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D. DEPARTMENT OF
POPULATION GENETICS
D-c. Division of Theoretical Genetics - Sumio
Sugano Group
RESEARCH
ACTIVITIES
(1)
Functional Genomics Based on the full-length cDNA
collection
Sumio Sugano
--We have been
constructing full-length cDNA libraries from
various human tissues and cells using oligo-capping
method. From these libraries, we have been
isolating a number of clones and determining their
5' end sequences. Using these 5' end sequence data,
we have selected about 30,000 clones and determined
entire sequences. Part of the result of this
activity and initial analysis of the fully
sequenced clones were published this
year11). We also gathered an
international consortium, H-invitational, for the
annotation of human full-length cDNAs with Takashi
Gojobori and Nomura Nobuo and made H-invitational
database6).
--The 5' end sequence
data of full-length cDNAs are indispensable for
identifying transcription start sites (tss). We
made and are maintaining database of tss, DBTSS,
with Kenta Nakai15). Using this
database, we compared human and mouse tss and
devised and evaluated promoter prediction
programs13) 14) 2). Furthermore, we
collaborated with Shin-Ichi Hashimoto and developed
a method to isolate a 5' tags of
mRNAs4).
--We also collaborated
with various groups to make full-length cDNA
libraries and to collect full-length cDNA clones.
This includes, Zebrafish3), red
alga7), and malaria16). We
also helped isolating various full-length cDNA
clones1) 5) 8) 9) 10) 17) 18).
--Finally, we made
very interesting finding that some of the small
open reading frames (ORF) within 5' un-translated
region (UTR) of mRNA do make small proteins. About
half of the mRNAs have small ORF in their 5' UTR.
Thus, there is a possibility that unexpectedly high
number of small proteins is translated from 5'
UTR.
PUBLICATIONS
Papers
1. Adachi, S., Jigami, T., Yasui, T.,
Nakano, T., Ohwada, S., Omori, Y., Sugano, S.,
Ohkawara, B., Shibuya, H., Nakamura, T. and
Akiyama, T., (2004). Role of a BCL9-related
beta-catenin-binding protein, B9L, in tumorigenesis
induced by aberrant activation of Wnt signaling.
Cancer Res. 64, 8496-8501.
2. Bajic, VB., Tan, SL., Suzuki, Y. and Sugano, S.
(2004). Promoter prediction analysis on the whole
human genome. Nat Biotechnol. 22,
1467-1473.
3. Gerhard, DS., Wagner, L., Feingold, EA.,
Shenmen, CM., Grouse, LH., Schuler, G., Klein, SL.,
Old, S., Rasooly, R., Good, P., Guyer, M., Peck,
AM., Derge, JG., Lipman, D., Collins, FS., Jang,
W., Sherry, S., Feolo, M., Misquitta, L., Lee, E.,
Rotmistrovsky, K., Greenhut, SF., Schaefer, CF.,
Buetow, K., Bonner, TI., Haussler, D., Kent, J.,
Kiekhaus, M., Furey, T., Brent, M., Prange, C.,
Schreiber, K., Shapiro, N., Bhat, NK., Hopkins,
RF., Hsie, F., Driscoll, T., Soares, MB., Casavant,
TL., Scheetz, TE., Brown-stein, MJ., Usdin, TB.,
Toshiyuki, S., Carninci, P., Piao, Y., Dudekula,
DB., Ko, MS., Kawakami, K., Suzuki, Y., Sugano, S.,
Gruber, CE., Smith, MR., Simmons, B., Moore, T.,
Waterman, R., Johnson, SL., Ruan, Y., Wei, CL.,
Mathavan, S., Gunaratne, PH., Wu, J., Garcia, AM.,
Hulyk, SW., Fuh, E., Yuan, Y., Sneed, A., Kowis,
C., Hodgson, A., Muzny, DM., McPherson, J., Gibbs,
RA., Fahey, J., Helton, E., Ketteman, M., Madan,
A., Rodrigues, S., Sanchez, A., Whiting, M.,
Madari, A., Young, AC., Wetherby, KD., Granite,
SJ., Kwong, PN., Brinkley, CP., Pearson, RL.,
Bouffard, GG., Blakesly, RW., Green, ED., Dickson,
MC., Rodriguez, AC., Grimwood, J., Schmutz, J.,
Myers, RM., Butterfield, YS., Griffith, M.,
Griffith, OL., Krzywinski, MI., Liao, N., Morrin,
R., Palmquist, D., Petrescu, AS., Skalska, U.,
Smailus, DE., Stott, JM., Schnerch, A., Schein,
JE., Jones, SJ., Holt, RA., Baross, A., Marra, MA.,
Clifton, S., Makowski, KA., Bosak, S. and Malek, J.
(2004). MGC Project Team. The status, quality, and
expansion of the NIH full-length cDNA project: the
Mammalian Gene Collection (MGC). Genome Res.
14, 2121-2127.
4. Hashimoto, SI., Suzuki, Y., Kasai, Y.,
Morohoshi, K., Yamada, T., Sese, J., Morishita, S.,
Sugano, S. and Matsushima, K. (2004). 5'-end SAGE
for the analysis of transcriptional start sites.
Nat Biotechnol. 22, 1146-1149, Epub Aug
8.
5. Huang, DY., Kuo, YY., Lai, JS., Suzuki, Y.,
Sugano, S. and Chang, ZF. (2004). GATA-1 and NF-Y
cooperate to mediate erythroid-specific
transcription of Gfi-1B gene. Nucleic Acids Res.
32, 3935-3946.
6. Imanishi, T., Itoh, T., Suzuki, Y., O'Donovan,
C., Fukuchi, S., Koyanagi, KO., Barrero, RA.,
Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., Yura,
K., Miyazaki, S., Ikeo, K., Homma, K., Kasprzyk,
A., Nishikawa, T., Hirakawa, M., Thierry-Mieg, J.,
Thierry-Mieg, D., Ashurst, J., Jia, L., Nakao, M.,
Thomas, MA., Mulder, N., Karavidopoulou, Y., Jin,
L., Kim, S., Yasuda, T., Lenhard, B., Eveno, E.,
Suzuki, Y., Yamasaki, C., Takeda, JI., Gough, C.,
Hilton, P., Fujii, Y., Sakai, H., Tanaka, S., Amid,
C., Bellgard, M., Bonaldo, Md, M., Bono, H.,
Bromberg, SK., Brookes, AJ., Bruford, E., Carninci,
P., Chelala, C., Couillault, C., Souza, SJ.,
Debily, MA., Devignes, MD., Dubchak, I., Endo, T.,
Estreicher, A., Eyras, E., Fukami-Kobayashi, K., R,
Gopinath, G., Graudens, E., Hahn, Y., Han, M., Han,
ZG., Hanada, K., Hanaoka, H., Harada, E.,
Hashimoto, K., Hinz, U., Hirai, M., Hishiki, T.,
Hopkinson, I., Imbeaud, S., Inoko, H., Kanapin, A.,
Kaneko, Y., Kasukawa, T., Kelso, J., Kersey, P.,
Kikuno, R., Kimura, K., Korn, B., Kuryshev, V.,
Makalowska, I., Makino, T., Mano, S.,
Mariage-Samson, R., Mashima, J., Matsuda, H.,
Mewes, HW., Minoshima, S., Nagai, K., Nagasaki, H.,
Nagata, N., Nigam, R., Ogasawara, O., Ohara, O.,
Ohtsubo, M., Okada, N., Okido, T., Oota, S., Ota,
M., Ota, T., Otsuki, T., Piatier-Tonneau, D.,
Poustka, A., Ren, SX., Saitou, N., Sakai, K.,
Sakamoto, S., Sakate, R., Schupp, I., Servant, F.,
Sherry, S., Shiba, R., Shimizu, N., Shimoyama, M.,
Simpson, AJ., Soares, B., Steward, C., Suwa, M.,
Suzuki, M., Takahashi, A., Tamiya, G., Tanaka, H.,
Taylor, T., Terwilliger, JD., Unneberg, P.,
Veeramachaneni, V., Watanabe, S., Wilming, L.,
Yasuda, N., Yoo, HS., Stodolsky, M., Makalowski,
W., Go, M., Nakai, K., Takagi, T., Kanehisa, M.,
Sakaki, Y., Quackenbush, J., Okazaki, Y.,
Hayashizaki, Y., Hide, W., Chakraborty, R.,
Nishikawa, K., Sugawara, H., Tateno, Y., Chen, Z.,
Oishi, M., Tonellato, P., Apweiler, R., Okubo, K.,
Wagner, L., Wiemann, S., Strausberg, RL., Isogai,
T., Auffray, C., Nomura, N., Gojobori, T. and
Sugano, S. (2004). Integrative Annotation of 21,037
Human Genes Validated by Full-Length cDNA Clones.
PLoS Biol. Apr 20 [Epub ahead of
print].
7. Matsuzaki, M., Misumi, O., Shin-I, T., Maruyama,
S., Takahara, M., Miyagishima, SY., Mori, T.,
Nishida, K., Yagisawa, F., Nishida, K., Yoshida,
Y., Nishimura, Y., Nakao, S., Kobayashi, T.,
Momoyama, Y., Higashiyama, T., Minoda, A., Sano,
M., Nomoto, H., Oishi, K., Hayashi, H., Ohta, F.,
Nishizaka, S., Haga, S., Miura, S., Morishita, T.,
Kabeya, Y., Terasawa, K., Suzuki, Y., Ishii, Y.,
Asakawa, S., Takano, H., Ohta, N., Kuroiwa, H.,
Tanaka, K., Shimizu, N., Sugano, S., Sato, N.,
Nozaki, H., Ogasawara, N., Kohara, Y. and Kuroiwa,
T. (2004). Genome sequence of the ultrasmall
unicellular red alga Cyanidioschyzon merolae 10D.
Nature. 428, 653-657.
8. Niida, A., Hiroko T., Kasai, M., Furukawa, Y.,
Nakamura, Y., Suzuki, Y., Sugano, S., Akiyama, T.
(2004). DKK1, a negative regulator of Wnt
signaling, is a target of the beta-catenin/TCF
pathway. Oncogene. 23, 8520-8526.
9. Noma, T., Yoshizawa, I., Sugano, S., Ogawa, N.
and Kawano, Y. (2004). Somatropin promotes
dermatophagoides farinae-specific IgE generation
independently of IL-4 and IL-10. Asian Pac J
Allergy Immunol. 22, 133-142.
10. Nonaka, H., Sugano, S. and Miyajima, A. (2004).
Serial analysis of gene expression in sinusoidal
endothelial cells from normal and injured mouse
liver. Biochem Biophys Res Commun. 324,
15-24.
11. Ota ,T., Suzuki, Y., Nishikawa, T., Otsuki, T.,
Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K.,
Sato, H., Nagai, K., Kimura, K., Makita, H.,
Sekine, M., Obayashi, M., Nishi, T., Shibahara, T.,
Tanaka, T., Ishii, S., Yamamoto, J., Saito, K.,
Kawai, Y., Isono, Y., Nakamura, Y., Nagahari, K.,
Murakami, K., Yasuda, T., Iwayanagi, T., Wagatsuma,
M., Shiratori, A., Sudo, H., Hosoiri, T., Kaku, Y.,
Kodaira, H., Kondo, H., Sugawara, M., Takahashi,
M., Kanda, K., Yokoi, T., Furuya, T., Kikkawa, E.,
Omura, Y., Abe, K., Kamihara, K., Katsuta, N.,
Sato, K., Tanikawa, M., Yamazaki, M., Ninomiya, K.,
Ishibashi, T., Yamashita, H., Murakawa, K.,
Fujimori, K., Tanai, H., Kimata, M., Watanabe, M.,
Hiraoka, S., Chiba, Y., Ishida, S., Ono, Y.,
Takiguchi, S., Watanabe, S., Yosida, M., Hotuta,
T., Kusano, J., Kanehori, K., Takahashi-Fujii, A.,
Hara, H., Tanase, TO., Nomura, Y., Togiya, S.,
Komai, F., Hara, R., Takeuchi, K., Arita, M.,
Imose, N., Musashino, K., Yuuki, H., Oshima, A.,
Sasaki, N., Aotsuka, S., Yoshikawa, Y., Matsunawa,
H., Ichihara, T., Shiohata, N., Sano, S., Moriya,
S., Momiyama, H., Satoh, N., Takami, S., Terashima,
Y., Suzuki, O., Nakagawa, S., Senoh, A., Mizoguchi,
H., Goto, Y., Shimizu, F., Wakebe, H., Hishigaki,
H., Watanabe, T., Sugiyama, A., Takemoto, M.,
Kawakami, B., Yamazaki, M., Watanabe, K., Kumagai,
A., Itakura, S., Fukuzumi, Y., Fujimori, Y.,
Komiyama, M., Tashiro, H., Tanigami, A., Fujiwara,
T., Ono, T., Yamada, K., Fujii, Y., Ozaki, K.,
Hirao, M., Ohmori, Y., Kawabata, A., Hikiji, T.,
Kobatake, N., Inagaki, H., Ikema, Y., Okamoto, S.,
Okitani, R., Kawakami, T., Noguchi, S., Itoh, T.,
Shigeta, K., Senba, T., Matsumura, K., Nakajima,
Y., Mizuno, T., Morinaga, M., Sasaki, M., Togashi,
T., Oyama, M., Hata, H., Watanabe, M., Komatsu, T.,
Mizushima-Sugano, J., Satoh, T., Shirai, Y.,
Takahashi, Y., Nakagawa, K., Okumura, K., Nagase,
T., Nomura, N., Kikuchi, H., Masuho, Y., Yamashita,
R., Nakai, K., Yada, T., Nakamura, Y., Ohara, O.,
Isogai, T. and Sugano, S. (2004). Complete
sequencing and characterization of 21,243
full-length human cDNAs. Nat Genet. 36,
40-45.
12. Oyama, M., Itagaki, C., Hata, H., Suzuki, Y.,
Izumi, T., Natsume, T., Isobe, T. and Sugano, S.
(2004). Analysis of small human proteins reveals
the translation of upstream open reading frames of
mRNAs. Genome Res. 10B, 2048-2052.
13. Suzuki, Y., Yamashita, R., Shirota, M.,
Sakakibara, Y., Chiba, J., Mizushima-Sugano, J.,
Kel, AE., Arakawa, T., Carninci, P., Kawai, J.,
Hayashizaki, Y., Takagi, T., Nakai, K. and Sugano,
S. (2004). Large-scale collection and
characterization of promoters of human and mouse
genes. In Silico Biol. 4 (3), 0036 [Epub
ahead of print].
14. Suzuki, Y., Yamashita, R., Shirota, M.,
Sakakibara, Y., Chiba, J., Mizushima-Sugano, J.,
Nakai, K. and Sugano, S. (2004). Sequence
comparison of human and mouse genes reveals a
homologous block structure in the promoter regions.
Genome Res. 14, 1711-1718.
15. Suzuki, Y., Yamashita, R., Sugano, S. and
Nakai, K. (2004). DBTSS, DataBase of
Transcriptional Start Sites: progress report 2004.
Nucleic Acids Res. 32, D78-81.
16. Watanabe, J., Sasaki, M., Suzuki, Y. and
Sugano, S. (2004). Full-malaria 2004: an enlarged
database for comparative studies of full-length
cDNAs of malaria parasites, Plasmodium species.
Nucleic Acids Res. 32, D334-338.
17. Yamada, S., Ohira, M., Horie, H., Ando, K.,
Takayasu, H., Suzuki, Y., Sugano, S., Hirata, T.,
Goto, T., Matsunaga, T., Hiyama, E., Hayashi, Y.,
Ando, H., Suita, S., Kaneko, M., Sasaki, F.,
Hashizume, K., Ohnuma, N. and Nakagawara, A.
(2004). Expression profiling and differential
screening between hepatoblastomas and the
corresponding normal livers: identification of high
expression of the PLK1 oncogene as a
poor-prognostic indicator of hepatoblastomas.
Oncogene. 23, 5901-5911.
18. Yu, L., Frith, MC., Suzuki, Y., Peterfreund,
RA., Gearan, T., Sugano, S., Schwarzschild, MA.,
Weng, Z., Fink, JS. and Chen, JF. (2004).
Characterization of genomic organization of the
adenosine A2A receptor gene by molecular and
bioinformatics analyses. Brain Res. 1000,
156-173.
Databases
19. http://dbtss.hgc.jp/
20. https://www.jbirc.aist.go.jp/hinv/index.jsp
SOCIAL CONTRIBUTIONS AND
OTHERS
Šw‰ïŠˆ“®
1. HUGO: Council
2. HUGO Pacific: Co-Chair
3. ˆâ“`ŽqŽ¡—Êw‰ï:•]‹cˆõ
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