Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells.

Inoue T, Kohro T, Tanaka T, Kanki Y, Li G, Poh HM, Mimura I, Kobayashi M, Taguchi A, Maejima T, Suehiro J, Sugiyama A, Kaneki K, Aruga H, Dong S, Stevens JF, Yamamoto S, Tsutsumi S, Fujita T, Ruan X, Aburatani H, Nangaku M, et al. Cellular-automaton model of the cooperative dynamics of RNA polymerase II during transcription in human cells. Genome Biol. 2014 Apr 10;15(4):R63. doi: 10.1186/gb-2014-15-4-r63.

Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements.

Inoue T, Kohro T, Tanaka T, Kanki Y, Li G, Poh HM, Mimura I, Kobayashi M, Taguchi A, Maejima T, Suehiro J, Sugiyama A, Kaneki K, Aruga H, Dong S, Stevens JF, Yamamoto S, Tsutsumi S, Fujita T, Ruan X, Aburatani H, Nangaku M, et al. Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements. Genome Biol. 2014 Apr 10;15(4):R63. doi: 10.1186/gb-2014-15-4-r63.

Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells.

Yukawa M, Akiyama T, Franke V, Mise N, Isagawa T, Suzuki Y, Suzuki MG, Vlahovicek K, Abe K, Aburatani H, Aoki F. Genome-wide analysis of the chromatin composition of histone H2A and H3 variants in mouse embryonic stem cells. PLoS One. 2014 Mar 21;9(3):e92689. doi: 10.1371/journal.pone.0092689. eCollection 2014.

Conjugation-free, visual, and quantitative evaluation of inhibitors on protein tyrosine kinases and phosphatases with a luminescent Tb(III) complex.

Akiba H, Sumaoka J, Hamakubo T, Komiyama M. Conjugation-free, visual, and quantitative evaluation of inhibitors on protein tyrosine kinases and phosphatases with a luminescent Tb(III) complex. Anal Bioanal Chem. 2014 May;406(12):2957-64. doi: 10.1007/s00216-014-7707-x. Epub 2014 Mar 21.

Concurrent activation of acetylation and tri-methylation of H3K27 in a subset of hepatocellular carcinoma with aggressive behavior.

Hayashi A, Yamauchi N, Shibahara J, Kimura H, Morikawa T, Ishikawa S, Nagae G, Nishi A, Sakamoto Y, Kokudo N, Aburatani H, Fukayama M. Concurrent activation of acetylation and tri-methylation of H3K27 in a subset of hepatocellular carcinoma with aggressive behavior. PLoS One. 2014 Mar 10;9(3):e91330. doi: 10.1371/journal.pone.0091330. eCollection 2014.

Methylation epigenotypes and genetic features in colorectal laterally spreading tumors.

Sakai E, Ohata K, Chiba H, Matsuhashi N, Doi N, Fukushima J, Endo H, Takahashi H, Tsuji S, Yagi K, Matsusaka K, Aburatani H, Nakajima A, Kaneda A. Methylation epigenotypes and genetic features in colorectal laterally spreading tumors. Int J Cancer. 2014 Oct 1;135(7):1586-95. doi: 10.1002/ijc.28814. Epub 2014 Mar 10.

Suppression of bone formation by osteoclastic expression of semaphorin 4D.

Kudo S, Caaveiro JM, Goda S, Nagatoishi S, Ishii K, Matsuura T, Sudou Y, Kodama T, Hamakubo T, Tsumoto K. Suppression of bone formation by osteoclastic expression of semaphorin 4D. Biochemistry. 2014 Mar 25;53(11):1742-52. doi: 10.1021/bi401341g. Epub 2014 Mar 10.

Identification and characterization of the X-dimer of human P-cadherin: implications for homophilic cell adhesion.

Kudo S, Caaveiro JM, Goda S, Nagatoishi S, Ishii K, Matsuura T, Sudou Y, Kodama T, Hamakubo T, Tsumoto K. Identification and characterization of the X-dimer of human P-cadherin: implications for homophilic cell adhesion. Biochemistry. 2014 Mar 25;53(11):1742-52. doi: 10.1021/bi401341g. Epub 2014 Mar 10.

Evidence for osteocyte regulation of bone homeostasis through RANKL expression.

Imamura K, Imamachi N, Akizuki G, Kumakura M, Kawaguchi A, Nagata K, Kato A, Kawaguchi Y, Sato H, Yoneda M, Kai C, Yada T, Suzuki Y, Yamada T, Ozawa T, Kaneki K, Inoue T, Kobayashi M, Kodama T, Wada Y, Sekimizu K, Akimitsu N. Evidence for osteocyte regulation of bone homeostasis through RANKL expression. Mol Cell. 2014 Feb 6;53(3):393-406. doi: 10.1016/j.molcel.2014.01.009. Erratum in: Mol Cell. 2014 Jun 19;54(6):1055.

Ets family members induce lymphangiogenesis through physical and functional interaction with Prox1.

Yuhashi K, Ohnishi S, Kodama T, Koike K, Kanamori H. Ets family members induce lymphangiogenesis through physical and functional interaction with Prox1. Virology. 2014 Feb;450-451:13-23. doi: 10.1016/j.virol.2013.11.036. Epub 2013 Dec 18.

Antitumor activity and induction of TP53-dependent apoptosis toward ovarian clear cell adenocarcinoma by the dual PI3K/mTOR inhibitor DS-7423.

Kashiyama T, Oda K, Ikeda Y, Shiose Y, Hirota Y, Inaba K, Makii C, Kurikawa R, Miyasaka A, Koso T, Fukuda T, Tanikawa M, Shoji K, Sone K, Arimoto T, Wada-Hiraike O, Kawana K, Nakagawa S, Matsuda K, McCormick F, Aburatani H, Yano T, et al. Antitumor activity and induction of TP53-dependent apoptosis toward ovarian clear cell adenocarcinoma by the dual PI3K/mTOR inhibitor DS-7423. PLoS One. 2014 Feb 4;9(2):e87220. doi: 10.1371/journal.pone.0087220. eCollection 2014.

Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome.

Arai E, Sakamoto H, Ichikawa H, Totsuka H, Chiku S, Gotoh M, Mori T, Nakatani T, Ohnami S, Nakagawa T, Fujimoto H, Wang L, Aburatani H, Yoshida T, Kanai Y. Multilayer-omics analysis of renal cell carcinoma, including the whole exome, methylome and transcriptome. Int J Cancer. 2014 Sep 15;135(6):1330-42. doi: 10.1002/ijc.28768. Epub 2014 May 2.

The miR-17/106-p38 axis is a key regulator of the neurogenic-to-gliogenic transition in developing neural stem/progenitor cells.

Naka-Kaneda H, Nakamura S, Igarashi M, Aoi H, Kanki H, Tsuyama J, Tsutsumi S, Aburatani H, Shimazaki T, Okano H. The miR-17/106-p38 axis is a key regulator of the neurogenic-to-gliogenic transition in developing neural stem/progenitor cells. Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1604-9. doi: 10.1073/pnas.1315567111. Epub 2014 Jan 13.

Exploration of liver cancer genomes.

Shibata T, Aburatani H. Exploration of liver cancer genomes. Nat Rev Gastroenterol Hepatol. 2014 Jun;11(6):340-9. doi: 10.1038/nrgastro.2014.6. Epub 2014 Jan 28. Review.

The role of the BH3-only protein Noxa in bone homeostasis.

Fruchart JC, Davignon J, Hermans MP, Al-Rubeaan K, Amarenco P, Assmann G, Barter P, Betteridge J, Bruckert E, Cuevas A, Farnier M, Ferrannini E, Fioretto P, Genest J, Ginsberg HN, Gotto AM Jr, Hu D, Kadowaki T, Kodama T, Krempf M, Matsuzawa Y, N̼̱ez-Cort̩s JM, et al. The role of the BH3-only protein Noxa in bone homeostasis. Cardiovasc Diabetol. 2014 Jan 24;13:26. doi: 10.1186/1475-2840-13-26. Review.

Retraction for Akimoto et al., Testis-specific protein on Y chromosome (TSPY) represses the activity of the androgen receptor in androgen-dependent testicular germ-cell tumors.

Akimoto C, Ueda T, Inoue K, Yamaoka I, Sakari M, Obara W, Fujioka T, Nagahara A, Nonomura N, Tsutsumi S, Aburatani H, Miki T, Matsumoto T, Kitagawa H, Kato S. Retraction for Akimoto et al., Testis-specific protein on Y chromosome (TSPY) represses the activity of the androgen receptor in androgen-dependent testicular germ-cell tumors. Proc Natl Acad Sci U S A. 2014 Feb 11;111(6):2398. doi: 10.1073/pnas.1323399111. Epub 2014 Jan 21. No abstract available.