Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate.

Hayashi G, Koyama K, Shiota H, Kamio A, Umeda T, Nagae G, Aburatani H, Okamoto A. Base-Resolution Analysis of 5-Hydroxymethylcytosine by One-Pot Bisulfite-Free Chemical Conversion with Peroxotungstate. J Am Chem Soc. 2016 Nov 2;138(43):14178-14181. Epub 2016 Oct 24.

Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells.

Ishimoto K, Kawamata N, Uchihara Y, Okubo M, Fujimoto R, Gotoh E, Kakinouchi K, Mizohata E, Hino N, Okada Y, Mochizuki Y, Tanaka T, Hamakubo T, Sakai J, Kodama T, Inoue T, Tachibana K, Doi T. Effects of Chronic Low-Dose Radiation on Human Neural Progenitor Cells. PLoS One. 2016 Oct 31;11(10):e0165766. doi: 10.1371/journal.pone.0165766. eCollection 2016.

Molecular Pathology and Novel Clinical Therapy for Uterine Leiomyosarcoma.

Hayashi T, Kawano M, Ichimura T, Ida K, Ando H, Zharhary D, Kanai Y, Aburatani H, Tonegawa S, Shiozawa T, Yaegashi N, Konishi I. Molecular Pathology and Novel Clinical Therapy for Uterine Leiomyosarcoma. Anticancer Res. 2016 Oct;36(10):4997-5007. Review.

Ubiquitination of Lysine 867 of the Human SETDB1 Protein Upregulates Its Histone H3 Lysine 9 (H3K9) Methyltransferase Activity.

Ishimoto K, Kawamata N, Uchihara Y, Okubo M, Fujimoto R, Gotoh E, Kakinouchi K, Mizohata E, Hino N, Okada Y, Mochizuki Y, Tanaka T, Hamakubo T, Sakai J, Kodama T, Inoue T, Tachibana K, Doi T. Ubiquitination of Lysine 867 of the Human SETDB1 Protein Upregulates Its Histone H3 Lysine 9 (H3K9) Methyltransferase Activity. PLoS One. 2016 Oct 31;11(10):e0165766. doi: 10.1371/journal.pone.0165766. eCollection 2016.

Loss of YAP1 defines neuroendocrine differentiation of lung tumors.

Ito T, Matsubara D, Tanaka I, Makiya K, Tanei ZI, Kumagai Y, Shiu SJ, Nakaoka HJ, Ishikawa S, Isagawa T, Morikawa T, Shinozaki-Ushiku A, Goto Y, Nakano T, Tsuchiya T, Tsubochi H, Komura D, Aburatani H, Dobashi Y, Nakajima J, Endo S, Fukayama M, et al. Loss of YAP1 defines neuroendocrine differentiation of lung tumors. Cancer Sci. 2016 Oct;107(10):1527-1538. doi: 10.1111/cas.13013. Epub 2016 Sep 9.

MDM2 is a potential therapeutic target and prognostic factor for ovarian clear cell carcinomas with wild type TP53.

Makii C, Oda K, Ikeda Y, Sone K, Hasegawa K, Uehara Y, Nishijima A, Asada K, Koso T, Fukuda T, Inaba K, Oki S, Machino H, Kojima M, Kashiyama T, Mori-Uchino M, Arimoto T, Wada-Hiraike O, Kawana K, Yano T, Fujiwara K, Aburatani H, et al. MDM2 is a potential therapeutic target and prognostic factor for ovarian clear cell carcinomas with wild type TP53. Oncotarget. 2016 Nov 15;7(46):75328-75338. doi: 10.18632/oncotarget.12175.

Smad4 is required to inhibit osteoclastogenesis and maintain bone mass.

Morita M, Yoshida S, Iwasaki R, Yasui T, Sato Y, Kobayashi T, Watanabe R, Oike T, Miyamoto K, Takami M, Ozato K, Deng CX, Aburatani H, Tanaka S, Yoshimura A, Toyama Y, Matsumoto M, Nakamura M, Kawana H, Nakagawa T, Miyamoto T. Smad4 is required to inhibit osteoclastogenesis and maintain bone mass. Sci Rep. 2016 Oct 12;6:35221. doi: 10.1038/srep35221.

Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1.

Aihara H, Nakagawa T, Mizusaki H, Yoneda M, Kato M, Doiguchi M, Imamura Y, Higashi M, Ikura T, Hayashi T, Kodama Y, Oki M, Nakayama T, Cheung E, Aburatani H, Takayama KI, Koseki H, Inoue S, Takeshima Y, Ito T. Histone H2A T120 Phosphorylation Promotes Oncogenic Transformation via Upregulation of Cyclin D1. Mol Cell. 2016 Oct 6;64(1):176-188. doi: 10.1016/j.molcel.2016.09.012.

Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems

Nishida K, Arazoe T, Yachie N, Banno S, Kakimoto M, Tabata M, Mochizuki M, Miyabe A, Araki M, Hara KY, Shimatani Z & Kondo A Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems Science 353, aaf8729

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data.

duVerle DA, Yotsukura S, Nomura S, Aburatani H, Tsuda K. CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data. BMC Bioinformatics. 2016 Sep 13;17(1):363. doi: 10.1186/s12859-016-1175-6.

Coupling CDH17 and CLDN18 markers for comprehensive membrane-targeted detection of human gastric cancer.

Matsusaka K, Ushiku T, Urabe M, Fukuyo M, Abe H, Ishikawa S, Seto Y, Aburatani H, Hamakubo T, Kaneda A, Fukayama M. Coupling CDH17 and CLDN18 markers for comprehensive membrane-targeted detection of human gastric cancer. Oncotarget. 2016 Sep 27;7(39):64168-64181. doi: 10.18632/oncotarget.11638.

Two subtypes of colorectal tumor with distinct molecular features in familial adenomatous polyposis.

Takane K, Matsusaka K, Ota S, Fukuyo M, Yue Y, Nishimura M, Sakai E, Matsushita K, Miyauchi H, Aburatani H, Nakatani Y, Takayama T, Matsubara H, Akagi K, Kaneda A. Two subtypes of colorectal tumor with distinct molecular features in familial adenomatous polyposis. Oncotarget. 2016 Dec 20;7(51):84003-84016. doi: 10.18632/oncotarget.11510.

The H3K9 methyltransferase Setdb1 regulates TLR4-mediated inflammatory responses in macrophages.

Hachiya R, Shiihashi T, Shirakawa I, Iwasaki Y, Matsumura Y, Oishi Y, Nakayama Y, Miyamoto Y, Manabe I, Ochi K, Tanaka M, Goda N, Sakai J, Suganami T, Ogawa Y. The H3K9 methyltransferase Setdb1 regulates TLR4-mediated inflammatory responses in macrophages. Sci Rep. 2016 Jun 28;6:28845. doi: 10.1038/srep28845.

Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development.

Nimura K, Yamamoto M, Takeichi M, Saga K, Takaoka K, Kawamura N, Nitta H, Nagano H, Ishino S, Tanaka T, Schwartz RJ, Aburatani H, Kaneda Y. Regulation of alternative polyadenylation by Nkx2-5 and Xrn2 during mouse heart development. Elife. 2016 Jun 22;5. pii: e16030. doi: 10.7554/eLife.16030.

Network-based analysis for identification of candidate genes for colorectal cancer progression.

Tsuji S, Midorikawa Y, Seki M, Takayama T, Sugiyama Y, Aburatani H. Network-based analysis for identification of candidate genes for colorectal cancer progression. Biochem Biophys Res Commun. 2016 Aug 5;476(4):534-40. doi: 10.1016/j.bbrc.2016.05.158. Epub 2016 May 30.

Transcriptional and epigenetic control of brown and beige adipose cell fate and function.

Inagaki T, Sakai J, Kajimura S. Transcriptional and epigenetic control of brown and beige adipose cell fate and function. Nat Rev Mol Cell Biol. 2016 Aug;17(8):480-95. doi: 10.1038/nrm.2016.62. Epub 2016 Jun 2. Review.