Publications

  1. HOME
  2. Publications

2024

  1. Sasa K, Son R, Oguchi A, Ashizawa K, Hasegawa N, Kubota D, Suehara Y, Takagi T, Okubo T, Akaike K, Sugimoto K,Takahashi M, Sakamoto K, Hashimoto T, Mine S, Fukunaga T, Ishijima M, Hayashi T, Yao T, Murakawa Y, Saito T. NTRK2expression in gastrointestinal stromal tumors with a special emphasis on the clinicopathological and prognostic impacts. Scientific Reports. 8;14(1):768 (2024)

2023

  1. Son R, Yamazawa K, Oguchi A, Suga M, Tamura M, Yanagita M, Murakawa Y, Kume S, Morphomics via Next-generation Electron Microscopy. Journal of Molecular Cell Biology. mjad081 (2023)
  2. Uehata T, Yamada S, Ori D, Vandenbon A, Giladi A, Jelinski A, Murakawa Y, Watanabe H, Takeuchi K, Toratani K, Mino T, Kiryu H, Standley DM, Tsujimura T, IkawaT, Kondoh G, Landthaler M, Kawamoto H, Rodewald HR, Amit I, Yamamoto R, Miyazaki M, Takeuchi O. Regulation of lymphoid-myeloid lineage bias through Regnase-1/3-mediated control of Nfkbiz. Blood. 18;143(3):243-257 (2023)
  3. Yoshikawa T, Oguchi A, Toriu N, Sato Y, Kobayashi T, Ogawa O, Haga H, Sakurai S, Yamamoto T, Murakawa Y, Yanagita M. Tertiary Lymphoid Tissues Are Microenvironments with Intensive Interactions between Immune Cells and Proinflammatory Parenchymal Cells in Aged Kidneys. Journal of the American Society of Nephrology. 1;34(10):1687-1708 (2023)
  4. Kitao M, Hayashi R, Nomi K, Kobayashi R, Katayama T, Takayanagi H, Oguchi A, Murakawa Y, Nishida K. Identification of BST2 as a conjunctival epithelial stem/progenitor cell marker. iScience. 5;26(7):107016 (2023)
  5. Kojima S, Koyama S, Ka M, Saito Y, Parrish EH, Endo M, Takata S, Mizukoshi M, Hikino K, Takeda A, Gelinas AF, HeatonSM, Koide R, Kamada AJ, Noguchi M, Hamada M; Biobank Japan Project Consortium; Kamatani Y, Murakawa Y, Ishigaki K,Nakamura Y, Ito K, Terao C, Momozawa Y, Parrish NF. Mobile element variation contributes to population-specific genomediversification, gene regulation and disease risk. Nature Genetics. 55(6):939-951 (2023)
  6. Koido M, Hon CC, Koyama S, Kawaji H, Murakawa Y, Ishigaki K, Ito K, Sese J, Parrish NF, Kamatani Y, Carninci P, Terao C, Prediction of the cell-type-specific transcription of non-coding RNAs from genome sequences via machine learning. Nature Biomedical Engineering. 7(6):830-844 (2023)
  7. Sakurada-Aono M, Sakamoto T, Kobayashi M, Takiuchi Y, Iwai F, Tada K, Sasanuma H, Hirabayashi S, Murakawa Y, Shirakawa K, Sakamoto C, Shindo K, Yasunaga JI, Matsuoka M, Pommier Y, Takeda S, Takaori-Kondo A. HTLV-1 bZIP factorimpairs DNA mismatch repair system. Biochemical and Biophysical Research Communications. 21;657:43-49 (2023)
  8. Gawriyski L, Jouhilahti EM, Yoshihara M, Fei L, Weltner J, Airenne TT, Trokovic R, Bhagat S, Tervaniemi MH, Murakawa Y, Salokas K, Liu X, Miettinen S, Bürglin TR, Sahu B, Otonkoski T, Johnson MS, Katayama S, Varjosalo M, Kere J. Comprehensive characterization of the embryonic factor LEUTX. iScience. 9;26(3):106172 (2023)
  9. Najnin RA, Al Mahmud MR, Rahman MM, Takeda S, Sasanuma H, Tanaka H, Murakawa Y, Shimizu N, Akter S, Takagi M, Sunada T, Akamatsu S, He G, Itou J, Toi M, Miyaji M, Tsutsui KM, Keeney S, Yamada S. ATM suppresses c-Myc overexpression in the mammary epithelium in response to estrogen. Cell Reports. 42(1):111909 (2023)

2022

  1. Kunishima N, Takeda Y, Hirose R, Kume S, Maeda M, Oguchi A, Yanagita M, Shibuya H, Tamura M, Kataoka Y, Murakawa Y, Ito K, Omote K. Compact Laboratory- Based X-ray Microscope Enabling Nondestructive 3D Structure Acquisition of Mouse Nephron with High Speed and Better User Accessibility. Microscopy - Oxford Academic. 71(6):315-323 (2022)
  2. Kageyama Y, Nakamura M, Igari Y, Yamaguchi S, Oguchi A, Murakawa Y, Hattori Y, Sasano Y. Expression of matrix metalloproteinase-3 and -10 is up-regulated in the periodontal tissues of aged mice. Journal of Periodontal Research. 57(4):733-741 (2022)
  3. Nakagawa R, Takasawa K, Gau M, Tsuji-Hosokawa A, Kawaji H, Murakawa Y, Takada S, Mikami M, Narumi S, Fukami M, Sreenivasan R, Maruyama T, Tucker EJ, Zhao L, Bowles J, Sinclair A, Koopman P, Hayashizaki Y, Morio T, Kashimada K. Two ovarian candidate enhancers, identified by time series enhancer RNA analyses, harbor rare genetic variations identified in ovarian insufficiency. Human Molecular Genetics. 31(13):2223-2235 (2022)
  4. Nagano M, Hu B, Yokobayashi S, Yamamura A, Umemura F, Coradin M, Ohta H, Yabuta Y, Ishikura Y, Okamoto I, Ikeda H, Kawahira N, Nosaka Y, Shimizu S, Kojima Y, Mizuta K, Kasahara T, Imoto Y, Meehan K, Stocsits R, Wutz G, Hiraoka Y, Murakawa Y, Yamamoto T, Tachibana K, Peters JM, Mirny LA, Garcia BA, Majewski J, Saitou M. Nucleome programming is required for the foundation of totipotency in mammalian germline development. The EMBO Journal. 41(13): e110600 (2022)
  5. Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience. 25(4):104137 (2022)
  6. Shiraki N, Maruyama K, Hayashi R, Oguchi A, Murakawa Y, Katayama T, Takigawa T, Sakimoto S, Quantock AJ, Tsujikawa M, Nishida K. PAX6-positive microglia evolve locally in hiPSC-derived ocular organoids. Stem Cell Report. 17(2):221-230 (2022)
  7. Sato Y, Oguchi A, Fukushima Y, Masuda K, Toriu N, Taniguchi K, Yoshikawa T, Cui X, Kondo M, Hosoi T, Komidori S, Shimizu Y, Fujita H, Jiang L, Kong Y, Yamanashi T, Seita J, Yamamoto T, Toyokuni S, Hamazaki Y, Hattori M, Yoshikai Y, Boor P, Floege J, Kawamoto H, Murakawa Y, Minato N, Yanagita M. CD153/CD30 signaling promotes age-dependent tertiary lymphoid tissue expansion and kidney injury. The Journal of Clinical Investigation. 132(2):e146071 (2022)
  8. Guerrini MM, Oguchi A, Suzuki A, Murakawa Y. Cap analysis of gene expression (CAGE) and noncoding regulatory elements. Seminars in Immunopathology. 44(1):127-136 (2022)

2021

  1. Jayakumar V, Nishimura O, Kadota M, Hirose N, Sano H, Murakawa Y, Yamamoto Y, Nakaya M, Tsukiyama T, Seita Y, Nakamura S, Kawai J, Sasaki E, Ema M, Kuraku S, Kawaji H, Sakakibara Y. Chromosomal-scale de novo genome assemblies of Cynomolgus Macaque and Common Marmoset. Scientific Data. 8, 159 (2021)
  2. Konishi Y, Ichise H, Watabe T, Oki C, Tsukiji S, Hamazaki Y, Murakawa Y, Takaori-Kondo A, Terai K, Matsuda M. Intravital Imaging Identifies the VEGF-TXA2 Axis as a Critical Promoter of PGE2 Secretion from Tumor Cells and Immune Evasion. Cancer Research 81, 4124-4132 (2021)
  3. Matsui H, Shirakawa K, Konishi Y, Hirabayashi S, Sarca AD, Fukuda H, Nomura R, Stanford E, Horisawa Y, Kazuma Y, Matsumoto T, Yamazaki H, Murakawa Y, Battivelli E, Verdin E, Koyanagi Y, Takaori-Kondo A. CAGE-seq reveals that HIV-1 latent infection does not trigger unique cellular responses in a Jurkat T cell model. Journal of Virology 02394-20 (2021)
  4. Sasaki K, Oguchi A, Cheng K, Murakawa Y, Okamoto I, Ohta H, Yabuta Y, Iwatani C, Tsuchiya H, Yamamoto T, Seita Y, Saitou M. The embryonic ontogeny of the gonadal somatic cells in mice and monkeys. Cell Reports 35, 109075 (2021)
  5. Yamamura Y, Furuichi K, Murakawa Y, Hirabayashi S, Yoshihara M, Sako K, Kitajima S, Toyama T, Iwata Y, Sakai N, Hosomichi K, Murphy PM, Tajima A, Okita K, Osafune K, Kaneko S, Wada T. Identification of candidate PAX2-regulated genes implicated in human kidney development. Scientific Reports 11, 9123 (2021)
  6. Hirabayashi S, Shirakawa K, Horisawa Y, Matsumoto T, Matsui H, Yamazaki H, Sarca AD, Kazuma Y, Nomura R, Konishi Y, Takeuchi S, Stanford E, Kawaji H, Murakawa Y, Takaori-Kondo A. APOBEC3B is preferentially expressed at the G2/M phase of cell cycle. Biochemical Biophysical Research Communications 546, 178-184 (2021)
  7. Takahashi T, Kawaji H, Murakawa Y, Hayashizaki Y, Murakami T, Yabushita Y, Homma Y, Kumamoto T, Matsuyama R, Endo I. Significance of HMGA2 expression as independent poor prognostic marker in perihilar and distal cholangiocarcinoma resected with curative intent. European Journal of Surgical Oncology 47, 394-400 (2021)

2020

  1. Ooki A, Onodera S,Saito A, Oguchi A, Murakawa Y, Sakamoto T, Sueishi K, Nishii Y, Azuma T. CAGE-seq analysis of osteoblast derived from cleidocranial dysplasia human induced pluripotent stem cells. Bone 141, 115582 (2020)

2019

  1. Hirabayashi S, Bhagat S., Matsuki Y, Takegami Y, Uehata T, Kanemaru A, Itoh M, Shirakawa K, Takaori-Kondo A, Takeuchi O, Carninci P, Katayama S, Hayashizaki Y, Kere J, Kawaji H, Murakawa Y. NET-CAGE Characterizes Dynamics and Topology of Human Transcribed Cis-regulatory Elements. Nature Genetics 51, 1369-1379 (2019)
  2. Miyazato P, Matsuo M, Tan BJY, Tokunaga M, Katsuya H, Islam S, Ito J, Murakawa Y, Satou Y. HTLV-1 contains a high CG dinucleotide content and is susceptible to the host antiviral protein ZAP. Retrovirology 16, 38 (2019)
  3. Hia F, Fan Yang S, Shichino Y, Yoshinaga M, Murakawa Y, Vandenbon A, Fukao A, Fujiwara T, Landthaler M, Natsume T, Adachi S, Iwasaki S, *Takeuchi O. Codon Optimality Confers GC-Rich-Induced Stability to mRNAs in Humans. EMBO Reports e48220. (2019)
  4. Yamazaki H, Shirakawa K, Matsumoto T, Hirabayashi S, Murakawa Y, Kobayashi M, Sarca AD, Kazuma Y, Matsui H, Maruyama W, Fukuda H, Shirakawa R, Shindo K, Ri M, Iida S, *Takaori-Kondo A. Endogenous APOBEC3B Overexpression Constitutively Generates DNA Substitutions and Deletions in Myeloma Cells. Scientific Reports 9, 7122 (2019)
  5. Yoshihara M, Oguchi A, Murakawa Y. Genomic Instability of iPSCs and Challenges in Their Clinical Applications. Advances in Experimental Medicine and Biology 1201, 23-47 (2019)

2018

  1. Bardales J, Wieser E, Kawaji H, Murakawa M, Darzacq X. Selective activation of alternative MYC core promoters by Wnt-responsive enhancers. Genes, 23, E270 (2018)

2017

  1. Yoshihara M, Araki A, Kasama Y, Sunayama M, Abe M, Nishida K, Kawaji H, Hayashizaki Y, Murakawa Y. Hotspots of de novo point mutations in induced pluripotent stem cells. Cell Reports, 21, 308-315. (2017)
  2. Takiuchi Y, Kobayashi M, Tada K, Iwai F, Sakurada M, Hirabayashi S, Nagata K, Shirakawa K, Shindo K, Yasunaga JI, Murakawa Y., Rajapakse V, Pommier Y, Matsuoka M, Takaori-Kondo A., HTLV-1 bZIP factor suppresses TDP1 expression through inhibition of NRF-1 in adult T-cell leukemia. Scientific Reports. 7, 12849 (2017)

2016

  1. Yoshihara M, Hayashizaki Y, Murakawa Y. Genomic stability of iPSCs: challenges towards their clinical applications. Stem Cell Reviews and Reports 13, 7-16 (2016)
  2. Murakawa Y, Yoshihara M, Kawaji H, Nishikawa M, Zayed H, Suzuki H, Fantom Consortium, Hayashizaki Y. Enhanced identification of transcriptinal enhancers provides mechanistic insights into diseases. Trends in Genetics 32, 76-88 (2016)
  3. Daniele Hasler D, Lehmann G, Murakawa Y, Klironomos F, Jakob L, Grässer F, Rajewsky N, Landthaler M, Meister G. The Lupus autoantigen La prevents mis-channeling of tRNA fragments into the human microRNA pathway. Molecular Cell 63, 110-124 (2016)

2015

  1. Murakawa Y, Hinz M, Mothes J, Schuetz A, Yasuda T, Mastrobuoni G, Friedel C.C, Dölken L, Kempa S, Schmidt-Supprian M, Heinemann U, Wolf J, Scheidereit C, Landthaler M. RC3H1 represses the IKK/NF-κB negative feedback regulator A20 by binding to a 3’UTR composite structure-sequence element. Nature Communications 6, 7367 (2015)
  2. Mino T, Murakawa Y, Fukao A, Vandenbon A, Wessels H, Ori D, Uehata T, Tartey S, Akira S, Suzuki Y, Vinueesa GG, Ohler U, Standley DM, Landthaler M, Fujiwara T, Takeuchi O. Regnase-1 and Roquin Regulate a Common Element in Inflammatory mRNAs by Spatiotemporally Distinct Mechanisms. Cell 161, 1058-1073 (2015)
  3. Kuespert M, Murakawa Y, Schäffler K, Vanselow J, Wolf E, Jurane, S, Schlosser A, Landthaler M and Fischer U. LARP4B is an AU-rich sequence associated factor that promotes mRNA accumulation and translation. RNA 21, 1294-1305 (2015)
  4. Adachi S, Murakawa Y, and Hiraga S. Dynamic nature of SecA and its associated proteins in Escherichia coli. Frontiers in Microbiology 6, 75 (2015)

2014

  1. Rybak-Wolf A (#), Jens M (#), Murakawa Y (#), Herzog M, Landthaler M, Rajewsky N. A variety of Dicer substrates in human and C.elegans. Cell 159, 1153-1167 (2014) (#co-first authors)
  2. Schuetz A, Murakawa Y, Rosenbaum E, Landthaler M, Heinemann U. Roquin binding to stem-loop mRNAs induces protein dimerization and involves a winged helix-turn-helix motif. Nature Communications 5, 5701 (2014)
  3. Adachi S, Murakawa Y, and Hiraga S. SecA defects are accompanied by dysregulation of MukB, DNA gyrase, chromosome partitioning and DNA superhelicity in Escherichia coli. Microbiology, 160 1648-1658 (2014)

2013

  1. Wang Y, Gogol-Doring A, Hu H, Frohler S, Ma Y, Jens M, Maaskola J, Murakawa Y, Quedenau C, Landthaler M, Kalscheuer V, Wieczorek D, Wang Y, Hu Y, Chen W. Integrative analysis revealed the molecular mechanism underlying RBM10-mediated splicing regulation. EMBO molecular medicine 5, 1431-1442 (2013)
  2. Liu Y, Hu W, Murakawa Y, Yin J, Wang G, Landthaler M, and Yan J. Cold-induced RNA-binding proteins regulate circadian gene expression by controlling alternative polyadenylation. Scientific reports, 3 2054 (2013)

2012

  1. Baltz AG, Munschauer M, Schwanhäusser B, Vasile A, Murakawa Y, Schueler M, Youngs N, Penfold-Brown D, Drew K, Milek M, Wyler E, Bonneau R, Selbach M, Dieterich C, Landthaler M. The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts. Molecular Cell 46 674-690 (2012)
  2. Murakawa Y, Miyagawa-Hayashino A, Ogura Y, Egawa H, Okamoto S, Soejima Y, Kurosawa M, Sumiyoshi S, Uemoto S, and Haga, H. Liver transplantation for severe hepatitis in patients with common variable immunodeficiency. Pediatric transplantation 16, E210-216 (2012)

2009

  1. Motegi A, Murakawa Y, and Takeda S. The vital link between the ubiquitin-proteasome pathway and DNA repair: impact on cancer therapy. Cancer letters 283, 1-9 (2009)

2007

  1. Murakawa Y, Sonoda E, Barber L.J, Zeng W, Yokomori K, Kimura H, Niimi A, Lehmann A, Zhao G.Y, Hochegger H, Boulton SJ, Takeda S. Inhibitors of the proteasome suppress homologous DNA recombination in mammalian cells. Cancer research, 67, 8536-8543 (2007)
  2. Zhao G.Y, Sonoda E, Barber L.J, Oka H, Murakawa Y, Yamada K, Ikura T, Wang X, Kobayashi M, Yamamoto, K Boulton S.J, Takeda S. A critical role for the ubiquitin-conjugating enzyme Ubc13 in initiating homologous recombination. Molecular Cell, 25, 663-675 (2007)
  3. Saberi A, Hochegger H, Szuts D, Lan L, Yasui A, Sale J.E, Taniguchi Y, Murakawa Y, Zeng W, Yokomori K, Helleday T, Teraoka H, Arakawa H, Buerstedde J.M, Takeda S. RAD18 and poly(ADP-ribose) polymerase independently suppress the access of nonhomologous end joining to double-strand breaks and facilitate homologous recombination-mediated repair. Molecular and cellular biology 27, 2562-2571 (2007)