Wei Dai
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Lin Wu
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China
| | - Jinke Wang
- State Key Laboratory of Bioelectronics, Southeast University, Sipailou 2, Nanjing, 210096, China.
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Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes. Nat Commun 2018; 9:336. [PMID: 29362365 PMCID: PMC5780524 DOI: 10.1038/s41467-017-02522-z] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 12/07/2017] [Indexed: 11/29/2022] Open
Abstract
Most studies of bacterial motility have examined small-scale (micrometer–centimeter) cell dispersal in monocultures. However, bacteria live in multispecies communities, where interactions with other microbes may inhibit or facilitate dispersal. Here, we demonstrate that motile bacteria in cheese rind microbiomes use physical networks created by filamentous fungi for dispersal, and that these interactions can shape microbial community structure. Serratia proteamaculans and other motile cheese rind bacteria disperse on fungal networks by swimming in the liquid layers formed on fungal hyphae. RNA-sequencing, transposon mutagenesis, and comparative genomics identify potential genetic mechanisms, including flagella-mediated motility, that control bacterial dispersal on hyphae. By manipulating fungal networks in experimental communities, we demonstrate that fungal-mediated bacterial dispersal can shift cheese rind microbiome composition by promoting the growth of motile over non-motile community members. Our single-cell to whole-community systems approach highlights the interactive dynamics of bacterial motility in multispecies microbiomes. Interactions with other microbes may inhibit or facilitate the dispersal of bacteria. Here, Zhang et al. use cheese rind microbiomes as a model to show that physical networks created by filamentous fungi can affect the dispersal of motile bacteria and thus shape the diversity of microbial communities.
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