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D’Alessandro G, Morales-Juarez DA, Richards SL, Nitiss KC, Serrano-Benitez A, Wang J, Thomas JC, Gupta V, Voigt A, Belotserkovskaya R, Goh CG, Bowden AR, Galanty Y, Beli P, Nitiss JL, Zagnoli-Vieira G, Jackson SP. RAD54L2 counters TOP2-DNA adducts to promote genome stability. SCIENCE ADVANCES 2023; 9:eadl2108. [PMID: 38055822 PMCID: PMC10699776 DOI: 10.1126/sciadv.adl2108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 11/07/2023] [Indexed: 12/08/2023]
Abstract
The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anticancer agents such as etoposide operate by stabilizing TOP2ccs, ultimately generating genotoxic TOP2-DNA protein cross-links that require processing and repair. Here, we identify RAD54 like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with tyrosyl-DNA phosphodiesterase 2 (TDP2) and TOP2 (ZATT/ZNF451) and independent of TDP2. Our work suggests a model wherein RAD54L2 recognizes sumoylated TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.
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Affiliation(s)
- Giuseppina D’Alessandro
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Sean L. Richards
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Juanjuan Wang
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
| | - John C. Thomas
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Andrea Voigt
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rimma Belotserkovskaya
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Chen Gang Goh
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Anne Ramsay Bowden
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Yaron Galanty
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Petra Beli
- Institute of Molecular Biology (IMB), Chromatin Biology & Proteomics, Mainz, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
| | | | - Guido Zagnoli-Vieira
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P. Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
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Tsuchiya M, Kong W, Hiraoka Y, Haraguchi T, Ogawa H. TBK1 inhibitors enhance transfection efficiency by suppressing p62/SQSTM1 phosphorylation. Genes Cells 2023; 28:68-77. [PMID: 36284367 DOI: 10.1111/gtc.12987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/18/2022] [Accepted: 10/23/2022] [Indexed: 01/19/2023]
Abstract
DNA transfection is an essential technique in the life sciences. Non-viral transfection reagents are widely used for transfection in basic science. However, low transfection efficiency is a problem in some cell types. This low efficiency can be primarily attributed to the intracellular degradation of transfected DNA by p62-dependent selective autophagy, specifically by p62 phosphorylated at the S403 residue (p62-S403-P). To achieve efficient DNA transfection, we focused on a phosphorylation process that generates p62-S403-P and investigated whether inhibition of this process affects transfection efficiency. One of the kinases that phosphorylate p62 is TBK1. The TBK1 gene depletion in murine embryonic fibroblast cells by genome editing caused a significant reduction or loss of p62-S405-P (equivalent to human S403-P) and enhanced transfection efficiency, suggesting that TBK1 is a major kinase that phosphorylates p62 at S403. Therefore, TBK1 is a viable target for drug treatment to increase transfection efficiency. Transfection efficiency was enhanced when cells were treated with one of the following TBK1 inhibitors BX795, MRT67307, or amlexanox. This effect was synergistically improved when the two inhibitors were used in combination. Our results indicate that TBK1 inhibitors enhanced transfection efficiency by suppressing p62 phosphorylation.
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Affiliation(s)
- Megumi Tsuchiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Weixia Kong
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Yasushi Hiraoka
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Tokuko Haraguchi
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
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3
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The scaffold protein p62 regulates adaptive thermogenesis through ATF2 nuclear target activation. Nat Commun 2020; 11:2306. [PMID: 32385399 PMCID: PMC7211001 DOI: 10.1038/s41467-020-16230-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 04/16/2020] [Indexed: 12/31/2022] Open
Abstract
During β-adrenergic stimulation of brown adipose tissue (BAT), p38 phosphorylates the activating transcription factor 2 (ATF2) which then translocates to the nucleus to activate the expression of Ucp1 and Pgc-1α. The mechanisms underlying ATF2 target activation are unknown. Here we demonstrate that p62 (Sqstm1) binds to ATF2 to orchestrate activation of the Ucp1 enhancer and Pgc-1α promoter. P62Δ69-251 mice show reduced expression of Ucp1 and Pgc-1α with impaired ATF2 genomic binding. Modulation of Ucp1 and Pgc-1α expression through p62 regulation of ATF2 signaling is demonstrated in vitro and in vivo in p62Δ69-251 mice, global p62−/− and Ucp1-Cre p62flx/flx mice. BAT dysfunction resulting from p62 deficiency is manifest after birth and obesity subsequently develops despite normal food intake, intestinal nutrient absorption and locomotor activity. In summary, our data identify p62 as a master regulator of BAT function in that it controls the Ucp1 pathway through regulation of ATF2 genomic binding. Beta-adrenergic stimulation of brown adipose tissue leads to thermogenesis via the activating transcription factor 2 (ATF2) mediated expression of the thermogenic genes Ucp1 and Pgc-1α. Here, the authors show that the scaffold protein p62 regulates brown adipose tissue function through modifying ATF2 genomic binding and subsequent Ucp1 and Pgc-1α induction.
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Nishizawa M, Walinda E, Morimoto D, Sugase K. Pinpoint analysis of a protein in slow exchange using F 1F 2-selective ZZ-exchange spectroscopy: assignment and kinetic analysis. JOURNAL OF BIOMOLECULAR NMR 2020; 74:205-211. [PMID: 32236785 DOI: 10.1007/s10858-020-00309-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
ZZ-exchange spectroscopy is widely used to study slow exchange processes in biomolecules, especially determination of exchange rates and assignment of minor peaks. However, if the exchange cross peaks overlap or the populations are skewed, kinetic analysis is hindered. In order to analyze slow exchange protein dynamics under such conditions, here we have developed a new method by combining ZZ-exchange and F1F2-selective NMR spectroscopy. We demonstrate the utility of this method by examining the monomer-dimer transition of the ubiquitin-associated domain of p62, successfully assigning the minor (monomeric) peaks and obtaining the exchange rates, which cannot be achieved by ZZ-exchange alone.
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Affiliation(s)
- Mayu Nishizawa
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Erik Walinda
- Department of Molecular and Cellular Physiology, Graduate School of Medicine, Kyoto University, Sakyo-ku Yoshida Konoe-cho, Kyoto, 606-8501, Japan
| | - Daichi Morimoto
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan
| | - Kenji Sugase
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-Daigaku Katsura, Nishikyo-Ku, Kyoto, 615-8510, Japan.
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Teeli AS, Leszczyński P, Krishnaswamy N, Ogawa H, Tsuchiya M, Śmiech M, Skarzynski D, Taniguchi H. Possible Mechanisms for Maintenance and Regression of Corpus Luteum Through the Ubiquitin-Proteasome and Autophagy System Regulated by Transcriptional Factors. Front Endocrinol (Lausanne) 2019; 10:748. [PMID: 31803139 PMCID: PMC6877548 DOI: 10.3389/fendo.2019.00748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
The corpus luteum (CL) is an important tissue of the female reproductive process which is established through ovulation of the mature follicle. Pulsatile release of prostaglandin F2α from the uterus leads to the regression of luteal cells and restarts the estrous cycle in most non-primate species. The rapid functional regression of the CL, which coincides with decrease of progesterone production, is followed by its structural regression. Although we now have a better understanding of how the CL is triggered to undergo programmed cell death, the precise mechanisms governing CL protein degradation in a very short period of luteolysis remains unknown. In this context, activation of ubiquitin-proteasome pathway (UPP), unfolded protein response (UPR) and autophagy are potential subcellular mechanisms involved. The ubiquitin-proteasome pathway (UPP) maintains tissue homeostasis in the face of both internal and external stressors. The UPP also controls physiological processes in many gonadal cells. Emerging evidence suggests that UPP dysfunction is involved in male and female reproductive tract dysfunction. Autophagy is activated when cells are exposed to different types of stressors such as hypoxia, starvation, and oxidative stress. While emerging evidence points to an important role for the UPP and autophagy in the CL, the key underlying transcriptional mechanisms have not been well-documented. In this review, we propose how CL regression may be governed by the ubiquitin-proteasome and autophagy pathways. We will further consider potential transcription factors which may regulate these events in the CL.
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Affiliation(s)
- Aamir S. Teeli
- Department of Experimental Embryology, The Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Poland
| | - Paweł Leszczyński
- Department of Experimental Embryology, The Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Poland
| | | | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Megumi Tsuchiya
- Graduate School of Frontier Biosciences, Osaka University, Suita, Japan
| | - Magdalena Śmiech
- Department of Experimental Embryology, The Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Poland
| | - Dariusz Skarzynski
- Department of Reproductive Immunology and Pathology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Hiroaki Taniguchi
- Department of Experimental Embryology, The Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzebiec, Poland
- *Correspondence: Hiroaki Taniguchi
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Baba T, Otake H, Inoue M, Sato T, Ishihara Y, Moon JY, Tsuchiya M, Miyabayashi K, Ogawa H, Shima Y, Wang L, Sato R, Yamazaki T, Suyama M, Nomura M, Choi MH, Ohkawa Y, Morohashi KI. Ad4BP/SF-1 regulates cholesterol synthesis to boost the production of steroids. Commun Biol 2018; 1:18. [PMID: 30271905 PMCID: PMC6123728 DOI: 10.1038/s42003-018-0020-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 02/14/2018] [Indexed: 11/09/2022] Open
Abstract
Housekeeping metabolic pathways such as glycolysis are active in all cell types. In addition, many types of cells are equipped with cell-specific metabolic pathways. To properly perform their functions, housekeeping and cell-specific metabolic pathways must function cooperatively. However, the regulatory mechanisms that couple metabolic pathways remain largely unknown. Recently, we showed that the steroidogenic cell-specific nuclear receptor Ad4BP/SF-1, which regulates steroidogenic genes, also regulates housekeeping glycolytic genes. Here, we identify cholesterogenic genes as the targets of Ad4BP/SF-1. Further, we reveal that Ad4BP/SF-1 regulates Hummr, a candidate mediator of cholesterol transport from endoplasmic reticula to mitochondria. Given that cholesterol is the starting material for steroidogenesis and is synthesized from acetyl-CoA, which partly originates from glucose, our results suggest that multiple biological processes involved in synthesizing steroid hormones are governed by Ad4BP/SF-1. To our knowledge, this study provides the first example where housekeeping and cell-specific metabolism are coordinated at the transcriptional level.
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Affiliation(s)
- Takashi Baba
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.,Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Hiroyuki Otake
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Miki Inoue
- Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Tetsuya Sato
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Yasuhiro Ishihara
- Laboratory of Molecular Brain Science, Graduate School of Integrated Arts and Sciences, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan
| | - Ju-Yeon Moon
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Megumi Tsuchiya
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Osaka, 565-0871, Japan
| | - Kanako Miyabayashi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Hidesato Ogawa
- Nuclear Dynamics Group, Graduate School of Frontier Biosciences, Osaka University, Yamadaoka 1-3, Osaka, 565-0871, Japan
| | - Yuichi Shima
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.,Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.,Department of Anatomy, Kawasaki Medical School, 577 Matsushima, Kurashiki, 701-0192, Japan
| | - Lixiang Wang
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ryuichiro Sato
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Takeshi Yamazaki
- Laboratory of Molecular Brain Science, Graduate School of Integrated Arts and Sciences, Hiroshima University, Kagamiyama 1-7-1, Higashi-Hiroshima, 739-8521, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Masatoshi Nomura
- Department of Medicine and Bioregulatory Science, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.,Division of Endocrinology and Metabolism, Department of Internal Medicine, Kurume University School of Medicine, Asahimachi 67, Kurume, 830-0011, Japan
| | - Man Ho Choi
- Molecular Recognition Research Center, Korea Institute of Science and Technology, Seoul, 02792, Korea
| | - Yasuyuki Ohkawa
- Division of Transcritomics, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan
| | - Ken-Ichirou Morohashi
- Department of Molecular Biology, Graduate School of Medical Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan. .,Department of Systems Life Sciences, Graduate School of Systems Life Sciences, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka, 812-8582, Japan.
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Lysosomal activity maintains glycolysis and cyclin E1 expression by mediating Ad4BP/SF-1 stability for proper steroidogenic cell growth. Sci Rep 2017; 7:240. [PMID: 28325912 PMCID: PMC5428257 DOI: 10.1038/s41598-017-00393-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Accepted: 02/21/2017] [Indexed: 12/21/2022] Open
Abstract
The development and differentiation of steroidogenic organs are controlled by Ad4BP/SF-1 (adrenal 4 binding protein/steroidogenic factor 1). Besides, lysosomal activity is required for steroidogenesis and also enables adrenocortical cell to survive during stress. However, the role of lysosomal activity on steroidogenic cell growth is as yet unknown. Here, we showed that lysosomal activity maintained Ad4BP/SF-1 protein stability for proper steroidogenic cell growth. Treatment of cells with lysosomal inhibitors reduced steroidogenic cell growth in vitro. Suppression of autophagy did not affect cell growth indicating that autophagy was dispensable for steroidogenic cell growth. When lysosomal activity was inhibited, the protein stability of Ad4BP/SF-1 was reduced leading to reduced S phase entry. Interestingly, treatment of cells with lysosomal inhibitors reduced glycolytic gene expression and supplying the cells with pyruvate alleviated the growth defect. ChIP-sequence/ChIP studies indicated that Ad4BP/SF-1 binds to the upstream region of Ccne1 (cyclin E1) gene during G1/S phase. In addition, treatment of zebrafish embryo with lysosomal inhibitor reduced the levels of the interrenal (adrenal) gland markers. Thus lysosomal activity maintains steroidogenic cell growth via stabilizing Ad4BP/SF-1 protein.
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Tsuchiya M, Karim MR, Matsumoto T, Ogawa H, Taniguchi H. A Protein Preparation Method for the High-throughput Identification of Proteins Interacting with a Nuclear Cofactor Using LC-MS/MS Analysis. J Vis Exp 2017. [PMID: 28190051 DOI: 10.3791/55077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Transcriptional coregulators are vital to the efficient transcriptional regulation of nuclear chromatin structure. Coregulators play a variety of roles in regulating transcription. These include the direct interaction with transcription factors, the covalent modification of histones and other proteins, and the occasional chromatin conformation alteration. Accordingly, establishing relatively quick methods for identifying proteins that interact within this network is crucial to enhancing our understanding of the underlying regulatory mechanisms. LC-MS/MS-mediated protein binding partner identification is a validated technique used to analyze protein-protein interactions. By immunoprecipitating a previously-identified member of a protein complex with an antibody (occasionally with an antibody for a tagged protein), it is possible to identify its unknown protein interactions via mass spectrometry analysis. Here, we present a method of protein preparation for the LC-MS/MS-mediated high-throughput identification of protein interactions involving nuclear cofactors and their binding partners. This method allows for a better understanding of the transcriptional regulatory mechanisms of the targeted nuclear factors.
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Affiliation(s)
| | - M Rezaul Karim
- Department of Biotechnology and Genetic Engineering, Jahangirnagar University
| | - Taro Matsumoto
- Division of Cell Regeneration and Transplantation, School of Medicine, Nihon University
| | - Hidesato Ogawa
- Graduate School of Frontier Biosciences, Osaka University;
| | - Hiroaki Taniguchi
- Division of Cell Regeneration and Transplantation, School of Medicine, Nihon University; Institute of Genetics and Animal Breeding of the Polish Academy of Sciences; Graduate School of Life and Medical Sciences, Doshisha University;
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