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Research Output

  • 658 Citations
  • 17 h-Index
  • 40 Article
  • 2 Comment/debate
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Article
2020

Chromatin integration labeling for mapping DNA-binding proteins and modifications with low input

Handa, T., Harada, A., Maehara, K., Sato, S., Nakao, M., Goto, N., Kurumizaka, H., Ohkawa, Y. & Kimura, H., Oct 1 2020, In : Nature Protocols. 15, 10, p. 3334-3360 27 p.

Research output: Contribution to journalArticle

2019

A chromatin integration labelling method enables epigenomic profiling with lower input

Harada, A., Maehara, K., Handa, T., Arimura, Y., Nogami, J., Hayashi-Takanaka, Y., Shirahige, K., Kurumizaka, H., Kimura, H. & Ohkawa, Y., Feb 1 2019, In : Nature Cell Biology. 21, 2, p. 287-296 10 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Biochemical analysis of nucleosome targeting by Tn5 transposase

Sato, S., Arimura, Y., Kujirai, T., Harada, A., Maehara, K., Nogami, J., Ohkawa, Y. & Kurumizaka, H., Aug 1 2019, In : Open Biology. 9, 8, 190116.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)
Open Access
3 Citations (Scopus)

Chromatin-bound CRM1 recruits SET-Nup214 and NPM1c onto HOX clusters causing aberrant HOX expression in leukemia cells

Oka, M., Mura, S., Otani, M., Miyamoto, Y., Nogami, J., Maehara, K., Harada, A., Tachibana, T., Yoneda, Y. & Ohkawa, Y., Nov 2019, In : eLife. 8, e46667.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Dmrt factors determine the positional information of cerebral cortical progenitors via differential suppression of homeobox genes

Konno, D., Kishida, C., Maehara, K., Ohkawa, Y., Kiyonari, H., Okada, S. & Matsuzaki, F., Aug 2019, In : Development (Cambridge). 146, 15, dev174243.

Research output: Contribution to journalArticle

Open Access
2 Citations (Scopus)

Sustained expression of HeyL is critical for the proliferation of muscle stem cells in overloaded muscle

Fukuda, S., Kaneshige, A., Kaji, T., Noguchi, Y. T., Takemoto, Y., Zhang, L., Tsujikawa, K., Kokubo, H., Uezumi, A., Maehara, K., Harada, A., Ohkawa, Y. & Fukada, S. I., Sep 2019, In : eLife. 8, e48284.

Research output: Contribution to journalArticle

Open Access
6 Citations (Scopus)

The Eleanor ncRNAs activate the topological domain of the ESR1 locus to balance against apoptosis

Abdalla, M. O. A., Yamamoto, T., Maehara, K., Nogami, J., Ohkawa, Y., Miura, H., Poonperm, R., Hiratani, I., Nakayama, H., Nakao, M. & Saitoh, N., Dec 1 2019, In : Nature communications. 10, 1, 3778.

Research output: Contribution to journalArticle

Open Access
6 Citations (Scopus)
2018

Cryo-EM structure of the nucleosome containing the ALB1 enhancer DNA sequence

Takizawa, Y., Tanaka, H., Machida, S., Koyama, M., Maehara, K., Ohkawa, Y., Wade, P. A., Wolf, M. & Kurumizaka, H., 2018, In : Open Biology. 8, 3, 170255.

Research output: Contribution to journalArticle

9 Citations (Scopus)
17 Citations (Scopus)

Histone H3.3 sub-variant H3mm7 is required for normal skeletal muscle regeneration

Harada, A., Maehara, K., Ono, Y., Taguchi, H., Yoshioka, K., Kitajima, Y., Xie, Y., Sato, Y., Iwasaki, T., Nogami, J., Okada, S., Komatsu, T., Semba, Y., Takemoto, T., Kimura, H., Kurumizaka, H. & Ohkawa, Y., Dec 1 2018, In : Nature communications. 9, 1, 1400.

Research output: Contribution to journalArticle

2 Citations (Scopus)

Sensitive detection of fluorescence in western blotting by merging images

Kondo, Y., Higa, S., Iwasaki, T., Matsumoto, T., Maehara, K., Harada, A., Baba, Y., Fujita, M. & Ohkawa, Y., Jan 2018, In : PloS one. 13, 1, e0191532.

Research output: Contribution to journalArticle

7 Citations (Scopus)
2017

Chd2 regulates chromatin for proper gene expression toward differentiation in mouse embryonic stem cells

Semba, Y., Harada, A., Maehara, K., Oki, S., Meno, C., Ueda, J., Yamagata, K., Suzuki, A., Onimaru, M., Nogami, J., Okada, S., Akashi, K. & Ohkawa, Y., Sep 1 2017, In : Nucleic acids research. 45, 15, p. 8758-8772 15 p.

Research output: Contribution to journalArticle

11 Citations (Scopus)

Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

Taguchi, H., Xie, Y., Horikoshi, N., Maehara, K., Harada, A., Nogami, J., Sato, K., Arimura, Y., Osakabe, A., Kujirai, T., Iwasaki, T., Semba, Y., Tachibana, T., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Apr 25 2017, In : Biochemistry. 56, 16, p. 2184-2196 13 p.

Research output: Contribution to journalArticle

6 Citations (Scopus)

Crystal structure of the overlapping dinucleosome composed of hexasome and octasome

Kato, D., Osakabe, A., Arimura, Y., Mizukami, Y., Horikoshi, N., Saikusa, K., Akashi, S., Nishimura, Y., Park, S. Y., Nogami, J., Maehara, K., Ohkawa, Y., Matsumoto, A., Kono, H., Inoue, R., Sugiyama, M. & Kurumizaka, H., Apr 14 2017, In : Science. 356, 6334, p. 205-208 4 p., 356.

Research output: Contribution to journalArticle

31 Citations (Scopus)

Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis

Ueda, J., Harada, A., Urahama, T., Machida, S., Maehara, K., Hada, M., Makino, Y., Nogami, J., Horikoshi, N., Osakabe, A., Taguchi, H., Tanaka, H., Tachiwana, H., Yao, T., Yamada, M., Iwamoto, T., Isotani, A., Ikawa, M., Tachibana, T., Okada, Y. & 4 others, Kimura, H., Ohkawa, Y., Kurumizaka, H. & Yamagata, K., Jan 17 2017, In : Cell Reports. 18, 3, p. 593-600 8 p.

Research output: Contribution to journalArticle

30 Citations (Scopus)

The requirement of Mettl3-promoted MyoD mRNA maintenance in proliferative myoblasts for skeletal muscle differentiation

Kudou, K., Komatsu, T., Nogami, J., Maehara, K., Harada, A., Saeki, H., Oki, E., Maehara, Y. & Ohkawa, Y., 2017, In : Open Biology. 7, 9, 170119.

Research output: Contribution to journalArticle

14 Citations (Scopus)

Thymine DNA glycosylase modulates DNA damage response and gene expression by base excision repair-dependent and independent mechanisms

Nakamura, T., Murakami, K., Tada, H., Uehara, Y., Nogami, J., Maehara, K., Ohkawa, Y., Saitoh, H., Nishitani, H., Ono, T., Nishi, R., Yokoi, M., Sakai, W. & Sugasawa, K., Apr 1 2017, In : Genes to Cells. 22, 4, p. 392-405 14 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)
2016

Chd5 Regulates MuERV-L/MERVL Expression in Mouse Embryonic Stem Cells Via H3K27me3 Modification and Histone H3.1/H3.2

Hayashi, M., Maehara, K., Harada, A., Semba, Y., Kudo, K., Takahashi, H., Oki, S., Meno, C., Ichiyanagi, K., Akashi, K. & Ohkawa, Y., Mar 2016, In : Journal of Cellular Biochemistry. 117, 3, p. 780-792 13 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Chromatin architecture may dictate the target site for DMC1, but not for RAD51, during homologous pairing

Kobayashi, W., Takaku, M., Machida, S., Tachiwana, H., Maehara, K., Ohkawa, Y. & Kurumizaka, H., Apr 7 2016, In : Scientific reports. 6, 24228.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Chromatin-prebound Crm1 recruits Nup98-HoxA9 fusion to induce aberrant expression of Hox cluster genes

Oka, M., Mura, S., Yamada, K., Sangel, P., Hirata, S., Maehara, K., Kawakami, K., Tachibana, T., Ohkawa, Y., Kimura, H. & Yoneda, Y., Jan 7 2016, In : eLife. 5, JANUARY2016, e09540.

Research output: Contribution to journalArticle

18 Citations (Scopus)

Exploration of nucleosome positioning patterns in transcription factor function

Maehara, K. & Ohkawa, Y., Jan 21 2016, In : Scientific reports. 6, 19620.

Research output: Contribution to journalArticle

4 Citations (Scopus)

Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis

Urahama, T., Harada, A., Maehara, K., Horikoshi, N., Sato, K., Sato, Y., Shiraishi, K., Sugino, N., Osakabe, A., Tachiwana, H., Kagawa, W., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Jan 15 2016, In : Epigenetics and Chromatin. 9, 1, 51.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Histone H4 lysine 20 acetylation is associated with gene repression in human cells

Kaimori, J. Y., Maehara, K., Hayashi-Takanaka, Y., Harada, A., Fukuda, M., Yamamoto, S., Ichimaru, N., Umehara, T., Yokoyama, S., Matsuda, R., Ikura, T., Nagao, K., Obuse, C., Nozaki, N., Takahara, S., Takao, T., Ohkawa, Y., Kimura, H. & Isaka, Y., Apr 11 2016, In : Scientific reports. 6, 24318.

Research output: Contribution to journalArticle

17 Citations (Scopus)

Identification of immunoglobulin gene sequences from a small read number of mRNA-seq using hybridomas

Kuniyoshi, Y., Maehara, K., Iwasaki, T., Hayashi, M., Semba, Y., Fujita, M., Sato, Y., Kimura, H., Harada, A. & Ohkawa, Y., Oct 2016, In : PloS one. 11, 10, e0165473.

Research output: Contribution to journalArticle

3 Citations (Scopus)

Structure and function of human histone H3.Y nucleosome

Kujirai, T., Horikoshi, N., Sato, K., Maehara, K., Machida, S., Osakabe, A., Kimura, H., Ohkawa, Y. & Kurumizaka, H., Jul 27 2016, In : Nucleic acids research. 44, 13, p. 6127-6141 15 p.

Research output: Contribution to journalArticle

19 Citations (Scopus)
2015

A cluster of noncoding RNAs activates the ESR1 locus during breast cancer adaptation

Tomita, S., Abdalla, M. O. A., Fujiwara, S., Matsumori, H., Maehara, K., Ohkawa, Y., Iwase, H., Saitoh, N. & Nakao, M., Apr 29 2015, In : Nature communications. 6, 6966.

Research output: Contribution to journalArticle

34 Citations (Scopus)

Agplus: A rapid and flexible tool for aggregation plots

Maehara, K. & Ohkawa, Y., Jul 31 2015, In : Bioinformatics. 31, 18, p. 3046-3047 2 p.

Research output: Contribution to journalArticle

9 Citations (Scopus)

Cdt1-binding protein GRWD1 is a novel histone-binding protein that facilitates MCM loading through its influence on chromatin architecture

Sugimoto, N., Maehara, K., Yoshida, K., Yasukouchi, S., Osano, S., Watanabe, S., Aizawa, M., Yugawa, T., Kiyono, T., Kurumizaka, H., Ohkawa, Y. & Fujita, M., 2015, In : Nucleic acids research. 43, 12, p. 5898-5911 14 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Distribution of histone H4 modifications as revealed by a panel of specific monoclonal antibodies

Hayashi-Takanaka, Y., Maehara, K., Harada, A., Umehara, T., Yokoyama, S., Obuse, C., Ohkawa, Y., Nozaki, N. & Kimura, H., Dec 1 2015, In : Chromosome Research. 23, 4, p. 753-766 14 p.

Research output: Contribution to journalArticle

22 Citations (Scopus)

Incorporation of histone H3.1 suppresses the lineage potential of skeletal muscle

Harada, A., Maehara, K., Sato, Y., Konno, D., Tachibana, T., Kimura, H. & Ohkawa, Y., Jan 30 2015, In : Nucleic acids research. 43, 2, p. 775-786 12 p.

Research output: Contribution to journalArticle

24 Citations (Scopus)

Influence of DNA methylation on positioning and DNA flexibility of nucleosomes with pericentric satellite DNA

Osakabe, A., Adachi, F., Arimura, Y., Maehara, K., Ohkawa, Y. & Kurumizaka, H., Oct 7 2015, In : Open Biology. 5, 10, 150128.

Research output: Contribution to journalArticle

12 Citations (Scopus)

Tissue-specific expression of histone H3 variants diversified after species separation

Maehara, K., Harada, A., Sato, Y., Matsumoto, M., Nakayama, K. I., Kimura, H. & Ohkawa, Y., Sep 17 2015, In : Epigenetics and Chromatin. 8, 1, 35.

Research output: Contribution to journalArticle

21 Citations (Scopus)
2014

Heterochromatin dynamics during the differentiation process revealed by the DNA methylation reporter mouse, methylRO

Ueda, J., Maehara, K., Mashiko, D., Ichinose, T., Yao, T., Hori, M., Sato, Y., Kimura, H., Ohkawa, Y. & Yamagata, K., Jun 3 2014, In : Stem Cell Reports. 2, 6, p. 910-924 15 p.

Research output: Contribution to journalArticle

26 Citations (Scopus)

Regulation of RNA polymerase II activation by histone acetylation in single living cells

Stasevich, T. J., Hayashi-Takanaka, Y., Sato, Y., Maehara, K., Ohkawa, Y., Sakata-Sogawa, K., Tokunaga, M., Nagase, T., Nozaki, N., McNally, J. G. & Kimura, H., Dec 11 2014, In : Nature. 516, 7530, p. 272-275 4 p.

Research output: Contribution to journalArticle

120 Citations (Scopus)

SraTailor: Graphical user interface software for processing and visualizing ChIP-seq data

Oki, S., Maehara, K., Ohkawa, Y. & Meno, C., Dec 1 2014, In : Genes to Cells. 19, 12, p. 919-926 8 p.

Research output: Contribution to journalArticle

14 Citations (Scopus)
2013

A co-localization model of paired ChIP-seq data using a large ENCODE data set enables comparison of multiple samples

Maehara, K., Odawara, J., Harada, A., Yoshimi, T., Nagao, K., Obuse, C., Akashi, K., Tachibana, T., Sakata, T. & Ohkawa, Y., Jan 2013, In : Nucleic acids research. 41, 1, p. 54-62 9 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Human TREX component Thoc5 affects alternative polyadenylation site choice by recruiting mammalian cleavage factor I

Katahira, J., Okuzaki, D., Inoue, H., Yoneda, Y., Maehara, K. & Ohkawa, Y., Aug 2013, In : Nucleic acids research. 41, 14, p. 7060-7072 13 p.

Research output: Contribution to journalArticle

37 Citations (Scopus)
2011

The classification of mRNA expression levels by the phosphorylation state of RNAPII CTD based on a combined genome-wide approach

Odawara, J., Harada, A., Yoshimi, T., Maehara, K., Tachibana, T., Okada, S., Akashi, K. & Ohkawa, Y., Oct 20 2011, In : BMC genomics. 12, 516.

Research output: Contribution to journalArticle

26 Citations (Scopus)