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Publications

Maezawa, S., Yukawa, M., Hasegawa, K, Wang, M, Alavattam, K. G., Barski., A., De Falco T., and Namekawa S. H. Polycomb suppresses a female gene regulatory network to ensure testicular differentiation. bioRxiv 2021.01.19.427322; doi: https://doi.org/10.1101/2021.01.19.427322

Alavattam, K.G, Maezawa, S, Andreassen, P.R, and Namekawa, S.H. Meiotic sex chromosome inactivation and XY body: A phase separation hypothesis. Cell Mol Life Sci. in press

Zhou, S, Sakashita, A, Yuan, S, and Namekawa, S.H. Retrotransposons in the mammalian male germline. Sexual Reproduction, in press

Sakashita, A, Ariura, M, and Namekawa, S.H. CRISPR-mediated activation of transposable elements in embryonic stem cells. Methods Mol Biol, in press

Jay, A, Reitz, D, Namekawa, S.H, Heyer, W.D. Cancer testis antigens and genomic instability: More than immunology. DNA Repair (Amst). 2021 Aug 17;108:103214. doi: 10.1016/j.dnarep.2021.103214.

Ruth KS, Day FR, Hussain J, Martínez-Marchal A, Aiken CE, Azad A, Thompson DJ, Knoblochova L, Abe H, Tarry-Adkins JL, Gonzalez JM, Fontanillas P, Claringbould A, Bakker OB, Sulem P, Walters RG, Terao C, Turon S, Horikoshi M, Lin K, Onland-Moret NC, Sankar A, Hertz EPT, Timshel PN, Shukla V, Borup R, Olsen KW, Aguilera P, Ferrer-Roda M, Huang Y, Stankovic S, Timmers PRHJ, Ahearn TU, Alizadeh BZ, Naderi E, Andrulis IL, Arnold AM, Aronson KJ, Augustinsson A, Bandinelli S, Barbieri CM, Beaumont RN, Becher H, Beckmann MW, Benonisdottir S, Bergmann S, Bochud M, Boerwinkle E, Bojesen SE, Bolla MK, Boomsma DI, Bowker N, Brody JA, Broer L, Buring JE, Campbell A, Campbell H, Castelao JE, Catamo E, Chanock SJ, Chenevix-Trench G, Ciullo M, Corre T, Couch FJ, Cox A, Crisponi L, Cross SS, Cucca F, Czene K, Smith GD, de Geus EJCN, de Mutsert R, De Vivo I, Demerath EW, Dennis J, Dunning AM, Dwek M, Eriksson M, Esko T, Fasching PA, Faul JD, Ferrucci L, Franceschini N, Frayling TM, Gago-Dominguez M, Mezzavilla M, García-Closas M, Gieger C, Giles GG, Grallert H, Gudbjartsson DF, Gudnason V, Guénel P, Haiman CA, Håkansson N, Hall P, Hayward C, He C, He W, Heiss G, Høffding MK, Hopper JL, Hottenga JJ, Hu F, Hunter D, Ikram MA, Jackson RD, Joaquim MDR, John EM, Joshi PK, Karasik D, Kardia SLR, Kartsonaki C, Karlsson R, Kitahara CM, Kolcic I, Kooperberg C, Kraft P, Kurian AW, Kutalik Z, La Bianca M, LaChance G, Langenberg C, Launer LJ, Laven JSE, Lawlor DA, Le Marchand L, Li J, Lindblom A, Lindstrom S, Lindstrom T, Linet M, Liu Y, Liu S, Luan J, Mägi R, Magnusson PKE, Mangino M, Mannermaa A, Marco B, Marten J, Martin NG, Mbarek H, McKnight B, Medland SE, Meisinger C, Meitinger T, Menni C, Metspalu A, Milani L, Milne RL, Montgomery GW, Mook-Kanamori DO, Mulas A, Mulligan AM, Murray A, Nalls MA, Newman A, Noordam R, Nutile T, Nyholt DR, Olshan AF, Olsson H, Painter JN, Patel AV, Pedersen NL, Perjakova N, Peters A, Peters U, Pharoah PDP, Polasek O, Porcu E, Psaty BM, Rahman I, Rennert G, Rennert HS, Ridker PM, Ring SM, Robino A, Rose LM, Rosendaal FR, Rossouw J, Rudan I, Rueedi R, Ruggiero D, Sala CF, Saloustros E, Sandler DP, Sanna S, Sawyer EJ, Sarnowski C, Schlessinger D, Schmidt MK, Schoemaker MJ, Schraut KE, Scott C, Shekari S, Shrikhande A, Smith AV, Smith BH, Smith JA, Sorice R, Southey MC, Spector TD, Spinelli JJ, Stampfer M, Stöckl D, van Meurs JBJ, Strauch K, Styrkarsdottir U, Swerdlow AJ, Tanaka T, Teras LR, Teumer A, Þorsteinsdottir U, Timpson NJ, Toniolo D, Traglia M, Troester MA, Truong T, Tyrrell J, Uitterlinden AG, Ulivi S, Vachon CM, Vitart V, Völker U, Vollenweider P, Völzke H, Wang Q, Wareham NJ, Weinberg CR, Weir DR, Wilcox AN, van Dijk KW, Willemsen G, Wilson JF, Wolffenbuttel BHR, Wolk A, Wood AR, Zhao W, Zygmunt M; Biobank-based Integrative Omics Study (BIOS) Consortium; eQTLGen Consortium; Biobank Japan Project; China Kadoorie Biobank Collaborative Group; kConFab Investigators; LifeLines Cohort Study; InterAct consortium; 23andMe Research Team, Chen Z, Li L, Franke L, Burgess S, Deelen P, Pers TH, Grøndahl ML, Andersen CY, Pujol A, Lopez-Contreras AJ, Daniel JA, Stefansson K, Chang-Claude J, van der Schouw YT, Lunetta KL, Chasman DI, Easton DF, Visser JA, Ozanne SE, Namekawa SH, Solc P, Murabito JM, Ong KK, Hoffmann ER, Murray A, Roig I, Perry JRB. Genetic insights into biological mechanisms governing human ovarian ageing. Nature. 2021 Aug;596(7872):393-397. doi: 10.1038/s41586-021-03779-7. Epub 2021 Aug 4. PMID: 34349265

Abe, H., Meduri, R., Li, Z., Andreassen, P.R., and Namekawa S. H. RNF8 is not required for histone-to-protamine exchange in spermiogenesis. Biol Reprod. 2021 Jul 5:ioab132.

Horisawa-Takada, Y., Kodera, C., Takemoto, K., Sakashita, A., Horisawa, K., Maeda, R., Shimada, R., Usuki, S., Fujimura, S., Tani, N., Matsuura, K., Akiyama, T., Suzuki, A., Niwa, H., Tachibana, M., Ohba, T., Katabuchi, H., Namekawa, S. H., Araki, K., Ishiguro, K. I. Meiosis-specific ZFP541 repressor complex promotes developmental progression of meiotic prophase towards completion during mouse spermatogenesis. Nat Commun. 2021 Jun 1;12(1):3184. 

Sakashita, A., Maezawa. S., Takahashi K., Alavattam, K. G., Yukawa, M., Barski., A., Pavlicev, M., and Namekawa S. H. Endogenous retroviruses drive species-specific germline transcriptomes in mammals. Nature Structural & Molecular Biology, September 7, 2020.

Maezawa. S., Sakashita, A., Yukawa, M., Chen, X., Takahashi, K, Alavattam, K. G., Weirauch, T., Barski., A., and Namekawa S. H. Super-enhancer switching drives a burst of gene expression at the mitosis-to-meiosis transition. Nature Structural & Molecular Biology, September 7, 2020.

Yeh, Y.H, Hu, M., Nakagawa, T., Sakashita, A., Yoshida, S., Maezawa. S., and Namekawa S. H. Isolation of Murine Spermatogenic Cells Using Vybrant DyeCycle Violet-based Sorting. J Vis Exp, August 14, 2020.

Nie. Y., Wilson. A., DeFalco. T.J., Meetei A., Namekawa S. H. and Pang Q. Fancd2 is required for the repression of germline transposable elements. Reproduction 2020 159(6):659-668

Alavattam, KG., and Namekawa S.H. Licensing meiotic progression. Biol Reprod, 2020 103(1):10-12

Alavattam, KG., Abe, H., Namekawa S.H. Pioneering meiotic recombination. Genes & Development, 2020 34(5-6):395-397

Che. L., Alavattam, K. G., Stambrook P.J. Namekawa S. H. and Du. C. BRUCE preserves genomic stability in the male germline of mice. Cell Death & Differentiation, 2020 27(8):2402-2416

Abe, H., Alavattam, K. G., Pang Q., Andreassen, P. R., Hegde, R. S., and Namekawa S. H. The initiation of meiotic sex chromosome inactivation sequesters DNA damage signaling from autosomes in mouse spermatogenesis. Current Biology, 2020 30(3):408-420.e5.

Dong, J., Cao, C., Wang, X., Wen, Y., Sakashita, A., Chen, S., Zhang, J., Zhang, Y., Zhou, L, Luo,. M, Liu, M., Liao, A., Namekawa, S.H., Yuan, S., UHRF1 suppresses retrotransposon and cooperates with PRMT5 and piRNA pathway in male germ cells. Nature Communications, 2019 10(1):4705

Alavattam, K. G., Maezawa, S., Sakashita A., Khoury, H., Barski, A., Kaplan, N., and Namekawa S. H. Attenuated chromatin compartmentalization in meiosis and its maturation in sperm development. Nature Structural & Molecular Biology, 2019 26(3):175-184

Sakashita, A., Wakai, T., Kawabata, Y., Nishimura, C., Sotomaru, Y., Alavattam, K. G., Namekawa, S. H., Kono, T. XY oocytes of sex-reversed females with a Sry mutation deviate from the normal developmental process beyond the mitotic stage. Biol Reprod, 2019 100(3):697-710.

Maezawa, S., Alavattam, K. G., Tatara, M., Nagai, R., Barski, A., and Namekawa S. H. A rapidly evolved domain, the SCML2 DNA-binding (SDB) repeats, contributes to chromatin binding of mouse SCML2. Biol Reprod, 2018, 100(2):409-419.

Maezawa, S., Hasegawa, K., Alavattam, K. G., Funakoshi, M., Sato, T., Barski, A., and Namekawa S. H. SCML2 promotes heterochromatin organization in late spermatogenesis. J Cell Sci,. 2018 131(17):jcs217125

Sakashita, A., Yeh, Y.H. V., Namekawa, S. H., Lin, S-P. Epigenomic and single-cell profiling of human spermatogonial stem cells. Stem Cell Investig 2018 5:11.

Maezawa. S., Hasegawa, K., Yukawa, M., Kubo, N., Sakashita, A., Alavattam, K. G., Sin, H. S., Kartashov, A. V., Sasaki. H., Barski, A., and Namekawa S. H. SCML2 facilitate H3K27me3 to establish bivalent domains in the male germline. PNAS, 2018 115(19):4957-4962.

Alavattam, K. G., Abe, H., Sakashita A. and Namekawa S. H. Chromosome spread analyses of meiotic sex chromosome inactivation. Methods Mol Biol. 2018 1861:113-129.

Adams, S., Maezawa. S., Alavattam, K. G., Abe, H., Sakashita, A., Shroder M., Broering T. J., Price, C. M., Barski, A., Andreassen, P. R., and Namekawa S. H. RNF8 and SCML2 cooperatively regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes. PloS Genet, 2018 14(2):e1007233.

Abe, H., Alavattam, K. G., Kato Y., Castrillon D. H., Pang Q., Andreassen, P. R., and Namekawa S. H. CHEK1 coordinates DNA damage signaling and meiotic progression in the male germline of mice. Hum Mol Genet. 2018 27(7):1136-1149.

Maezawa, S., Yukawa, M., Alavattam, K. G., Barski, A., and Namekawa S. H. Dynamic reorganization of open chromatin underlies diverse transcriptomes during spermatogenesis. Nucleic Acids Res, 2018 27(7):1136-1149.

Maezawa, S., Hasegawa, K., Yukawa, M., Sakashita, A., Alavattam, K. G., Andreassen, P. R., Vidal, M., Koseki. H., Barski, A., and Namekawa S. H. PRC1 directs timely activation of germline genes in spermatogenesis. Genes Dev, 2017 31: 1693-1703.

Zhang, T., Du, W., Wilson, A. F., Namekawa, S. H., Andreassen, P. R, Ruhikanta, Meetei A., and Pang, Q. Fancd2 in vivo interaction network reveals a non-canonical role in mitochondrial function. Sci Rep, 2017 7:45626.

Alavattam, K. G., Kato, Y., Sin, H. S., Maezawa. S., Kowalski, I., Pang, Q., Andreassen, P. R., and Namekawa S. H. Elucidation of the Fanconi anemia protein network in meiosis and its function in the regulation of histone modifications. Cell Rep, 2016 17(4):1141-1157.

Sun, S., Payer, B., Namekawa S. H., An, J. Y., Press, W., Catalan-dibene, J., Sunwoo, H., and Lee, J. T. Xist imprinting is promoted by the hemizygous state in the male germline. Proc Natl Acad Sci U S A. 2015 112(47):14415-22.

Du, W., Amarachintha, S., Erden, O., Wilson, A., Meetei A., Andreassen, P. R., Namekawa S. H., and Pang, Q., Fancb deficiency impairs hematopoietic stem cell function. Sci Rep. 2015 5:18127

Sin, H. S., Kartashov, A. V., Hasegawa, K., Barski, A., and Namekawa S. H. Poised chromatin and bivalent domains facilitate the mitosis-to-meiosis transition in the male germline. BMC Biol, 13:53.

Kato, Y., Alavattam, K. G., Sin, H. S., Meetei A., Pang, Q., Andreassen, P. R., and Namekawa S. H. FANCB is essential in the male germline and regulates H3K9 methylation on the sex chromosomes during meiosis. Hum Mol Genet, 24(18):5234-49.

Broering, T. J., Wang, Y.-L., Pandey, R. N., Hegde R. S, Wang, S.-C and Namekawa S. H. BAZ1B is dispensable for H2AX phosphorylation on Tyrosine 142 during spermatogenesis. Biol Open 2015. 4(7):873-84.

Hu, Y. C., and Namekawa S. H. Functional significance of the sex chromosomes during spermatogenesis. Reproduction 2015 149(6): R265-R277.

Zhang, T., Wilson, A. F., Mahmood, Ali A., Namekawa, S. H., Andreassen, P. R, Ruhikanta, Meetei A., and Pang, Q. Loss of Faap20 Causes Hematopoietic Stem and Progenitor Cell Depletion in Mice Under Genotoxic Stress. Stem Cells, 2015 33(7):2320-2330.

Hasegawa, K., Sin, H. S., Maezawa, S., Broering, T.J., Kartashov, A. V., Alavattam, K. G., Ichijima, Y., Zhang, F., Bacon, W. C., Greis, K. D., Andreassen, P. R., Barski, A., and Namekawa S. H. SCML2 establishes the male germline-specific epigenome through regulation of histone H2A ubiquitination. Dev Cell, 2015 32(5):574-88.

Broering, T. J., Alavattam, K. G., Sadreyev, R. I., Ichijima, Y., Kato, Y., Hasegawa, K., Camerini-Otero, R. D., Lee, J. T., Andreassen, P. R., and Namekawa S. H. BRCA1 establishes DNA damage signaling and pericentric heterochromatin of the X chromosome in male meiosis. J Cell Biol., 2014 205(5):663-75.

Namekawa, S. H. Slide preparation method to preserve three-dimensional chromatin architecture of testicular germ cells. J Vis Exp., 2013 (83):e50819.

Hasegawa, K., Namekawa, S. H. and Saga, Y. MEK/ERK signaling directly and indirectly contributes to the cyclical self-renewal of spermatogonial stem cells. 2013 Stem Cells, ;31(11):2517-27.

Sin, H. S., and Namekawa, S. H. The great escape: active genes on inactive sex chromosomes and their evolutionary implications. Epigenetics, 2013 Sep;8(9):887-92.

Sin, H. S., Barski, A., Zhang, F., Kartashov, A. V., Nussenzweig, A., Chen, J., Andreassen, P. R., and Namekawa, S. H. RNF8 regulates active epigenetic modifications and escape gene activation from inactive sex chromosomes in postmeiotic spermatids. Genes Dev, 2012 26(24):2737-2748

Wu, Q., Song, R., Ortogero, N., Zheng, H., Evanoff, R., Small, C. L., Griswold, M. D., Namekawa, S. H., Royo, H., Turner, J. M., Yan, W. The RNase III enzyme DROSHA is essential for microRNA production and spermatogenesis. J Biol Chem, 2012 287(30):25173-90.

Ichijima, Y., Sin, H. S., and Namekawa, S. H. Sex chromosome inactivation in germ cells: Emerging roles of DNA damage response pathways. Cell. Mol. Life. Sci, 2012 69(15):2559-72.

Sin, H. S., Ichijima, Y., Koh, E., Namiki, M., and Namekawa, S. H. Human post meiotic sex chromatin and its impact on sex chromosome evolution. Genome Res, 2012 22(5):827-36.

Anguera, M. C., Ma, W., Clift, D., Namekawa, S. H., Kelleher III, R. J, and Lee, J. T. Tsx produces a long noncoding RNA and has general functions in the germline, stem cells, and brain. PloS Genet,. 2011 Sep;7(9):e1002248.

Payer, B., Lee, J. T., and Namekawa, S. H. X-inactivation and X-reactivation: Epigenetic hallmarks of mammalian reproduction and pluripotent stem cells. Hum Genet, 2011 130(2):265-80.

Ichijima, Y., Ichijima, M., Lou, Z., Nussenzweig, A., Camerini-Otero, R. D., Chen, J., Andreassen, P. R., and Namekawa, S. H. MDC1 directs chromosome-wide silencing of the sex chromosomes in male germ cells. Genes Dev, 2011 25(9):959-71

Namekawa, S. H., and Lee, J. T. Detection of nascent RNA, single-copy DNA, and protein localization by immunoFISH in murine germ cells and pre-implantation embryos. Nature Protocols. 2011 6(3):270-84.

Nordstrand, L. M., Svärd, J., Larsen, E., Nilsen, A., Ougland, R., Furu, K., Lien, G. F., Rognes, T., Namekawa, S. H., Lee, J. T. and Klungland, A. Mice lacking alkbh1 display sex-ratio distortion and unilateral eye defects. PloS One, 2011 5(11):e13827.

Namekawa, S. H., Payer, B., Huynh K. D., Jaenisch, R., and Lee, J. T. Two-step imprinted X-inactivation: Repeat vs genic silencing in the mice. Mol Cell Biol 2010 30(13):3187-205.

Zhang, L. F., Ogawa, Y., Ahn, J. Y., Namekawa, S. H., Silva, S. S., and Lee, J. T. Telomeric RNAs mark sex chromosomes in stem cells. Genetics. 2009 182(3):685-98. Epub 2009 Apr 20.

Namekawa, S. H. and Lee, J. T. XY and ZW: is meiotic sex chromosome inactivation the rule in evolution? PLoS Genet. 2009 5(5):e1000493.

Sugawara H., Iwabata K., Koshiyama A., Yanai T., Daikuhara Y., Namekawa S. H., Hamada F. N., and Sakaguchi K. Coprinus cinereus Mer3 is required for synaptonemal complex formation during meiosis. Chromosoma, 2009 118, 127-139.

Ishii, S., Koshiyama, A., Hamada, F. N., Nara, T. Y., Iwabata, K., Sakaguchi, K.,* and Namekawa, S. H. Interaction between Lim15/Dmc1 and the homologue of the large subunit of CAF-1 – a molecular link between recombination and chromatin assembly during meiosis. FEBS J, 275, 2032-2041

Namekawa, S. H., VandeBerg, J. L., McCarrey, J. R., and Lee, J. T. Sex chromosome silencing in the marsupial male germ line. Proc Natl Acad Sci U S A, 2007 104, 9730-9735.

Kim, S., Namekawa, S. H., Niswander, L. M., Ward, J. O., Lee, J. T., Bardwell, V. J., and Zarkower, D. A mammal-specific Doublesex homolog associates with male sex chromatin and is required for male meiosis. PLoS Genet, 2007 3, e62.

Hamada, F. N., Koshiyama, A., Namekawa, S. H., Ishii, S., Iwabata, K., Nara, T., Yamaguchi, T., Ishizaki, T., Sakaguchi, K., and Sawado, T. Coprinus Proliferating Cell Nuclear Antigen (PCNA) interacts with Lim15/Dmc1 but does not stimulate its strand transfer activity. Biochem Biophys Res Commun, 2007 352, 836-842

Koshiyama, A, Hamada, F.N., Namekawa, S.H., Iwabata, K., Sugawara, H., Sakamoto, A., Ishizaki, T., and Sakaguchi, K. Sumoylation of a meiosis-specific RecA homolog, Lim15/Dmc1, via interaction with the small ubiquitin-related modifier (SUMO)-conjugating enzyme Ubc9. FEBS J, 2006 273, 4003-4012.

Namekawa, S. H., Park, P. J., Zhang, L. F., Shima, J. E., McCarrey, J. R., Griswold, M. D., and Lee, J. T. Postmeiotic sex chromatin in the male germline of mice. Curr Biol, 2006 16, 660-667.

Namekawa, S. H., Iwabata, K., Sugawara, H., Hamada, F. N., Koshiyama, A., Chiku, H., Kamada, T., and Sakaguchi, K. Knockdown of LIM15/DMC1 in the Mushroom Coprinus cinereus by double-stranded RNA-mediated gene silencing. Microbiology, 2005 151, 3669-3678

Iwabata, K., Koshiyama, A., Yamaguchi, T., Sugawara, H., Hamada, F. N., Namekawa, S. H., Ishii S, Ishizaki T, Chiku, H., Nara, T., and Sakaguchi, K. DNA topoisomerase II interacts with Lim15/Dmc1 in meiosis. Nucleic Acids Res, 2005 33, 5809-5818

Yamaguchi, T., Namekawa, S. H., Hamada, F. N., Kasai, N., Nara, T., Watanabe, K., Iwabata, K., Ishizaki, T., Ishii, S., Koshiyama, A., Inagaki, S., Kimura, S., and Sakaguchi, K. Expression of flap endonuclease-1 during meiosis in a basidiomycete, Coprinus cinereus. Fungal Genet Biol, 2004 41, 493-500.

Namekawa, S. H., Hamada, F. N., and Sakaguchi, K. Latest frontiers of meiosis research in Coprinus cinereus. Seikagaku (in Japanese), 2004 76, 1450-1454.

Namekawa, S., Hamada, F., Ishii, S., Ichijima, Y., Yamaguchi, T., Nara, T., Kimura, S., Ishizaki, T., Iwabata, K., Koshiyama, A., Teraoka, H., and Sakaguchi, K. Coprinus cinereus DNA ligase I during meiotic development. Biochim Biophys Acta, 2003 1627, 47-55.

Namekawa, S., Hamada, F., Sawado, T., Ishii, S., Nara, T., Ishizaki, T., Ohuchi, T., Arai, T., and Sakaguchi, K. Dissociation of DNA polymerase alpha-primase complex during meiosis in Coprinus cinereus. Eur J Biochem, 2003 270, 2137-2146.

Namekawa, S., Ichijima, Y., Hamada, F., Kasai, N., Iwabata, K., Nara, T., Teraoka, H., Sugawara, F., and Sakaguchi, K. DNA ligase IV from a basidiomycete, Coprinus cinereus, and its expression during meiosis. Microbiology, 2003 149, 2119-2128.

Kimura, S., Uchiyama, Y., Kasai, N., Namekawa, S., Saotome, A., Ueda, T., Ando, T., Ishibashi, T., Oshige, M., Furukawa, T., et al. A novel DNA polymerase homologous to Escherichia coli DNA polymerase I from a higher plant, rice (Oryza sativa L.). Nucleic Acids Res, 2002 30, 1585-1592.

Hamada, F., Namekawa, S., Kasai, N., Nara, T., Kimura, S., Sugawara, F., and Sakaguchi, K. Proliferating cell nuclear antigen from a basidiomycete, Coprinus cinereus. Alternative truncation and expression in meiosis. Eur J Biochem, 2002 269, 164-174.

Ishizaki, T., Tosaka, A., Nara, T., Aoshima, N., Namekawa, S., Watanabe, K., Hamada, F., Omori, A., and Sakaguchi, K. Leucine aminopeptidase during meiotic development. Eur J Biochem, 2002 269, 826-832.

Nara, T., Hamada, F., Namekawa, S., and Sakaguchi, K. Strand exchange reaction in vitro and DNA-dependent ATPase activity of recombinant LIM15/DMC1 and RAD51 proteins from Coprinus cinereus. Biochem Biophys Res Commun, 2001 285, 92-97.