1
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Qiao Z, Nguyen LC, Yang D, Dann C, Thomas DM, Henn M, Valdespino A, Swenson CS, Oakes SA, Rosner MR, Moellering RE. Direct inhibition of tumor hypoxia response with synthetic transcriptional repressors. Nat Chem Biol 2024:10.1038/s41589-024-01716-z. [PMID: 39215099 DOI: 10.1038/s41589-024-01716-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 08/01/2024] [Indexed: 09/04/2024]
Abstract
Many oncogenic transcription factors (TFs) are considered to be undruggable because of their reliance on large protein-protein and protein-DNA interfaces. TFs such as hypoxia-inducible factors (HIFs) and X-box-binding protein 1 (XBP1) are induced by hypoxia and other stressors in solid tumors and bind to unfolded protein response element (UPRE) and hypoxia-induced response element (HRE) motifs to control oncogenic gene programs. Here, we report a strategy to create synthetic transcriptional repressors (STRs) that mimic the basic leucine zipper domain of XBP1 and recognize UPRE and HRE motifs. A lead molecule, STR22, binds UPRE and HRE DNA sequences with high fidelity and competes with both TFs in cells. Under hypoxia, STR22 globally suppresses HIF1α binding to HRE-containing promoters and enhancers, inhibits hypoxia-induced gene expression and blocks protumorigenic phenotypes in triple-negative breast cancer (TNBC) cells. In vivo, intratumoral and systemic STR22 treatment inhibited hypoxia-dependent gene expression, primary tumor growth and metastasis of TNBC tumors. These data validate a novel strategy to target the tumor hypoxia response through coordinated inhibition of TF-DNA binding.
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Affiliation(s)
- Zeyu Qiao
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Long C Nguyen
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Dongbo Yang
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Christopher Dann
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Deborah M Thomas
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Madeline Henn
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Andrea Valdespino
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA
| | - Colin S Swenson
- Department of Chemistry, The University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Scott A Oakes
- Department of Pathology, The University of Chicago, Chicago, IL, USA
| | - Marsha Rich Rosner
- Ben May Department for Cancer Research, The University of Chicago, Chicago, IL, USA.
| | - Raymond E Moellering
- Department of Chemistry, The University of Chicago, Chicago, IL, USA.
- Institute for Genomics and Systems Biology, The University of Chicago, Chicago, IL, USA.
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2
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Speltz TE, Qiao Z, Swenson CS, Shangguan X, Coukos JS, Lee CW, Thomas DM, Santana J, Fanning SW, Greene GL, Moellering RE. Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains. Nat Biotechnol 2023; 41:541-551. [PMID: 36302987 PMCID: PMC10392954 DOI: 10.1038/s41587-022-01504-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 09/08/2022] [Indexed: 01/16/2023]
Abstract
Despite unequivocal roles in disease, transcription factors (TFs) remain largely untapped as pharmacologic targets due to the challenges in targeting protein-protein and protein-DNA interactions. Here we report a chemical strategy to generate modular synthetic transcriptional repressors (STRs) derived from the bHLH domain of MAX. Our synthetic approach yields chemically stabilized tertiary domain mimetics that cooperatively bind the MYC/MAX consensus E-box motif with nanomolar affinity, exhibit specificity that is equivalent to or beyond that of full-length TFs and directly compete with MYC/MAX protein for DNA binding. A lead STR directly inhibits MYC binding in cells, downregulates MYC-dependent expression programs at the proteome level and inhibits MYC-dependent cell proliferation. Co-crystallization and structure determination of a STR:E-box DNA complex confirms retention of DNA recognition in a near identical manner as full-length bHLH TFs. We additionally demonstrate structure-blind design of STRs derived from alternative bHLH-TFs, confirming that STRs can be used to develop highly specific mimetics of TFs targeting other gene regulatory elements.
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Affiliation(s)
- Thomas E Speltz
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Zeyu Qiao
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Colin S Swenson
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Xianghang Shangguan
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - John S Coukos
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Christopher W Lee
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Deborah M Thomas
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Jesse Santana
- Department of Chemistry, University of Chicago, Chicago, IL, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Sean W Fanning
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
- Department of Cancer Biology, Loyola University Chicago, Chicago, IL, USA
| | - Geoffrey L Greene
- Ben May Department for Cancer Research, University of Chicago, Chicago, IL, USA
| | - Raymond E Moellering
- Department of Chemistry, University of Chicago, Chicago, IL, USA.
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, IL, USA.
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3
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Functional Comparison between VP64-dCas9-VP64 and dCas9-VP192 CRISPR Activators in Human Embryonic Kidney Cells. Int J Mol Sci 2021; 22:ijms22010397. [PMID: 33401508 PMCID: PMC7795359 DOI: 10.3390/ijms22010397] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Reversal in the transcriptional status of desired genes has been exploited for multiple research, therapeutic, and biotechnological purposes. CRISPR/dCas9-based activators can activate transcriptionally silenced genes after being guided by gene-specific gRNA(s). Here, we performed a functional comparison between two such activators, VP64-dCas9-VP64 and dCas9-VP192, in human embryonic kidney cells by the concomitant targeting of POU5F1 and SOX2. We found 22- and 6-fold upregulations in the mRNA level of POU5F1 by dCas9-VP192 and VP64-dCas9-VP64, respectively. Likewise, SOX2 was up-regulated 4- and 2-fold using dCas9-VP192 and VP64dCas9VP64, respectively. For the POU5F1 protein level, we observed 3.7- and 2.2-fold increases with dCas9-VP192 and VP64-dCas9-VP64, respectively. Similarly, the SOX2 expression was 2.4- and 2-fold higher with dCas9-VP192 and VP64-dCas9-VP64, respectively. We also confirmed that activation only happened upon co-transfecting an activator plasmid with multiplex gRNA plasmid with a high specificity to the reference genes. Our data revealed that dCas9-VP192 is more efficient than VP64-dCas9-VP64 for activating reference genes.
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4
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Huang HM, Stephan P, Kries H. Engineering DNA-Templated Nonribosomal Peptide Synthesis. Cell Chem Biol 2020; 28:221-227.e7. [PMID: 33238159 DOI: 10.1016/j.chembiol.2020.11.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/16/2020] [Accepted: 11/03/2020] [Indexed: 12/23/2022]
Abstract
Diffusive escape of intermediates limits the rate enhancement that nanocontainers or macromolecular scaffolds can provide for artificial biocatalytic cascades. Nonribosomal peptide synthetases (NRPSs) naturally form gigantic assembly lines and prevent escape by covalently tethering intermediates. Here, we have built DNA-templated NRPS (DT-NRPS) by adding zinc-finger tags to split NRPS modules. The zinc fingers direct the NRPS modules to 9-bp binding sites on a DNA strand, where they form a catalytically active enzyme cascade. Geometric constraints of the DT-NRPSs were investigated using the template DNA as a molecular ruler. Up to four DT-NRPS modules were assembled on DNA to synthesize peptides. DT-NRPSs outperform previously reported DNA-templated enzyme cascades in terms of DNA acceleration, which demonstrates that covalent intermediate channeling is possible along the DNA template. Attachment of assembly line enzymes to a DNA scaffold is a promising catalytic strategy for the sequence-controlled biosynthesis of nonribosomal peptides and other polymers.
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Affiliation(s)
- Hsin-Mei Huang
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Philipp Stephan
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany
| | - Hajo Kries
- Junior Research Group Biosynthetic Design of Natural Products, Leibniz Institute for Natural Product Research and Infection Biology (HKI) e.V., Beutenbergstr. 11a, 07745 Jena, Germany.
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5
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Liu J, Lian X, Liu F, Yan X, Cheng C, Cheng L, Sun X, Shi Z. Identification of Novel Key Targets and Candidate Drugs in Oral Squamous Cell Carcinoma. Curr Bioinform 2020. [DOI: 10.2174/1574893614666191127101836] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Background:
Oral Squamous Cell Carcinoma (OSCC) is the most common malignant
epithelial neoplasm. It is located within the top 10 ranking incidence of cancers with a poor
prognosis and low survival rates. New breakthroughs of therapeutic strategies are therefore needed
to improve the survival rate of OSCC harboring patients.
Objective:
Since targeted therapy is considered as the most promising therapeutic strategies in
cancer, it is of great significance to identify novel targets and drugs for the treatment of OSCC.
Methods:
A series of bioinformatics approaches were launched to identify the hub proteins and
their potential agents. Microarray analysis and several online functional activity network analysis
were firstly utilized to recognize drug targets in OSCC. Subsequently, molecular docking was used
to screen their potential drugs from the specs chemistry database. At the same time, the assessment
of ligand-based virtual screening model was also evaluated.
Results:
In this study, two microarray data (GSE31056, GSE23558) were firstly selected and
analyzed to get consensus candidate genes including 681 candidate genes. Additionally, we
selected 33 candidate genes based on whether they belong to the kinases and transcription factors
and further clustered candidate hub targets based on functions and signaling pathways with
significant enrichment analysis by using DAVID and STRING online databases. Then, core PPI
network was then identified and we manually selected GRB2 and IGF1 as the key drug targets
according to the network analysis and previous references. Lastly, virtual screening was performed
to identify potential small molecules which could target these two targets, and such small
molecules can serve as the promising candidate agents for future drug development.
Conclusion:
In summary, our study might provide novel insights for understanding of the
underlying molecular events of OSCC, and our discovered candidate targets and candidate agents
could be used as the promising therapeutic strategies for the treatment of OSCC.
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Affiliation(s)
- Juan Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xinjie Lian
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Feng Liu
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xueling Yan
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Chunyan Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Lijia Cheng
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
| | - Xiaolin Sun
- Department of Radiotherapy, the Central Hospital of Xuzhou, Xuzhou 221000, China
| | - Zheng Shi
- School of Medicine & Sichuan Industrial Institute of Antibiotics & Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu 610015, China
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6
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Chen CD, Rudy MA, Zeldich E, Abraham CR. A method to specifically activate the Klotho promoter by using zinc finger proteins constructed from modular building blocks and from naturally engineered Egr1 transcription factor backbone. FASEB J 2020; 34:7234-7246. [PMID: 32347987 DOI: 10.1096/fj.202000171r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/03/2020] [Accepted: 03/08/2020] [Indexed: 12/20/2022]
Abstract
There is an unmet need for treatments for diseases associated with aging. The antiaging, life-extending, and cognition-enhancing protein Klotho is neuroprotective due to its anti-inflammatory, antioxidative, and pro-myelinating effects. In addition, Klotho is also a tumor suppressor and has beneficial roles in multiple organs. Klotho is downregulated as part of the aging process. Thus, upregulating Klotho in the brain may lead to novel therapeutics to people suffering or at risk for neurodegenerative diseases such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis, and demyelinating diseases such as multiple sclerosis. We attempted to upregulate Klotho for its beneficial effects in the brain and elsewhere. Here, we describe a method to specifically activate Klotho gene expression. To accomplish this task, we designed zinc finger proteins (ZFPs) targeting within -300 bps of the human Klotho promoter. We designed the ZPF constructs either de novo from modular building blocks, or modified sequences from the natural endogenous Egr1 transcription factor backbone structure. Egr1 is known to upregulate Klotho expression. We tested the transcriptional activation effects of these ZFPs in a dual luciferase coincidence reporter system under the control of 4-kb promoter of human Klotho in stable HEK293 cells and in HK-2 cells that express Klotho protein endogenously. We found that the best ZFPs are the de novo designed ones targeting -250 bps of Klotho promoter and one of the Egr1-binding sites. We further enhanced Klotho's activation using p65-Rta transcriptional activation domains in addition to VP64. These upregulation approaches could be useful for studying Klotho's protective effects and designing Klotho boosting therapeutics for future in vivo experiments.
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Affiliation(s)
- Ci-Di Chen
- Klogene Therapeutics, Inc, Boston, MA, USA
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7
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Tsagkaris C, Papakosta V, Miranda AV, Zacharopoulou L, Danilchenko V, Matiashova L, Dhar A. Gene Therapy for Angelman Syndrome: Contemporary Approaches and Future Endeavors. Curr Gene Ther 2020; 19:359-366. [DOI: 10.2174/1566523220666200107151025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 11/28/2019] [Accepted: 01/01/2020] [Indexed: 01/20/2023]
Abstract
Background:
Angelman Syndrome (AS) is a congenital non inherited neurodevelopmental
disorder. The contemporary AS management is symptomatic and it has been accepted that gene therapy
may play a key role in the treatment of AS.
Objective:
The purpose of this study is to summarize existing and suggested gene therapy approaches
to Angelman syndrome.
Methods:
This is a literature review. Pubmed and Scopus databases were researched with keywords
(gene therapy, Angelman’s syndrome, neurological disorders, neonates). Peer-reviewed studies that
were closely related to gene therapies in Angelman syndrome and available in English, Greek, Ukrainian
or Indonesian were included. Studies that were published before 2000 were excluded and did not
align with the aforementioned criteria.
Results:
UBE3A serves multiple roles in signaling and degradation procedures. Although the restoration
of UBE3A expression rather than targeting known activities of the molecule would be the optimal
therapeutic goal, it is not possible so far. Reinstatement of paternal UBE3A appears as an adequate alternative.
This can be achieved by administering topoisomerase-I inhibitors or reducing UBE3A antisense
transcript (UBE3A-ATS), a molecule which silences paternal UBE3A.
Conclusion:
Understanding UBE3A imprinting unravels the path to an etiologic treatment of AS.
Gene therapy models tested on mice appeared less effective than anticipated pointing out that activation
of paternal UBE3A cannot counteract the existing CNS defects. On the other hand, targeting abnormal
downstream cell signaling pathways has provided promising rescue effects. Perhaps, combined
reinstatement of paternal UBE3A expression with abnormal signaling pathways-oriented treatment is
expected to provide better therapeutic effects. However, AS gene therapy remains debatable in pharmacoeconomics
and ethics context.
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Affiliation(s)
| | | | | | | | - Valeriia Danilchenko
- Department of Pediatrics #1 with Propaedeutics and Neonatology, Ukrainian Medical Stomatological Academy, Poltava, Ukraine
| | | | - Amrit Dhar
- Government Medical College, Jammu and Kashmir, India
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8
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Nakata E, Dinh H, Nguyen TM, Morii T. DNA binding adaptors to assemble proteins of interest on DNA scaffold. Methods Enzymol 2019; 617:287-322. [PMID: 30784406 DOI: 10.1016/bs.mie.2018.12.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
DNA nanostructures serve as the ideal scaffolds to assemble materials of interest. Among these, proteins are of particularly interesting class of molecules to assemble because of their huge functional variability. Sequence-specific DNA binding proteins have been applied as adaptors to stably locate the fused proteins at defined positions of DNA scaffold in high loading yields. The strategy allows to control the number of enzyme molecules and to maintain the catalytic activity. By fusing a chemoselective self-ligating protein tag to the DNA binding protein, the modular adaptors formed covalent bonds at respective sequences on DNA scaffold with fast reaction kinetics. Application of a set of orthogonal modular adaptors enables spatial organization of multiple types of enzymes.
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Affiliation(s)
- Eiji Nakata
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | - Huyen Dinh
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan
| | | | - Takashi Morii
- Institute of Advanced Energy, Kyoto University, Uji, Kyoto, Japan.
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9
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Hober S, Lindbo S, Nilvebrant J. Bispecific applications of non-immunoglobulin scaffold binders. Methods 2019; 154:143-152. [DOI: 10.1016/j.ymeth.2018.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/24/2018] [Accepted: 09/28/2018] [Indexed: 12/13/2022] Open
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10
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Klann TS, Black JB, Gersbach CA. CRISPR-based methods for high-throughput annotation of regulatory DNA. Curr Opin Biotechnol 2018; 52:32-41. [PMID: 29500989 DOI: 10.1016/j.copbio.2018.02.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 02/11/2018] [Indexed: 02/07/2023]
Abstract
Developments in CRISPR/Cas9-based technologies provide a new paradigm in functional screening of the genome. Conventional screening methods have focused on high-throughput perturbations of the protein-coding genome with technologies such as RNAi. However, equivalent methods for perturbing the non-coding genome have not existed until recently. CRISPR-based screening of genomic DNA has enabled the study of both genes and non-coding gene regulatory elements. Here we review recent progress in assigning function to the non-coding genome using CRISPR-based genomic and epigenomic screens, and discuss the prospects of these technologies to transforming our understanding of genome structure and regulation.
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Affiliation(s)
- Tyler S Klann
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, United States
| | - Joshua B Black
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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11
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Heiderscheit EA, Eguchi A, Spurgat MC, Ansari AZ. Reprogramming cell fate with artificial transcription factors. FEBS Lett 2018; 592:888-900. [PMID: 29389011 DOI: 10.1002/1873-3468.12993] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 01/15/2018] [Accepted: 01/24/2018] [Indexed: 01/10/2023]
Abstract
Transcription factors (TFs) reprogram cell states by exerting control over gene regulatory networks and the epigenetic landscape of a cell. Artificial transcription factors (ATFs) are designer regulatory proteins comprised of modular units that can be customized to overcome challenges faced by natural TFs in establishing and maintaining desired cell states. Decades of research on DNA-binding proteins and synthetic molecules has provided a molecular toolkit for ATF design and the construction of genome-scale libraries of ATFs capable of phenotypic manipulation and reprogramming of cell states. Here, we compare the unique strengths and limitations of different ATF platforms, highlight the advantages of cooperative assembly, and present the potential of ATF libraries in revealing gene regulatory networks that govern cell fate choices.
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Affiliation(s)
- Evan A Heiderscheit
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Asuka Eguchi
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Mackenzie C Spurgat
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
| | - Aseem Z Ansari
- Department of Biochemistry, University of Wisconsin - Madison, WI, USA.,The Genome Center of Wisconsin, University of Wisconsin - Madison, WI, USA
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12
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Pyles B, Bailus BJ, O'Geen H, Segal DJ. Purified Protein Delivery to Activate an Epigenetically Silenced Allele in Mouse Brain. Methods Mol Biol 2018; 1767:227-239. [PMID: 29524138 PMCID: PMC6281562 DOI: 10.1007/978-1-4939-7774-1_12] [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: 12/17/2022]
Abstract
The ability to activate or repress specific genes in the brain could have a tremendous impact for understanding and treating neurological disorders. Artificial transcription factors based on zinc finger, TALE, and CRISPR/Cas9 programmable DNA-binding platforms have been widely used to regulate the expression of specific genes in cultured cells, but their delivery into the brain represents a critical challenge to apply such tools in live animals. In previous work, we developed a purified, zinc finger-based artificial transcription factor that could be injected systemically, cross the blood-brain barrier, and alter expression of a specific gene in the brain of an adult mouse model of Angelman syndrome. Importantly, our mode of delivery produced widespread distribution throughout the brain. Here we describe our most current methods for the production and purification of the factor, dosage optimization, and use of live animal fluorescence imaging to visualize the kinetics of distribution.
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Affiliation(s)
- Benjamin Pyles
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - Barbara J Bailus
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, USA.
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13
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Ren C, Adams AN, Pyles B, Bailus BJ, O'Geen H, Segal DJ. In Vivo Applications of Cell-Penetrating Zinc-Finger Transcription Factors. Methods Mol Biol 2018; 1867:239-251. [PMID: 30155828 PMCID: PMC6296463 DOI: 10.1007/978-1-4939-8799-3_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Artificial transcription factors based on zinc finger, TALE, and CRISPR/Cas9 programmable DNA-binding platforms have been widely used to regulate the expression of specific genes in cultured cells, but their delivery into organs such as the brain represents a critical challenge to apply such tools in live animals. In previous work, we developed a zinc-finger-based artificial transcription factor harboring a cell-penetrating peptide (CPP) that could be injected systemically, cross the blood-brain barrier, and alter expression of a specific gene in the brain of an adult mouse. Importantly, our mode of delivery produced widespread distribution throughout the brain. Here we describe methods for the production and purification of the factor, testing CPP activity in cells, and testing CPP activity in mice.
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Affiliation(s)
- Chonghua Ren
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
- Guangzhou Key Laboratory of Insect Development Regulation and Application Research, South China Normal University, Guangzhou, China
| | - Alexa N Adams
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
| | - Benjamin Pyles
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
| | - Barbara J Bailus
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
- The Buck Institute for Research on Aging, Novato, CA, USA
| | - Henriette O'Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA
| | - David J Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, CA, USA.
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14
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Li Y, Liu X, Tang H, Yang H, Meng X. RNA Sequencing Uncovers Molecular Mechanisms Underlying Pathological Complete Response to Chemotherapy in Patients with Operable Breast Cancer. Med Sci Monit 2017; 23:4321-4327. [PMID: 28880852 PMCID: PMC5600194 DOI: 10.12659/msm.903272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background This study aimed to identify key genes contributing to pathological complete response (pCR) to chemotherapy by mRNA sequencing (RNA-seq). Material/Methods RNA was extracted from the frozen biopsy tissue of patients with pathological complete response and patients with non-pathological complete response. Sequencing was performed on the HiSeq2000 platform. Differentially expressed genes (DEGs) were identified between the pCR group and non-pCR (NpCR) group. Pathway enrichment analysis of DEGs was performed. A protein-protein interaction network was constructed, then module analysis was performed to identify a subnetwork. Finally, transcription factors were predicted. Results A total of 673 DEGs were identified, including 419 upregulated ones and 254 downregulated ones. The PPI network constructed consisted of 276 proteins forming 471 PPI pairs, and a subnetwork containing 18 protein nodes was obtained. Pathway enrichment analysis revealed that PLCB4 and ADCY6 were enriched in pathways renin secretion, gastric acid secretion, gap junction, inflammatory mediator regulation of TRP channels, retrograde endocannabinoid signaling, melanogenesis, cGMP-PKG signaling pathway, calcium signaling pathway, chemokine signaling pathway, cAMP signaling pathway, and rap1 signaling pathway. CNR1 was enriched in the neuroactive ligand-receptor interaction pathway, retrograde endocannabinoid signaling pathway, and rap1 signaling pathway. The transcription factor-gene network consists of 15 transcription factors and 16 targeted genes, of which 5 were downregulated and 10 were upregulated. Conclusions We found key genes that may contribute to pCR to chemotherapy, such as PLCB4, ADCY6, and CNR1, as well as some transcription factors.
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Affiliation(s)
- Yongfeng Li
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Xiaozhen Liu
- Department of Pathology, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Hongchao Tang
- 2nd Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, China (mainland)
| | - Hongjian Yang
- Department of Breast Surgery, Zhejiang Cancer Hospital, Hangzhou, Zhejiang, China (mainland)
| | - Xuli Meng
- Department of General Surgery, Tongde Hospital of Zhejiang Province, Hangzhou, Zhejiang, China (mainland)
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15
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Huang S, Feng C, Chen L, Huang Z, Zhou X, Li B, Wang LL, Chen W, Lv FQ, Li TS. Molecular Mechanisms of Mild and Severe Pneumonia: Insights from RNA Sequencing. Med Sci Monit 2017; 23:1662-1673. [PMID: 28381820 PMCID: PMC5390720 DOI: 10.12659/msm.900782] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND This study aimed to uncover the molecular mechanisms underlying mild and severe pneumonia by use of mRNA sequencing (RNA-seq). MATERIAL AND METHODS RNA was extracted from the peripheral blood of patients with mild pneumonia, severe pneumonia, and healthy controls. Sequencing was performed on the HiSeq4000 platform. After filtering, clean reads were mapped to the human reference genome hg19. Differentially expressed genes (DEGs) were identified between the control group and the mild or severe group. A transcription factor-gene network was constructed for each group. Biological process (BP) terms enriched by DEGs in the network were analyzed and these genes were also mapped to the Connectivity map to search for small-molecule drugs. RESULTS A total of 199 and 560 DEGs were identified from the mild group and severe group, respectively. A transcription factor-gene network consisting of 215 nodes and another network consisting of 451 nodes were constructed in the mild group and severe group, respectively, and 54 DEGs (e.g., S100A9 and S100A12) were found to be common, with consistent differential expression changes in the 2 groups. Genes in the transcription factor-gene network for the mild group were mainly enriched in 13 BP terms, especially defense and inflammatory response (e.g., S100A8) and spermatogenesis, while the top BP terms enriched by genes in the severe group include response to oxidative stress (CCL5), wound healing, and regulation of cell differentiation (CCL5), and of the cellular protein metabolic process. CONCLUSIONS S100A9 and S100A12 may have a role in the pathogenesis of pneumonia: S100A9 and CXCL1 may contribute solely in mild pneumonia, and CCL5 and CXCL11 may contribute in severe pneumonia.
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Affiliation(s)
- Sai Huang
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland).,Department of Hematology, Chinese People's Liberation Army (PLA) General Hospital, Beijing, China (mainland)
| | - Cong Feng
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Li Chen
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Zhi Huang
- Electrical and Computer Engineering, Purdue University, Indianapolis, IN, USA
| | - Xuan Zhou
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Bei Li
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Li-Li Wang
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Wei Chen
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Fa-Qin Lv
- Department of Ultrasound, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
| | - Tan-Shi Li
- Department of Emergency, General Hospital of The People's Liberation Army (PLA), Beijing, China (mainland)
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16
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Redchuk TA, Omelina ES, Chernov KG, Verkhusha VV. Near-infrared optogenetic pair for protein regulation and spectral multiplexing. Nat Chem Biol 2017; 13:633-639. [PMID: 28346403 DOI: 10.1038/nchembio.2343] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 01/10/2017] [Indexed: 12/18/2022]
Abstract
Multifunctional optogenetic systems are in high demand for use in basic and biomedical research. Near-infrared-light-inducible binding of bacterial phytochrome BphP1 to its natural PpsR2 partner is beneficial for simultaneous use with blue-light-activatable tools. However, applications of the BphP1-PpsR2 pair are limited by the large size, multidomain structure and oligomeric behavior of PpsR2. Here, we engineered a single-domain BphP1 binding partner, Q-PAS1, which is three-fold smaller and lacks oligomerization. We exploited a helix-PAS fold of Q-PAS1 to develop several near-infrared-light-controllable transcription regulation systems, enabling either 40-fold activation or inhibition. The light-induced BphP1-Q-PAS1 interaction allowed modification of the chromatin epigenetic state. Multiplexing the BphP1-Q-PAS1 pair with a blue-light-activatable LOV-domain-based system demonstrated their negligible spectral crosstalk. By integrating the Q-PAS1 and LOV domains in a single optogenetic tool, we achieved tridirectional protein targeting, independently controlled by near-infrared and blue light, thus demonstrating the superiority of Q-PAS1 for spectral multiplexing and engineering of multicomponent systems.
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Affiliation(s)
- Taras A Redchuk
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Evgeniya S Omelina
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Konstantin G Chernov
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Department of Anatomy and Structural Biology and Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York, USA
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17
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Carroll BL, Pulkoski-Gross MJ, Hannun YA, Obeid LM. CHK1 regulates NF-κB signaling upon DNA damage in p53- deficient cells and associated tumor-derived microvesicles. Oncotarget 2017; 7:18159-70. [PMID: 26921248 PMCID: PMC4951279 DOI: 10.18632/oncotarget.7566] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 01/23/2016] [Indexed: 12/15/2022] Open
Abstract
The recently discovered CHK1-Suppressed (CS) pathway is activated by inhibition or loss of the checkpoint kinase CHK1, promoting an apoptotic response to DNA damage mediated by caspase-2 in p53-deficient cells. Although functions of the CS-pathway have been investigated biochemically, it remains unclear whether and how CHK1 inhibition can be regulated endogenously and whether this constitutes a key component of the DNA damage response (DDR). Here, we present data that define the first endogenous activation of the CS-pathway whereby, upon DNA damage, wild type p53 acts as an endogenous regulator of CHK1 levels that modulates caspase-2 activation. Moreover, we demonstrate that persistence of CHK1 levels in response to DNA damage in p53-deficient cancer cells, leads to CHK1-mediated activation of NF-κB and induction of NF-κB-regulated genes in cells and in associated tumor-derived microvesicles (TMVs), both of which are abrogated by loss or inhibition of CHK1. These data define a novel role for CHK1 in the DDR pathway as a regulator NF-κB activity. Our data provide evidence that targeting CHK1 in p53-deficient cancers may abrogate NF-κB signaling that is associated with increased cellular survival and chemoresistance.
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Affiliation(s)
- Brittany L Carroll
- Stony Brook Cancer Center and The Department of Medicine, Stony Brook, New York, USA
| | - Michael J Pulkoski-Gross
- Stony Brook Cancer Center and The Department of Medicine, Stony Brook, New York, USA.,Pharmacological Sciences, Stony Brook University, Health Sciences Center, Stony Brook, New York, USA
| | - Yusuf A Hannun
- Stony Brook Cancer Center and The Department of Medicine, Stony Brook, New York, USA
| | - Lina M Obeid
- Stony Brook Cancer Center and The Department of Medicine, Stony Brook, New York, USA.,Northport Veterans Affairs Medical Center, Northport, New York, USA
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18
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Hamed MY, Arya G. Zinc finger protein binding to DNA: an energy perspective using molecular dynamics simulation and free energy calculations on mutants of both zinc finger domains and their specific DNA bases. J Biomol Struct Dyn 2016. [PMID: 26196228 DOI: 10.1080/07391102.2015.1068224] [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] [Indexed: 10/23/2022]
Abstract
Energy calculations based on MM-GBSA were employed to study various zinc finger protein (ZF) motifs binding to DNA. Mutants of both the DNA bound to their specific amino acids were studied. Calculated energies gave evidence for a relationship between binding energy and affinity of ZF motifs to their sites on DNA. ΔG values were -15.82(12), -3.66(12), and -12.14(11.6) kcal/mol for finger one, finger two, and finger three, respectively. The mutations in the DNA bases reduced the value of the negative energies of binding (maximum value for ΔΔG = 42Kcal/mol for F1 when GCG mutated to GGG, and ΔΔG = 22 kcal/mol for F2, the loss in total energy of binding originated in the loss in electrostatic energies upon mutation (r = .98). The mutations in key amino acids in the ZF motif in positions-1, 2, 3, and 6 showed reduced binding energies to DNA with correlation coefficients between total free energy and electrostatic was .99 and with Van der Waal was .93. Results agree with experimentally found selectivity which showed that Arginine in position-1 is specific to G, while Aspartic acid (D) in position 2 plays a complicated role in binding. There is a correlation between the MD calculated free energies of binding and those obtained experimentally for prepared ZF motifs bound to triplet bases in other reports (), our results may help in the design of ZF motifs based on the established recognition codes based on energies and contributing energies to the total energy.
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Affiliation(s)
- Mazen Y Hamed
- a Department of Chemistry , Birzeit University , P. O. Box 14 Birzeit, Palestine
| | - Gaurav Arya
- b Department of Nanoengineering , University of California , San Diego, 9500 Gilman Dr., MC-0448, La Jolla , CA 92093-0448 , USA
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19
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Abstract
CRISPR-Cas9 technology has rapidly changed the landscape for how biologists and bioengineers study and manipulate the genome. Derived from the bacterial adaptive immune system, CRISPR-Cas9 has been coopted and repurposed for a variety of new functions, including the activation or repression of gene expression (termed CRISPRa or CRISPRi, respectively). This represents an exciting alternative to previously used repression or activation technologies such as RNA interference (RNAi) or the use of gene overexpression vectors. We have only just begun exploring the possibilities that CRISPR technology offers for gene regulation and the control of cell identity and behavior. In this review, we describe the recent advances of CRISPR-Cas9 technology for gene regulation and outline advantages and disadvantages of CRISPRa and CRISPRi (CRISPRa/i) relative to alternative technologies.
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20
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Understanding Transcription Factor Regulation by Integrating Gene Expression and DNase I Hypersensitive Sites. BIOMED RESEARCH INTERNATIONAL 2015; 2015:757530. [PMID: 26425553 PMCID: PMC4573618 DOI: 10.1155/2015/757530] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/16/2015] [Indexed: 12/20/2022]
Abstract
Transcription factors are proteins that bind to DNA sequences to regulate gene transcription. The transcription factor binding sites are short DNA sequences (5-20 bp long) specifically bound by one or more transcription factors. The identification of transcription factor binding sites and prediction of their function continue to be challenging problems in computational biology. In this study, by integrating the DNase I hypersensitive sites with known position weight matrices in the TRANSFAC database, the transcription factor binding sites in gene regulatory region are identified. Based on the global gene expression patterns in cervical cancer HeLaS3 cell and HelaS3-ifnα4h cell (interferon treatment on HeLaS3 cell for 4 hours), we present a model-based computational approach to predict a set of transcription factors that potentially cause such differential gene expression. Significantly, 6 out 10 predicted functional factors, including IRF, IRF-2, IRF-9, IRF-1 and IRF-3, ICSBP, belong to interferon regulatory factor family and upregulate the gene expression levels responding to the interferon treatment. Another factor, ISGF-3, is also a transcriptional activator induced by interferon alpha. Using the different transcription factor binding sites selected criteria, the prediction result of our model is consistent. Our model demonstrated the potential to computationally identify the functional transcription factors in gene regulation.
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21
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Wei H, Wang Z. Engineering RNA-binding proteins with diverse activities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:597-613. [DOI: 10.1002/wrna.1296] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 07/09/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Huanhuan Wei
- Key Laboratory of Computational Biology; MPG-CAS Partner Institute of Computational Biology; Shanghai China
| | - Zefeng Wang
- Key Laboratory of Computational Biology; MPG-CAS Partner Institute of Computational Biology; Shanghai China
- Department of Pharmacology; University of North Carolina at Chapel Hill; Chapel Hill NC USA
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22
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Gebbing M, Bergmann T, Schulz E, Ehrhardt A. Gene therapeutic approaches to inhibit hepatitis B virus replication. World J Hepatol 2015; 7:150-164. [PMID: 25729471 PMCID: PMC4342598 DOI: 10.4254/wjh.v7.i2.150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/23/2014] [Accepted: 11/19/2014] [Indexed: 02/06/2023] Open
Abstract
Acute and chronic hepatitis B virus (HBV) infections remain to present a major global health problem. The infection can be associated with acute symptomatic or asymptomatic hepatitis which can cause chronic inflammation of the liver and over years this can lead to cirrhosis and the development of hepatocellular carcinomas. Currently available therapeutics for chronically infected individuals aim at reducing viral replication and to slow down or stop the progression of the disease. Therefore, novel treatment options are needed to efficiently combat and eradicate this disease. Here we provide a state of the art overview of gene therapeutic approaches to inhibit HBV replication. We discuss non-viral and viral approaches which were explored to deliver therapeutic nucleic acids aiming at reducing HBV replication. Types of delivered therapeutic nucleic acids which were studied since many years include antisense oligodeoxynucleotides and antisense RNA, ribozymes and DNAzymes, RNA interference, and external guide sequences. More recently designer nucleases gained increased attention and were exploited to destroy the HBV genome. In addition we mention other strategies to reduce HBV replication based on delivery of DNA encoding dominant negative mutants and DNA vaccination. In combination with available cell culture and animal models for HBV infection, in vitro and in vivo studies can be performed to test efficacy of gene therapeutic approaches. Recent progress but also challenges will be specified and future perspectives will be discussed. This is an exciting time to explore such approaches because recent successes of gene therapeutic strategies in the clinic to treat genetic diseases raise hope to find alternative treatment options for patients chronically infected with HBV.
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23
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Liu Z, Borlak J, Tong W. Deciphering miRNA transcription factor feed-forward loops to identify drug repurposing candidates for cystic fibrosis. Genome Med 2014; 6:94. [PMID: 25484921 PMCID: PMC4256829 DOI: 10.1186/s13073-014-0094-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 10/23/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Cystic fibrosis (CF) is a fatal genetic disorder caused by mutations in the CF transmembrane conductance regulator (CFTR) gene that primarily affects the lungs and the digestive system, and the current drug treatment is mainly able to alleviate symptoms. To improve disease management for CF, we considered the repurposing of approved drugs and hypothesized that specific microRNA (miRNA) transcription factors (TF) gene networks can be used to generate feed-forward loops (FFLs), thus providing treatment opportunities on the basis of disease specific FFLs. METHODS Comprehensive database searches revealed significantly enriched TFs and miRNAs in CF and CFTR gene networks. The target genes were validated using ChIPBase and by employing a consensus approach of diverse algorithms to predict miRNA gene targets. STRING analysis confirmed protein-protein interactions (PPIs) among network partners and motif searches defined composite FFLs. Using information extracted from SM2miR and Pharmaco-miR, an in silico drug repurposing pipeline was established based on the regulation of miRNA/TFs in CF/CFTR networks. RESULTS In human airway epithelium, a total of 15 composite FFLs were constructed based on CFTR specific miRNA/TF gene networks. Importantly, nine of them were confirmed in patient samples and CF epithelial cells lines, and STRING PPI analysis provided evidence that the targets interacted with each other. Functional analysis revealed that ubiquitin-mediated proteolysis and protein processing in the endoplasmic reticulum dominate the composite FFLs, whose major functions are folding, sorting, and degradation. Given that the mutated CFTR gene disrupts the function of the chloride channel, the constructed FFLs address mechanistic aspects of the disease and, among 48 repurposing drug candidates, 26 were confirmed with literature reports and/or existing clinical trials relevant to the treatment of CF patients. CONCLUSION The construction of FFLs identified promising drug repurposing candidates for CF and the developed strategy may be applied to other diseases as well.
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Affiliation(s)
- Zhichao Liu
- />Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079 USA
| | - Jürgen Borlak
- />Centre for Pharmacology and Toxicology, Hannover Medical School, Carl-Neuberg-Straße 1, 30625 Hannover, Germany
| | - Weida Tong
- />Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079 USA
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24
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Funabashi H, Yanagi S, Suzuki S, Mie M, Kobatake E. Assembly of zinc finger motif-fused enzymes on a dsDNA scaffold for catalyzing consecutive reactions with a proximity effect. Biotechnol Lett 2014; 37:109-14. [PMID: 25216646 DOI: 10.1007/s10529-014-1644-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/14/2014] [Indexed: 11/25/2022]
Abstract
The feasibility of assembling enzymes, catalyzing consecutive reactions, on to a double-stranded DNA (dsDNA) scaffold utilizing zinc finger motifs is described. The catalytic activities of two zinc finger motif-fused enzymes catalyzing a bioluminescence reaction with energy recycling, namely pyruvate phosphate dikinase and firefly luciferase, have been evaluated. Bioluminescence measurements with dsDNA scaffolds coding a different distance between the binding sites for each zinc finger motif-fused enzyme confirmed the effect of the distance, proving the proximity effect of ATP recycling presumed to be the result of efficient intermediate diffusion. Thus, fusion to zinc finger motifs offers a promising option for the assembly of bi-enzymes, catalyzing a consecutive reaction, onto a dsDNA scaffold with a proximity effect.
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Affiliation(s)
- Hisakage Funabashi
- Department of Biological Information, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Midori-ku, Yokohama, 226-8501, Japan,
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25
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van Tol N, van der Zaal BJ. Artificial transcription factor-mediated regulation of gene expression. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 225:58-67. [PMID: 25017160 DOI: 10.1016/j.plantsci.2014.05.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 05/22/2014] [Accepted: 05/23/2014] [Indexed: 06/03/2023]
Abstract
The transcriptional regulation of endogenous genes with artificial transcription factors (TFs) can offer new tools for plant biotechnology. Three systems are available for mediating site-specific DNA recognition of artificial TFs: those based on zinc fingers, TALEs, and on the CRISPR/Cas9 technology. Artificial TFs require an effector domain that controls the frequency of transcription initiation at endogenous target genes. These effector domains can be transcriptional activators or repressors, but can also have enzymatic activities involved in chromatin remodeling or epigenetic regulation. Artificial TFs are able to regulate gene expression in trans, thus allowing them to evoke dominant mutant phenotypes. Large scale changes in transcriptional activity are induced when the DNA binding domain is deliberately designed to have lower binding specificity. This technique, known as genome interrogation, is a powerful tool for generating novel mutant phenotypes. Genome interrogation has clear mechanistic and practical advantages over activation tagging, which is the technique most closely resembling it. Most notably, genome interrogation can lead to the discovery of mutant phenotypes that are unlikely to be found when using more conventional single gene-based approaches.
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Affiliation(s)
- Niels van Tol
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Bert J van der Zaal
- Department of Molecular and Developmental Genetics, Institute of Biology Leiden, Leiden University, Sylvius Laboratory, Sylviusweg 72, 2333 BE Leiden, The Netherlands.
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26
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Kabadi AM, Gersbach CA. Engineering synthetic TALE and CRISPR/Cas9 transcription factors for regulating gene expression. Methods 2014; 69:188-97. [PMID: 25010559 DOI: 10.1016/j.ymeth.2014.06.014] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Revised: 06/26/2014] [Accepted: 06/27/2014] [Indexed: 12/22/2022] Open
Abstract
Engineered DNA-binding proteins that can be targeted to specific sites in the genome to manipulate gene expression have enabled many advances in biomedical research. This includes generating tools to study fundamental aspects of gene regulation and the development of a new class of gene therapies that alter the expression of endogenous genes. Designed transcription factors have entered clinical trials for the treatment of human diseases and others are in preclinical development. High-throughput and user-friendly platforms for designing synthetic DNA-binding proteins present innovative methods for deciphering cell biology and designing custom synthetic gene circuits. We review two platforms for designing synthetic transcription factors for manipulating gene expression: Transcription activator-like effectors (TALEs) and the RNA-guided clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system. We present an overview of each technology and a guide for designing and assembling custom TALE- and CRISPR/Cas9-based transcription factors. We also discuss characteristics of each platform that are best suited for different applications.
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Affiliation(s)
- Ami M Kabadi
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States
| | - Charles A Gersbach
- Department of Biomedical Engineering, Duke University, Durham, NC 27708, United States; Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, United States; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, NC 27710, United States.
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27
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Hashim Z, Teoh ST, Bamba T, Fukusaki E. Construction of a metabolome library for transcription factor-related single gene mutants of Saccharomyces cerevisiae. J Chromatogr B Analyt Technol Biomed Life Sci 2014; 966:83-92. [PMID: 24974314 DOI: 10.1016/j.jchromb.2014.05.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 05/17/2014] [Accepted: 05/19/2014] [Indexed: 01/08/2023]
Abstract
Transcription factors (TFs) play an important role in gene regulation, providing control for cells to adapt to ever changing environments and different physiological states. Although great effort has been taken to study TFs through DNA-protein binding and microarray gene expression experiments, the understanding of transcriptional regulation is still lacking, due to lack of information that links TF regulatory events and final phenotypic change. Here, we focused on metabolites as the final readouts of gene transcription process. We performed metabolite profiling of 154 Saccharomyces cerevisiae's single gene knockouts each defective in a gene encoding transcription factor and built a metabolome library consists of 84 metabolites with good reproducibility. Using the metabolome dataset, we obtained significant correlations and identified differential strains that exhibit altered metabolism compared to control. This work presents a novel metabolome dataset library which will be invaluable for researchers working on transcriptional regulation and yeast biology in general.
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Affiliation(s)
- Zanariah Hashim
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Shao Thing Teoh
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Takeshi Bamba
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichiro Fukusaki
- Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
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28
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Abstract
Current technology enables the production of highly specific genome modifications with excellent efficiency and specificity. Key to this capability are targetable DNA cleavage reagents and cellular DNA repair pathways. The break made by these reagents can produce localized sequence changes through inaccurate nonhomologous end joining (NHEJ), often leading to gene inactivation. Alternatively, user-provided DNA can be used as a template for repair by homologous recombination (HR), leading to the introduction of desired sequence changes. This review describes three classes of targetable cleavage reagents: zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR/Cas RNA-guided nucleases (RGNs). As a group, these reagents have been successfully used to modify genomic sequences in a wide variety of cells and organisms, including humans. This review discusses the properties, advantages, and limitations of each system, as well as the specific considerations required for their use in different biological systems.
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Affiliation(s)
- Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112;
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29
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Chen W, Qian Y, Wu X, Sun Y, Wu X, Cheng X. Inhibiting replication of begomoviruses using artificial zinc finger nucleases that target viral-conserved nucleotide motif. Virus Genes 2014; 48:494-501. [PMID: 24474330 DOI: 10.1007/s11262-014-1041-4] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 01/16/2014] [Indexed: 11/26/2022]
Abstract
Geminiviridae consists of a large group of single-stranded DNA viruses that cause tremendous losses worldwide. Frequent mixed infection and high rates of recombination and mutation allow them to adapt rapidly to new hosts and overcome hosts' resistances. Therefore, an effective strategy able to confer plants with resistance against multiple begomoviruses is needed. In the present study, artificial zinc finger proteins were designed based on a conserved sequence motif of begomoviruses. DNA-binding affinities and specificities of these artificial zinc fingers were evaluated using electrophoretic mobility shift assay. Artificial zinc finger nuclease (AZFNs) were then constructed based on the ones with the highest DNA-binding affinities. In vitro digest and transient expression assay showed that these AZFNs can efficiently cleave the target sequence and inhibit the replication of different begomoviruses. These results suggest that artificial zinc finger protein technology may be used to achieve resistance against multiple begomoviruses.
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Affiliation(s)
- Wei Chen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 310036, Zhejiang, People's Republic of China
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Li BQ, Feng KY, Ding J, Cai YD. Predicting DNA-binding sites of proteins based on sequential and 3D structural information. Mol Genet Genomics 2014; 289:489-99. [PMID: 24448651 DOI: 10.1007/s00438-014-0812-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 01/04/2014] [Indexed: 11/26/2022]
Abstract
Protein-DNA interactions play important roles in many biological processes. To understand the molecular mechanisms of protein-DNA interaction, it is necessary to identify the DNA-binding sites in DNA-binding proteins. In the last decade, computational approaches have been developed to predict protein-DNA-binding sites based solely on protein sequences. In this study, we developed a novel predictor based on support vector machine algorithm coupled with the maximum relevance minimum redundancy method followed by incremental feature selection. We incorporated not only features of physicochemical/biochemical properties, sequence conservation, residual disorder, secondary structure, solvent accessibility, but also five three-dimensional (3D) structural features calculated from PDB data to predict the protein-DNA interaction sites. Feature analysis showed that 3D structural features indeed contributed to the prediction of DNA-binding site and it was demonstrated that the prediction performance was better with 3D structural features than without them. It was also shown via analysis of features from each site that the features of DNA-binding site itself contribute the most to the prediction. Our prediction method may become a useful tool for identifying the DNA-binding sites and the feature analysis described in this paper may provide useful insights for in-depth investigations into the mechanisms of protein-DNA interaction.
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Affiliation(s)
- Bi-Qing Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People's Republic of China
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Manipulation of RNA Using Engineered Proteins with Customized Specificity. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2014; 825:199-225. [DOI: 10.1007/978-1-4939-1221-6_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Cheng AW, Wang H, Yang H, Shi L, Katz Y, Theunissen TW, Rangarajan S, Shivalila CS, Dadon DB, Jaenisch R. Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system. Cell Res 2013; 23:1163-71. [PMID: 23979020 PMCID: PMC3790238 DOI: 10.1038/cr.2013.122] [Citation(s) in RCA: 567] [Impact Index Per Article: 51.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2013] [Revised: 08/10/2013] [Accepted: 08/13/2013] [Indexed: 02/07/2023] Open
Abstract
Technologies allowing for specific regulation of endogenous genes are valuable for the study of gene functions and have great potential in therapeutics. We created the CRISPR-on system, a two-component transcriptional activator consisting of a nuclease-dead Cas9 (dCas9) protein fused with a transcriptional activation domain and single guide RNAs (sgRNAs) with complementary sequence to gene promoters. We demonstrate that CRISPR-on can efficiently activate exogenous reporter genes in both human and mouse cells in a tunable manner. In addition, we show that robust reporter gene activation in vivo can be achieved by injecting the system components into mouse zygotes. Furthermore, we show that CRISPR-on can activate the endogenous IL1RN, SOX2, and OCT4 genes. The most efficient gene activation was achieved by clusters of 3-4 sgRNAs binding to the proximal promoters, suggesting their synergistic action in gene induction. Significantly, when sgRNAs targeting multiple genes were simultaneously introduced into cells, robust multiplexed endogenous gene activation was achieved. Genome-wide expression profiling demonstrated high specificity of the system.
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Affiliation(s)
- Albert W Cheng
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Computational and Systems Biology Program, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Haoyi Wang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Hui Yang
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Linyu Shi
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Yarden Katz
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Chikdu S Shivalila
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Daniel B Dadon
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rudolf Jaenisch
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Colombo J, Provazzi PJS, Calmon MF, Pires LC, Rodrigues NC, Petl P, Fossey MA, de Souza FP, Canduri F, Rahal P. Expression, purification and molecular analysis of the human ZNF706 protein. Biol Proced Online 2013; 15:10. [PMID: 24060497 PMCID: PMC3848911 DOI: 10.1186/1480-9222-15-10] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 09/14/2013] [Indexed: 01/14/2023] Open
Abstract
Background The ZNF706 gene encodes a protein that belongs to the zinc finger family of proteins and was found to be highly expressed in laryngeal cancer, making the structure and function of ZNF706 worthy of investigation. In this study, we expressed and purified recombinant human ZNF706 that was suitable for structural analysis in Escherichia coli BL21(DH3). Findings ZNF706 mRNA was extracted from a larynx tissue sample, and cDNA was ligated into a cloning vector using the TOPO method. ZNF706 protein was expressed according to the E. coli expression system procedures and was purified using a nickel-affinity column. The structural qualities of recombinant ZNF706 and quantification alpha, beta sheet, and other structures were obtained by spectroscopy of circular dichroism. ZNF706's structural modeling showed that it is composed of α-helices (28.3%), β-strands (19.4%), and turns (20.9%), in agreement with the spectral data from the dichroism analysis. Conclusions We used circular dichroism and molecular modeling to examine the structure of ZNF706. The results suggest that human recombinant ZNF706 keeps its secondary structures and is appropriate for functional and structural studies. The method of expressing ZNF706 protein used in this study can be used to direct various functional and structural studies that will contribute to the understanding of its function as well as its relationship with other biological molecules and its putative role in carcinogenesis.
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Affiliation(s)
- Jucimara Colombo
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | | | - Marilia Freitas Calmon
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Lilian Campos Pires
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Nathália Campos Rodrigues
- Institute of Chemistry of São Carlos, Department of Chemistry and Molecular Physics, University of São Paulo - USP, CEP: 13560-970, São Carlos /SP, Brazil
| | - Paulo Petl
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Marcelo Andrés Fossey
- Department of Physics, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Fátima Pereira de Souza
- Department of Physics, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
| | - Fernanda Canduri
- Institute of Chemistry of São Carlos, Department of Chemistry and Molecular Physics, University of São Paulo - USP, CEP: 13560-970, São Carlos /SP, Brazil
| | - Paula Rahal
- Department of Biology, São Paulo State University - UNESP, CEP: 15054-000, São José do Rio Preto /SP, Brazil
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Ye Z, Zhang W, Liu L, Chen G, Shen Z, Zhou N. Fabrication of a colorimetric biosensing platform for the detection of protein–DNA interaction. Biosens Bioelectron 2013; 46:108-12. [DOI: 10.1016/j.bios.2013.02.028] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2012] [Revised: 02/01/2013] [Accepted: 02/16/2013] [Indexed: 10/27/2022]
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Juárez-Moreno K, Erices R, Beltran AS, Stolzenburg S, Cuello-Fredes M, Owen GI, Qian H, Blancafort P. Breaking through an epigenetic wall: re-activation of Oct4 by KRAB-containing designer zinc finger transcription factors. Epigenetics 2013; 8:164-76. [PMID: 23314702 DOI: 10.4161/epi.23503] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The gene Oct4 encodes a transcription factor critical for the maintenance of pluripotency and self-renewal in embryonic stem cells. In addition, improper re-activation of Oct4 contributes to oncogenic processes. Herein, we describe a novel designer zinc finger protein (ZFP) capable of upregulating the endogenous Oct4 promoter in a panel of breast and ovarian cell lines carrying a silenced gene. In some ovarian tumor lines, the ZFP triggered a strong reactivation of Oct4, with levels of expression comparable with exogenous Oct4 cDNA delivery. Surprisingly, the reactivation of Oct4 required a KRAB domain for effective upregulation of the endogenous gene. While KRAB-containing ZFPs are traditionally described as transcriptional repressors, our results suggest that these proteins could, in certain genomic contexts, function as potent activators and, thus, outline an emerging novel function of KRAB-ZFPs. In addition, we document a novel ZFP that could be used for the epigenetic reprograming of cancer cells.
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Affiliation(s)
- Karla Juárez-Moreno
- Department of Pharmacology, University of North Carolina School of Medicine, Chapel Hill, NC, USA
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36
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Zhu C, Gupta A, Hall VL, Rayla AL, Christensen RG, Dake B, Lakshmanan A, Kuperwasser C, Stormo GD, Wolfe SA. Using defined finger-finger interfaces as units of assembly for constructing zinc-finger nucleases. Nucleic Acids Res 2013; 41:2455-65. [PMID: 23303772 PMCID: PMC3575815 DOI: 10.1093/nar/gks1357] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) have been used for genome engineering in a wide variety of organisms; however, it remains challenging to design effective ZFNs for many genomic sequences using publicly available zinc-finger modules. This limitation is in part because of potential finger–finger incompatibility generated on assembly of modules into zinc-finger arrays (ZFAs). Herein, we describe the validation of a new set of two-finger modules that can be used for building ZFAs via conventional assembly methods or a new strategy—finger stitching—that increases the diversity of genomic sequences targetable by ZFNs. Instead of assembling ZFAs based on units of the zinc-finger structural domain, our finger stitching method uses units that span the finger–finger interface to ensure compatibility of neighbouring recognition helices. We tested this approach by generating and characterizing eight ZFAs, and we found their DNA-binding specificities reflected the specificities of the component modules used in their construction. Four pairs of ZFNs incorporating these ZFAs generated targeted lesions in vivo, demonstrating that stitching yields ZFAs with robust recognition properties.
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Affiliation(s)
- Cong Zhu
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Ankit Gupta
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Victoria L. Hall
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Amy L. Rayla
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Ryan G. Christensen
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Benjamin Dake
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Abirami Lakshmanan
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Charlotte Kuperwasser
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Gary D. Stormo
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
| | - Scot A. Wolfe
- Program in Gene Function and Expression, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA 01605, Department of Genetics, Washington University School of Medicine, St Louis, MO, USA 63108 and Molecular Oncology Research Institute (MORI), Tufts University School of Medicine, Boston, MA, USA 02111
- *To whom correspondence should be addressed. Tel: +1 508 856 3953; Fax: +1 508 856 5460;
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Verzele D, Madder A. Synthetic Progress in cMyc-Max Oncoprotein Miniaturization: Semi-Online Monitoring Gives Solid-Phase Access to Hydrophobic b(-HLH-)ZIP Peptidosteroid Tweezers. European J Org Chem 2012. [DOI: 10.1002/ejoc.201201235] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Fu F, Voytas DF. Zinc Finger Database (ZiFDB) v2.0: a comprehensive database of C₂H₂ zinc fingers and engineered zinc finger arrays. Nucleic Acids Res 2012. [PMID: 23203887 PMCID: PMC3531203 DOI: 10.1093/nar/gks1167] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
ZiFDB (Zinc Finger Database, http://zifdb.msi.umn.edu) is a web-accessible database that houses information on individual C2H2 zinc fingers (ZFs) and engineered zinc finger arrays (ZFAs). ZiFDB serves as a resource for biologists interested in engineering ZFAs for use as sequence-specific DNA-binding reagents. Here, we describe four new features of ZiFDB: (i) the database allows users to input new ZFs and ZFAs; (ii) a shadow database temporarily stores user-submitted data, pending approval by the database curator and subsequent loading into the persistent database; (iii) ZiFDB contains 181 Context-Dependent Assembly (CoDA) ZFAs, which were generated by this newly described ZFA engineering platform; and (iv) the database also now contains 319 F1F2 CoDA units and 334 F2F3 CoDA units that can be used to construct CoDA arrays. In total, the new release of ZiFDB contains 1226 ZFs and 1123 ZFAs.
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Affiliation(s)
- Fengli Fu
- Department of Genetics, University of Minnesota, 6-160 Jackson Hall, 321 Church Street SE, Minneapolis, MN 55455, USA
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Joung JK, Sander JD. TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 2012; 14:49-55. [PMID: 23169466 DOI: 10.1038/nrm3486] [Citation(s) in RCA: 1028] [Impact Index Per Article: 85.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Engineered nucleases enable the targeted alteration of nearly any gene in a wide range of cell types and organisms. The newly-developed transcription activator-like effector nucleases (TALENs) comprise a nonspecific DNA-cleaving nuclease fused to a DNA-binding domain that can be easily engineered so that TALENs can target essentially any sequence. The capability to quickly and efficiently alter genes using TALENs promises to have profound impacts on biological research and to yield potential therapeutic strategies for genetic diseases.
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Affiliation(s)
- J Keith Joung
- Massachusetts General Hospital, Molecular Pathology Unit, the Center for Computational and Integrative Biology, and the Center for Cancer Research, Harvard Medical School, Department of Pathology, 149 13th Street, 6th floor, Charlestown, Massachusetts 02129, USA.
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40
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Mercer AC, Gaj T, Fuller RP, Barbas CF. Chimeric TALE recombinases with programmable DNA sequence specificity. Nucleic Acids Res 2012; 40:11163-72. [PMID: 23019222 PMCID: PMC3510496 DOI: 10.1093/nar/gks875] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Site-specific recombinases are powerful tools for genome engineering. Hyperactivated variants of the resolvase/invertase family of serine recombinases function without accessory factors, and thus can be re-targeted to sequences of interest by replacing native DNA-binding domains (DBDs) with engineered zinc-finger proteins (ZFPs). However, imperfect modularity with particular domains, lack of high-affinity binding to all DNA triplets, and difficulty in construction has hindered the widespread adoption of ZFPs in unspecialized laboratories. The discovery of a novel type of DBD in transcription activator-like effector (TALE) proteins from Xanthomonas provides an alternative to ZFPs. Here we describe chimeric TALE recombinases (TALERs): engineered fusions between a hyperactivated catalytic domain from the DNA invertase Gin and an optimized TALE architecture. We use a library of incrementally truncated TALE variants to identify TALER fusions that modify DNA with efficiency and specificity comparable to zinc-finger recombinases in bacterial cells. We also show that TALERs recombine DNA in mammalian cells. The TALER architecture described herein provides a platform for insertion of customized TALE domains, thus significantly expanding the targeting capacity of engineered recombinases and their potential applications in biotechnology and medicine.
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Affiliation(s)
- Andrew C Mercer
- The Skaggs Institute for Chemical Biology and Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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41
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Wieland M, Fussenegger M. Engineering Molecular Circuits Using Synthetic Biology in Mammalian Cells. Annu Rev Chem Biomol Eng 2012; 3:209-34. [DOI: 10.1146/annurev-chembioeng-061010-114145] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Markus Wieland
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
| | - Martin Fussenegger
- Department of Biosystems Science and Bioengineering, ETH Zurich, CH-4058 Basel, Switzerland; ,
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42
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Ausländer S, Wieland M, Fussenegger M. Smart medication through combination of synthetic biology and cell microencapsulation. Metab Eng 2012; 14:252-60. [DOI: 10.1016/j.ymben.2011.06.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/11/2011] [Accepted: 06/09/2011] [Indexed: 01/05/2023]
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Imanishi M, Matsumura K, Tsuji S, Nakaya T, Negi S, Futaki S, Sugiura Y. Zn(II) binding and DNA binding properties of ligand-substituted CXHH-type zinc finger proteins. Biochemistry 2012; 51:3342-8. [PMID: 22482427 DOI: 10.1021/bi300236m] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
CCHH-type zinc fingers are among the most common DNA binding motifs found in eukaryotes. In a previous report, we substituted the second ligand cysteine residue with aspartic acid, producing a Zn(II)-responsive transcription factor; this indicates that a ligand substitution is a possible design target of an engineered zinc finger peptide. Despite the importance of Zn(II) binding with respect to the folding and DNA binding properties of a zinc finger peptide, no study about the effects of ligand substitution on both Zn(II) binding and DNA binding properties has been reported. Here, we substituted a conserved cysteine (C) with other zinc-coordinated amino acid residues, histidine (H), aspartic acid (D), and glutamic acid (E), to create CXHH-type zinc finger peptides (X = C, H, D, and E). The Zn(II)-dependent conformational change was observed in all peptides; however, the Zn(II) binding affinity and metal coordination geometry of the peptides were different. Gel mobility shift assays showed that the Zn(II)-bound forms of the ligand-substituted derivatives retain DNA binding ability, while the DNA binding affinity decreased in the following manner: CCHH > CDHH > CEHH ≫ CHHH. The DNA binding sequence preferences of the ligand-substituted derivatives were similar to that of the wild type in the context of the full three-finger DNA-binding domain of transcription factor Zif268. These results indicate that artificial zinc finger proteins with various DNA binding affinities that respond to a diverse range of Zn(II) concentrations can be designed by substituting the Zn(II) ligand.
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Affiliation(s)
- Miki Imanishi
- Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan.
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44
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Rivenbark AG, Stolzenburg S, Beltran AS, Yuan X, Rots MG, Strahl BD, Blancafort P. Epigenetic reprogramming of cancer cells via targeted DNA methylation. Epigenetics 2012; 7:350-60. [PMID: 22419067 DOI: 10.4161/epi.19507] [Citation(s) in RCA: 156] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
An obstacle in the treatment of human diseases such as cancer is the inability to selectively and effectively target historically undruggable targets such as transcription factors. Here, we employ a novel technology using artificial transcription factors (ATFs) to epigenetically target gene expression in cancer cells. We show that site-specific DNA methylation and long-term stable repression of the tumor suppressor Maspin and the oncogene SOX2 can be achieved in breast cancer cells via zinc-finger ATFs targeting DNA methyltransferase 3a (DNMT3a) to the promoters of these genes. Using this approach, we show Maspin and SOX2 downregulation is more significant as compared with transient knockdown, which is also accompanied by stable phenotypic reprogramming of the cancer cell. These findings indicate that multimodular Zinc Finger Proteins linked to epigenetic editing domains can be used as novel cell resources to selectively and heritably alter gene expression patterns to stably reprogram cell fate.
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Affiliation(s)
- Ashley G Rivenbark
- Department of Pharmacology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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45
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Patterns and plasticity in RNA-protein interactions enable recruitment of multiple proteins through a single site. Proc Natl Acad Sci U S A 2012; 109:6054-9. [PMID: 22467831 DOI: 10.1073/pnas.1200521109] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
mRNA control hinges on the specificity and affinity of proteins for their RNA binding sites. Regulatory proteins must bind their own sites and reject even closely related noncognate sites. In the PUF [Pumilio and fem-3 binding factor (FBF)] family of RNA binding proteins, individual proteins discriminate differences in the length and sequence of binding sites, allowing each PUF to bind a distinct battery of mRNAs. Here, we show that despite these differences, the pattern of RNA interactions is conserved among PUF proteins: the two ends of the PUF protein make critical contacts with the two ends of the RNA sites. Despite this conserved "two-handed" pattern of recognition, the RNA sequence is flexible. Among the binding sites of yeast Puf4p, RNA sequence dictates the pattern in which RNA bases are flipped away from the binding surface of the protein. Small differences in RNA sequence allow new modes of control, recruiting Puf5p in addition to Puf4p to a single site. This embedded information adds a new layer of biological meaning to the connections between RNA targets and PUF proteins.
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46
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Egelkrout E, Rajan V, Howard JA. Overproduction of recombinant proteins in plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2012; 184:83-101. [PMID: 22284713 DOI: 10.1016/j.plantsci.2011.12.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Revised: 12/06/2011] [Accepted: 12/09/2011] [Indexed: 05/21/2023]
Abstract
Recombinant protein production in microbial hosts and animal cell cultures has revolutionized the pharmaceutical and industrial enzyme industries. Plants as alternative hosts for the production of recombinant proteins are being actively pursued, taking advantage of their unique characteristics. The key to cost-efficient production in any system is the level of protein accumulation, which is inversely proportional to the cost. Levels of up to 5 g/kg biomass have been obtained in plants, making this production system competitive with microbial hosts. Increasing protein accumulation at the cellular level by varying host, germplasm, location of protein accumulation, and transformation procedure is reviewed. At the molecular level increased expression by improving transcription, translation and accumulation of the protein is critically evaluated. The greatest increases in protein accumulation will occur when various optimized parameters are more fully integrated with each other. Because of the complex nature of plants, this will take more time and effort to accomplish than has been the case for the simpler unicellular systems. However the potential for plants to become one of the major avenues for protein production appears very promising.
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Affiliation(s)
- Erin Egelkrout
- Applied Biotechnology Institute, Cal Poly Technology Park, Building 83, San Luis Obispo, CA 93407, USA
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Nomura W, Masuda A, Ohba K, Urabe A, Ito N, Ryo A, Yamamoto N, Tamamura H. Effects of DNA binding of the zinc finger and linkers for domain fusion on the catalytic activity of sequence-specific chimeric recombinases determined by a facile fluorescent system. Biochemistry 2012; 51:1510-7. [PMID: 22304662 DOI: 10.1021/bi201878x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Artificial zinc finger proteins (ZFPs) consist of Cys(2)-His(2)-type modules composed of ∼30 amino acids with a ββα structure that coordinates a zinc ion. ZFPs that recognize specific DNA target sequences can substitute for the binding domains of enzymes that act on DNA to create designer enzymes with programmable sequence specificity. The most studied of these engineered enzymes are zinc finger nucleases (ZFNs). ZFNs have been widely used to model organisms and are currently in human clinical trials with an aim of therapeutic gene editing. Difficulties with ZFNs arise from unpredictable mutations caused by nonhomologous end joining and off-target DNA cleavage and mutagenesis. A more recent strategy that aims to address the shortcomings of ZFNs involves zinc finger recombinases (ZFRs). A thorough understanding of ZFRs and methods for their modification promises powerful new tools for gene manipulation in model organisms as well as in gene therapy. In an effort to design efficient and specific ZFRs, the effects of the DNA binding affinity of the zinc finger domains and the linker sequence between ZFPs and recombinase catalytic domains have been assessed. A plasmid system containing ZFR target sites was constructed for evaluation of catalytic activities of ZFRs with variable linker lengths and numbers of zinc finger modules. Recombination efficiencies were evaluated by restriction enzyme analysis of isolated plasmids after reaction in Escherichia coli and changes in EGFP fluorescence in mammalian cells. The results provide information relevant to the design of ZFRs that will be useful for sequence-specific genome modification.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioengineering, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo 101-0062, Japan.
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Huang X, Narayanaswamy R, Fenn K, Szpakowski S, Sasaki C, Costa J, Blancafort P, Lizardi PM. Sequence-specific biosensors report drug-induced changes in epigenetic silencing in living cells. DNA Cell Biol 2012; 31 Suppl 1:S2-10. [PMID: 22313050 DOI: 10.1089/dna.2011.1537] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Treatment with demethylating drugs can induce demethylation and reactivation of abnormally silenced tumor suppressor genes in cancer cells, but it can also induce potentially deleterious loss of methylation of repetitive elements. To enable the observation of unwanted drug effects related to loss of methylation of repetitive DNA, we have developed a novel biosensor capable of reporting changes in DNA accessibility via luminescence, in living cells. The biosensor design comprises two independent modules, each with a polydactyl zinc finger domain fused to a half intein and to a split-luciferase domain that can be joined by conditional protein splicing after binding to adjacent DNA targets. We show that an artificial zinc finger design specifically targeting DNA sequences near the promoter region of the L1PA2 subfamily of Line-1 retroelements is able to generate luminescent signals, reporting loss of epigenetic silencing and increased DNA accessibility of retroelements in human cells treated with the demethylating drugs decitabine or 5-azacytidine.
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Affiliation(s)
- Xudong Huang
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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Nakata E, Liew FF, Uwatoko C, Kiyonaka S, Mori Y, Katsuda Y, Endo M, Sugiyama H, Morii T. Zinc-Finger Proteins for Site-Specific Protein Positioning on DNA-Origami Structures. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108199] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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