1
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Li X, Wang J, Curtin K, Li P. Microfluidic Continuous Flow DNA Fragmentation based on a Vibrating Sharp-tip. MICROFLUIDICS AND NANOFLUIDICS 2022; 26:104. [PMID: 38130602 PMCID: PMC10735211 DOI: 10.1007/s10404-022-02610-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 11/07/2022] [Indexed: 12/23/2023]
Abstract
Fragmentation of DNA into short fragments is of great importance for detecting and studying DNAs. Current microfluidic methods of DNA fragmentation are either inefficient for generating small fragments or rely on microbubbles. Here, we report a DNA fragmentation method in a 3D-printed microfluidic device, which allows efficient continuous flow fragmentation of genomic DNAs without the need for microbubbles. This method is enabled by localized acoustic streaming induced by a single vibrating sharp-tip. Genomic DNAs were fragmented into 700 to 3000 bp fragments with a low power consumption of ~140 mW. The system demonstrated successful fragmentation under a wide range of flow rates from 1 to 50 μL/min without the need for air bubbles. Finally, the utility of the continuous DNA fragmentation method was demonstrated to accelerate the DNA hybridization process for biosensing. Due to the small footprint, continuous flow and bubble-free operation, and high fragmentation efficiency, this method demonstrated great potential for coupling with other functional microfluidic units to achieve an integrated DNA analysis platform.
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Affiliation(s)
- Xiaojun Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Jing Wang
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
| | - Kathrine Curtin
- Department of Mechanical and Aerospace Engineering, West Virginia University, Morgantown, WV, USA
| | - Peng Li
- C. Eugene Bennett Department of Chemistry, West Virginia University, Morgantown, WV, USA
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2
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Fan L, Wang J, Deng P, Wang Y, Zhang A, Yang M, Zeng G. Foxhead box D1 promotes the partial epithelial-to-mesenchymal transition of laryngeal squamous cell carcinoma cells via transcriptionally activating the expression of zinc finger protein 532. Bioengineered 2022; 13:3057-3069. [PMID: 35112956 PMCID: PMC8973586 DOI: 10.1080/21655979.2021.2024978] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The presence of cervical lymph node metastases has been considered as the most important adverse prognostic factor for patients with laryngeal squamous cell carcinoma (LSCC). However, the underlying mechanisms remain to be fully revealed. In this study, we explored the expression profile of Foxhead box D1 (FOXD1), its association with epithelial-to-mesenchymal transition (EMT), and its downstream targets in LSCC. Bioinformatic analysis was performed based on the LSCC subset of The Cancer Genome Atlas-Head and Neck Squamous Cell Carcinoma (TCGA-HSNC) and Chromatin immunoprecipitation (ChIP)-seq data from Cistrome Data Browser. LSCC cell lines AMC-HN-8 and TU212 were used for in vitro studies. Results showed that FOXD1 upregulation was associated with poor prognosis of LSCC. FOXD1 knockdown reduced N-cadherin and Vimentin expression but increased E-cadherin expression in AMC-HN-8 cells. Its overexpression showed opposite effects in TU212 cells. FOXD1 could bind to the promoter of ZNF532 and activate its transcription. ZNF532 overexpression enhanced the invasion of both AMC-HN-8 and TU212 cells. In comparison, its knockdown significantly impaired their invasion. ZNF532 knockdown nearly abrogated the alterations of EMT markers caused by FOXD1 overexpression. Its overexpression largely rescued the phenotypes caused by FOXD1 knockdown. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that ZNF532 correlated genes are largely enriched in extracellular matrix regulations. LSCC patients with high ZNF532 expression (top 50%) had a significantly worse progression-free survival. In summary, this study confirmed that FOXD1 promotes partial-EMT of LSCC cells via transcriptionally activating the expression of ZNF532.
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Affiliation(s)
- Liang Fan
- Department of Otorhinolaryngology Head and Neck Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
| | - Jinxiu Wang
- Department of Otorhinolaryngology Head and Neck Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
| | - Pingping Deng
- Department of Otorhinolaryngology Head and Neck Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
| | - Yuanyuan Wang
- Department of Anesthesia, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
| | - Aiping Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
| | - Mengsheng Yang
- Otorhinolaryngology Head and Neck Surgery, Gansu Provincial Hospital, Lanzhou, Gansu, China
| | - Gang Zeng
- Department of Otorhinolaryngology Head and Neck Surgery, Jingmen No. 1 People's Hospital, Jingmen, Hubei, China
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3
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Keresztessy Z, Erdos E, Ozgyin L, Kádas J, Horváth J, Zahuczky G, Balint BL. Development of an antibody control system using phage display. J Biotechnol 2019; 300:63-69. [PMID: 31129070 DOI: 10.1016/j.jbiotec.2019.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
While chromatin immunoprecipitation has become a widely-used method in the field of transcription regulation studies, serious limitations connected to the complexity and relatively little standardization of the method serve as obstacles for its use in clinical research. In this paper we introduce a method for developing bacteriophage-based controls for the better standardization of the chromatin immunoprecipitation reactions. Random phage display libraries were selected with ChIP-grade antibodies for several rounds and individual monoclonal phages were isolated. These monoclonal phages can be propagated, characterized, capillary sequenced and if needed later cloned from in-silico data. Using such control tools allows for a better characterization of the immunoprecipitation stage needed for further clinical research in the field of chromatin-immunoprecipitation-based studies.
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Affiliation(s)
- Zsolt Keresztessy
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - Edina Erdos
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - Lilla Ozgyin
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - János Kádas
- UD-GenoMed Medical Genomic Technologies Ltd., 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - József Horváth
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - Gábor Zahuczky
- UD-GenoMed Medical Genomic Technologies Ltd., 98 Nagyerdei krt., H-4032 Debrecen, Hungary
| | - Balint L Balint
- Genomic Medicine and Bioinformatic Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 98 Nagyerdei krt., H-4032 Debrecen, Hungary.
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4
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Bomsztyk K, Mar D, Wang Y, Denisenko O, Ware C, Frazar CD, Blattler A, Maxwell AD, MacConaghy BE, Matula TJ. PIXUL-ChIP: integrated high-throughput sample preparation and analytical platform for epigenetic studies. Nucleic Acids Res 2019; 47:e69. [PMID: 30927002 PMCID: PMC6614803 DOI: 10.1093/nar/gkz222] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/25/2022] Open
Abstract
Chromatin immunoprecipitation (ChIP) is the most widely used approach for identification of genome-associated proteins and their modifications. We have previously introduced a microplate-based ChIP platform, Matrix ChIP, where the entire ChIP procedure is done on the same plate without sample transfers. Compared to conventional ChIP protocols, the Matrix ChIP assay is faster and has increased throughput. However, even with microplate ChIP assays, sample preparation and chromatin fragmentation (which is required to map genomic locations) remains a major bottleneck. We have developed a novel technology (termed 'PIXUL') utilizing an array of ultrasound transducers for simultaneous shearing of samples in standard 96-well microplates. We integrated PIXUL with Matrix ChIP ('PIXUL-ChIP'), that allows for fast, reproducible, low-cost and high-throughput sample preparation and ChIP analysis of 96 samples (cell culture or tissues) in one day. Further, we demonstrated that chromatin prepared using PIXUL can be used in an existing ChIP-seq workflow. Thus, the high-throughput capacity of PIXUL-ChIP provides the means to carry out ChIP-qPCR or ChIP-seq experiments involving dozens of samples. Given the complexity of epigenetic processes, the use of PIXUL-ChIP will advance our understanding of these processes in health and disease, as well as facilitate screening of epigenetic drugs.
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Affiliation(s)
- Karol Bomsztyk
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- To whom correspondence should be addressed. Tel. +1 206 616 7949;
| | - Daniel Mar
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
| | - Yuliang Wang
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, WA 98195, USA
| | - Oleg Denisenko
- UW Medicine South Lake Union, University of Washington, Seattle, WA 98109, USA
| | - Carol Ware
- Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA 98109, USA
| | - Christian D Frazar
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | | | - Adam D Maxwell
- Department of Urology, University of Washington School of Medicine, Seattle, WA 98195, USA
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Brian E MacConaghy
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
| | - Thomas J Matula
- Center for Industrial and Medical Ultrasound, Applied Physics Laboratory, University of Washington, Seattle, WA 98195, USA
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5
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Abstract
Chromatin immunoprecipitation (ChIP) is a powerful and sensitive technique that is widely used to study DNA-protein interactions. It enables an unbiased genome-wide analysis of transcriptional changes during several biological processes including cellular differentiation. Here, we describe a step-by-step protocol to identify histone modifications, transcription factor, and co-factor binding to chromatin in skeletal myoblasts. We discuss critical steps during cell harvesting, sonication, and immunoprecipitation and provide notes to evade common pitfalls.
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Affiliation(s)
- Vinay Kumar Rao
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore, Singapore
| | - Shilpa Rani Shankar
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Reshma Taneja
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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6
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Dall'Acqua A, Sonego M, Pellizzari I, Pellarin I, Canzonieri V, D'Andrea S, Benevol S, Sorio R, Giorda G, Califano D, Bagnoli M, Militello L, Mezzanzanica D, Chiappetta G, Armenia J, Belletti B, Schiappacassi M, Baldassarre G. CDK6 protects epithelial ovarian cancer from platinum-induced death via FOXO3 regulation. EMBO Mol Med 2018; 9:1415-1433. [PMID: 28778953 PMCID: PMC5623833 DOI: 10.15252/emmm.201607012] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is an infrequent but highly lethal disease, almost invariably treated with platinum‐based therapies. Improving the response to platinum represents a great challenge, since it could significantly impact on patient survival. Here, we report that silencing or pharmacological inhibition of CDK6 increases EOC cell sensitivity to platinum. We observed that, upon platinum treatment, CDK6 phosphorylated and stabilized the transcription factor FOXO3, eventually inducing ATR transcription. Blockage of this pathway resulted in EOC cell death, due to altered DNA damage response accompanied by increased apoptosis. These observations were recapitulated in EOC cell lines in vitro, in xenografts in vivo, and in primary tumor cells derived from platinum‐treated patients. Consistently, high CDK6 and FOXO3 expression levels in primary EOC predict poor patient survival. Our data suggest that CDK6 represents an actionable target that can be exploited to improve platinum efficacy in EOC patients. As CDK4/6 inhibitors are successfully used in cancer patients, our findings can be immediately transferred to the clinic to improve the outcome of EOC patients.
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Affiliation(s)
- Alessandra Dall'Acqua
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Maura Sonego
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Ilenia Pellizzari
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Ilenia Pellarin
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Vincenzo Canzonieri
- Division of Pathology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Sara D'Andrea
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Sara Benevol
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Roberto Sorio
- Division of Medical Oncology C, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Giorgio Giorda
- Division of Gynecology-Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Daniela Califano
- Genomica Funzionale, Istituto Nazionale Tumori -IRCCS- Fondazione G Pascale, Naples, Italy
| | - Marina Bagnoli
- Molecular Therapies Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori Milan, Milan, Italy
| | - Loredana Militello
- Division of Medical Oncology C, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Delia Mezzanzanica
- Molecular Therapies Unit, Department of Experimental Oncology and Molecular Medicine, Fondazione IRCCS Istituto Nazionale dei Tumori Milan, Milan, Italy
| | - Gennaro Chiappetta
- Genomica Funzionale, Istituto Nazionale Tumori -IRCCS- Fondazione G Pascale, Naples, Italy
| | - Joshua Armenia
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Barbara Belletti
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Monica Schiappacassi
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
| | - Gustavo Baldassarre
- Division of Molecular Oncology, CRO Aviano, IRCCS, National Cancer Institute, Aviano, Italy
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7
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Chiarella AM, Quimby AL, Mehrab-Mohseni M, Velasco B, Kasoji SK, Davis IJ, Dayton PA, Hathaway NA, Pattenden SG. Cavitation Enhancement Increases the Efficiency and Consistency of Chromatin Fragmentation from Fixed Cells for Downstream Quantitative Applications. Biochemistry 2018; 57:2756-2761. [PMID: 29658277 DOI: 10.1021/acs.biochem.8b00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the most sensitive, time-consuming, and variable steps of chromatin immunoprecipitation (ChIP) is chromatin sonication. Traditionally, this process can take hours to properly sonicate enough chromatin for multiple ChIP assays. Further, the length of sheared DNA is often inconsistent. In order to faithfully measure chemical and structural changes at the chromatin level, sonication needs to be reliable. Thus, chromatin fragmentation by sonication represents a significant bottleneck to downstream quantitative analysis. To improve the consistency and efficiency of chromatin sonication, we developed and tested a cavitation enhancing reagent based on sonically active nanodroplets. Here, we show that nanodroplets increase sonication efficiency by 16-fold and provide more consistent levels of chromatin fragmentation. Using the previously characterized chromatin in vivo assay (CiA) platform, we generated two distinct chromatin states in order to test nanodroplet-assisted sonication sensitivity in measuring post-translational chromatin marks. By comparing euchromatin to chemically induced heterochromatin at the same CiA:Oct4 locus, we quantitatively measure the capability of our new sonication technique to resolve differences in chromatin structure. We confirm that nanodroplet-assisted sonication results are indistinguishable from those of samples processed with traditional sonication in downstream applications. While the processing time for each sample was reduced from 38.4 to 2.3 min, DNA fragment distribution sizes were significantly more consistent with a coefficient of variation 2.7 times lower for samples sonicated in the presence of nanodroplets. In conclusion, sonication utilizing the nanodroplet cavitation enhancement reagent drastically reduces the amount of processing time and provides consistently fragmented chromatin of high quality for downstream applications.
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Affiliation(s)
- Anna M Chiarella
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Curriculum in Genetics and Molecular Biology , The University of North Carolina , Chapel Hill , North Carolina 27514 , United States
| | - Austin L Quimby
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Marjan Mehrab-Mohseni
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Brian Velasco
- Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Sandeep K Kasoji
- Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Ian J Davis
- Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Departments of Genetics and Pediatrics , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Paul A Dayton
- Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Joint Department of Biomedical Engineering , The University of North Carolina and North Carolina State University , Chapel Hill , North Carolina 27599 , United States
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Curriculum in Genetics and Molecular Biology , The University of North Carolina , Chapel Hill , North Carolina 27514 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
| | - Samantha G Pattenden
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States.,Lineberger Comprehensive Cancer Center , The University of North Carolina , Chapel Hill , North Carolina 27599 , United States
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8
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Truch J, Telenius J, Higgs DR, Gibbons RJ. How to Tackle Challenging ChIP-Seq, with Long-Range Cross-Linking, Using ATRX as an Example. Methods Mol Biol 2018; 1832:105-130. [PMID: 30073524 DOI: 10.1007/978-1-4939-8663-7_6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Chromatin immunoprecipitation coupled with high-throughput, next-generation DNA sequencing (ChIP-seq) has enabled researchers to establish the genome-wide patterns of chromatin modifications and binding of chromatin-associated proteins. Well-established protocols produce robust ChIP-seq data for many proteins by sequencing the DNA obtained following immunoprecipitation of fragmented chromatin using a wide range of specific antibodies. In general, the quality of these data mainly depends on the specificity and avidity of the antibody used. However, even using optimal antibodies, ChIP-seq can become more challenging when the protein associates with chromatin via protein-protein interactions rather than directly binding DNA. An example of such a protein is the alpha-thalassaemia mental retardation X-linked (ATRX) protein; a chromatin remodeler that associates with the histone chaperone DAXX, in the deposition of the replication-independent histone variant H3.3 and plays an important role in maintaining chromatin integrity. Inherited mutations of ATRX cause syndromal mental retardation (ATR-X Syndrome) whereas acquired mutations are associated with myelodysplasia, acute myeloid leukemia (ATMDS syndrome), and a range of solid tumors. Therefore, high quality ChIP-seq data have been needed to analyze the genome-wide distribution of ATRX, to advance our understanding of its normal role and to comprehend how mutations contribute to human disease. Here, we describe an optimized ChIP-seq protocol for ATRX which can also be used to produce high quality data sets for other challenging proteins which are indirectly associated with DNA and complement the ChIP-seq toolkit for genome-wide analyses of histone chaperon complexes and associated chromatin remodelers. Although not a focus of this chapter, we will also provide some insight for the analysis of the large dataset generated by ChIP-seq. Even though this protocol has been fully optimized for ATRX, it should also provide guidance for efficient ChIP-seq analysis, using the appropriate antibodies, for other proteins interacting indirectly with DNA.
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Affiliation(s)
- Julia Truch
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Jelena Telenius
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Douglas R Higgs
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Richard J Gibbons
- Medical Research Council (MRC) Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK.
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9
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Analysis of Epigenetic Regulation of Hypoxia-Induced Epithelial-Mesenchymal Transition in Cancer Cells by Quantitative Chromatin Immunoprecipitation of Histone Deacetylase 3 (HDAC3). Methods Mol Biol 2017; 1436:23-9. [PMID: 27246206 DOI: 10.1007/978-1-4939-3667-0_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Epigenetics plays a key role in gene expression control. Histone modifications including acetylation/deacetylation or methylation/demethylation are major epigenetic mechanisms known to regulate epithelial-mesenchymal transition (EMT)-associated gene expression during hypoxia-induced cancer metastasis. Chromatin immunoprecipitation (ChIP) assay is a powerful tool for investigation of histone modification patterns of genes of interest. In this chapter, we describe a protocol that uses chromatin immunoprecipitation (ChIP) to analyze the epigenetic regulation of EMT marker genes by deacetylation of acetylated Histone 3 Lys 4 (H3K4Ac) under hypoxia in a head and neck cancer cell line FaDu cells. Not only a method of ChIP coupled by real-time quantitative PCR but also the detailed conditions are provided based on our previously published studies.
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10
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Wang F, Wu D, Fu H, He F, Xu C, Zhou J, Li D, Li G, Xu J, Wu Q, Chen J, Su L, Wang W, Zhang S. Cofilin 1 promotes bladder cancer and is regulated by TCF7L2. Oncotarget 2017; 8:92043-92054. [PMID: 29190896 PMCID: PMC5696162 DOI: 10.18632/oncotarget.20664] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 06/27/2017] [Indexed: 01/22/2023] Open
Abstract
Earlier reports demonstrated that Cofilin expression is increased in bladder cancer samples, though its function remains unknown. Here, we found that Cofilin 1 expression was higher in bladder cancer tissues than in paracancerous tissues. Overexpression of Cofilin 1 promoted, while Cofilin 1 knockdown inhibited, proliferation, migration, and invasion in the T24 and RT4 bladder cancer cell lines. In addition, Cofilin 1 overexpression increased, while Cofilin 1 knockdown decreased, bladder tumor volumes in mouse xenograft experiments. Transcription factor 7-like 2 (TCF7L2) targeted the promoter of the Cofilin 1 gene, and TCF7L2 knockdown or mutations in the Cofilin 1 promoter dramatically decreased Cofilin 1 transcription. TCF7L2 promoted cell proliferation and migration and increased Cofilin 1 protein levels in RT4 and T24 cells. Thus, TCF7L2 contributed to Cofilin 1-induced promotion of bladder cancer development by binding to the Cofilin 1 promoter and increasing its expression.
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Affiliation(s)
- Fei Wang
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Dinglan Wu
- The Clinical Innovation & Research Center (CIRC), Shenzhen Hospital, Southern Medical University, Shenzhen, China
| | - Housheng Fu
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Fengrong He
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Congjie Xu
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Jiaquan Zhou
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Daoyuan Li
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Guoping Li
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Jianbing Xu
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Qinghui Wu
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Jianxiang Chen
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Liangju Su
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Weifu Wang
- Department of Urology, People's Hospital of Hainan Province, Haikou, China
| | - Shufang Zhang
- Central Laboratory, Haikou People's Hospital, Central South University Xiangya School of Medicine Affiliated Haikou Hospital, Haikou, China
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11
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Lee HG, Choi YR, Seo PJ. Increased STM expression is associated with drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2016; 201:79-84. [PMID: 27448723 DOI: 10.1016/j.jplph.2016.07.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/17/2016] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
In higher plants, shoot apical meristem (SAM) maintains cell division activity in order to give rise to aerial plant organs. Several lines of evidence have suggested that plants ensure stem cell proliferation activity in response to various external stimuli, thereby contributing to plant adaptation and fitness. Here, we report that the abscisic acid (ABA)-inducible R2R3-type MYB96 transcription factor regulates transcript accumulation of SHOOT MERISTEMLESS (STM) possibly to contribute to plant adaptation to environmental stress. STM was up-regulated in MYB96-overexpressing activation-tagging myb96-ox plants, but down-regulated in MYB96-deficient myb96-1 mutant plants, even in the presence of ABA. Notably, the MYB96 transcription factor bound directly to the STM promoter. In addition, consistent with the role of MYB96 in drought tolerance, transgenic plants overexpressing STM (35S:STM-MYC) were more tolerant to drought stress. These observations suggest that the MYB96-STM module contributes to enhancing plant tolerance to drought stress.
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Affiliation(s)
- Hong Gil Lee
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Yee-Ram Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Pil Joon Seo
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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12
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Finegersh A, Homanics GE. Chromatin immunoprecipitation and gene expression analysis of neuronal subtypes after fluorescence activated cell sorting. J Neurosci Methods 2016; 263:81-8. [PMID: 26868730 DOI: 10.1016/j.jneumeth.2016.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 01/15/2016] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
BACKGROUND With advances in cell capture, gene expression can now be studied in neuronal subtypes and single cells; however, studying epigenetic mechanisms that underlie these changes presents challenges. Moreover, chromatin immunoprecipitation (ChIP) protocols optimized for low cell number do not adequately address technical issues and cell loss while preparing tissue for fluorescence activated cell sorting (FACS). Developing a reliable FACS-ChIP protocol without the need for pooling tissue from multiple animals would enable study of epigenetic mechanisms in neuronal subtypes. METHODS FACS was used to isolate dopamine 1 receptor (D1R) expressing cells from the nucleus accumbens (NAc) of a commercially available BAC transgenic mouse strain. D1R+ cells were used to study gene expression as well as histone modifications at gene promoters using a novel native ChIP protocol. RESULTS Isolated cells had enrichment of the dopamine 1 receptor (D1R) mRNA and nearly undetectable levels of GFAP and D2R mRNA. ChIP analysis demonstrated the association of activating or repressive histone modifications with highly expressed or silent gene promoters, respectively. COMPARISON WITH EXISTING METHODS The ChIP protocol developed in this paper enables characterization of histone modifications from ∼30,000 FAC-sorted neurons. CONCLUSIONS We describe a one day FACS-ChIP protocol that can be applied to epigenetic studies of neuronal subtypes without pooling tissue.
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Affiliation(s)
- Andrey Finegersh
- University of Pittsburgh, Departments of Anesthesiology and Pharmacology & Chemical Biology, 6060 Biomedical Science Tower-3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States
| | - Gregg E Homanics
- University of Pittsburgh, Departments of Anesthesiology and Pharmacology & Chemical Biology, 6060 Biomedical Science Tower-3, 3501 Fifth Avenue, Pittsburgh, PA 15261, United States.
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13
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Cao Z, Lu C. A Microfluidic Device with Integrated Sonication and Immunoprecipitation for Sensitive Epigenetic Assays. Anal Chem 2016; 88:1965-72. [PMID: 26745449 PMCID: PMC4741277 DOI: 10.1021/acs.analchem.5b04707] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
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Epigenetic
studies increasingly require analysis of a small number
of cells that are of one specific type and derived from patients or
animals. In this report, we demonstrate a simple microfluidic device
that integrates sonication and immunoprecipitation (IP) for epigenetic
assays, such as chromatin immunoprecipitation (ChIP) and methylated
DNA immunoprecipitation (MeDIP). By incorporating an ultrasonic transducer
with a microfluidic chamber, we implemented microscale sonication
for both shearing chromatin/DNA and mixing/washing of IP beads. Such
integration allowed highly sensitive tests starting with 100 cross-linked
cells for ChIP or 500 pg of genomic DNA for MeDIP (compared to 106–107 cells for ChIP and 1–10 μg
of DNA for MeDIP in conventional assays). The entire on-chip process
of sonication and IP took only 1 h. Our tool will be useful for highly
sensitive epigenetic studies based on a small quantity of sample.
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Affiliation(s)
- Zhenning Cao
- Department of Biomedical Engineering and Mechanics, Virginia Tech , Blacksburg, Virginia 24061, United States
| | - Chang Lu
- Department of Chemical Engineering, Virginia Tech , Blacksburg, Virginia 24061, United States
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14
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MYB96 shapes the circadian gating of ABA signaling in Arabidopsis. Sci Rep 2016; 6:17754. [PMID: 26725725 PMCID: PMC4698719 DOI: 10.1038/srep17754] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 11/03/2015] [Indexed: 11/22/2022] Open
Abstract
Circadian clocks regulate the rhythms of biological activities with a period of approximately 24-hours and synchronize plant metabolism and physiology with the environmental cycles. The clock also gates responses to environmental stresses to maximize fitness advantages. Here we report that the MYB96 transcription factor is connected with the clock oscillator to shape the circadian gating of abscisic acid (ABA) responses. MYB96 directly binds to the TIMING OF CAB EXPRESSION 1 (TOC1) promoter to positively regulate its expression. The use of myb96 mutant plants shows that this regulation is essential for the gated induction of TOC1 by ABA. In turn, MYB96 induction by ABA is also altered in toc1-3 mutant plants. The increased tolerance to drought of MYB96 over-expressing plants is decreased in the toc1-3 mutant background, suggesting that MYB96 and TOC1 intersect the circadian clock and ABA signaling. The MYB96-TOC1 function might be also regulated by the clock component CIRCADIAN CLOCK-ASSOCIATED 1 (CCA1), which binds to the MYB96 promoter and alters its circadian expression. Thus, a complex circuitry of CCA1-MYB96-TOC1 regulatory interactions provides the mechanistic basis underlying the connection between circadian and stress signaling to optimize plant fitness to ambient stresses.
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15
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Effect of BIX-01294 on H3K9me2 levels and the imprinted gene Snrpn in mouse embryonic fibroblast cells. Biosci Rep 2015; 35:BSR20150064. [PMID: 26285804 PMCID: PMC4613706 DOI: 10.1042/bsr20150064] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 07/31/2015] [Indexed: 11/27/2022] Open
Abstract
BIX-01294 (a diazepin-quinazolin-amine derivative) has important biological effects and its epigenetic regulation at imprinting control regions is highly complex. BIX-01294 may reduce global H3K9me2 levels and affect epigenetic modifications of small nuclear ribonucleoprotein N (Snrpn) in MEFs. Histone H3 lysine 9 dimethylation (H3K9me2) hypermethylation is thought to be a major influential factor in cellular reprogramming, such as somatic cell nuclear transfer (SCNT) and induction of pluripotent stem cells (iPSCs). The diazepin-quinazolin-amine derivative (BIX-01294) specifically inhibits the activity of histone methyltransferase EHMT2 (euchromatic histone-lysine N-methyltransferase 2) and reduces H3K9me2 levels in cells. The imprinted gene small nuclear ribonucleoprotein N (Snrpn) is of particular interest because of its important biological functions. The objective of the present study was to investigate the effect of BIX-01294 on H3K9me2 levels and changes in Snrpn DNA methylation and histone H3K9me2 in mouse embryonic fibroblasts (MEFs). Results showed that 1.3 μM BIX-01294 markedly reduced global levels of H3K9me2 with almost no cellular toxicity. There was a significant decrease in H3K9me2 in promoter regions of the Snrpn gene after BIX-01294 treatment. A significant increase in methylation of the Snrpn differentially methylated region 1 (DMR1) and slightly decreased transcript levels of Snrpn were found in BIX-01294-treated MEFs. These results suggest that BIX-01294 may reduce global levels of H3K9me2 and affect epigenetic modifications of Snrpn in MEFs.
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16
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Kasoji SK, Pattenden SG, Malc EP, Jayakody CN, Tsuruta JK, Mieczkowski PA, Janzen WP, Dayton PA. Cavitation Enhancing Nanodroplets Mediate Efficient DNA Fragmentation in a Bench Top Ultrasonic Water Bath. PLoS One 2015; 10:e0133014. [PMID: 26186461 PMCID: PMC4505845 DOI: 10.1371/journal.pone.0133014] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 06/23/2015] [Indexed: 01/16/2023] Open
Abstract
A perfluorocarbon nanodroplet formulation is shown to be an effective cavitation enhancement agent, enabling rapid and consistent fragmentation of genomic DNA in a standard ultrasonic water bath. This nanodroplet-enhanced method produces genomic DNA libraries and next-generation sequencing results indistinguishable from DNA samples fragmented in dedicated commercial acoustic sonication equipment, and with higher throughput. This technique thus enables widespread access to fast bench-top genomic DNA fragmentation.
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Affiliation(s)
- Sandeep K. Kasoji
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, and North Carolina State University, Raleigh, North Carolina, United States of America
| | - Samantha G. Pattenden
- Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ewa P. Malc
- Department of Genetics, High Throughput Sequencing Facility, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Chatura N. Jayakody
- Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - James K. Tsuruta
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, and North Carolina State University, Raleigh, North Carolina, United States of America
- Department of Pediatrics, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Piotr A. Mieczkowski
- Department of Genetics, High Throughput Sequencing Facility, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - William P. Janzen
- Center for Integrative Chemical Biology and Drug Discovery, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Paul A. Dayton
- Joint Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina, and North Carolina State University, Raleigh, North Carolina, United States of America
- * E-mail:
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17
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The E3 Ubiquitin Ligase COP1 Regulates Thermosensory Flowering by Triggering GI Degradation in Arabidopsis. Sci Rep 2015; 5:12071. [PMID: 26159740 PMCID: PMC4498190 DOI: 10.1038/srep12071] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 06/10/2015] [Indexed: 12/22/2022] Open
Abstract
Floral transition is influenced by environmental factors such as light and temperature. Plants are capable of integrating photoperiod and ambient temperature signaling into their developmental program. Despite extensive investigations on individual genetic pathways, little is known about the molecular components that integrate both pathways. Here, we demonstrate that the RING finger–containing E3 ubiquitin ligase CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) acts as an integrator of photoperiod and ambient temperature signaling. In addition to the role in photoperiodic destabilization of CONSTANS (CO), COP1 also regulates temperature sensitivity by controlling the degradation of GIGANTEA (GI). COP1-impaired mutants showed reduced sensitivity to low ambient temperature. Notably, COP1 is more stabilized at low temperature and accelerates GI turnover in a 26S proteasome-dependent manner. The direct association of GI with the promoter of FLOWERING LOCUS T (FT) was reduced because of its ambient temperature-dependent protein stability control, and thus COP1-triggered GI turnover delays flowering at low temperatures via a CO-independent pathway. Taken together, our findings indicate that environmental conditions regulate the stability of COP1, and conditional specificity of its target selection stimulates proper developmental responses and ensures reproductive success.
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18
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Lee HG, Seo PJ. The MYB96-HHP module integrates cold and abscisic acid signaling to activate the CBF-COR pathway in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 82:962-977. [PMID: 25912720 DOI: 10.1111/tpj.12866] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 04/20/2015] [Accepted: 04/21/2015] [Indexed: 05/20/2023]
Abstract
Various environmental stresses limit plant growth, development, and reproductive success. Plants have therefore evolved sophisticated adaptive responses to deal with environmental challenges. The responses of plants to environmental stresses are mainly mediated by abscisic acid (ABA)-dependent and ABA-independent signaling pathways. While these two pathways have been implicated to play discrete roles in abiotic stress responses, accumulating evidence suggests that they are also intertwined. Here, we report that an R2R3-type MYB transcription factor, MYB96, integrates the ABA and cold signaling pathways. In addition to its role in ABA-mediated drought responses, MYB96 is also induced by cold stress in an ABA-independent manner and subsequently activates freezing tolerance. Notably, MYB96 regulates HEPTAHELICAL PROTEIN (HHP) genes by binding to their promoters. The HHP proteins, in turn, interact with C-REPEAT BINDING FACTOR (CBF) upstream regulators, such as INDUCER OF CBF EXPRESSION 1 (ICE1), ICE2, and CALMODULIN-BINDING TRANSCRIPTION ACTIVATOR 3 (CAMTA3). The specific interactive networks of HHPs with the CBF upstream regulators are necessary to facilitate transcriptional activation of the CBF regulon under stressful conditions. Together, the MYB96-HHP module integrates ABA-dependent and ABA-independent signals and activates the CBF pathway, ensuring plant adaptation to a wide range of adverse environmental fluctuations.
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Affiliation(s)
- Hong Gil Lee
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju, 561-756, Korea
| | - Pil Joon Seo
- Department of Bioactive Material Sciences and Research Center of Bioactive Materials, Chonbuk National University, Jeonju, 561-756, Korea
- Department of Chemistry and Research Institute of Physics and Chemistry, Chonbuk National University, Jeonju, 561-756, Korea
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19
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KMT1E-mediated chromatin modifications at the FcγRIIb promoter regulate thymocyte development. Genes Immun 2015; 16:162-9. [PMID: 25569264 DOI: 10.1038/gene.2014.70] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 08/28/2014] [Accepted: 11/06/2014] [Indexed: 11/09/2022]
Abstract
This work examines the role the lysine methyltransferase KMT1E (Setdb1) in thymocyte development. We have developed and described a T cell-specific conditional knockout of Setdb1. A partial block was seen at the double-positive to single-positive transition, causing reduced numbers of single-positive T cells in the thymus and periphery. Knockout thymocytes had reduced numbers of CD69(+) and T-cell receptor TCRβ(+) cells and increased numbers of apoptotic cells in the double-positive compartment, suggesting an alteration in the selection process. Transcriptional profiling of thymocytes revealed that Setdb1 deletion derepresses expression of FcγRIIb, the inhibitory Fc receptor. We demonstrate that a KMT1E-containing complex directly interacts with the FcγRIIb promoter and that histone H3 at lysine 9 tri-methylation at this promoter is dependent on Setdb1 expression. Derepression of FcγRIIb causes exacerbated signaling through the TCR complex, with specifically increased phosphorylation of ZAP70, affecting selection. This work identifies KMT1E as a novel repressor of FcγRIIb and identifies an underappreciated role of FcγRIIb in fine tuning thymocyte development.
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20
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SH2B1β interacts with STAT3 and enhances fibroblast growth factor 1-induced gene expression during neuronal differentiation. Mol Cell Biol 2014; 34:1003-19. [PMID: 24396070 DOI: 10.1128/mcb.00940-13] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Neurite outgrowth is an essential process during neuronal differentiation as well as neuroregeneration. Thus, understanding the molecular and cellular control of neurite outgrowth will benefit patients with neurological diseases. We have previously shown that overexpression of the signaling adaptor protein SH2B1β promotes fibroblast growth factor 1 (FGF1)-induced neurite outgrowth (W. F. Lin, C. J. Chen, Y. J. Chang, S. L. Chen, I. M. Chiu, and L. Chen, Cell. Signal. 21:1060-1072, 2009). SH2B1β also undergoes nucleocytoplasmic shuttling and regulates a subset of neurotrophin-induced genes. Although these findings suggest that SH2B1β regulates gene expression, the nuclear role of SH2B1β was not known. In this study, we show that SH2B1β interacts with the transcription factor, signal transducer, and activator of transcription 3 (STAT3) in neuronal PC12 cells, cortical neurons, and COS7 fibroblasts. By affecting the subcellular distribution of STAT3, SH2B1β increased serine phosphorylation and the concomitant transcriptional activity of STAT3. As a result, overexpressing SH2B1β enhanced FGF1-induced expression of STAT3 target genes Egr1 and Cdh2. Chromatin immunoprecipitation assays further reveal that, in response to FGF1, overexpression of SH2B1β promotes the in vivo occupancy of STAT3-Sp1 heterodimers at the promoter of Egr1 and Cdh2. These findings establish a central role of SH2B1β in orchestrating signaling events to transcriptional activation through interacting and regulating STAT3-containing complexes during neuronal differentiation.
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21
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Nielsen R, Mandrup S. Genome-wide profiling of transcription factor binding and epigenetic marks in adipocytes by ChIP-seq. Methods Enzymol 2014; 537:261-79. [PMID: 24480351 DOI: 10.1016/b978-0-12-411619-1.00014-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The recent advances in high-throughput sequencing combined with various other technologies have allowed detailed and genome-wide insight into the transcriptional networks that control adipogenesis. Chromatin immunoprecipitation (ChIP) combined with high-throughput sequencing (ChIP-seq) is one of the most widely used of these technologies. Using these methods, association of transcription factors, cofactors, and epigenetic marks can be mapped to DNA in a genome-wide manner. Here, we provide a detailed protocol for performing ChIP-seq analyses in preadipocytes and adipocytes. We have focused mainly on critical points, limitations of the assay, and quality controls required in order to obtain reproducible ChIP-seq data.
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Affiliation(s)
- Ronni Nielsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark.
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22
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Benedetti R, Conte M, Carafa V, Della Ventura B, Altucci C, Velotta R, Stunnenberg HG, Altucci L, Nebbioso A. Analysis of chromatin-nuclear receptor interactions by laser-chromatin immunoprecipitation. Methods Mol Biol 2014; 1204:25-34. [PMID: 25182758 DOI: 10.1007/978-1-4939-1346-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Better defining the dynamics of biomolecular interactions is an important step in understanding molecular biology and cellular processes. DNA-protein interactions, and specifically hormone-triggered DNA-nuclear receptor interactions, are key events which are still poorly understood. To date, the most commonly used approach in studying chromatin interactions is the immunoprecipitation of chemically cross-linked chromatin (ChIP) coupled with single gene or global genomic analyses. Currently, establishing a stable interplay between nucleic acids and proteins (DNA-protein cross-link) is mainly obtained through conventional, diffusion-triggered, chemical methods using formaldehyde. Here we describe an alternative method, called Laser-ChIP (LChIP), for the specific analysis of interactions between chromatin and nuclear receptors driven by a UV laser energy source. Photo-induced cross-linking in LChIP is achieved very rapidly, allowing the study of transient interactions, depending on laser source parameters.
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Affiliation(s)
- Rosaria Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale-II Università di Napoli, Via L. De Crecchio, 7, 80138, Naples, Italy
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23
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Zakaria Z, Umi S, Mokhtar S, Mokhtar U, Zaiharina M, Aziz A, Hoh B. Methodology An alternate method for DNA and RNA extraction from clotted blood. GENETICS AND MOLECULAR RESEARCH 2013; 12:302-11. [DOI: 10.4238/2013.february.4.4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Nguyen-Duc T, Peeters E, Muyldermans S, Charlier D, Hassanzadeh-Ghassabeh G. Nanobody(R)-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites. Nucleic Acids Res 2012; 41:e59. [PMID: 23275538 PMCID: PMC3597646 DOI: 10.1093/nar/gks1342] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Nanobodies® are single-domain antibody fragments derived from camelid heavy-chain antibodies. Because of their small size, straightforward production in Escherichia coli, easy tailoring, high affinity, specificity, stability and solubility, nanobodies® have been exploited in various biotechnological applications. A major challenge in the post-genomics and post-proteomics era is the identification of regulatory networks involving nucleic acid-protein and protein-protein interactions. Here, we apply a nanobody® in chromatin immunoprecipitation followed by DNA microarray hybridization (ChIP-chip) for genome-wide identification of DNA-protein interactions. The Lrp-like regulator Ss-LrpB, arguably one of the best-studied specific transcription factors of the hyperthermophilic archaeon Sulfolobus solfataricus, was chosen for this proof-of-principle nanobody®-assisted ChIP. Three distinct Ss-LrpB-specific nanobodies®, each interacting with a different epitope, were generated for ChIP. Genome-wide ChIP-chip with one of these nanobodies® identified the well-established Ss-LrpB binding sites and revealed several unknown target sequences. Furthermore, these ChIP-chip profiles revealed auxiliary operator sites in the open reading frame of Ss-lrpB. Our work introduces nanobodies® as a novel class of affinity reagents for ChIP. Taking into account the unique characteristics of nanobodies®, in particular, their short generation time, nanobody®-based ChIP is expected to further streamline ChIP-chip and ChIP-Seq experiments, especially in organisms with no (or limited) possibility of genetic manipulation.
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Affiliation(s)
- Trong Nguyen-Duc
- Research group of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussel, Belgium
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Greenberg ES, Chong KK, Huynh KT, Tanaka R, Hoon DSB. Epigenetic biomarkers in skin cancer. Cancer Lett 2012; 342:170-7. [PMID: 22289720 DOI: 10.1016/j.canlet.2012.01.020] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2011] [Revised: 01/05/2012] [Accepted: 01/15/2012] [Indexed: 02/08/2023]
Abstract
Epigenetic aberrations have been associated with cutaneous melanoma tumorigenesis and progression including dysregulated DNA gene promoter region methylation, histone modification, and microRNA. Several of these major epigenetic aberrations have been developed into biomarkers. Epigenetic biomarkers can be detected in tissue and in blood as circulating DNA in melanoma patients. There is strong evidence that biomarkers in cutaneous melanoma will have an important role as companions to therapeutics and overall patient management. Important progress has been made in epigenetic melanoma biomarker development and verification of clinical utility, and this review discusses some of the key current developments and existing challenges.
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Affiliation(s)
- Edward S Greenberg
- Department of Molecular Oncology, John Wayne Cancer Institute at Saint John's Health Center, Santa Monica, CA, USA
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