Structural perspectives on transcription in chromatin

Authors: Sekine, Shun-ichi, Ehara, Haruhiko, Kujirai, Tomoya, Kurumizaka, Hitoshi

Source: In Trends in Cell Biology March 2024 34(3):211-224

Cryo-EM structures of RNA polymerase II–nucleosome complexes rewrapping transcribed DNA

Authors: Akatsu, Munetaka, Ehara, Haruhiko, Kujirai, Tomoya, Fujita, Risa, Ito, Tomoko, Osumi, Ken, Ogasawara, Mitsuo, Takizawa, Yoshimasa, Sekine, Shun-ichi, Kurumizaka, Hitoshi

Source: In Journal of Biological Chemistry December 2023 299(12)

High-Speed Atomic Force Microscopy Reveals Spontaneous Nucleosome Sliding of H2A.Z at the Subsecond Time Scale

Authors: Morioka, Shin, Sato, Shoko, Horikoshi, Naoki, Kujirai, Tomoya, Tomita, Takuya, Baba, Yudai, Kakuta, Takahiro, Ogoshi, Tomoki, Puppulin, Leonardo, Sumino, Ayumi

Source: Nano letters. 23(5):1696-1704

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN631870180&indx=1&recIds=ETOCRN631870180

Structural Basis of Damaged Nucleotide Recognition by Transcribing RNA Polymerase II in the Nucleosome

Authors: Osumi, Ken, Kujirai, Tomoya, Ehara, Haruhiko, Ogasawara, Mitsuo, Kinoshita, Chiaki, Saotome, Mika, Kagawa, Wataru, Sekine, Shun-ichi, Takizawa, Yoshimasa, Kurumizaka, Hitoshi

Source: In Journal of Molecular Biology 1 July 2023 435(13)

Method for Evaluating Effects of Non-coding RNAs on Nucleosome Stability

Authors: Dacher, Mariko, Fujita, Risa, Kujirai, Tomoya, Kurumizaka, Hitoshi

Source: Methods in molecular biology. 2509:195-208

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN629743028&indx=1&recIds=ETOCRN629743028

Structural and biochemical analyses of the nucleosome containing Komagataella pastoris histones

Authors: Fukushima, Yutaro, Hatazawa, Suguru, Hirai, Seiya, Kujirai, Tomoya, Ehara, Haruhiko, Sekine, Shun-ichi, Takizawa, Yoshimasa, Kurumizaka, Hitoshi

Source: Journal of biochemistry. 172(2):79-88

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100157070278.0x000001&indx=1&recIds=ETOCvdc_100157070278.0x000001

Live-cell epigenome manipulation by synthetic histone acetylation catalyst system

Authors: Fujiwara, Yusuke, Yamanashi, Yuki, Fujimura, Akiko, Sato, Yuko, Kujirai, Tomoya, Kurumizaka, Hitoshi, Kimura, Hiroshi, Yamatsugu, Kenzo, Kawashima, Shigehiro A., Kanai, Motomu

Source: Proceedings of the National Academy of Sciences of the United States of America, 2021 Jan . 118(4), 1-8.

Access URL: https://www.jstor.org/stable/27006017

Cryo-EM and biochemical analyses of the nucleosome containing the human histone H3 variant H3.8.

Authors: Hirai, Seiya^1,2 (AUTHOR), Kujirai, Tomoya¹ (AUTHOR), Akatsu, Munetaka^1,2 (AUTHOR), Ogasawara, Mitsuo¹ (AUTHOR), Ehara, Haruhiko³ (AUTHOR), Sekine, Shun-ichi³ (AUTHOR), Ohkawa, Yasuyuki⁴ (AUTHOR), Takizawa, Yoshimasa¹ (AUTHOR), Kurumizaka, Hitoshi^1,2,3 (AUTHOR) kurumizaka@iqb.u-tokyo.ac.jp

Source: Journal of Biochemistry. Nov2023, Vol. 174 Issue 6, p549-559. 11p.

Subject Terms: *CHROMATIN, *RNA polymerase II, *BASE pairs

Contributions of Histone Variants in Nucleosome Structure and Function

Authors: Kurumizaka, Hitoshi, Kujirai, Tomoya, Takizawa, Yoshimasa

Source: In Journal of Molecular Biology 19 March 2021 433(6)

Chemical catalyst manipulating cancer epigenome and transcription.

Authors: Yamanashi, Yuki, Takamaru, Shinpei, Okabe, Atsushi, Kaito, Satoshi, Azumaya, Yuto, Kamimura, Yugo R., Yamatsugu, Kenzo, Kujirai, Tomoya, Kurumizaka, Hitoshi, Iwama, Atsushi, Kaneda, Atsushi, Kawashima, Shigehiro A., Kanai, Motomu

Source: Nature Communications; 1/24/2025, Vol. 16 Issue 1, p1-15, 15p

Subject Terms: ELONGATION factors (Biochemistry), GENETIC engineering, HISTONE acetylation, GENETIC transcription, CANCER chemotherapy

Organoruthenium-catalyzed chemical protein synthesis to elucidate the functions of epigenetic modifications on heterochromatin factorsElectronic supplementary information (ESI) available. See DOI: 10.1039/d1sc00731a

Authors: Kamo, Naoki, Kujirai, Tomoya, Kurumizaka, Hitoshi, Murakami, Hiroshi, Hayashi, Gosuke, Okamoto, Akimitsu

Source: Chemical science. 12(16):5926-5937

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100120018163.0x000001&indx=1&recIds=ETOCvdc_100120018163.0x000001

Structural insights into how Cas9 targets nucleosomes.

Authors: Nagamura, Reina, Kujirai, Tomoya, Kato, Junko, Shuto, Yutaro, Kusakizako, Tsukasa, Hirano, Hisato, Endo, Masaki, Toki, Seiichi, Saika, Hiroaki, Kurumizaka, Hitoshi, Nureki, Osamu

Source: Nature Communications; 12/30/2024, Vol. 15 Issue 1, p1-10, 10p

Subject Terms: GENOME editing, LIFE sciences, CRISPRS, GEL electrophoresis, DNA, CHROMATIN, ENDONUCLEASES

Structural Transition of the Nucleosome during Transcription Elongation.

Authors: Kujirai, Tomoya^1,2 (AUTHOR) haruhiko.ehara@riken.jp, Ehara, Haruhiko² (AUTHOR) shunichi.sekine@riken.jp, Sekine, Shun-ichi² (AUTHOR), Kurumizaka, Hitoshi^1,2 (AUTHOR) kurumizaka@iqb.u-tokyo.ac.jp

Source: Cells (2073-4409). May2023, Vol. 12 Issue 10, p1388. 19p.

Subject Terms: *HISTONES, *RNA polymerase II, *RNA polymerases, *TRANSGENIC organisms

Transcription through the nucleosome

Authors: Kujirai, Tomoya, Kurumizaka, Hitoshi

Source: In Current Opinion in Structural Biology April 2020 61:42-49

The N‐terminal and C‐terminal halves of histone H2A.Z independently function in nucleosome positioning and stability

Authors: Sato, Shoko, Tanaka, Naoki, Arimura, Yasuhiro, Kujirai, Tomoya, Kurumizaka, Hitoshi

Source: Genes to cells. 25(8):538-546

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100107535573.0x000001&indx=1&recIds=ETOCvdc_100107535573.0x000001

Insights into chromatin transcription from RNA polymerase II-nucleosome structures

Authors: Kujirai, Tomoya

Source: Seikagaku. 92(4):527-535

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCRN624672937&indx=1&recIds=ETOCRN624672937

Synthetic hyperacetylation of nucleosomal histonesElectronic supplementary information (ESI) available: Synthetic procedures, experimental details and Fig. S1–S4 (PDF). See DOI: 10.1039/d0cb00029a

Authors: Kajino, Hidetoshi, Nagatani, Tomomi, Oi, Miku, Kujirai, Tomoya, Kurumizaka, Hitoshi, Nishiyama, Atsuya, Nakanishi, Makoto, Yamatsugu, Kenzo, Kawashima, Shigehiro A., Kanai, Motomu

Source: RSC chemical biology. 1(2):56-59

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100110136070.0x000001&indx=1&recIds=ETOCvdc_100110136070.0x000001

Structural insight into nucleosome transcription by RNA polymerase II with elongation factors

Authors: Ehara, Haruhiko, Kujirai, Tomoya, Fujino, Yuka, Shirouzu, Mikako, Kurumizaka, Hitoshi, Sekine, Shun-ichi

Source: Science, 2019 Feb . 363(6428), 744-747.

Access URL: https://www.jstor.org/stable/26611694

Nucleosomal DNA unwinding pathway through canonical and non-canonical histone disassembly.

Authors: Nozawa, Hikaru, Nagae, Fritz, Ogihara, Satoshi, Hirano, Rina, Yamazaki, Hirohito, Iizuka, Ryo, Akatsu, Munetaka, Kujirai, Tomoya, Takada, Shoji, Kurumizaka, Hitoshi, Uemura, Sotaro

Source: Communications Biology; 9/14/2024, Vol. 7 Issue 1, p1-9, 9p

Subject Terms: DNA denaturation, MOLECULAR dynamics, GENETIC transcription regulation, HISTONES, MOLECULAR interactions

BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A.

Authors: Hoshii, Takayuki, Kikuchi, Sota, Kujirai, Tomoya, Masuda, Takeshi, Ito, Tomoko, Yasuda, Satoshi, Matsumoto, Makoto, Rahmutulla, Bahityar, Fukuyo, Masaki, Murata, Takeshi, Kurumizaka, Hitoshi, Kaneda, Atsushi

Source: Nucleic Acids Research; 9/9/2024, Vol. 52 Issue 16, p9463-9480, 18p