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Promoter-proximal pausing and its release: molecular mechanisms and physiological functions.
Chiba K, Yamamoto J, Yamaguchi Y, Handa H. Chiba K, et al. Among authors: yamamoto j. Exp Cell Res. 2010 Oct 15;316(17):2723-30. doi: 10.1016/j.yexcr.2010.05.036. Epub 2010 Jun 10. Exp Cell Res. 2010. PMID: 20541545 Review.
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.
Kimura K, Wakamatsu A, Suzuki Y, Ota T, Nishikawa T, Yamashita R, Yamamoto J, Sekine M, Tsuritani K, Wakaguri H, Ishii S, Sugiyama T, Saito K, Isono Y, Irie R, Kushida N, Yoneyama T, Otsuka R, Kanda K, Yokoi T, Kondo H, Wagatsuma M, Murakawa K, Ishida S, Ishibashi T, Takahashi-Fujii A, Tanase T, Nagai K, Kikuchi H, Nakai K, Isogai T, Sugano S. Kimura K, et al. Among authors: yamamoto j. Genome Res. 2006 Jan;16(1):55-65. doi: 10.1101/gr.4039406. Epub 2005 Dec 12. Genome Res. 2006. PMID: 16344560 Free PMC article.
NELF interacts with CBC and participates in 3' end processing of replication-dependent histone mRNAs.
Narita T, Yung TM, Yamamoto J, Tsuboi Y, Tanabe H, Tanaka K, Yamaguchi Y, Handa H. Narita T, et al. Among authors: yamamoto j. Mol Cell. 2007 May 11;26(3):349-65. doi: 10.1016/j.molcel.2007.04.011. Mol Cell. 2007. PMID: 17499042
Identification and functional analyses of 11,769 full-length human cDNAs focused on alternative splicing.
Wakamatsu A, Kimura K, Yamamoto J, Nishikawa T, Nomura N, Sugano S, Isogai T. Wakamatsu A, et al. Among authors: yamamoto j. DNA Res. 2009 Dec;16(6):371-83. doi: 10.1093/dnares/dsp022. Epub 2009 Oct 30. DNA Res. 2009. PMID: 19880432 Free PMC article.
DSIF, the Paf1 complex, and Tat-SF1 have nonredundant, cooperative roles in RNA polymerase II elongation.
Chen Y, Yamaguchi Y, Tsugeno Y, Yamamoto J, Yamada T, Nakamura M, Hisatake K, Handa H. Chen Y, et al. Among authors: yamamoto j. Genes Dev. 2009 Dec 1;23(23):2765-77. doi: 10.1101/gad.1834709. Genes Dev. 2009. PMID: 19952111 Free PMC article.
Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation.
Kim S, Yamamoto J, Chen Y, Aida M, Wada T, Handa H, Yamaguchi Y. Kim S, et al. Among authors: yamamoto j. Genes Cells. 2010 Sep 1;15(9):1003-13. doi: 10.1111/j.1365-2443.2010.01436.x. Epub 2010 Jul 29. Genes Cells. 2010. PMID: 20695905
DSIF and NELF interact with Integrator to specify the correct post-transcriptional fate of snRNA genes.
Yamamoto J, Hagiwara Y, Chiba K, Isobe T, Narita T, Handa H, Yamaguchi Y. Yamamoto J, et al. Nat Commun. 2014 Jun 27;5:4263. doi: 10.1038/ncomms5263. Nat Commun. 2014. PMID: 24968874
Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex.
Cao QF, Yamamoto J, Isobe T, Tateno S, Murase Y, Chen Y, Handa H, Yamaguchi Y. Cao QF, et al. Among authors: yamamoto j. Mol Cell Biol. 2015 Oct;35(20):3459-70. doi: 10.1128/MCB.00601-15. Epub 2015 Jul 27. Mol Cell Biol. 2015. PMID: 26217014 Free PMC article.
Correction for Cao et al., Characterization of the Human Transcription Elongation Factor Rtf1: Evidence for Nonoverlapping Functions of Rtf1 and the Paf1 Complex.
Cao QF, Yamamoto J, Isobe T, Tateno S, Murase Y, Chen Y, Handa H, Yamaguchi Y. Cao QF, et al. Among authors: yamamoto j. Mol Cell Biol. 2015 Dec;35(23):4093. doi: 10.1128/MCB.00914-15. Mol Cell Biol. 2015. PMID: 26518638 Free PMC article. No abstract available.
Human protein factory for converting the transcriptome into an in vitro-expressed proteome,
Goshima N, Kawamura Y, Fukumoto A, Miura A, Honma R, Satoh R, Wakamatsu A, Yamamoto J, Kimura K, Nishikawa T, Andoh T, Iida Y, Ishikawa K, Ito E, Kagawa N, Kaminaga C, Kanehori K, Kawakami B, Kenmochi K, Kimura R, Kobayashi M, Kuroita T, Kuwayama H, Maruyama Y, Matsuo K, Minami K, Mitsubori M, Mori M, Morishita R, Murase A, Nishikawa A, Nishikawa S, Okamoto T, Sakagami N, Sakamoto Y, Sasaki Y, Seki T, Sono S, Sugiyama A, Sumiya T, Takayama T, Takayama Y, Takeda H, Togashi T, Yahata K, Yamada H, Yanagisawa Y, Endo Y, Imamoto F, Kisu Y, Tanaka S, Isogai T, Imai J, Watanabe S, Nomura N. Goshima N, et al. Among authors: yamamoto j. Nat Methods. 2008 Dec;5(12):1011-7. doi: 10.1038/nmeth.1273. Nat Methods. 2008. PMID: 19054851
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