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24 results on '"Sakakibara, Yuta"'

1. Attention Sharing in a Virtual Environment Attracts Others

Author

Narumi, Takuji, Sakakibara, Yuta, Tanikawa, Tomohiro, Hirose, Michitaka, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, and Yamamoto, Sakae, editor

Published
2017
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3. Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2

Author

Fukuzawa, Hironobu, Takanashi, Tsukasa, Kukk, Edwin, Motomura, Koji, Wada, Shin-ichi, Nagaya, Kiyonobu, Ito, Yuta, Nishiyama, Toshiyuki, Nicolas, Christophe, Kumagai, Yoshiaki, Iablonskyi, Denys, Mondal, Subhendu, Tachibana, Tetsuya, You, Daehyun, Yamada, Syuhei, Sakakibara, Yuta, Asa, Kazuki, Sato, Yuhiro, Sakai, Tsukasa, Matsunami, Kenji, Umemoto, Takayuki, Kariyazono, Kango, Kajimoto, Shinji, Sotome, Hikaru, Johnsson, Per, Schöffler, Markus S., Kastirke, Gregor, Kooser, Kuno, Liu, Xiao-Jing, Asavei, Theodor, Neagu, Liviu, Molodtsov, Serguei, Ochiai, Kohei, Kanno, Manabu, Yamazaki, Kaoru, Owada, Shigeki, Ogawa, Kanade, Katayama, Tetsuo, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Ghosh, Aryya, Gokhberg, Kirill, Cederbaum, Lorenz S., Kuleff, Alexander I., Fukumura, Hiroshi, Kishimoto, Naoki, Rudenko, Artem, Miron, Catalin, Kono, Hirohiko, and Ueda, Kiyoshi

Published
2019
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5. Probing gaseous molecular structure by molecular-frame photoelectron angular distributions.

Author

Fukuzawa, Hironobu, Yamada, Syuhei, Sakakibara, Yuta, Tachibana, Tetsuya, Ito, Yuta, Takanashi, Tsukasa, Nishiyama, Toshiyuki, Sakai, Tsukasa, Nagaya, Kiyonobu, Saito, Norio, Oura, Masaki, Stener, Mauro, Decleva, Piero, and Ueda, Kiyoshi

Subjects
PHOTOELECTRONS, MOLECULAR structure, MOLECULAR probes, TIME-dependent density functional theory, DEPENDENCY (Psychology)
Abstract

Carbon 1s photoelectron angular distributions of an iodomethane molecule were measured relative to the recoil-frame determined by the momentum correlation between I+ and C H 3 + at photoelectron energies of 3, 6.1, and 12 eV. The energy dependent behavior of the recoil-frame photoelectron angular distributions is reproduced reasonably well by the time-dependent density functional theory with B-spline methods. We discuss potential applications of the fully differential photoelectron angular distribution measurements in the molecular frame to three-dimensional molecular structural determinations identifying the directions and lengths of the bonds. [ABSTRACT FROM AUTHOR]

Published
2019
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8. Suppression of thermal nanoplasma emission in clusters strongly ionized by hard x-rays

Author

Kumagai, Yoshiaki, Jurek, Zoltan, Xu, Weiqing, Saxena, Vikrant, Fukuzawa, Hironobu, Motomura, Koji, Iablonskyi, Denys, Nagaya, Kiyonobu, Wada, Shin-ichi, Ito, Yuta, Takanashi, Tsukasa, Yamada, Shuhei, Sakakibara, Yuta, Hiraki, Toshiyuki Nishiyama, Umemoto, Takayuki, Patanen, Minna, Bozek, John D., Dancus, Ioan, Cernaianu, Mihail, Miron, Catalin, Bauer, Tobias, Mucke, Melanie, Kukk, Edwin, Owada, Shigeki, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Son, Sang-Kil, Ziaja, Beata, Santra, Robin, Ueda, Kiyoshi, Kumagai, Yoshiaki, Jurek, Zoltan, Xu, Weiqing, Saxena, Vikrant, Fukuzawa, Hironobu, Motomura, Koji, Iablonskyi, Denys, Nagaya, Kiyonobu, Wada, Shin-ichi, Ito, Yuta, Takanashi, Tsukasa, Yamada, Shuhei, Sakakibara, Yuta, Hiraki, Toshiyuki Nishiyama, Umemoto, Takayuki, Patanen, Minna, Bozek, John D., Dancus, Ioan, Cernaianu, Mihail, Miron, Catalin, Bauer, Tobias, Mucke, Melanie, Kukk, Edwin, Owada, Shigeki, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Son, Sang-Kil, Ziaja, Beata, Santra, Robin, and Ueda, Kiyoshi

Abstract

Using electron and ion spectroscopy, we studied the electron and nuclear dynamics in similar to 50 000-atom large krypton clusters, following excitation with an intense hard x-ray pulse. Beyond the single pulse experiment, we also present the results of a time-resolved, x-ray pump-near-infrared probe measurement that allows one to learn about the time evolution of the system. After core ionization of the atoms by x-ray photons, trapped Auger and secondary electrons form a nanoplasma in which the krypton ions are embedded, according to the already published scenario. While the ion data show expected features, the electron emission spectra miss the expected pump-probe delay-dependent enhancement except for a slight enhancement in the energy range below 2 eV. Theoretical simulations help to reveal that, due to the deep trapping potential of the ions during the long time expansion accompanied by electron-ion recombination, thermal emission from the transient nanoplasma becomes quenched.

Published
2021
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9. Suppression of thermal nanoplasma emission in clusters strongly ionized by hard x-rays

Author

Kumagai, Yoshiaki, primary, Jurek, Zoltan, additional, Xu, Weiqing, additional, Saxena, Vikrant, additional, Fukuzawa, Hironobu, additional, Motomura, Koji, additional, Iablonskyi, Denys, additional, Nagaya, Kiyonobu, additional, Wada, Shin-ichi, additional, Ito, Yuta, additional, Takanashi, Tsukasa, additional, Yamada, Shuhei, additional, Sakakibara, Yuta, additional, Hiraki, Toshiyuki Nishiyama, additional, Umemoto, Takayuki, additional, Patanen, Minna, additional, Bozek, John D, additional, Dancus, Ioan, additional, Cernaianu, Mihail, additional, Miron, Catalin, additional, Bauer, Tobias, additional, Mucke, Melanie, additional, Kukk, Edwin, additional, Owada, Shigeki, additional, Togashi, Tadashi, additional, Tono, Kensuke, additional, Yabashi, Makina, additional, Son, Sang-Kil, additional, Ziaja, Beata, additional, Santra, Robin, additional, and Ueda, Kiyoshi, additional

Published
2021
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10. Sequence comparison of human and mouse genes reveals a homologous block structure in the promoter regions

Author

Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, Nakai, Kenta, and Sugano, Sumio

Subjects
Human genome -- Research, Genetic transcription -- Research, Genes -- Research, Health
Abstract

The large-scale comparative sequence analyses of putative promoter regions between human and mouse genes are presented. Results showed that the overall sequence similarity between human and mouse at neutral sites is 53-54%, while evaluating relics of ancestral repeats.

Published
2004

13. Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2

Author

30273436, Fukuzawa, Hironobu, Takanashi, Tsukasa, Kukk, Edwin, Motomura, Koji, Wada, Shin-ichi, Nagaya, Kiyonobu, Ito, Yuta, Nishiyama, Toshiyuki, Nicolas, Christophe, Kumagai, Yoshiaki, Iablonskyi, Denys, Mondal, Subhendu, Tachibana, Tetsuya, You, Daehyun, Yamada, Syuhei, Sakakibara, Yuta, Asa, Kazuki, Sato, Yuhiro, Sakai, Tsukasa, Matsunami, Kenji, Umemoto, Takayuki, Kariyazono, Kango, Kajimoto, Shinji, Sotome, Hikaru, Johnsson, Per, Schöffler, Markus S., Kastirke, Gregor, Kooser, Kuno, Liu, Xiao-Jing, Asavei, Theodor, Neagu, Liviu, Molodtsov, Serguei, Ochiai, Kohei, Kanno, Manabu, Yamazaki, Kaoru, Owada, Shigeki, Ogawa, Kanade, Katayama, Tetsuo, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Ghosh, Aryya, Gokhberg, Kirill, Cederbaum, Lorenz S., Kuleff, Alexander I., Fukumura, Hiroshi, Kishimoto, Naoki, Rudenko, Artem, Miron, Catalin, Kono, Hirohiko, Ueda, Kiyoshi, 30273436, Fukuzawa, Hironobu, Takanashi, Tsukasa, Kukk, Edwin, Motomura, Koji, Wada, Shin-ichi, Nagaya, Kiyonobu, Ito, Yuta, Nishiyama, Toshiyuki, Nicolas, Christophe, Kumagai, Yoshiaki, Iablonskyi, Denys, Mondal, Subhendu, Tachibana, Tetsuya, You, Daehyun, Yamada, Syuhei, Sakakibara, Yuta, Asa, Kazuki, Sato, Yuhiro, Sakai, Tsukasa, Matsunami, Kenji, Umemoto, Takayuki, Kariyazono, Kango, Kajimoto, Shinji, Sotome, Hikaru, Johnsson, Per, Schöffler, Markus S., Kastirke, Gregor, Kooser, Kuno, Liu, Xiao-Jing, Asavei, Theodor, Neagu, Liviu, Molodtsov, Serguei, Ochiai, Kohei, Kanno, Manabu, Yamazaki, Kaoru, Owada, Shigeki, Ogawa, Kanade, Katayama, Tetsuo, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Ghosh, Aryya, Gokhberg, Kirill, Cederbaum, Lorenz S., Kuleff, Alexander I., Fukumura, Hiroshi, Kishimoto, Naoki, Rudenko, Artem, Miron, Catalin, Kono, Hirohiko, and Ueda, Kiyoshi

Abstract

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation.

Published
2019

14. Following the Birth of a Nanoplasma Produced by an Ultrashort Hard-X-Ray Laser in Xenon Clusters

Author

Kumagai, Yoshiaki, primary, Fukuzawa, Hironobu, additional, Motomura, Koji, additional, Iablonskyi, Denys, additional, Nagaya, Kiyonobu, additional, Wada, Shin-ichi, additional, Ito, Yuta, additional, Takanashi, Tsukasa, additional, Sakakibara, Yuta, additional, You, Daehyun, additional, Nishiyama, Toshiyuki, additional, Asa, Kazuki, additional, Sato, Yuhiro, additional, Umemoto, Takayuki, additional, Kariyazono, Kango, additional, Kukk, Edwin, additional, Kooser, Kuno, additional, Nicolas, Christophe, additional, Miron, Catalin, additional, Asavei, Theodor, additional, Neagu, Liviu, additional, Schöffler, Markus S., additional, Kastirke, Gregor, additional, Liu, Xiao-jing, additional, Owada, Shigeki, additional, Katayama, Tetsuo, additional, Togashi, Tadashi, additional, Tono, Kensuke, additional, Yabashi, Makina, additional, Golubev, Nikolay V., additional, Gokhberg, Kirill, additional, Cederbaum, Lorenz S., additional, Kuleff, Alexander I., additional, and Ueda, Kiyoshi, additional

Published
2018
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15. Following the Birth of a Nanoplasma Produced by an Ultrashort Hard-X-Ray Laser in Xenon Clusters

Author

30273436, Kumagai, Yoshiaki, Fukuzawa, Hironobu, Motomura, Koji, Iablonskyi, Denys, Nagaya, Kiyonobu, Wada, Shin-ichi, Ito, Yuta, Takanashi, Tsukasa, Sakakibara, Yuta, You, Daehyun, Nishiyama, Toshiyuki, Asa, Kazuki, Sato, Yuhiro, Umemoto, Takayuki, Kariyazono, Kango, Kukk, Edwin, Kooser, Kuno, Nicolas, Christophe, Miron, Catalin, Asavei, Theodor, Neagu, Liviu, Schöffler, Markus S., Kastirke, Gregor, Liu, Xiao-jing, Owada, Shigeki, Katayama, Tetsuo, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Golubev, Nikolay V., Gokhberg, Kirill, Cederbaum, Lorenz S., Kuleff, Alexander I., Ueda, Kiyoshi, 30273436, Kumagai, Yoshiaki, Fukuzawa, Hironobu, Motomura, Koji, Iablonskyi, Denys, Nagaya, Kiyonobu, Wada, Shin-ichi, Ito, Yuta, Takanashi, Tsukasa, Sakakibara, Yuta, You, Daehyun, Nishiyama, Toshiyuki, Asa, Kazuki, Sato, Yuhiro, Umemoto, Takayuki, Kariyazono, Kango, Kukk, Edwin, Kooser, Kuno, Nicolas, Christophe, Miron, Catalin, Asavei, Theodor, Neagu, Liviu, Schöffler, Markus S., Kastirke, Gregor, Liu, Xiao-jing, Owada, Shigeki, Katayama, Tetsuo, Togashi, Tadashi, Tono, Kensuke, Yabashi, Makina, Golubev, Nikolay V., Gokhberg, Kirill, Cederbaum, Lorenz S., Kuleff, Alexander I., and Ueda, Kiyoshi

Abstract

X-ray free-electron lasers (XFELs) made available a new regime of x-ray intensities, revolutionizing the ultrafast structure determination and laying the foundations of the novel field of nonlinear x-ray optics. Although earlier studies revealed nanoplasma formation when an XFEL pulse interacts with any nanometer-scale matter, the formation process itself has never been decrypted and its timescale was unknown. Here we show that time-resolved ion yield measurements combined with a near-infrared laser probe reveal a surprisingly ultrafast population (∼ 12 fs), followed by a slower depopulation (∼ 250 fs) of highly excited states of atomic fragments generated in the process of XFEL-induced nanoplasma formation. Inelastic scattering of Auger electrons and interatomic Coulombic decay are suggested as the mechanisms populating and depopulating, respectively, these excited states. The observed response occurs within the typical x-ray pulse durations and affects x-ray scattering, thus providing key information on the foundations of x-ray imaging with XFELs.

Published
2018

17. Evidence for Efficient Pathway to Produce Slow Electrons by Ground-state Dication in Clusters

Author

You, Daehyun, primary, Fukuzawa, Hironobu, additional, Sakakibara, Yuta, additional, Takanashi, Tsukasa, additional, Ito, Yuta, additional, Maliyar, Gianluigi G., additional, Motomura, Koji, additional, Nagaya, Kiyonobu, additional, Nishiyama, Toshiyuki, additional, Asa, Kazuki, additional, Sato, Yuhiro, additional, Saito, Norio, additional, Oura, Masaki, additional, Schöffler, Markus, additional, Kastirke, Gregor, additional, Hergenhahn, Uwe, additional, Stumpf, Vasili, additional, Gohkberg, Kirill, additional, Kuleff, Alexander I., additional, Cederbaum, Lorenz S., additional, and Ueda, Kiyoshi, additional

Published
2017
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18. Distinct class of putative 'non-conserved' promoters in humans: Comparative studies of alternative promoters of human and mouse genes

Author

Tsuritani, Katsuki, Irie, Takuma, Yamashita, Riu, Sakakibara, Yuta, Sugano, Sumio, Nakai, Kenta, Suzuki, Yutaka, Wakaguri, Hiroyuki, Kanai, Akinori, and Mizushima-Sugano; Junko

Subjects
Animal genetics -- Research, Human genetics -- Research, Genetic research, Health
Abstract

Large-scale comparative studies of putative alternative promoters (PAPs) between human and mouse counterpart genes are described. The study of the PAPs suggests that there are two distinct classes of promoters in humans, with one class of promoters emerging frequently during evolution.

Published
2007

19. Ultrafast Coulomb explosion of a diiodomethane molecule induced by an X-ray free-electron laser pulse

Author

Takanashi, Tsukasa, primary, Nakamura, Kosuke, additional, Kukk, Edwin, additional, Motomura, Koji, additional, Fukuzawa, Hironobu, additional, Nagaya, Kiyonobu, additional, Wada, Shin-ichi, additional, Kumagai, Yoshiaki, additional, Iablonskyi, Denys, additional, Ito, Yuta, additional, Sakakibara, Yuta, additional, You, Daehyun, additional, Nishiyama, Toshiyuki, additional, Asa, Kazuki, additional, Sato, Yuhiro, additional, Umemoto, Takayuki, additional, Kariyazono, Kango, additional, Ochiai, Kohei, additional, Kanno, Manabu, additional, Yamazaki, Kaoru, additional, Kooser, Kuno, additional, Nicolas, Christophe, additional, Miron, Catalin, additional, Asavei, Theodor, additional, Neagu, Liviu, additional, Schöffler, Markus, additional, Kastirke, Gregor, additional, Liu, Xiao-Jing, additional, Rudenko, Artem, additional, Owada, Shigeki, additional, Katayama, Tetsuo, additional, Togashi, Tadashi, additional, Tono, Kensuke, additional, Yabashi, Makina, additional, Kono, Hirohiko, additional, and Ueda, Kiyoshi, additional

Published
2017
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20. Femtosecond Time-resolved Study on Nanoplasma Dynamics of Xenon Clusters Irradiated with High Intensity Hard X-rays at SACL

Author

Kumagai, Yoshiaki, primary, Fukuzawa, Hironobu, additional, Motomura, Koji, additional, Iablonskyi, Denis, additional, Nagaya, Kiyonobu, additional, Wada, Shin-ich, additional, Ito, Yuta, additional, Takanashi, Tsukasa, additional, Sakakibara, Yuta, additional, You, Daehyun, additional, Nishiyama, Toshiyuki, additional, Asa, Kazuki, additional, Sato, Yuhiro, additional, Umemoto, Takayuki, additional, Kariyazono, Kango, additional, Kukk, Edwin, additional, Kooser, Kuno, additional, Nicolas, Christophe, additional, Miron, Catalin, additional, Asavei, Theodor, additional, Neagu, Liviu, additional, Schöffler, Markus, additional, Kastirke, Gregor, additional, Liu, Xiao-jing, additional, Owada, Shigeki, additional, Katayama, Tetsuo, additional, Togashi, Tadashi, additional, Tono, Kensuke, additional, Yabashi, Makina, additional, Yao, Makoto, additional, and Ueda, Kiyoshi, additional

Published
2016
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21. Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome

Author

Sakakibara, Yuta, primary, Irie, Takuma, additional, Suzuki, Yutaka, additional, Yamashita, Riu, additional, Wakaguri, Hiroyuki, additional, Kanai, Akinori, additional, Chiba, Joe, additional, Takagi, Toshihisa, additional, Mizushima-Sugano, Junko, additional, Hashimoto, Shin-ichi, additional, Nakai, Kenta, additional, and Sugano, Sumio, additional

Published
2007
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22. Large-Scale Collection and Characterization of Promoters of Human and Mouse Genes.

Author

Suzuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, Kel, Alexander E., Arakawa, Takahiro, Carninci, Piero, Kawai, Jun, Hayashizaki, Yoshihide, Takagi, Toshihisa, Nakai, Kenta, and Sugano, Sumio

Subjects
NUCLEOTIDE sequence, GENES, DNA, TRANSCRIPTION factors, GENETIC transcription, GENETIC code
Abstract

We report the generation and initial characterization of a large-scale collection of sequences of putative promoter regions (PPRs) of human and mouse genes. Based on our unique collection of 400,225 and 580,209 human and mouse full-length cDNAs, we determined exact transcriptional start sites (TSSs). Using positional information of the TSSs, we could retrieve adjacent sequences as PPRs for 8,793 and 6,875 human and mouse genes, respectively. The positions of the PPRs were 4 kb upstream to previously reported 5'-ends of cDNAs on average, demonstrating that full-length cDNA information is indispensable for this purpose. Among those PPRs supported by experimentally validated TSSs, 3,324 could be paired as mutually homologous genes between human and mouse and were used for the comprehensive comparative studies. The sequence identities in the proximal regions of the TSSs were 45% on average, and 22,794 putative transcription factor binding sites that are conserved between human and mouse were identified. The data resource created in the present work and the results of the sequences' initial characterization should lay the firm foundation for deciphering the transcriptional modulations of human genes. All the data were deposited and made available through a database for comparative studies, DBTSS. [ABSTRACT FROM AUTHOR]

Published
2004
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23. Real-time observation of X-ray-induced intramolecular and interatomic electronic decay in CH2I2.

Author

Fukuzawa, Hironobu, Takanashi, Tsukasa, Kukk, Edwin, Motomura, Koji, Wada, Shin-ichi, Nagaya, Kiyonobu, Ito, Yuta, Nishiyama, Toshiyuki, Nicolas, Christophe, Kumagai, Yoshiaki, Iablonskyi, Denys, Mondal, Subhendu, Tachibana, Tetsuya, You, Daehyun, Yamada, Syuhei, Sakakibara, Yuta, Asa, Kazuki, Sato, Yuhiro, Sakai, Tsukasa, and Matsunami, Kenji

Abstract

The increasing availability of X-ray free-electron lasers (XFELs) has catalyzed the development of single-object structural determination and of structural dynamics tracking in real-time. Disentangling the molecular-level reactions triggered by the interaction with an XFEL pulse is a fundamental step towards developing such applications. Here we report real-time observations of XFEL-induced electronic decay via short-lived transient electronic states in the diiodomethane molecule, using a femtosecond near-infrared probe laser. We determine the lifetimes of the transient states populated during the XFEL-induced Auger cascades and find that multiply charged iodine ions are issued from short-lived (∼20 fs) transient states, whereas the singly charged ones originate from significantly longer-lived states (∼100 fs). We identify the mechanisms behind these different time scales: contrary to the short-lived transient states which relax by molecular Auger decay, the long-lived ones decay by an interatomic Coulombic decay between two iodine atoms, during the molecular fragmentation. Understanding strong X-ray induced phenomena is important for applications of X-ray free-electron laser imaging. Here, the authors show time-resolved measurements of X-ray free-electron laser induced electronic decay of CH2I2 molecule probed with NIR pulses and identify mechanisms behind different transient states lifetimes. [ABSTRACT FROM AUTHOR]

Published
2019
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24. Sequence Comparison of Human and Mouse Genes Reveals a Homologous Block Structure in the Promoter Regions.

Author

Susuki, Yutaka, Yamashita, Riu, Shirota, Matsuyuki, Sakakibara, Yuta, Chiba, Joe, Mizushima-Sugano, Junko, Nakai, Kenta, and Sugano, Sumio

Subjects
*GENES, *PROMOTERS (Genetics), *GENETIC transcription, *NUCLEOTIDES, *TRANSCRIPTION factors, *HUMAN genetics, *ANIMAL genetics, *GENETICS
Abstract

Comparative sequence analysis was carried out for the regions adjacent to experimentally validated transcriptional start sites (TSSs), using 3324 pairs of human and mouse genes. We aligned the upstream putative promoter sequences over the 1-kb proximal regions and found that the sequence conservation could not be further extended at, on average, 510 bp upstream positions of the TSSs. This discontinuous manner of the sequence conservation revealed a ‘block’ structure in about one-third of the putative promoter regions. Consistently, we also observed that G+C content and CpG frequency were significantly different inside and outside the blocks. Within the blocks, the sequence identity was uniformly 65% regardless of their length. About 90% of the previously characterized transcription factor binding sites were located within those blocks. In 46% of the blocks, the 5′ ends were bounded by interspersed repetitive elements, some of which may have nucleated the genomic rearrangements. The length of the blocks was shortest in the promoters of genes encoding transcription factors and of genes whose expression patterns are brain specific, which suggests that the evolutional diversifications in the transcriptional modulations should be the most marked in these populations of genes. [ABSTRACT FROM AUTHOR]

Published
2004

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