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Bhandari S, Hong K, Miyawaki-Kuwakado A, Tomimatsu K, Kim YI, Nam IK, Sagerström CG, Nakamura M, Choe SK. nudt7 gene depletion causes transcriptomic change in early development of zebrafish. J Biochem 2022; 173:53-63. [PMID: 36270274 DOI: 10.1093/jb/mvac086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 09/23/2022] [Accepted: 10/20/2022] [Indexed: 12/29/2022] Open
Abstract
The Nudt family has been identified as enzymes performing Coenzyme A to 3'5'-ADP + 4'-phospho pantetheine catalysis. The members of this family have been shown to be particularly involved in lipid metabolism, while their involvement in gene regulation through regulating transcription or mRNA metabolism has also been suggested. Here, we focused on peroxisomal NUDT7, possessing enzymatic activity similar to that of its paralog, peroxisomal NUDT19, which is involved in mRNA degradation. No reports have been published about the Nudt family in zebrafish. Our transcriptomic data showed that the Nudt family members are highly expressed around zygotic gene activation (ZGA) in developing zebrafish embryos. Therefore, we confirmed the computational prediction that the products of the nudt7 gene in zebrafish were localized in the peroxisome and highly expressed in early embryogenesis. The depletion of nudt7 genes by the CRISPR/Cas9 system did not affect development; however, it decreased the rate of transcription in ZGA. In addition, H3K27ac ChIP-seq analysis demonstrated that this decrease in transcription was correlated with the genome-wide decrease of H3K27ac level. This study suggests that peroxisomal Nudt7 functions in regulating transcription in ZGA via formation of the H3K27ac domain in active chromatin.
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Key Words
- ChIP-seq.Abbreviations: (ChIP-seq), chromatin immunoprecipitation sequencing; (CRISPR), clustered regularly interspaced short palindromic repeats; (DEG), differentially expressed genes; (DHA), docosahexaenoic acid; (EGFP), enhanced green fluorescence protein; (ERK), extracellular-signal-regulated kinase; (FDR), false discovery rate; (GO), gene ontology; (H3K27ac), histone 3 acetylated at lysine 27; (hpf), hours post-fertilization; (IGV), Integrative Genome Viewer; (KO), knockout; (Nudt), Nudix; (PCA), principal component analysis; (Pex), peroxin; (PTS1), peroxisomal localization signal sequence 1; (TSS), transcription start site; (WT), wild-type; (ZGA), zygotic gene activation
- Nudt family
- RNA-seq
- zebrafish
- zygotic gene activation
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Affiliation(s)
- Sushil Bhandari
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - KwangHeum Hong
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - Atsuko Miyawaki-Kuwakado
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 8128582 Japan
| | - Kosuke Tomimatsu
- Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 8128582 Japan
| | - Yong-Il Kim
- Department of Medicine, Graduate School, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - In-Koo Nam
- Institute of Brain Science, Wonkwang University, 460 Iksadae-ro, Iksan, 54538 South Korea
| | - Charles G Sagerström
- Department of Pediatrics, University of Colorado Medical School, 13001 East 17th Place, Campus Box C290, Aurora, CO 80045, USA
| | - Mako Nakamura
- Faculty of Agriculture, Kyushu University, 744 Motooka Nishi-Ku, Fukuoka, 8190395 Japan
| | - Seong-Kyu Choe
- Department of Microbiology, Wonkwang University School of Medicine, 460 Iksadae-ro, Iksan, 54538 South Korea
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2
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Tomimatsu K, Bihary D, Olan I, Parry AJ, Schoenfelder S, Chan ASL, Slater GSC, Ito Y, Rugg-Gunn PJ, Kirschner K, Bermejo-Rodriguez C, Seko T, Kugoh H, Shiraishi K, Sayama K, Kimura H, Fraser P, Narita M, Samarajiwa SA, Narita M. Locus-specific induction of gene expression from heterochromatin loci during cellular senescence. Nat Aging 2022; 2:31-45. [PMID: 37118356 DOI: 10.1038/s43587-021-00147-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/04/2021] [Indexed: 04/30/2023]
Abstract
Senescence is a fate-determined state, accompanied by reorganization of heterochromatin. Although lineage-appropriate genes can be temporarily repressed through facultative heterochromatin, stable silencing of lineage-inappropriate genes often involves the constitutive heterochromatic mark, histone H3 lysine 9 trimethylation (H3K9me3). The fate of these heterochromatic genes during senescence is unclear. In the present study, we show that a small number of lineage-inappropriate genes, exemplified by the LCE2 skin genes, are derepressed during senescence from H3K9me3 regions in fibroblasts. DNA FISH experiments reveal that these gene loci, which are condensed at the nuclear periphery in proliferative cells, are decompacted during senescence. Decompaction of the locus is not sufficient for LCE2 expression, which requires p53 and C/EBPβ signaling. NLRP3, which is predominantly expressed in macrophages from an open topologically associated domain (TAD), is also derepressed in senescent fibroblasts due to the local disruption of the H3K9me3-rich TAD that contains it. NLRP3 has been implicated in the amplification of inflammatory cytokine signaling in senescence and aging, highlighting the functional relevance of gene induction from 'permissive' H3K9me3 regions in senescent cells.
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Affiliation(s)
- Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Shiga University of Medical Science, Shiga, Japan
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK
- VIB-KU Leuven Center for Cancer Biology, Leuven, Belgium
| | - Ioana Olan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
| | - Stefan Schoenfelder
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
| | - Adelyne S L Chan
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Guy St C Slater
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- International University of Health and Welfare, Tochigi, Japan
| | | | - Kristina Kirschner
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Institute for Cancer Sciences, University of Glasgow, Glasgow, UK
| | - Camino Bermejo-Rodriguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, UK
| | - Tomomi Seko
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Hiroyuki Kugoh
- Department of Biomedical Science, Institute of Regenerative Medicine and Biofunction, Graduate School of Medical Science, Tottori University, Yonago, Japan
- Chromosome Engineering Research Center, Tottori University, Yonago, Japan
| | - Ken Shiraishi
- Department of Dermatology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Koji Sayama
- Department of Dermatology, Graduate School of Medicine, Ehime University, Toon, Japan
| | - Hiroshi Kimura
- Tokyo Tech World Research Hub Initiative and Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Peter Fraser
- Nuclear Dynamics Programme, The Babraham Institute, Cambridge, UK
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- Tokyo Tech World Research Hub Initiative and Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan.
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3
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Hirai S, Tomimatsu K, Miyawaki-Kuwakado A, Takizawa Y, Komatsu T, Tachibana T, Fukushima Y, Takeda Y, Negishi L, Kujirai T, Koyama M, Ohkawa Y, Kurumizaka H. Unusual nucleosome formation and transcriptome influence by the histone H3mm18 variant. Nucleic Acids Res 2021; 50:72-91. [PMID: 34929737 PMCID: PMC8855299 DOI: 10.1093/nar/gkab1137] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 10/22/2021] [Accepted: 10/29/2021] [Indexed: 11/14/2022] Open
Abstract
Histone H3mm18 is a non-allelic H3 variant expressed in skeletal muscle and brain
in mice. However, its function has remained enigmatic. We found that H3mm18 is
incorporated into chromatin in cells with low efficiency, as compared to H3.3.
We determined the structures of the nucleosome core particle (NCP) containing
H3mm18 by cryo-electron microscopy, which revealed that the entry/exit DNA
regions are drastically disordered in the H3mm18 NCP. Consistently, the H3mm18
NCP is substantially unstable in vitro. The forced expression
of H3mm18 in mouse myoblast C2C12 cells markedly suppressed muscle
differentiation. A transcriptome analysis revealed that the forced expression of
H3mm18 affected the expression of multiple genes, and suppressed a group of
genes involved in muscle development. These results suggest a novel gene
expression regulation system in which the chromatin landscape is altered by the
formation of unusual nucleosomes with a histone variant, H3mm18, and provide
important insight into understanding transcription regulation by chromatin.
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Affiliation(s)
- Seiya Hirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka812-0054, Japan
| | - Atsuko Miyawaki-Kuwakado
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka812-0054, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Tetsuro Komatsu
- Institute for Molecular and Cellular Regulation, Gunma University, 3-39-15, Showa-machi, Maebashi, Gunma371-8512, Japan
| | - Taro Tachibana
- Department of Bioengineering, Graduate School of Engineering, Osaka City University, Sugimoto, Sumiyoshi-ku, Osaka558-8585, Japan
| | - Yutaro Fukushima
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Yasuko Takeda
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Masako Koyama
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi, Fukuoka812-0054, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo113-0032, Japan
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4
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Maehara K, Tomimatsu K, Harada A, Tanaka K, Sato S, Fukuoka M, Okada S, Handa T, Kurumizaka H, Saitoh N, Kimura H, Ohkawa Y. Modeling population size independent tissue epigenomes by ChIL-seq with single thin sections. Mol Syst Biol 2021; 17:e10323. [PMID: 34730297 PMCID: PMC8564819 DOI: 10.15252/msb.202110323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 11/25/2022] Open
Abstract
Recent advances in genome‐wide technologies have enabled analyses using small cell numbers of even single cells. However, obtaining tissue epigenomes with cell‐type resolution from large organs and tissues still remains challenging, especially when the available material is limited. Here, we present a ChIL‐based approach for analyzing the diverse cellular dynamics at the tissue level using high‐depth epigenomic data. “ChIL for tissues” allows the analysis of a single tissue section and can reproducibly generate epigenomic profiles from several tissue types, based on the distribution of target epigenomic states, tissue morphology, and number of cells. The proposed method enabled the independent evaluation of changes in cell populations and gene activation in cells from regenerating skeletal muscle tissues, using a statistical model of RNA polymerase II distribution on gene loci. Thus, the integrative analyses performed using ChIL can elucidate in vivo cell‐type dynamics of tissues.
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Affiliation(s)
- Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kaori Tanaka
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Shoko Sato
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Megumi Fukuoka
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Seiji Okada
- Division of Pathophysiology, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Noriko Saitoh
- Division of Cancer Biology, The Cancer Institute of Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Hiroshi Kimura
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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5
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Miyawaki-Kuwakado A, Wu Q, Harada A, Tomimatsu K, Fujii T, Maehara K, Ohkawa Y. Transcriptome analysis of gene expression changes upon enzymatic dissociation in skeletal myoblasts. Genes Cells 2021; 26:530-540. [PMID: 33987903 DOI: 10.1111/gtc.12870] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 04/30/2021] [Accepted: 05/07/2021] [Indexed: 11/28/2022]
Abstract
Single-cell RNA-sequencing analysis is one of the most effective tools for understanding specific cellular states. The use of single cells or pooled cells in RNA-seq analysis requires the isolation of cells from a tissue or culture. Although trypsin or more recently cold-active protease (CAP) has been used for cell dissociation, the extent to which the gene expression changes are suppressed has not been clarified. To this end, we conducted detailed profiling of the enzyme-dependent gene expression changes in mouse skeletal muscle progenitor cells, focusing on the enzyme treatment time, amount and temperature. We found that the genes whose expression was changed by the enzyme treatment could be classified in a time-dependent manner and that there were genes whose expression was changed independently of the enzyme treatment time, amount and temperature. This study will be useful as reference data for genes that should be excluded or considered for RNA-seq analysis using enzyme isolation methods.
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Affiliation(s)
- Atsuko Miyawaki-Kuwakado
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Qianmei Wu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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6
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Elgaabari A, Miyawaki-Kuwakado A, Tomimatsu K, Wu Q, Tokunaga K, Izumi W, Suzuki T, Tatsumi R, Nakamura M. Epigenetic effects induced by the ectopic expression of Pax7 in 3T3-L1. J Biochem 2021; 170:107-117. [PMID: 33729538 DOI: 10.1093/jb/mvab030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 03/07/2021] [Indexed: 11/14/2022] Open
Abstract
Although skeletal muscle cells and adipocytes are derived from the same mesoderm, they do not transdifferentiate in vivo and are strictly distinct at the level of gene expression. To elucidate some of the regulatory mechanisms underlying this strict distinction, Pax7, a myogenic factor, was ectopically expressed in 3T3-L1 adipose progenitor cells to perturb their adipocyte differentiation potential. Transcriptome analysis showed that ectopic expression of Pax7 repressed the expression of some adipocyte genes and induced expression of some skeletal muscle cell genes. We next profiled the epigenomic state altered by Pax7 expression using H3K27ac, an activating histone mark, and H3K27me3, a repressive histone mark, as indicators. Our results show that ectopic expression of Pax7 did not result in the formation of H3K27ac at loci of skeletal muscle-related genes, but instead resulted in the formation of H3K27me3 at adipocyte-related gene loci. These findings suggest that the primary function of ectopic Pax7 expression is the formation of H3K27me3, and muscle gene expression results from secondary regulation.
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Affiliation(s)
- Alaa Elgaabari
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura.,Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, 812-8582, Japan
| | - Atsuko Miyawaki-Kuwakado
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kosuke Tomimatsu
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Qianmei Wu
- Department of Bioresource Sciences, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, 819-0395, Japan
| | - Kosuke Tokunaga
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Wakana Izumi
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Takahiro Suzuki
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Ryuichi Tatsumi
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
| | - Mako Nakamura
- Alaa Elgaabari, Atsuko Miyawaki-Kuwakado, Kosuke Tomimatsu, Qianmei Wu, Kosuke Tokunaga, Wakana Izumi, Takahiro Suzuki, Ryuichi Tatsumi, Mako Nakamura
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7
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Wu Q, Fujii T, Harada A, Tomimatsu K, Miyawaki-Kuwakado A, Fujita M, Maehara K, Ohkawa Y. Genome-wide analysis of chromatin structure changes upon MyoD binding in proliferative myoblasts during the cell cycle. J Biochem 2021; 169:653-661. [PMID: 33479729 DOI: 10.1093/jb/mvab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/24/2020] [Indexed: 11/13/2022] Open
Abstract
MyoD, a myogenic differentiation protein, has been studied for its critical role in skeletal muscle differentiation. MyoD-expressing myoblasts have a potency to be differentiated with proliferation of ectopic cells. However, little is known about the effect on chromatin structure of MyoD binding in proliferative myoblasts. In this study, we evaluated the chromatin structure around MyoD-bound genome regions during the cell cycle by chromatin immunoprecipitation sequencing. Genome-wide analysis of histone modifications was performed in proliferative mouse C2C12 myoblasts during three phases (G1, S, G2/M) of the cell cycle. We found that MyoD-bound genome regions had elevated levels of active histone modifications, such as H3K4me1/2/3, and H3K27ac, compared with MyoD-unbound genome regions during the cell cycle. We also demonstrated that the elevated H3K4me2/3 modification level was maintained during the cell cycle, whereas the H3K27ac and H3K4me1 modification levels decreased to the same level as MyoD-unbound genome regions during the later phases. Immunoblot analysis revealed that MyoD abundance was high in the G1 phase then decreased in the S and G2/M phases. Our results suggest that MyoD binding formed selective epigenetic memories with H3K4me2/3 during the cell cycle in addition to myogenic gene induction via active chromatin formation coupled with transcription.
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Affiliation(s)
- Qianmei Wu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Takeru Fujii
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan.,Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Akihito Harada
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Kosuke Tomimatsu
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Atsuko Miyawaki-Kuwakado
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Masatoshi Fujita
- Department of Cellular Biochemistry, Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan
| | - Kazumitsu Maehara
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
| | - Yasuyuki Ohkawa
- Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka, 812-0054, Japan
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8
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Nagasawa M, Tomimatsu K, Terada K, Kondo K, Miyazaki K, Miyazaki M, Motooka D, Okuzaki D, Yoshida T, Kageyama S, Kawamoto H, Kawauchi A, Agata Y. Long non-coding RNA MANCR is a target of BET bromodomain protein BRD4 and plays a critical role in cellular migration and invasion abilities of prostate cancer. Biochem Biophys Res Commun 2020; 526:128-134. [PMID: 32199616 DOI: 10.1016/j.bbrc.2020.03.043] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 03/09/2020] [Indexed: 01/03/2023]
Abstract
Androgen receptor (AR)-negative castration-resistant prostate cancer (CRPC) is highly aggressive and is resistant to most of the current therapies. Bromodomain and extra terminal domain (BET) protein BRD4 binds to super-enhancers (SEs) that drive high expression of oncogenes in many cancers. A BET inhibitor, JQ1, has been found to suppress the malignant phenotypes of prostate cancer cells, however, the target genes of JQ1 remain largely unknown. Here we show that SE-associated genes specific for AR-negative CRPC PC3 cells include genes involved in migration and invasion, and that JQ1 impairs migration and invasion of PC3 cells. We identified a long non-coding RNA, MANCR, which was markedly down-regulated by JQ1, and found that BRD4 binds to the MANCR locus. MANCR knockdown led to a significant decrease in migration and invasion of PC3 cells. Furthermore, RNA sequencing analysis revealed that expression of the genes involved in migration and invasion was altered by MANCR knockdown. In summary, our data demonstrate that MANCR plays a critical role in migration and invasion of PC3 cells.
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Affiliation(s)
- Masayuki Nagasawa
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan; Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Kosuke Tomimatsu
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Koji Terada
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Kenta Kondo
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan
| | - Kazuko Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Masaki Miyazaki
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Okuzaki
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Yoshida
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Susumu Kageyama
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Hiroshi Kawamoto
- Laboratory of Immunology, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan
| | - Akihiro Kawauchi
- Department of Urology, Shiga University of Medical Science, Shiga, Japan
| | - Yasutoshi Agata
- Department of Biochemistry and Molecular Biology, Shiga University of Medical Science, Shiga, Japan.
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9
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Parry AJ, Hoare M, Bihary D, Hänsel-Hertsch R, Smith S, Tomimatsu K, Mannion E, Smith A, D'Santos P, Russell IA, Balasubramanian S, Kimura H, Samarajiwa SA, Narita M. NOTCH-mediated non-cell autonomous regulation of chromatin structure during senescence. Nat Commun 2018; 9:1840. [PMID: 29743479 PMCID: PMC5943456 DOI: 10.1038/s41467-018-04283-9] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Senescent cells interact with the surrounding microenvironment achieving diverse functional outcomes. We have recently identified that NOTCH1 can drive 'lateral induction' of a unique senescence phenotype in adjacent cells by specifically upregulating the NOTCH ligand JAG1. Here we show that NOTCH signalling can modulate chromatin structure autonomously and non-autonomously. In addition to senescence-associated heterochromatic foci (SAHF), oncogenic RAS-induced senescent (RIS) cells exhibit a massive increase in chromatin accessibility. NOTCH signalling suppresses SAHF and increased chromatin accessibility in this context. Strikingly, NOTCH-induced senescent cells, or cancer cells with high JAG1 expression, drive similar chromatin architectural changes in adjacent cells through cell-cell contact. Mechanistically, we show that NOTCH signalling represses the chromatin architectural protein HMGA1, an association found in multiple human cancers. Thus, HMGA1 is involved not only in SAHFs but also in RIS-driven chromatin accessibility. In conclusion, this study identifies that the JAG1-NOTCH-HMGA1 axis mediates the juxtacrine regulation of chromatin architecture.
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Affiliation(s)
- Aled J Parry
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Matthew Hoare
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Dóra Bihary
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Robert Hänsel-Hertsch
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Stephen Smith
- Department of Pathology, Addenbrooke's Hospital, University of Cambridge, Cambridge, CB2 0QQ, UK
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Elizabeth Mannion
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Amy Smith
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paula D'Santos
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - I Alasdair Russell
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Hiroshi Kimura
- Cell Biology Centre, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, 226-8503, Japan
| | - Shamith A Samarajiwa
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Robinson Way, Cambridge, CB2 0RE, UK.
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10
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Tomimatsu K, Kokura K, Nishida T, Yoshimura Y, Kazuki Y, Narita M, Oshimura M, Ohbayashi T. Multiple expression cassette exchange via TP901-1, R4, and Bxb1 integrase systems on a mouse artificial chromosome. FEBS Open Bio 2017; 7:306-317. [PMID: 28286726 PMCID: PMC5337897 DOI: 10.1002/2211-5463.12169] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 11/17/2016] [Accepted: 11/24/2016] [Indexed: 01/21/2023] Open
Abstract
The site-specific excision of a target DNA sequence for genetic knockout or lineage tracing is a powerful tool for investigating biological systems. Currently, site-specific recombinases (SSRs), such as Cre or Flp recombination target cassettes, have been successfully excised or inverted by a single SSR to regulate transgene expression. However, the use of a single SSR might restrict the complex control of gene expression. This study investigated the potential for expanding the multiple regulation of transgenes using three different integrase systems (TP901-1, R4, and Bxb1). We designed three excision cassettes that expressed luciferase, where the luciferase expression could be exchanged to a fluorescent protein by site-specific recombination. Individual cassettes that could be regulated independently by a different integrase were connected in tandem and inserted into a mouse artificial chromosome (MAC) vector in Chinese hamster ovary cells. The transient expression of an integrase caused the targeted luciferase activity to be lost and fluorescence was activated. Additionally, the integrase system enabled the specific excision of targeted DNA sequences without cross-reaction with the other recombination targets. These results suggest that the combined use of these integrase systems in a defined locus on a MAC vector permits the multiple regulation of transgene expression and might contribute to genomic or cell engineering.
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Affiliation(s)
- Kosuke Tomimatsu
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
- Japan Society for the Promotion of ScienceTokyoJapan
| | - Kenji Kokura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Division of Human Genome ScienceDepartment of Molecular and Cellular BiologySchool of Life SciencesFaculty of MedicineTottori UniversityYonagoJapan
| | - Tadashi Nishida
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
| | - Yuki Yoshimura
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
- Central Institute for Experimental AnimalsKawasakiJapan
| | - Yasuhiro Kazuki
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Masashi Narita
- Cancer Research UK Cambridge InstituteLi Ka Shing CentreUniversity of CambridgeUK
| | - Mitsuo Oshimura
- Chromosome Engineering Research CenterTottori UniversityYonagoJapan
- Department of Biomedical ScienceInstitute of Regenerative Medicine and BiofunctionGraduate School of Medical SciencesTottori UniversityYonagoJapan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and TechnologyTottori UniversityYonagoJapan
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11
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Hoare M, Ito Y, Kang TW, Weekes MP, Matheson NJ, Patten DA, Shetty S, Parry AJ, Menon S, Salama R, Antrobus R, Tomimatsu K, Howat W, Lehner PJ, Zender L, Narita M. NOTCH1 mediates a switch between two distinct secretomes during senescence. Nat Cell Biol 2016; 18:979-92. [PMID: 27525720 PMCID: PMC5008465 DOI: 10.1038/ncb3397] [Citation(s) in RCA: 303] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 07/12/2016] [Indexed: 12/15/2022]
Abstract
Senescence, a persistent form of cell-cycle arrest, is often associated with a diverse secretome, which provides complex functionality for senescent cells within the tissue microenvironment. We show that oncogene-induced senescence is accompanied by a dynamic fluctuation of NOTCH1 activity, which drives a TGF-β-rich secretome, while suppressing the senescence-associated pro-inflammatory secretome through inhibition of C/EBPβ. NOTCH1 and NOTCH1-driven TGF-β contribute to 'lateral induction of senescence' through a juxtacrine NOTCH-JAG1 pathway. In addition, NOTCH1 inhibition during senescence facilitates upregulation of pro-inflammatory cytokines, promoting lymphocyte recruitment and senescence surveillance in vivo. As enforced activation of NOTCH1 signalling confers a near mutually exclusive secretory profile compared with typical senescence, our data collectively indicate that the dynamic alteration of NOTCH1 activity during senescence dictates a functional balance between these two distinct secretomes: one representing TGF-β and the other pro-inflammatory cytokines, highlighting that NOTCH1 is a temporospatial controller of secretome composition.
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Affiliation(s)
- Matthew Hoare
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
| | - Yoko Ito
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Tae-Won Kang
- Division of Translational Gastrointestinal Oncology, Dept. of Internal Medicine I, University Hospital Tuebingen, Otfried-Mueller-Strasse 12, 72076 Tuebingen, Germany & Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Michael P. Weekes
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Nicholas J. Matheson
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Daniel A. Patten
- National Institute of Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), Centre for Liver Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Shishir Shetty
- National Institute of Health Research (NIHR) Birmingham Liver Biomedical Research Unit (BRU), Centre for Liver Research, University of Birmingham, Birmingham, B15 2TT, UK
| | - Aled J. Parry
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Suraj Menon
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Rafik Salama
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Robin Antrobus
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Kosuke Tomimatsu
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - William Howat
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Paul J. Lehner
- University of Cambridge, Department of Medicine, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
- University of Cambridge, Cambridge Institute for Medical Research, Addenbrooke's Hospital, Cambridge, CB2 0XY, UK
| | - Lars Zender
- Division of Translational Gastrointestinal Oncology, Dept. of Internal Medicine I, University Hospital Tuebingen, Otfried-Mueller-Strasse 12, 72076 Tuebingen, Germany & Translational Gastrointestinal Oncology Group within the German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Masashi Narita
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
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12
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Abstract
Cellular senescence is often accompanied by the production of secreted proteins that mediate the diverse effects of senescence on the tissue microenvironment. The mammalian target of rapamycin (mTOR), a master regulator of protein synthesis, is now shown to control the senescence-associated secretory phenotype by modulating gene transcription and mRNA translation and stabilization.
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Affiliation(s)
- Kosuke Tomimatsu
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
| | - Masashi Narita
- University of Cambridge, Cancer Research UK Cambridge Institute, Robinson Way, Cambridge, CB2 0RE, UK
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13
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Kirschner K, Samarajiwa SA, Cairns JM, Menon S, Pérez-Mancera PA, Tomimatsu K, Bermejo-Rodriguez C, Ito Y, Chandra T, Narita M, Lyons SK, Lynch AG, Kimura H, Ohbayashi T, Tavaré S, Narita M. Phenotype specific analyses reveal distinct regulatory mechanism for chronically activated p53. PLoS Genet 2015; 11:e1005053. [PMID: 25790137 PMCID: PMC4366240 DOI: 10.1371/journal.pgen.1005053] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 02/02/2015] [Indexed: 01/15/2023] Open
Abstract
The downstream functions of the DNA binding tumor suppressor p53 vary depending on the cellular context, and persistent p53 activation has recently been implicated in tumor suppression and senescence. However, genome-wide information about p53-target gene regulation has been derived mostly from acute genotoxic conditions. Using ChIP-seq and expression data, we have found distinct p53 binding profiles between acutely activated (through DNA damage) and chronically activated (in senescent or pro-apoptotic conditions) p53. Compared to the classical 'acute' p53 binding profile, 'chronic' p53 peaks were closely associated with CpG-islands. Furthermore, the chronic CpG-island binding of p53 conferred distinct expression patterns between senescent and pro-apoptotic conditions. Using the p53 targets seen in the chronic conditions together with external high-throughput datasets, we have built p53 networks that revealed extensive self-regulatory 'p53 hubs' where p53 and many p53 targets can physically interact with each other. Integrating these results with public clinical datasets identified the cancer-associated lipogenic enzyme, SCD, which we found to be directly repressed by p53 through the CpG-island promoter, providing a mechanistic link between p53 and the 'lipogenic phenotype', a hallmark of cancer. Our data reveal distinct phenotype associations of chronic p53 targets that underlie specific gene regulatory mechanisms.
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Affiliation(s)
- Kristina Kirschner
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Shamith A. Samarajiwa
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Jonathan M. Cairns
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Suraj Menon
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Pedro A. Pérez-Mancera
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Camino Bermejo-Rodriguez
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Yoko Ito
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Tamir Chandra
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masako Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Scott K. Lyons
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Andy G. Lynch
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan
| | - Tetsuya Ohbayashi
- Research Center for Bioscience and Technology, Tottori University, Yonago, Japan
| | - Simon Tavaré
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, United Kingdom
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14
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Jung YS, Matsumoto SE, Yamashita M, Tomimatsu K, Teruya K, Katakura Y, Shirahata S. Propionibacterium AcnesActs as an Adjuvant inin VitroImmunization of Human Peripheral Blood Mononuclear Cells. Biosci Biotechnol Biochem 2014; 71:1963-9. [PMID: 17690460 DOI: 10.1271/bbb.70159] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We have established an in vitro immunization protocol whereby human peripheral blood mononuclear cells (PBMCs) are initially treated with L-leucyl-L-leucine methyl ester (LLME) and subsequently sensitized with antigen in the presence of interleukin (IL)-2, IL-4, and adjuvant. This protocol resulted in the production of antigen-specific antibodies. PBMCs are potentiated to react with exogenous antigens upon treatment with LLME. We are using this system to investigate the immunomodulatory activity of additives. In the present study, we aimed to evaluate the immunomodulatory activity of Propionibacterium acnes (P. acnes), which is known to exhibit various immunomodulatory effects in murine models, using this in vitro immunization protocol. P. acnes was found to augment the production of antigen-specific antibodies by PBMC, possibly through increased production of inflammatory cytokines and/or increased T-B cell interaction. P. acnes hence appears to act as an adjuvant in the antibody response in in vitro immunization.
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Affiliation(s)
- Yeon Suk Jung
- Department of Genetic Resources Technology, Faculty of Agriculture, Kyushu University, Hakozaki, Fukuoka, Japan
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15
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Abstract
Human monoclonal antibody has great potential for treatment of various diseases utilizing their specificity against antigens. We have shown an in vitro immunization (IVI) protocol inducing antigen-specific immune responses in human peripheral blood mononuclear cells (PBMCs) for efficient production of human monoclonal antibodies. By using IVI method antigen specific antibody genes can be efficiently obtained because of increasing production of antigen-specific antibodies from in vitro immunized PBMCs. This IVI protocol will be widely applied for combination with several display methods and enhance the production of human monoclonal antibodies.
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Affiliation(s)
- Kosuke Tomimatsu
- Faculty of Agriculture, Department of Bioscience and Biotechnology, Kyushu University, Fukuoka, Japan
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16
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Tomimatsu K, Matsumoto SE, Tanaka H, Yamashita M, Nakanishi H, Teruya K, Kazuno S, Kinjo T, Hamasaki T, Kusumoto KI, Kabayama S, Katakura Y, Shirahata S. A rapid screening and production method using a novel mammalian cell display to isolate human monoclonal antibodies. Biochem Biophys Res Commun 2013; 441:59-64. [DOI: 10.1016/j.bbrc.2013.10.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Accepted: 10/04/2013] [Indexed: 11/29/2022]
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17
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Sadaie M, Salama R, Carroll T, Tomimatsu K, Chandra T, Young AR, Narita M, Pérez-Mancera PA, Bennett DC, Chong H, Kimura H, Narita M. Redistribution of the Lamin B1 genomic binding profile affects rearrangement of heterochromatic domains and SAHF formation during senescence. Genes Dev 2013; 27:1800-8. [PMID: 23964094 PMCID: PMC3759696 DOI: 10.1101/gad.217281.113] [Citation(s) in RCA: 205] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 07/22/2013] [Indexed: 12/14/2022]
Abstract
Senescence is a stress-responsive form of stable cell cycle exit. Senescent cells have a distinct gene expression profile, which is often accompanied by the spatial redistribution of heterochromatin into senescence-associated heterochromatic foci (SAHFs). Studying a key component of the nuclear lamina lamin B1 (LMNB1), we report dynamic alterations in its genomic profile and their implications for SAHF formation and gene regulation during senescence. Genome-wide mapping reveals that LMNB1 is depleted during senescence, preferentially from the central regions of lamina-associated domains (LADs), which are enriched for Lys9 trimethylation on histone H3 (H3K9me3). LMNB1 knockdown facilitates the spatial relocalization of perinuclear H3K9me3-positive heterochromatin, thus promoting SAHF formation, which could be inhibited by ectopic LMNB1 expression. Furthermore, despite the global reduction in LMNB1 protein levels, LMNB1 binding increases during senescence in a small subset of gene-rich regions where H3K27me3 also increases and gene expression becomes repressed. These results suggest that LMNB1 may contribute to senescence in at least two ways due to its uneven genome-wide redistribution: first, through the spatial reorganization of chromatin and, second, through gene repression.
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Affiliation(s)
- Mahito Sadaie
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Rafik Salama
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Thomas Carroll
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Kosuke Tomimatsu
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
- Research Centre for Bioscience and Technology, Tottori University, Tottori 683-8503, Japan
| | - Tamir Chandra
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Andrew R.J. Young
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Masako Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Pedro A. Pérez-Mancera
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Dorothy C. Bennett
- Biomedical Sciences Research Centre, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Heung Chong
- Cellular Pathology, Division of Biomedical Sciences, St. George's, University of London, London SW17 0RE, United Kingdom
| | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Osaka 565-0871, Japan
| | - Masashi Narita
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge CB2 0RE, United Kingdom
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18
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Matsumoto SE, Yamashita M, Katakura Y, Aiba Y, Tomimatsu K, Kabayama S, Teruya K, Shirahata S. A rapid and efficient strategy to generate antigen-specific human monoclonal antibody by in vitro immunization and the phage display method. J Immunol Methods 2008; 332:2-9. [DOI: 10.1016/j.jim.2007.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2007] [Revised: 11/30/2007] [Accepted: 12/05/2007] [Indexed: 11/30/2022]
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19
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Yoshimura Y, Tomimatsu K, Nishimura T, Miyake A, Hashimoto N. Studies on condensed-heterocyclic azolium cephalosporins. V. Synthesis and antibacterial activity of 3-(condensed-triazolo-pyridinium, -pyrimidinium, and -pyridazinium)-methyl cephalosporins. J Antibiot (Tokyo) 1992; 45:721-34. [PMID: 1624374 DOI: 10.7164/antibiotics.45.721] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
As a part of our studies on cephalosporins bearing condensed-heterocyclic azolium methyl groups at the 3 position in the cephalosporin nucleus, we describe here the synthesis and antibacterial activity of 7 beta-[2-(2-aminothiazol-4-yl)2(Z)-methoxyiminoacetamido] cephalosporins (1-16, 7 beta-[2-(2-amino-5-chlorothiazol-4-yl)-2(Z)- methoxyiminoacetamido] cephalosporins (17,18) and 7 beta-[2-(5-amino- 1,2,4-thiadiazol-3-yl)-2(Z)-methoxyiminoacetamido) cephalosporins (19-23) containing a variety of condensed-heterocyclic triazolium methyl groups at the 3 position in the cephalosporin nucleus. These cephalosporins exhibited potent antibacterial activity, and it appears that condensed-heterocyclic triazolium as well as condensed-heterocyclic imidazolium rings are effective moieties for improving antibacterial activity and the spectrum of activity. Among the cephalosporins tested, 7 beta-[2-(2-aminothiazol-4-yl)-2(Z)-methoxyiminoacetamido]-3-(5- methyl[1,2,3]triazolo-[1,5-alpha]pyridinium-1-yl)methyl-3-cephem-4- carboxylate (9) and 7 beta-[2-(2-aminothiazol-4-yl)-2(Z)-methoxyiminoacetamido]-3-(6- methoxy[1,2,4]triazolo[1,5-alpha]pyridinium-1-yl)methyl-3-cephem-4- carboxylate (11) showed good antibacterial activity.
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Affiliation(s)
- Y Yoshimura
- Chemistry Research Laboratory, Takeda Chemical Industries, Ltd., Osaka, Japan
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20
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Ito H, Tomimatsu K. [Proceedings: Weight loading and speed in mountain climbing]. Nihon Seirigaku Zasshi 1974; 36:408. [PMID: 4478638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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21
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Maekawa K, Fukuda Y, Tomimatsu K. [Interaction between estrogen and progestogen in a vaginal smear of ovariectomized and partially hepatectomized rats]. Zasshi Tokyo Ika Daigaku 1969; 27:69-75. [PMID: 5816200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
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22
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Maekawa K, Fukuda Y, Tomimatsu K. [Effects of respiration-stimulatory substances on branchial and intestinal respiration of the loach, Misgurnus anguillicaudatus]. Zasshi Tokyo Ika Daigaku 1967; 25:737-40. [PMID: 5625997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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