K
Kazuhiro R. Nitta
Researcher at Juntendo University
Publications - 35
Citations - 3639
Kazuhiro R. Nitta is an academic researcher from Juntendo University. The author has contributed to research in topics: Gene & Mitochondrial disease. The author has an hindex of 14, co-authored 30 publications receiving 2802 citations. Previous affiliations of Kazuhiro R. Nitta include Fujitsu & University of Tokyo.
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Journal ArticleDOI
DNA-Binding Specificities of Human Transcription Factors
Arttu Jolma,Jian Yan,Tom Whitington,Jarkko Toivonen,Kazuhiro R. Nitta,Pasi Rastas,Ekaterina Morgunova,Martin Enge,Mikko Taipale,Gong-Hong Wei,Kimmo Palin,Juan M. Vaquerizas,Renaud Vincentelli,Nicholas M. Luscombe,Timothy P. Hughes,Patrick Lemaire,Esko Ukkonen,Teemu Kivioja,Teemu Kivioja,Jussi Taipale,Jussi Taipale +20 more
TL;DR: Global analysis of the data revealed that homodimer orientation and spacing preferences, and base-stacking interactions, have a larger role in TF-DNA binding than previously appreciated.
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Impact of cytosine methylation on DNA binding specificities of human transcription factors.
Yimeng Yin,Ekaterina Morgunova,Arttu Jolma,Eevi Kaasinen,Biswajyoti Sahu,Syed Khund-Sayeed,Pratyush Kumar Das,Teemu Kivioja,Kashyap Dave,Fan Zhong,Kazuhiro R. Nitta,Minna Taipale,Alexander Popov,Paul A. Ginno,Silvia Domcke,Silvia Domcke,Jian Yan,Dirk Schübeler,Dirk Schübeler,Charles Vinson,Jussi Taipale,Jussi Taipale +21 more
TL;DR: This work systematically analyzed binding specificities of full-length transcription factors and extended DNA binding domains to unmethylated and CpG-methylated DNA by using methylation-sensitive SELEX (systematic evolution of ligands by exponential enrichment).
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DNA-dependent formation of transcription factor pairs alters their binding specificity
Arttu Jolma,Yimeng Yin,Kazuhiro R. Nitta,Kashyap Dave,Alexander Popov,Minna Taipale,Martin Enge,Teemu Kivioja,Ekaterina Morgunova,Jussi Taipale,Jussi Taipale +10 more
TL;DR: The results indicate that the DNA molecule commonly plays an active role in cooperative interactions that define the gene regulatory lexicon.
Journal ArticleDOI
Conservation of transcription factor binding specificities across 600 million years of bilateria evolution
Kazuhiro R. Nitta,Arttu Jolma,Yimeng Yin,Ekaterina Morgunova,Teemu Kivioja,Junaid Akhtar,Korneel Hens,Jarkko Toivonen,Bart Deplancke,Eileen E. M. Furlong,Jussi Taipale +10 more
TL;DR: This analysis revealed that TF binding specificities are highly conserved between Drosophila and mammals, and that for orthologous TFs, the similarity extends even to the level of very subtle dinucleotide binding preferences.
Journal ArticleDOI
The interaction landscape between transcription factors and the nucleosome.
Fangjie Zhu,Lucas Farnung,Eevi Kaasinen,Biswajyoti Sahu,Yimeng Yin,Bei Wei,Svetlana O. Dodonova,Kazuhiro R. Nitta,Ekaterina Morgunova,Minna Taipale,Minna Taipale,Patrick Cramer,Patrick Cramer,Jussi Taipale,Jussi Taipale,Jussi Taipale +15 more
TL;DR: This work reveals notable differences in the binding of transcription factors to free and nucleosomal DNA, and uncovers a diverse interaction landscape between transcription factors and the nucleosome.