51
|
Qin Q, Fan J, Zheng R, Wan C, Mei S, Wu Q, Sun H, Brown M, Zhang J, Meyer CA, Liu XS. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP-seq data. Genome Biol 2020; 21:32. [PMID: 32033573 PMCID: PMC7007693 DOI: 10.1186/s13059-020-1934-6] [Citation(s) in RCA: 141] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
We developed Lisa (http://lisa.cistrome.org/) to predict the transcriptional regulators (TRs) of differentially expressed or co-expressed gene sets. Based on the input gene sets, Lisa first uses histone mark ChIP-seq and chromatin accessibility profiles to construct a chromatin model related to the regulation of these genes. Using TR ChIP-seq peaks or imputed TR binding sites, Lisa probes the chromatin models using in silico deletion to find the most relevant TRs. Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performance of imputed TR cistromes and outperformed alternative methods in identifying the perturbed TRs.
Collapse
Affiliation(s)
- Qian Qin
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
- Center of Molecular Medicine, Children's Hospital of Fudan University, Shanghai, 201102, China
| | - Jingyu Fan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Rongbin Zheng
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Changxin Wan
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Shenglin Mei
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Qiu Wu
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Hanfei Sun
- Clinical Translational Research Center, Shanghai Pulmonary Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200433, China
| | - Myles Brown
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02215, USA
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA
| | - Jing Zhang
- Stem Cell Translational Research Center, Tongji Hospital, School of Life Science and Technology, Tongji University, Shanghai, 200065, China.
| | - Clifford A Meyer
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| | - X Shirley Liu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
- Department of Data Sciences, Dana-Farber Cancer Institute and Harvard T.H. Chan School of Public Health, Boston, MA, 02215, USA.
| |
Collapse
|
52
|
Meadows SK, Brandsmeier LA, Newberry KM, Betti MJ, Nesmith AS, Mackiewicz M, Partridge EC, Mendenhall EM, Myers RM. Epitope Tagging ChIP-Seq of DNA Binding Proteins Using CETCh-Seq. Methods Mol Biol 2020; 2117:3-34. [PMID: 31960370 DOI: 10.1007/978-1-0716-0301-7_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chromatin immunoprecipitation followed by next-generation DNA sequencing (ChIP-seq) has been used to identify transcription factor (TF) binding proteins throughout the genome. Unfortunately, this approach traditionally requires commercially available, ChIP-seq grade antibodies that frequently fail to generate acceptable datasets. To obtain data for the many TFs for which there is no appropriate antibody, we recently developed a new method for performing ChIP-seq by epitope tagging endogenous TFs using CRISPR/Cas9 genome editing technology (CETCh-seq). Here, we describe our general protocol of CETCh-seq for both adherent and nonadherent cell lines using a commercially available FLAG antibody.
Collapse
Affiliation(s)
- Sarah K Meadows
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | | | - Amy S Nesmith
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,University of Alabama in Huntsville, Huntsville, AL, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| |
Collapse
|
53
|
Muhammad II, Kong SL, Akmar Abdullah SN, Munusamy U. RNA-seq and ChIP-seq as Complementary Approaches for Comprehension of Plant Transcriptional Regulatory Mechanism. Int J Mol Sci 2019; 21:E167. [PMID: 31881735 PMCID: PMC6981605 DOI: 10.3390/ijms21010167] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Revised: 12/19/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The availability of data produced from various sequencing platforms offer the possibility to answer complex questions in plant research. However, drawbacks can arise when there are gaps in the information generated, and complementary platforms are essential to obtain more comprehensive data sets relating to specific biological process, such as responses to environmental perturbations in plant systems. The investigation of transcriptional regulation raises different challenges, particularly in associating differentially expressed transcription factors with their downstream responsive genes. In this paper, we discuss the integration of transcriptional factor studies through RNA sequencing (RNA-seq) and Chromatin Immunoprecipitation sequencing (ChIP-seq). We show how the data from ChIP-seq can strengthen information generated from RNA-seq in elucidating gene regulatory mechanisms. In particular, we discuss how integration of ChIP-seq and RNA-seq data can help to unravel transcriptional regulatory networks. This review discusses recent advances in methods for studying transcriptional regulation using these two methods. It also provides guidelines for making choices in selecting specific protocols in RNA-seq pipelines for genome-wide analysis to achieve more detailed characterization of specific transcription regulatory pathways via ChIP-seq.
Collapse
Affiliation(s)
- Isiaka Ibrahim Muhammad
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Sze Ling Kong
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| | - Siti Nor Akmar Abdullah
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Selangor 43400, Malaysia
| | - Umaiyal Munusamy
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, Selangor 43400, Malaysia; (I.I.M.); (S.L.K.); (U.M.)
| |
Collapse
|
54
|
Zitnik M, Nguyen F, Wang B, Leskovec J, Goldenberg A, Hoffman MM. Machine Learning for Integrating Data in Biology and Medicine: Principles, Practice, and Opportunities. AN INTERNATIONAL JOURNAL ON INFORMATION FUSION 2019; 50:71-91. [PMID: 30467459 PMCID: PMC6242341 DOI: 10.1016/j.inffus.2018.09.012] [Citation(s) in RCA: 222] [Impact Index Per Article: 44.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include myriad properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of all the factors relevant to understanding a phenomenon such as a disease. Integrative methods that combine data from multiple technologies have thus emerged as critical statistical and computational approaches. The key challenge in developing such approaches is the identification of effective models to provide a comprehensive and relevant systems view. An ideal method can answer a biological or medical question, identifying important features and predicting outcomes, by harnessing heterogeneous data across several dimensions of biological variation. In this Review, we describe the principles of data integration and discuss current methods and available implementations. We provide examples of successful data integration in biology and medicine. Finally, we discuss current challenges in biomedical integrative methods and our perspective on the future development of the field.
Collapse
Affiliation(s)
- Marinka Zitnik
- Department of Computer Science, Stanford University,
Stanford, CA, USA
| | - Francis Nguyen
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Bo Wang
- Hikvision Research Institute, Santa Clara, CA, USA
| | - Jure Leskovec
- Department of Computer Science, Stanford University,
Stanford, CA, USA
- Chan Zuckerberg Biohub, San Francisco, CA, USA
| | - Anna Goldenberg
- Genetics & Genome Biology, SickKids Research Institute,
Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| | - Michael M. Hoffman
- Department of Medical Biophysics, University of Toronto,
Toronto, ON, Canada
- Princess Margaret Cancer Centre, Toronto, ON, Canada
- Department of Computer Science, University of Toronto,
Toronto, ON, Canada
- Vector Institute, Toronto, ON, Canada
| |
Collapse
|
55
|
Zhao K, Cheng S, Miao N, Xu P, Lu X, Zhang Y, Wang M, Ouyang X, Yuan X, Liu W, Lu X, Zhou P, Gu J, Zhang Y, Qiu D, Jin Z, Su C, Peng C, Wang JH, Dong MQ, Wan Y, Ma J, Cheng H, Huang Y, Yu Y. A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation. Nat Cell Biol 2019; 21:1261-1272. [PMID: 31570835 DOI: 10.1038/s41556-019-0396-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022]
Abstract
The repression of transposons by the Piwi-interacting RNA (piRNA) pathway is essential to protect animal germ cells. In Drosophila, Panoramix enforces transcriptional silencing by binding to the target-engaged Piwi-piRNA complex, although the precise mechanisms by which this occurs remain elusive. Here, we show that Panoramix functions together with a germline-specific paralogue of a nuclear export factor, dNxf2, and its cofactor dNxt1 (p15), to suppress transposon expression. The transposon RNA-binding protein dNxf2 is required for animal fertility and Panoramix-mediated silencing. Transient tethering of dNxf2 to nascent transcripts leads to their nuclear retention. The NTF2 domain of dNxf2 competes dNxf1 (TAP) off nucleoporins, a process required for proper RNA export. Thus, dNxf2 functions in a Panoramix-dNxf2-dependent TAP/p15 silencing (Pandas) complex that counteracts the canonical RNA exporting machinery and restricts transposons to the nuclear peripheries. Our findings may have broader implications for understanding how RNA metabolism modulates heterochromatin formation.
Collapse
Affiliation(s)
- Kang Zhao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Sha Cheng
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Na Miao
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Ping Xu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,National Engineering Laboratory of AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Xiaohua Lu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yuhan Zhang
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China.,State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Ming Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xuan Ouyang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xun Yuan
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Xin Lu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Peng Zhou
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Gu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Yiqun Zhang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Ding Qiu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zhaohui Jin
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Chen Su
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Chao Peng
- National Facility for Protein Science in Shanghai, Zhangjiang Lab, Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai, China
| | - Jian-Hua Wang
- Graduate School of Peking Union Medical College and Chinese Academy of Sciences of Medical Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China.,Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, China
| | - Youzhong Wan
- National Engineering Laboratory of AIDS Vaccine, Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai, China
| | - Hong Cheng
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Huang
- University of Chinese Academy of Sciences, Beijing, China. .,State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai, China. .,Shanghai Key Laboratory of Biliary Tract Disease Research, Shanghai Research Center of Biliary Tract Disease, Department of General Surgery, Xinhua Hospital, affiliated with Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Yang Yu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. .,University of Chinese Academy of Sciences, Beijing, China.
| |
Collapse
|
56
|
Deegan DF, Engel N. Sexual Dimorphism in the Age of Genomics: How, When, Where. Front Cell Dev Biol 2019; 7:186. [PMID: 31552249 PMCID: PMC6743004 DOI: 10.3389/fcell.2019.00186] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 08/22/2019] [Indexed: 12/26/2022] Open
Abstract
In mammals, sex chromosomes start to program autosomal gene expression and epigenetic patterns very soon after fertilization. Yet whether the resulting sex differences are perpetuated throughout development and how they connect to the sex-specific expression patterns in adult tissues is not known. There is a dearth of information on the timing and continuity of sex biases during development. It is also unclear whether sex-specific selection operates during embryogenesis. On the other hand, there is mounting evidence that all adult tissues exhibit sex-specific expression patterns, some of which are independent of hormonal influence and due to intrinsic regulatory effects of the sex chromosome constitution. There are many diseases with origins during embryogenesis that also exhibit sex biases. Epigenetics has provided us with viable mechanisms to explain how the genome stores the memory of developmental events. We propose that some of these marks can be traced back to the sex chromosomes, which interact with the autosomes and establish sex-specific epigenetic features soon after fertilization. Sex-biased epigenetic marks that linger after reprograming may reveal themselves at the transcriptional level at later developmental stages and possibly, throughout the lifespan. Detailed molecular information on the ontogeny of sex biases would also elucidate the sex-specific selective pressures operating on embryos and how compensatory mechanisms evolved to resolve sexual conflict.
Collapse
Affiliation(s)
| | - Nora Engel
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, United States
| |
Collapse
|
57
|
Blanchard Z, Vahrenkamp JM, Berrett KC, Arnesen S, Gertz J. Estrogen-independent molecular actions of mutant estrogen receptor 1 in endometrial cancer. Genome Res 2019; 29:1429-1441. [PMID: 31362937 PMCID: PMC6724674 DOI: 10.1101/gr.244780.118] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 07/23/2019] [Indexed: 01/14/2023]
Abstract
Estrogen receptor 1 (ESR1) mutations have been identified in hormone therapy-resistant breast cancer and primary endometrial cancer. Analyses in breast cancer suggest that mutant ESR1 exhibits estrogen-independent activity. In endometrial cancer, ESR1 mutations are associated with worse outcomes and less obesity, however, experimental investigation of these mutations has not been performed. Using a unique CRISPR/Cas9 strategy, we introduced the D538G mutation, a common endometrial cancer mutation that alters the ligand binding domain of ESR1, while epitope tagging the endogenous locus. We discovered estrogen-independent mutant ESR1 genomic binding that is significantly altered from wild-type ESR1. The D538G mutation impacted expression, including a large set of nonestrogen-regulated genes, and chromatin accessibility, with most affected loci bound by mutant ESR1. Mutant ESR1 is distinct from constitutive ESR1 activity because mutant-specific changes are not recapitulated with prolonged estrogen exposure. Overall, the D538G mutant ESR1 confers estrogen-independent activity while causing additional regulatory changes in endometrial cancer cells that are distinct from breast cancer cells.
Collapse
Affiliation(s)
- Zannel Blanchard
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jeffery M Vahrenkamp
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Kristofer C Berrett
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Spencer Arnesen
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jason Gertz
- Department of Oncological Sciences, University of Utah, Salt Lake City, Utah 84112, USA
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| |
Collapse
|
58
|
Bressan RB, Pollard SM. Genome Editing in Human Neural Stem and Progenitor Cells. Results Probl Cell Differ 2019; 66:163-182. [PMID: 30209659 DOI: 10.1007/978-3-319-93485-3_7] [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] [Indexed: 02/11/2024]
Abstract
Experimental tools for precise manipulation of mammalian genomes enable reverse genetic approaches to explore biology and disease. Powerful genome editing technologies built upon designer nucleases, such as CRISPR/Cas9, have recently emerged. Parallel progress has been made in methodologies for the expansion and differentiation of human pluripotent and tissue stem cells. Together these innovations provide a remarkable new toolbox for human cellular genetics and are opening up vast opportunities for discoveries and applications across the breadth of life sciences research. In this chapter, we review the emergence of genome editing technologies and how these are being deployed in studies of human neurobiology, neurological disease, and neuro-oncology. We focus our discussion on CRISPR/Cas9 and its application in studies of human neural stem and progenitor cells.
Collapse
Affiliation(s)
- Raul Bardini Bressan
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine and Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, UK.
| |
Collapse
|
59
|
Niu W, Parent JM. Modeling genetic epilepsies in a dish. Dev Dyn 2019; 249:56-75. [DOI: 10.1002/dvdy.79] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 06/21/2019] [Accepted: 06/21/2019] [Indexed: 02/07/2023] Open
Affiliation(s)
- Wei Niu
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
| | - Jack M. Parent
- Department of Neurology and Neuroscience Graduate ProgramUniversity of Michigan Medical Center and VA Ann Arbor Healthcare System Ann Arbor Michigan
| |
Collapse
|
60
|
Lin DW, Chung BP, Huang JW, Wang X, Huang L, Kaiser P. Microhomology-based CRISPR tagging tools for protein tracking, purification, and depletion. J Biol Chem 2019; 294:10877-10885. [PMID: 31138654 DOI: 10.1074/jbc.ra119.008422] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/07/2019] [Indexed: 12/26/2022] Open
Abstract
Work in yeast models has benefitted tremendously from the insertion of epitope or fluorescence tags at the native gene locus to study protein function and behavior under physiological conditions. In contrast, work in mammalian cells largely relies on overexpression of tagged proteins because high-quality antibodies are only available for a fraction of the mammalian proteome. CRISPR/Cas9-mediated genome editing has recently emerged as a powerful genome-modifying tool that can also be exploited to insert various tags and fluorophores at gene loci to study the physiological behavior of proteins in most organisms, including mammals. Here we describe a versatile toolset for rapid tagging of endogenous proteins. The strategy utilizes CRISPR/Cas9 and microhomology-mediated end joining repair for efficient tagging. We provide tools to insert 3×HA, His6FLAG, His6-Biotin-TEV-RGSHis6, mCherry, GFP, and the auxin-inducible degron tag for compound-induced protein depletion. This approach and the developed tools should greatly facilitate functional analysis of proteins in their native environment.
Collapse
Affiliation(s)
| | | | | | - Xiaorong Wang
- Physiology and Biophysics, University of California, Irvine, California 92617
| | - Lan Huang
- Physiology and Biophysics, University of California, Irvine, California 92617
| | | |
Collapse
|
61
|
HiBiT-qIP, HiBiT-based quantitative immunoprecipitation, facilitates the determination of antibody affinity under immunoprecipitation conditions. Sci Rep 2019; 9:6895. [PMID: 31053795 PMCID: PMC6499798 DOI: 10.1038/s41598-019-43319-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/31/2019] [Indexed: 12/23/2022] Open
Abstract
The affinity of an antibody for its antigen serves as a critical parameter for antibody evaluation. The evaluation of antibody-antigen affinity is essential for a successful antibody-based assay, particularly immunoprecipitation (IP), due to its strict dependency on antibody performance. However, the determination of antibody affinity or its quantitative determinant, the dissociation constant (Kd), under IP conditions is difficult. In the current study, we used a NanoLuc-based HiBiT system to establish a HiBiT-based quantitative immunoprecipitation (HiBiT-qIP) assay for determining the Kd of antigen-antibody interactions in solution. The HiBiT-qIP method measures the amount of immunoprecipitated proteins tagged with HiBiT in a simple yet quantitative manner. We used this method to measure the Kd values of epitope tag-antibody interactions. To accomplish this, FLAG, HA, V5, PA and Ty1 epitope tags in their monomeric, dimeric or trimeric form were fused with glutathione S-transferase (GST) and the HiBiT peptide, and these tagged GST proteins were mixed with cognate monoclonal antibodies in IP buffer for the assessment of the apparent Kd values. This HiBiT-qIP assay showed a considerable variation in the Kd values among the examined antibody clones. Additionally, the use of epitope tags in multimeric form revealed a copy number-dependent increase in the apparent affinity.
Collapse
|
62
|
BRD9 defines a SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors. Nat Commun 2019; 10:1881. [PMID: 31015438 PMCID: PMC6479050 DOI: 10.1038/s41467-019-09891-7] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 04/03/2019] [Indexed: 12/22/2022] Open
Abstract
Bromodomain-containing protein 9 (BRD9) is a recently identified subunit of SWI/SNF(BAF) chromatin remodeling complexes, yet its function is poorly understood. Here, using a genome-wide CRISPR-Cas9 screen, we show that BRD9 is a specific vulnerability in pediatric malignant rhabdoid tumors (RTs), which are driven by inactivation of the SMARCB1 subunit of SWI/SNF. We find that BRD9 exists in a unique SWI/SNF sub-complex that lacks SMARCB1, which has been considered a core subunit. While SMARCB1-containing SWI/SNF complexes are bound preferentially at enhancers, we show that BRD9-containing complexes exist at both promoters and enhancers. Mechanistically, we show that SMARCB1 loss causes increased BRD9 incorporation into SWI/SNF thus providing insight into BRD9 vulnerability in RTs. Underlying the dependency, while its bromodomain is dispensable, the DUF3512 domain of BRD9 is essential for SWI/SNF integrity in the absence of SMARCB1. Collectively, our results reveal a BRD9-containing SWI/SNF subcomplex is required for the survival of SMARCB1-mutant RTs. Mutations of the SWI/SNF chromatin-remodeling complex member SMARCB1 can cause malignant rhaboid tumors. Here the authors report a BRD9-containing SWI/SNF subcomplex that lacks SMARCB1 and its requirement for the survival of rhaboid tumors.
Collapse
|
63
|
Venters BJ. Insights from resolving protein-DNA interactions at near base-pair resolution. Brief Funct Genomics 2019; 17:80-88. [PMID: 29211822 DOI: 10.1093/bfgp/elx043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
One of the central goals in molecular biology is to understand how cell-type-specific expression patterns arise through selective recruitment of RNA polymerase II (Pol II) to a subset of gene promoters. Pol II needs to be recruited to a precise genomic position at the proper time to produce messenger RNA from a DNA template. Ostensibly, transcription is a relatively simple cellular process; yet, experimentally measuring and then understanding the combinatorial possibilities of transcriptional regulators remain a daunting task. Since its introduction in 1985, chromatin immunoprecipitation (ChIP) has remained a key tool for investigating protein-DNA contacts in vivo. Over 30 years of intensive research using ChIP have provided numerous insights into mechanisms of gene regulation. As functional genomic technologies improve, they present new opportunities to address key biological questions. ChIP-exo is a refined version of ChIP-seq that significantly reduces background signal, while providing near base-pair mapping resolution for protein-DNA interactions. This review discusses the evolution of the ChIP assay over the years; the methodological differences between ChIP-seq, ChIP-exo and ChIP-nexus; and highlight new insights into epigenetic and transcriptional mechanisms that were uniquely enabled with the near base-pair resolution of ChIP-exo.
Collapse
|
64
|
Wilkinson B, Evgrafov O, Zheng D, Hartel N, Knowles JA, Graham NA, Ichida J, Coba MP. Endogenous Cell Type-Specific Disrupted in Schizophrenia 1 Interactomes Reveal Protein Networks Associated With Neurodevelopmental Disorders. Biol Psychiatry 2019; 85:305-316. [PMID: 29961565 PMCID: PMC6251761 DOI: 10.1016/j.biopsych.2018.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 04/03/2018] [Accepted: 05/03/2018] [Indexed: 11/17/2022]
Abstract
BACKGROUND Disrupted in schizophrenia 1 (DISC1) has been implicated in a number of psychiatric diseases along with neurodevelopmental phenotypes such as the proliferation and differentiation of neural progenitor cells. While there has been significant effort directed toward understanding the function of DISC1 through the determination of its protein-protein interactions within an in vitro setting, endogenous interactions involving DISC1 within a cell type-specific setting relevant to neural development remain unclear. METHODS Using CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein 9) genome engineering technology, we inserted an endogenous 3X-FLAG tag at the C-terminus of the canonical DISC1 gene in human induced pluripotent stem cells (iPSCs). We further differentiated these cells and used affinity purification to determine protein-protein interactions involving DISC1 in iPSC-derived neural progenitor cells and astrocytes. RESULTS We were able to determine 151 novel cell type-specific proteins present in DISC1 endogenous interactomes. The DISC1 interactomes can be clustered into several subcomplexes that suggest novel DISC1 cell-specific functions. In addition, the DISC1 interactome in iPSC-derived neural progenitor cells associates in a connected network containing proteins found to harbor de novo mutations in patients affected by schizophrenia and contains a subset of novel interactions that are known to harbor syndromic mutations in neurodevelopmental disorders. CONCLUSIONS Endogenous DISC1 interactomes within iPSC-derived human neural progenitor cells and astrocytes are able to provide context to DISC1 function in a cell type-specific setting relevant to neural development and enables the integration of psychiatric disease risk factors within a set of defined molecular functions.
Collapse
Affiliation(s)
- Brent Wilkinson
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Oleg Evgrafov
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - DongQing Zheng
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - Nicolas Hartel
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - James A. Knowles
- Department of Cell Biology, SUNY Downstate Medical Center, Brooklyn, NY 11203, USA
| | - Nicholas A. Graham
- Mork Family Department of Chemical Engineering and Materials Science, University of Southern California, Los Angeles, CA 90033, USA
| | - Justin Ichida
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Department of Stem Cell Biology and Regenerative Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Eli and Edythe Broad CIRM Center for Regenerative Medicine and Stem Cell Research at USC
| | - Marcelo P. Coba
- Zilkha Neurogenetic Institute, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Department of Psychiatry and Behavioral Sciences, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA,Corresponding Author: Marcelo P. Coba, Keck School of Medicine, University of Southern California, Zilkha Neurogenetic Institute, 1501 San Pablo St, Los Angeles, CA 90033, USA. Phone: 323-442-4345.
| |
Collapse
|
65
|
Doan ND, DiChiara AS, Del Rosario AM, Schiavoni RP, Shoulders MD. Mass Spectrometry-Based Proteomics to Define Intracellular Collagen Interactomes. Methods Mol Biol 2019; 1944:95-114. [PMID: 30840237 DOI: 10.1007/978-1-4939-9095-5_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We present the development, optimization, and application of constructs, cell lines, covalent cross-linking methods, and immunoprecipitation strategies that enable robust and accurate determination of collagen interactomes via mass spectrometry-based proteomics. Using collagen type-I as an example, protocols for working with large, repetitive, and GC-rich collagen genes are described, followed by strategies for engineering cells that stably and inducibly express antibody epitope-tagged collagen-I. Detailed steps to optimize collagen interactome cross-linking and perform immunoprecipitations are then presented. We conclude with a discussion of methods to elute collagen interactomes and prepare samples for mass spectrometry-mediated identification of interactors. Throughout, caveats and potential problems researchers may encounter when working with collagen are discussed. We note that the protocols presented herein may be readily adapted to define interactomes of other collagen types, as well as to determine comparative interactomes of normal and disease-causing collagen variants using quantitative isotopic labeling (SILAC)- or isobaric mass tags (iTRAQ or TMT)-based mass spectrometry analysis.
Collapse
Affiliation(s)
- Ngoc-Duc Doan
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Andrew S DiChiara
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | | | - Matthew D Shoulders
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
66
|
Lau CH. Applications of CRISPR-Cas in Bioengineering, Biotechnology, and Translational Research. CRISPR J 2018; 1:379-404. [PMID: 31021245 DOI: 10.1089/crispr.2018.0026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
CRISPR technology is rapidly evolving, and the scope of CRISPR applications is constantly expanding. CRISPR was originally employed for genome editing. Its application was then extended to epigenome editing, karyotype engineering, chromatin imaging, transcriptome, and metabolic pathway engineering. Now, CRISPR technology is being harnessed for genetic circuits engineering, cell signaling sensing, cellular events recording, lineage information reconstruction, gene drive, DNA genotyping, miRNA quantification, in vivo cloning, site-directed mutagenesis, genomic diversification, and proteomic analysis in situ. It has also been implemented in the translational research of human diseases such as cancer immunotherapy, antiviral therapy, bacteriophage therapy, cancer diagnosis, pathogen screening, microbiota remodeling, stem-cell reprogramming, immunogenomic engineering, vaccine development, and antibody production. This review aims to summarize the key concepts of these CRISPR applications in order to capture the current state of play in this fast-moving field. The key mechanisms, strategies, and design principles for each technological advance are also highlighted.
Collapse
Affiliation(s)
- Cia-Hin Lau
- Department of Biomedical Engineering, City University of Hong Kong , Hong Kong, SAR, China
| |
Collapse
|
67
|
Yamakawa T, Waer C, Itakura K. AT-rich interactive domain 5B regulates androgen receptor transcription in human prostate cancer cells. Prostate 2018; 78:1238-1247. [PMID: 30027545 DOI: 10.1002/pros.23699] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 07/05/2018] [Indexed: 01/22/2023]
Abstract
BACKGROUND The androgen receptor (AR) is one of the most important and dynamically regulated factors in prostate cancer (PCa) progression. Despite the importance of AR expression regulation, the precise mechanisms are not fully understood. ARID5B, an AT-rich interaction domain DNA-binding motif-containing transcription factor, is expressed higher in primary PCa than normal prostate, and correlated with AR expression. We therefore hypothesized that ARID5B could regulate AR expression. METHODS Correlation between AR and ARID5B expression was analyzed using publicly and commercially available microarray data. To examine the role of ARID5B in AR expression, ARID5B was knocked down in VCaP and LNCaP cells, then mRNA and protein levels of AR were measured and an in vitro cell proliferation assay was performed. Chromatin immunoprecipitation was performed to further examine molecular mechanisms. RESULTS Knockdown of ARID5B suppressed the AR mRNA and protein expression in VCaP and LNCaP cells and decreased in vitro cell proliferation. Suppression of ARID5B decreased the occupancy of active RNA polymerase II in the AR promoter, indicating that ARID5B regulates AR transcription. The active histone mark, H3K4me3, occupancy was decreased with ARID5B knockdown. CONCLUSION Our study revealed that AR transcription is positively regulated by ARID5B through H3K4me3 recruitment in the AR promoter. Our findings reveal novel mechanisms of AR transcription, which is dynamically regulated in prostate tumor progression.
Collapse
Affiliation(s)
- Takahiro Yamakawa
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Christi Waer
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| | - Keiichi Itakura
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, California
| |
Collapse
|
68
|
Haploinsufficiency of the intellectual disability gene SETD5 disturbs developmental gene expression and cognition. Nat Neurosci 2018; 21:1717-1727. [DOI: 10.1038/s41593-018-0266-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/26/2018] [Indexed: 12/11/2022]
|
69
|
Brien GL, Remillard D, Shi J, Hemming ML, Chabon J, Wynne K, Dillon ET, Cagney G, Van Mierlo G, Baltissen MP, Vermeulen M, Qi J, Fröhling S, Gray NS, Bradner JE, Vakoc CR, Armstrong SA. Targeted degradation of BRD9 reverses oncogenic gene expression in synovial sarcoma. eLife 2018; 7:41305. [PMID: 30431433 PMCID: PMC6277197 DOI: 10.7554/elife.41305] [Citation(s) in RCA: 117] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/11/2018] [Indexed: 12/14/2022] Open
Abstract
Synovial sarcoma tumours contain a characteristic fusion protein, SS18-SSX, which drives disease development. Targeting oncogenic fusion proteins presents an attractive therapeutic opportunity. However, SS18-SSX has proven intractable for therapeutic intervention. Using a domain-focused CRISPR screen we identified the bromodomain of BRD9 as a critical functional dependency in synovial sarcoma. BRD9 is a component of SS18-SSX containing BAF complexes in synovial sarcoma cells; and integration of BRD9 into these complexes is critical for cell growth. Moreover BRD9 and SS18-SSX co-localize extensively on the synovial sarcoma genome. Remarkably, synovial sarcoma cells are highly sensitive to a novel small molecule degrader of BRD9, while other sarcoma subtypes are unaffected. Degradation of BRD9 induces downregulation of oncogenic transcriptional programs and inhibits tumour progression in vivo. We demonstrate that BRD9 supports oncogenic mechanisms underlying the SS18-SSX fusion in synovial sarcoma and highlight targeted degradation of BRD9 as a potential therapeutic opportunity in this disease.
Collapse
Affiliation(s)
- Gerard L Brien
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Remillard
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Junwei Shi
- Department of Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Matthew L Hemming
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States.,Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Jonathon Chabon
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Kieran Wynne
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Eugène T Dillon
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Gerard Cagney
- School of Biomolecular and Biomedical Science and Conway Institute, University College Dublin, Dublin, Ireland
| | - Guido Van Mierlo
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Marijke P Baltissen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Jun Qi
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - Stefan Fröhling
- German Cancer Consortium, Heidelberg, Germany.,Section for Personalized Oncology, Heidelberg University Hospital, Heidelberg, Germany.,Division of Translational Oncology, National Center for Tumor Diseases Heidelberg and German Cancer Research Center, Heidelberg, Germany
| | - Nathanael S Gray
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | - James E Bradner
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| | | | - Scott A Armstrong
- Department of Pediatric Oncology, Dana Farber Cancer Institute, Boston Children's Hospital and Harvard Medical School, Boston, United States
| |
Collapse
|
70
|
Isolation of mitochondria from Saccharomyces cerevisiae using magnetic bead affinity purification. PLoS One 2018; 13:e0196632. [PMID: 29698455 PMCID: PMC5919621 DOI: 10.1371/journal.pone.0196632] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 04/16/2018] [Indexed: 11/30/2022] Open
Abstract
Isolated mitochondria are widely used to study the function of the organelle. Typically, mitochondria are prepared using differential centrifugation alone or in conjunction with density gradient ultracentrifugation. However, mitochondria isolated using differential centrifugation contain membrane or organelle contaminants, and further purification of crude mitochondria by density gradient ultracentrifugation requires large amounts of starting material, and is time-consuming. Mitochondria have also been isolated by irreversible binding to antibody-coated magnetic beads. We developed a method to prepare mitochondria from budding yeast that overcomes many of the limitations of other methods. Mitochondria are tagged by insertion of 6 histidines (6xHis) into the TOM70 (Translocase of outer membrane 70) gene at its chromosomal locus, isolated using Ni-NTA (nickel (II) nitrilotriacetic acid) paramagnetic beads and released from the magnetic beads by washing with imidazole. Mitochondria prepared using this method contain fewer contaminants, and are similar in ultrastructure as well as protein import and cytochrome c oxidase complex activity compared to mitochondria isolated by differential centrifugation. Moreover, this isolation method is amenable to small samples, faster than purification by differential and density gradient centrifugation, and more cost-effective than purification using antibody-coated magnetic beads. Importantly, this method can be applied to any cell type where the genetic modification can be introduced by CRISPR or other methods.
Collapse
|
71
|
Dewari PS, Southgate B, Mccarten K, Monogarov G, O'Duibhir E, Quinn N, Tyrer A, Leitner MC, Plumb C, Kalantzaki M, Blin C, Finch R, Bressan RB, Morrison G, Jacobi AM, Behlke MA, von Kriegsheim A, Tomlinson S, Krijgsveld J, Pollard SM. An efficient and scalable pipeline for epitope tagging in mammalian stem cells using Cas9 ribonucleoprotein. eLife 2018; 7:e35069. [PMID: 29638216 PMCID: PMC5947990 DOI: 10.7554/elife.35069] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/10/2018] [Indexed: 01/09/2023] Open
Abstract
CRISPR/Cas9 can be used for precise genetic knock-in of epitope tags into endogenous genes, simplifying experimental analysis of protein function. However, Cas9-assisted epitope tagging in primary mammalian cell cultures is often inefficient and reliant on plasmid-based selection strategies. Here, we demonstrate improved knock-in efficiencies of diverse tags (V5, 3XFLAG, Myc, HA) using co-delivery of Cas9 protein pre-complexed with two-part synthetic modified RNAs (annealed crRNA:tracrRNA) and single-stranded oligodeoxynucleotide (ssODN) repair templates. Knock-in efficiencies of ~5-30%, were achieved without selection in embryonic stem (ES) cells, neural stem (NS) cells, and brain-tumor-derived stem cells. Biallelic-tagged clonal lines were readily derived and used to define Olig2 chromatin-bound interacting partners. Using our novel web-based design tool, we established a 96-well format pipeline that enabled V5-tagging of 60 different transcription factors. This efficient, selection-free and scalable epitope tagging pipeline enables systematic surveys of protein expression levels, subcellular localization, and interactors across diverse mammalian stem cells.
Collapse
Affiliation(s)
- Pooran Singh Dewari
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Benjamin Southgate
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Katrina Mccarten
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - German Monogarov
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Eoghan O'Duibhir
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Niall Quinn
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Ashley Tyrer
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Marie-Christin Leitner
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Colin Plumb
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Maria Kalantzaki
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Carla Blin
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Rebecca Finch
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Raul Bardini Bressan
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Gillian Morrison
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc.CoralvilleUnited States
| | - Alex von Kriegsheim
- Institute of Genetics and Molecular Medicine, Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
| | - Simon Tomlinson
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| | - Jeroen Krijgsveld
- German Cancer Research CenterUniversity of HeidelbergHeidelbergGermany
| | - Steven M Pollard
- Edinburgh Cancer Research United Kingdom CentreUniversity of EdinburghEdinburghUnited Kingdom
- MRC Centre for Regenerative MedicineUniversity of EdinburghEdinburghUnited Kingdom
| |
Collapse
|
72
|
Applications of CRISPR/Cas System to Bacterial Metabolic Engineering. Int J Mol Sci 2018; 19:ijms19041089. [PMID: 29621180 PMCID: PMC5979482 DOI: 10.3390/ijms19041089] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/02/2018] [Accepted: 04/03/2018] [Indexed: 01/10/2023] Open
Abstract
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) adaptive immune system has been extensively used for gene editing, including gene deletion, insertion, and replacement in bacterial and eukaryotic cells owing to its simple, rapid, and efficient activities in unprecedented resolution. Furthermore, the CRISPR interference (CRISPRi) system including deactivated Cas9 (dCas9) with inactivated endonuclease activity has been further investigated for regulation of the target gene transiently or constitutively, avoiding cell death by disruption of genome. This review discusses the applications of CRISPR/Cas for genome editing in various bacterial systems and their applications. In particular, CRISPR technology has been used for the production of metabolites of high industrial significance, including biochemical, biofuel, and pharmaceutical products/precursors in bacteria. Here, we focus on methods to increase the productivity and yield/titer scan by controlling metabolic flux through individual or combinatorial use of CRISPR/Cas and CRISPRi systems with introduction of synthetic pathway in industrially common bacteria including Escherichia coli. Further, we discuss additional useful applications of the CRISPR/Cas system, including its use in functional genomics.
Collapse
|
73
|
Abstract
Advances in Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated system (CRISPR/Cas9) has dramatically reshaped our ability to edit genomes. The scientific community is using CRISPR/Cas9 for various biotechnological and medical purposes. One of its most important uses is developing potential therapeutic strategies against diseases. CRISPR/Cas9 based approaches have been increasingly applied to the treatment of human diseases like cancer, genetic, immunological and neurological disorders and viral diseases. These strategies using CRISPR/Cas9 are not only therapy oriented but can also be used for disease modeling as well, which in turn can lead to the improved understanding of mechanisms of various infectious and genetic diseases. In addition, CRISPR/Cas9 system can also be used as programmable antibiotics to kill the bacteria sequence specifically and therefore can bypass multidrug resistance. Furthermore, CRISPR/Cas9 based gene drive may also hold the potential to limit the spread of vector borne diseases. This bacterial and archaeal adaptive immune system might be a therapeutic answer to previous incurable diseases, of course rigorous testing is required to corroborate these claims. In this review, we provide an insight about the recent developments using CRISPR/Cas9 against various diseases with respect to disease modeling and treatment, and what future perspectives should be noted while using this technology.
Collapse
|
74
|
Tosti L, Ashmore J, Tan BSN, Carbone B, Mistri TK, Wilson V, Tomlinson SR, Kaji K. Mapping transcription factor occupancy using minimal numbers of cells in vitro and in vivo. Genome Res 2018; 28:592-605. [PMID: 29572359 PMCID: PMC5880248 DOI: 10.1101/gr.227124.117] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 03/05/2018] [Indexed: 01/11/2023]
Abstract
The identification of transcription factor (TF) binding sites in the genome is critical to understanding gene regulatory networks (GRNs). While ChIP-seq is commonly used to identify TF targets, it requires specific ChIP-grade antibodies and high cell numbers, often limiting its applicability. DNA adenine methyltransferase identification (DamID), developed and widely used in Drosophila, is a distinct technology to investigate protein–DNA interactions. Unlike ChIP-seq, it does not require antibodies, precipitation steps, or chemical protein–DNA crosslinking, but to date it has been seldom used in mammalian cells due to technical limitations. Here we describe an optimized DamID method coupled with next-generation sequencing (DamID-seq) in mouse cells and demonstrate the identification of the binding sites of two TFs, POU5F1 (also known as OCT4) and SOX2, in as few as 1000 embryonic stem cells (ESCs) and neural stem cells (NSCs), respectively. Furthermore, we have applied this technique in vivo for the first time in mammals. POU5F1 DamID-seq in the gastrulating mouse embryo at 7.5 d post coitum (dpc) successfully identified multiple POU5F1 binding sites proximal to genes involved in embryo development, neural tube formation, and mesoderm-cardiac tissue development, consistent with the pivotal role of this TF in post-implantation embryo. This technology paves the way to unprecedented investigation of TF–DNA interactions and GRNs in specific cell types of limited availability in mammals, including in vivo samples.
Collapse
Affiliation(s)
- Luca Tosti
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - James Ashmore
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Boon Siang Nicholas Tan
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Benedetta Carbone
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Tapan K Mistri
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Valerie Wilson
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Simon R Tomlinson
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| | - Keisuke Kaji
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh BioQuarter, Edinburgh, EH16 4UU, Scotland, United Kingdom
| |
Collapse
|
75
|
Charpentier M, Khedher AHY, Menoret S, Brion A, Lamribet K, Dardillac E, Boix C, Perrouault L, Tesson L, Geny S, De Cian A, Itier JM, Anegon I, Lopez B, Giovannangeli C, Concordet JP. CtIP fusion to Cas9 enhances transgene integration by homology-dependent repair. Nat Commun 2018; 9:1133. [PMID: 29556040 PMCID: PMC5859065 DOI: 10.1038/s41467-018-03475-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 02/16/2018] [Indexed: 12/18/2022] Open
Abstract
In genome editing with CRISPR-Cas9, transgene integration often remains challenging. Here, we present an approach for increasing the efficiency of transgene integration by homology-dependent repair (HDR). CtIP, a key protein in early steps of homologous recombination, is fused to Cas9 and stimulates transgene integration by HDR at the human AAVS1 safe harbor locus. A minimal N-terminal fragment of CtIP, designated HE for HDR enhancer, is sufficient to stimulate HDR and this depends on CDK phosphorylation sites and the multimerization domain essential for CtIP activity in homologous recombination. HDR stimulation by Cas9-HE, however, depends on the guide RNA used, a limitation that may be overcome by testing multiple guides to the locus of interest. The Cas9-HE fusion is simple to use and allows obtaining twofold or more efficient transgene integration than that with Cas9 in several experimental systems, including human cell lines, iPS cells, and rat zygotes.
Collapse
Affiliation(s)
- M Charpentier
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - A H Y Khedher
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
- Translational Sciences, Sanofi, 13 Quai Jules Guesde, F-94400, Vitry-sur-Seine, France
| | - S Menoret
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - A Brion
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - K Lamribet
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - E Dardillac
- Equipe Labellisée Ligue Contre le Cancer, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, CNRS UMR 8200, 114 rue Edouard Vaillant, Villejuif, F-94805, France
| | - C Boix
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - L Perrouault
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - L Tesson
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - S Geny
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - A De Cian
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - J M Itier
- Translational Sciences, Sanofi, 13 Quai Jules Guesde, F-94400, Vitry-sur-Seine, France
| | - I Anegon
- Centre de Recherche en Transplantation et Immunologie UMR1064, INSERM, Université de Nantes, CHU de Nantes, 30 Avenue Jean Monnet, F-44093, Nantes, France
| | - B Lopez
- Equipe Labellisée Ligue Contre le Cancer, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, CNRS UMR 8200, 114 rue Edouard Vaillant, Villejuif, F-94805, France
| | - C Giovannangeli
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France
| | - J P Concordet
- Museum National d'Histoire Naturelle, INSERM U1154, CNRS UMR 7196, Sorbonne Universités, 43 rue Cuvier, Paris, F-75231, France.
| |
Collapse
|
76
|
Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Brief Funct Genomics 2018; 17:116-137. [PMID: 29529131 PMCID: PMC5889016 DOI: 10.1093/bfgp/ely004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Advances in the methods for detecting protein-DNA interactions have played a key role in determining the directions of research into the mechanisms of transcriptional regulation. The most recent major technological transformation happened a decade ago, with the move from using tiling arrays [chromatin immunoprecipitation (ChIP)-on-Chip] to high-throughput sequencing (ChIP-seq) as a readout for ChIP assays. In addition to the numerous other ways in which it is superior to arrays, by eliminating the need to design and manufacture them, sequencing also opened the door to carrying out comparative analyses of genome-wide transcription factor occupancy across species and studying chromatin biology in previously less accessible model and nonmodel organisms, thus allowing us to understand the evolution and diversity of regulatory mechanisms in unprecedented detail. Here, we review the biological insights obtained from such studies in recent years and discuss anticipated future developments in the field.
Collapse
Affiliation(s)
- Georgi K Marinov
- Corresponding author: Georgi K. Marinov, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. E-mail:
| | | |
Collapse
|
77
|
Chai M, Sanosaka T, Okuno H, Zhou Z, Koya I, Banno S, Andoh-Noda T, Tabata Y, Shimamura R, Hayashi T, Ebisawa M, Sasagawa Y, Nikaido I, Okano H, Kohyama J. Chromatin remodeler CHD7 regulates the stem cell identity of human neural progenitors. Genes Dev 2018; 32:165-180. [PMID: 29440260 PMCID: PMC5830929 DOI: 10.1101/gad.301887.117] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022]
Abstract
Multiple congenital disorders often present complex phenotypes, but how the mutation of individual genetic factors can lead to multiple defects remains poorly understood. In the present study, we used human neuroepithelial (NE) cells and CHARGE patient-derived cells as an in vitro model system to identify the function of chromodomain helicase DNA-binding 7 (CHD7) in NE-neural crest bifurcation, thus revealing an etiological link between the central nervous system (CNS) and craniofacial anomalies observed in CHARGE syndrome. We found that CHD7 is required for epigenetic activation of superenhancers and CNS-specific enhancers, which support the maintenance of the NE and CNS lineage identities. Furthermore, we found that BRN2 and SOX21 are downstream effectors of CHD7, which shapes cellular identities by enhancing a CNS-specific cellular program and indirectly repressing non-CNS-specific cellular programs. Based on our results, CHD7, through its interactions with superenhancer elements, acts as a regulatory hub in the orchestration of the spatiotemporal dynamics of transcription factors to regulate NE and CNS lineage identities.
Collapse
Affiliation(s)
- MuhChyi Chai
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.,Gene Regulation Research, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
| | - Tsukasa Sanosaka
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Hironobu Okuno
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Zhi Zhou
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Ikuko Koya
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Satoe Banno
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tomoko Andoh-Noda
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yoshikuni Tabata
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan.,E-WAY Research Laboratory, Discovery, Medicine Creation, Neurology Business Group, Tsukuba, Ibaraki 300-2635, Japan
| | - Rieko Shimamura
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Tetsutaro Hayashi
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - Masashi Ebisawa
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - Yohei Sasagawa
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan
| | - Itoshi Nikaido
- Bioinformatics Research Unit, Advanced Center for Computing and Communication, RIKEN, Wako, Saitama 351-0198, Japan.,Single-Cell Omics Research Unit, RIKEN Center for Developmental Biology, Wako, Saitama 351-0198, Japan
| | - Hideyuki Okano
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Jun Kohyama
- Department of Physiology, Keio University School of Medicine, Shinjuku-ku, Tokyo 160-8582, Japan
| |
Collapse
|
78
|
Regulation of Sensing, Transportation, and Catabolism of Nitrogen Sources in Saccharomyces cerevisiae. Microbiol Mol Biol Rev 2018; 82:82/1/e00040-17. [PMID: 29436478 DOI: 10.1128/mmbr.00040-17] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Nitrogen is one of the most important essential nutrient sources for biogenic activities. Regulation of nitrogen metabolism in microorganisms is complicated and elaborate. For this review, the yeast Saccharomyces cerevisiae was chosen to demonstrate the regulatory mechanism of nitrogen metabolism because of its relative clear genetic background. Current opinions on the regulation processes of nitrogen metabolism in S. cerevisiae, including nitrogen sensing, transport, and catabolism, are systematically reviewed. Two major upstream signaling pathways, the Ssy1-Ptr3-Ssy5 sensor system and the target of rapamycin pathway, which are responsible for sensing extracellular and intracellular nitrogen, respectively, are discussed. The ubiquitination of nitrogen transporters, which is the most general and efficient means for controlling nitrogen transport, is also summarized. The following metabolic step, nitrogen catabolism, is demonstrated at two levels: the transcriptional regulation process related to GATA transcriptional factors and the translational regulation process related to the general amino acid control pathway. The interplay between nitrogen regulation and carbon regulation is also discussed. As a model system, understanding the meticulous process by which nitrogen metabolism is regulated in S. cerevisiae not only could facilitate research on global regulation mechanisms and yeast metabolic engineering but also could provide important insights and inspiration for future studies of other common microorganisms and higher eukaryotic cells.
Collapse
|
79
|
Korona D, Koestler SA, Russell S. Engineering the Drosophila Genome for Developmental Biology. J Dev Biol 2017; 5:jdb5040016. [PMID: 29615571 PMCID: PMC5831791 DOI: 10.3390/jdb5040016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/07/2017] [Accepted: 12/08/2017] [Indexed: 02/07/2023] Open
Abstract
The recent development of transposon and CRISPR-Cas9-based tools for manipulating the fly genome in vivo promises tremendous progress in our ability to study developmental processes. Tools for introducing tags into genes at their endogenous genomic loci facilitate imaging or biochemistry approaches at the cellular or subcellular levels. Similarly, the ability to make specific alterations to the genome sequence allows much more precise genetic control to address questions of gene function.
Collapse
Affiliation(s)
- Dagmara Korona
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Stefan A Koestler
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| | - Steven Russell
- Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.
| |
Collapse
|
80
|
Ramaker RC, Savic D, Hardigan AA, Newberry K, Cooper GM, Myers RM, Cooper SJ. A genome-wide interactome of DNA-associated proteins in the human liver. Genome Res 2017; 27:1950-1960. [PMID: 29021291 PMCID: PMC5668951 DOI: 10.1101/gr.222083.117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 08/22/2017] [Indexed: 12/13/2022]
Abstract
Large-scale efforts like the ENCODE Project have made tremendous progress in cataloging the genomic binding patterns of DNA-associated proteins (DAPs), such as transcription factors (TFs). However, most chromatin immunoprecipitation-sequencing (ChIP-seq) analyses have focused on a few immortalized cell lines whose activities and physiology differ in important ways from endogenous cells and tissues. Consequently, binding data from primary human tissue are essential to improving our understanding of in vivo gene regulation. Here, we identify and analyze more than 440,000 binding sites using ChIP-seq data for 20 DAPs in two human liver tissue samples. We integrated binding data with transcriptome and phased WGS data to investigate allelic DAP interactions and the impact of heterozygous sequence variation on the expression of neighboring genes. Our tissue-based data set exhibits binding patterns more consistent with liver biology than cell lines, and we describe uses of these data to better prioritize impactful noncoding variation. Collectively, our rich data set offers novel insights into genome function in human liver tissue and provides a valuable resource for assessing disease-related disruptions.
Collapse
Affiliation(s)
- Ryne C Ramaker
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA
| | - Kimberly Newberry
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA
| |
Collapse
|
81
|
Kanca O, Bellen HJ, Schnorrer F. Gene Tagging Strategies To Assess Protein Expression, Localization, and Function in Drosophila. Genetics 2017; 207:389-412. [PMID: 28978772 PMCID: PMC5629313 DOI: 10.1534/genetics.117.199968] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 06/13/2017] [Indexed: 01/15/2023] Open
Abstract
Analysis of gene function in complex organisms relies extensively on tools to detect the cellular and subcellular localization of gene products, especially proteins. Typically, immunostaining with antibodies provides these data. However, due to cost, time, and labor limitations, generating specific antibodies against all proteins of a complex organism is not feasible. Furthermore, antibodies do not enable live imaging studies of protein dynamics. Hence, tagging genes with standardized immunoepitopes or fluorescent tags that permit live imaging has become popular. Importantly, tagging genes present in large genomic clones or at their endogenous locus often reports proper expression, subcellular localization, and dynamics of the encoded protein. Moreover, these tagging approaches allow the generation of elegant protein removal strategies, standardization of visualization protocols, and permit protein interaction studies using mass spectrometry. Here, we summarize available genomic resources and techniques to tag genes and discuss relevant applications that are rarely, if at all, possible with antibodies.
Collapse
Affiliation(s)
- Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, Texas 77030
- Program in Developmental Biology, Baylor College of Medicine, Houston, Texas 77030
- Department of Neuroscience, Baylor College of Medicine, Houston, Texas 77030
- Howard Hughes Medical Institute, Houston, Texas 77030
| | - Frank Schnorrer
- Developmental Biology Institute of Marseille (IBDM), UMR 7288, CNRS, Aix-Marseille Université, 13288, France
| |
Collapse
|
82
|
Liu JL. Sparks of the CRISPR explosion: Applications in medicine and agriculture. J Genet Genomics 2017; 44:413-414. [DOI: 10.1016/j.jgg.2017.09.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Indexed: 12/14/2022]
|
83
|
Diwan A, Ninawe A, Harke S. Gene editing (CRISPR-Cas) technology and fisheries sector. CANADIAN JOURNAL OF BIOTECHNOLOGY 2017. [DOI: 10.24870/cjb.2017-000108] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
84
|
Lin J, Zhou Y, Liu J, Chen J, Chen W, Zhao S, Wu Z, Wu N. Progress and Application of CRISPR/Cas Technology in Biological and Biomedical Investigation. J Cell Biochem 2017; 118:3061-3071. [DOI: 10.1002/jcb.26198] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2017] [Accepted: 06/06/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Jiachen Lin
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Yangzhong Zhou
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Internal Medicine, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Jiaqi Liu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Department of Breast Surgical Oncology, National Cancer Center/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijingChina
| | - Jia Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Weisheng Chen
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Sen Zhao
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
| | - Zhihong Wu
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Central Laboratory, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
| | - Nan Wu
- Department of Orthopedic Surgery, Peking Union Medical College HospitalPeking Union Medical College and Chinese Academy of Medical SciencesBeijingChina
- Beijing Key Laboratory for Genetic Research of Skeletal DeformityBeijingChina
- Medical Research Center of OrthopedicsChinese Academy of Medical SciencesBeijingChina
- Department of Molecular and Human GeneticsBaylor College of MedicineHoustonTexas
| |
Collapse
|
85
|
Xiong X, Zhang Y, Yan J, Jain S, Chee S, Ren B, Zhao H. A Scalable Epitope Tagging Approach for High Throughput ChIP-Seq Analysis. ACS Synth Biol 2017; 6:1034-1042. [PMID: 28215080 DOI: 10.1021/acssynbio.6b00358] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Eukaryotic transcriptional factors (TFs) typically recognize short genomic sequences alone or together with other proteins to modulate gene expression. Mapping of TF-DNA interactions in the genome is crucial for understanding the gene regulatory programs in cells. While chromatin immunoprecipitation followed by sequencing (ChIP-Seq) is commonly used for this purpose, its application is severely limited by the availability of suitable antibodies for TFs. To overcome this limitation, we developed an efficient and scalable strategy named cmChIP-Seq that combines the clustered regularly interspaced short palindromic repeats (CRISPR) technology with microhomology mediated end joining (MMEJ) to genetically engineer a TF with an epitope tag. We demonstrated the utility of this tool by applying it to four TFs in a human colorectal cancer cell line. The highly scalable procedure makes this strategy ideal for ChIP-Seq analysis of TFs in diverse species and cell types.
Collapse
Affiliation(s)
- Xiong Xiong
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Yanxiao Zhang
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
| | - Jian Yan
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Biosciences and Nutrition, Karolinska Institutet, 141 83 Huddinge, Sweden
| | - Surbhi Jain
- Department
of Biochemistry, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| | - Sora Chee
- Department
of Cellular and Molecular Medicine, Institute of Genome Medicine,
Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California 92093, United States
| | - Bing Ren
- Ludwig Institute for Cancer Research, 9500 Gilman Drive, La Jolla, California 92093, United States
- Department
of Cellular and Molecular Medicine, Institute of Genome Medicine,
Moores Cancer Center, University of California San Diego, School of Medicine, San Diego, California 92093, United States
| | - Huimin Zhao
- Department
of Chemical and Biomolecular Engineering, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
- Departments
of Chemistry and Bioengineering, Carl R. Woese Institute for Genomic
Biology, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801, United States
| |
Collapse
|
86
|
|
87
|
Powell SK, Gregory J, Akbarian S, Brennand KJ. Application of CRISPR/Cas9 to the study of brain development and neuropsychiatric disease. Mol Cell Neurosci 2017; 82:157-166. [PMID: 28549865 DOI: 10.1016/j.mcn.2017.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/22/2017] [Indexed: 12/18/2022] Open
Abstract
CRISPR/Cas9 technology has transformed our ability to manipulate the genome and epigenome, from efficient genomic editing to targeted localization of effectors to specific loci. Through the manipulation of DNA- and histone-modifying enzyme activities, activation or repression of gene expression, and targeting of transcriptional regulators, the role of gene-regulatory and epigenetic pathways in basic biology and disease processes can be directly queried. Here, we discuss emerging CRISPR-based methodologies, with specific consideration of neurobiological applications of human induced pluripotent stem cell (hiPSC)-based models.
Collapse
Affiliation(s)
- S K Powell
- Medical Scientist Training Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - J Gregory
- Instructional Technology Group, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - S Akbarian
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - K J Brennand
- Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States; Department of Genetics and Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| |
Collapse
|
88
|
Bressan RB, Dewari PS, Kalantzaki M, Gangoso E, Matjusaitis M, Garcia-Diaz C, Blin C, Grant V, Bulstrode H, Gogolok S, Skarnes WC, Pollard SM. Efficient CRISPR/Cas9-assisted gene targeting enables rapid and precise genetic manipulation of mammalian neural stem cells. Development 2017; 144:635-648. [PMID: 28096221 PMCID: PMC5312033 DOI: 10.1242/dev.140855] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 12/15/2016] [Indexed: 01/09/2023]
Abstract
Mammalian neural stem cell (NSC) lines provide a tractable model for discovery across stem cell and developmental biology, regenerative medicine and neuroscience. They can be derived from foetal or adult germinal tissues and continuously propagated in vitro as adherent monolayers. NSCs are clonally expandable, genetically stable, and easily transfectable - experimental attributes compatible with targeted genetic manipulations. However, gene targeting, which is crucial for functional studies of embryonic stem cells, has not been exploited to date in NSC lines. Here, we deploy CRISPR/Cas9 technology to demonstrate a variety of sophisticated genetic modifications via gene targeting in both mouse and human NSC lines, including: (1) efficient targeted transgene insertion at safe harbour loci (Rosa26 and AAVS1); (2) biallelic knockout of neurodevelopmental transcription factor genes; (3) simple knock-in of epitope tags and fluorescent reporters (e.g. Sox2-V5 and Sox2-mCherry); and (4) engineering of glioma mutations (TP53 deletion; H3F3A point mutations). These resources and optimised methods enable facile and scalable genome editing in mammalian NSCs, providing significant new opportunities for functional genetic analysis.
Collapse
Affiliation(s)
| | - Pooran Singh Dewari
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Maria Kalantzaki
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Ester Gangoso
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Mantas Matjusaitis
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Claudia Garcia-Diaz
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Carla Blin
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Vivien Grant
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Harry Bulstrode
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - Sabine Gogolok
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| | - William C Skarnes
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Steven M Pollard
- MRC Centre for Regenerative Medicine, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
89
|
Van Nostrand EL, Gelboin-Burkhart C, Wang R, Pratt GA, Blue SM, Yeo GW. CRISPR/Cas9-mediated integration enables TAG-eCLIP of endogenously tagged RNA binding proteins. Methods 2016; 118-119:50-59. [PMID: 28003131 DOI: 10.1016/j.ymeth.2016.12.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 12/08/2016] [Accepted: 12/10/2016] [Indexed: 12/22/2022] Open
Abstract
Identification of in vivo direct RNA targets for RNA binding proteins (RBPs) provides critical insight into their regulatory activities and mechanisms. Recently, we described a methodology for enhanced crosslinking and immunoprecipitation followed by high-throughput sequencing (eCLIP) using antibodies against endogenous RNA binding proteins. However, in many cases it is desirable to profile targets of an RNA binding protein for which an immunoprecipitation-grade antibody is lacking. Here we describe a scalable method for using CRISPR/Cas9-mediated homologous recombination to insert a peptide tag into the endogenous RNA binding protein locus. Further, we show that TAG-eCLIP performed using tag-specific antibodies can yield the same robust binding profiles after proper control normalization as eCLIP with antibodies against endogenous proteins. Finally, we note that antibodies against commonly used tags can immunoprecipitate significant amounts of antibody-specific RNA, emphasizing the need for paired controls alongside each experiment for normalization. TAG-eCLIP enables eCLIP profiling of new native proteins where no suitable antibody exists, expanding the RBP-RNA interaction landscape.
Collapse
Affiliation(s)
- Eric L Van Nostrand
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Chelsea Gelboin-Burkhart
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Ruth Wang
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Gabriel A Pratt
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Steven M Blue
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA
| | - Gene W Yeo
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA, USA; Stem Cell Program, University of California at San Diego, La Jolla, CA, USA; Institute for Genomic Medicine, University of California at San Diego, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA; Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Molecular Engineering Laboratory, A*STAR, Singapore.
| |
Collapse
|
90
|
CRISPR-Cas9 mediated genetic engineering for the purification of the endogenous integrator complex from mammalian cells. Protein Expr Purif 2016; 128:101-8. [PMID: 27546450 DOI: 10.1016/j.pep.2016.08.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 08/12/2016] [Accepted: 08/16/2016] [Indexed: 01/14/2023]
Abstract
The Integrator Complex (INT) is a large multi-subunit protein complex, containing at least 14 subunits and a host of associated factors. These protein components have been established through pulldowns of overexpressed epitope tagged subunits or by using antibodies raised against specific subunits. Here, we utilize CRISPR/Cas9 gene editing technology to introduce N-terminal FLAG epitope tags into the endogenous genes that encode Integrator subunit 4 and 11 within HEK293T cells. We provide specific details regarding design, approaches for facile screening, and our observed frequency of successful recombination. Finally, using silver staining, Western blotting and LC-MS/MS we compare the components of INT of purifications from CRISPR derived lines to 293T cells overexpressing FLAG-INTS11 to define a highly resolved constituency of mammalian INT.
Collapse
|
91
|
Brown A, Woods WS, Perez-Pinera P. Multiplexed Targeted Genome Engineering Using a Universal Nuclease-Assisted Vector Integration System. ACS Synth Biol 2016; 5:582-8. [PMID: 27159246 DOI: 10.1021/acssynbio.6b00056] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Engineered nucleases are capable of efficiently modifying complex genomes through introduction of targeted double-strand breaks. However, mammalian genome engineering remains limited by low efficiency of heterologous DNA integration at target sites, which is typically performed through homologous recombination, a complex, ineffective and costly process. In this study, we developed a multiplexable and universal nuclease-assisted vector integration system for rapid generation of gene knock outs using selection that does not require customized targeting vectors, thereby minimizing the cost and time frame needed for gene editing. Importantly, this system is capable of remodeling native mammalian genomes through integration of DNA, up to 50 kb, enabling rapid generation and screening of multigene knockouts from a single transfection. These results support that nuclease assisted vector integration is a robust tool for genome-scale gene editing that will facilitate diverse applications in synthetic biology and gene therapy.
Collapse
Affiliation(s)
- Alexander Brown
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois 61801, United States
| |
Collapse
|
92
|
Yan H, Tian S, Slager SL, Sun Z. ChIP-seq in studying epigenetic mechanisms of disease and promoting precision medicine: progresses and future directions. Epigenomics 2016; 8:1239-58. [PMID: 27319740 DOI: 10.2217/epi-2016-0053] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used for mapping histone modifications, histone proteins, chromatin regulators, transcription factors and other DNA-binding proteins. It has played a significant role in our understanding of disease mechanisms and in exploring epigenetic changes for potential clinical applications. However, the conventional protocol requires large amounts of starting material and does not quantify the actual occupancy, limiting its applications in clinical settings. Herein we summarize the latest progresses in utilizing ChIP-seq to link epigenetic alterations to disease initiation and progression, and the implications in precision medicine. We provide an update on the newly developed ChIP-seq protocols, especially those suitable for scare clinical samples. Technical and analytical challenges are outlined together with recommendations for improvement. Finally, future directions in expediting ChIP-seq use in clinic are discussed.
Collapse
Affiliation(s)
- Huihuang Yan
- Division of Biomedical Statistics & Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Shulan Tian
- Division of Biomedical Statistics & Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Susan L Slager
- Division of Biomedical Statistics & Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| | - Zhifu Sun
- Division of Biomedical Statistics & Informatics, Department of Health Sciences Research, Mayo Clinic, 200 1st Street SW, Rochester, MN 55905, USA
| |
Collapse
|
93
|
Partridge EC, Watkins TA, Mendenhall EM. Every transcription factor deserves its map: Scaling up epitope tagging of proteins to bypass antibody problems. Bioessays 2016; 38:801-11. [PMID: 27311628 DOI: 10.1002/bies.201600028] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Genome-wide identification of transcription factor binding sites with the ChIP-seq method is an extremely important scientific endeavor - one that should ideally be performed for every transcription factor in as many cell types as possible. A major hurdle on the way to this goal is the necessity for a specific, ChIP-grade antibody for each transcription factor of interest, which is often not available. Here, we describe CETCh-seq, a recently published method utilizing genome engineering with the CRISPR/Cas9 system to circumvent the need for a specific antibody. Using the CETCh-seq method, targeted genomic editing results in an epitope-tagged transcription factor, which is recognized by a well-characterized, standard antibody, efficacious for ChIP-seq. We have used CETCh-seq in human cancer cell lines as well as mouse embryonic stem cells. We find that roughly 60% of transcription factors tagged using CETCh-seq produce a high quality ChIP-seq map, a significant improvement over traditional antibody-based methods.
Collapse
Affiliation(s)
| | | | - Eric M Mendenhall
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.,University of Alabama in Huntsville, AL, USA
| |
Collapse
|
94
|
Engel KL, Mackiewicz M, Hardigan AA, Myers RM, Savic D. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol 2016; 57:40-50. [PMID: 27224938 DOI: 10.1016/j.semcdb.2016.05.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/06/2016] [Accepted: 05/18/2016] [Indexed: 12/18/2022]
Abstract
Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research.
Collapse
Affiliation(s)
- Krysta L Engel
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Mark Mackiewicz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Andrew A Hardigan
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States; Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Daniel Savic
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States.
| |
Collapse
|
95
|
Vandemoortele G, Gevaert K, Eyckerman S. Proteomics in the genome engineering era. Proteomics 2015; 16:177-87. [DOI: 10.1002/pmic.201500262] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Revised: 09/22/2015] [Accepted: 10/15/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Giel Vandemoortele
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Kris Gevaert
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| | - Sven Eyckerman
- VIB Medical Biotechnology Center; Ghent Belgium
- Department of Biochemistry; Ghent University; Ghent Belgium
| |
Collapse
|