ゲノム科学研究室   
    ■I. 研究業績■
　著書・総説

15. Kato H, Hiraki-Kamon K, Eitoku M, Kiyosawa H, Neeley C, and Okazaki Y: Exploring standards
　　for industrializing human induced pluripotent cells, Pharm. Bioprocess. 3, 199-213, 2015.
14. Kohama C and Kiyosawa H: Genome-wide analysis of sense-antisense transcripts,in “Non-coding RNAs
　　and Epigenetic Regulation of Gene Expression:Drivers of Natural Selection” (Morris KV ed.),
　　pp. 3-29, Caister Academic Press, Norwich, U.K., 2012.
13. Numata K and Kiyosawa H: Genome-wide impact of endogenous antisense transcripts in eukaryotes.
　　Front. Biosci. 17, 300-315, 2012.
12. 沼田興治、清澤秀孔：次世代テクノロジーがあぶりだす未知のncRNAとその機能、実験医学 29、1709-1715、2011.
11. 分担執筆：「機能性RNAの分子生物学」（編者：河合剛太、清澤秀孔）、（株）クバプロ、2010.
　（分担執筆者[あいうえお順]：牛田千里、影山裕二、金井昭夫、河合剛太、清澤秀孔、黒崎直子、剣持直哉、坂本泰一、原田和雄）
　（第１章：分担執筆、第7章：単独執筆）
10. 清澤秀孔：マウスの内在性アンチセンスRNA、蛋白質　核酸　酵素52、441-448、2007.
  9. 清澤秀孔：mRNA型非翻訳性RNA、医学のあゆみ220、196-198、2007.
  8. 清澤秀孔、土井貴裕：新規機能性RNA分子による遺伝子発現プロファイリング
　　- マイクロRNAとナチュラル・アンチセンスRNA、「医学のあゆみ – 消化器疾患　state of arts, Ver.3」、245-251、2006.
  7. 清澤秀孔：マウスにおける内在性アンチセンス転写産物の解析、
　　「機能性non-coding RNA」、pp. 99-114、（株）クバプロ、2006.
  6. 清澤秀孔：マウスゲノムとナチュラル・アンチセンスRNA、
　　「躍進するRNA研究」実験医学（増刊）22、2488-2494、2004.
  5. 清澤秀孔：マッピング−ゲノム解読以前と以降、及び、マウス完全長cDNAの重要性、　
　　医学のあゆみ200、302-306、2002.
  4. 清澤秀孔、林崎良英：マウス遺伝子エンサイクロペディア・プロジェクト　—新規疾患関連遺伝子の同定に向けて、
　　蛋白質　核酸　酵素46（臨時増刊号）、2365-2370、2001.
  3. 清澤秀孔、林崎良英：マウスゲノム解析の現状、化学と生物39、504-512、2001.
  2. 清澤秀孔：疾患遺伝子とポジショナルキャンディデートクローニング、
　　「解読されたゲノム情報をどう活かすか」現代化学増刊40、pp. 63-69、東京化学同人、2001.
  1. 和中明生、金沢賢也、清澤秀孔、今泉和則、高木勉：新規遺伝子DP5による神経細胞死の制御、
　　「神経細胞死と機能分子」、 pp. 51-67、（株）クバプロ、1998.
 
 
   
 
 
 
 
   
 
   
   
   
   
   
   
   
   
    　原著論文

49. Eitoku M, Kato H, Suganuma N, and Kiyosawa H: Markers associated with neuron-specific Ube3a imprinting during
　　neuronal differentiation of mouse embryonic stem cells. Cytotechnology，70, 45-53, 2018.
48. Mbelambela EP, Hirota R, Eitoku M, Muchanga SMJ, Kiyosawa H, Yasumitsu-Lovell K, Lawanga OL,and Suganuma N:
　　Occupation exposed to road-traffic emissions and respiratory health among Congolese transit workers,
　　particularly bus conductors, in Kinshasa: a cross-sectional study. Environ. Health Prev.Med.22, 11, 2017.
47. Noguchi N, Eitoku M, Kiyosawa H, and Suganuma N: Fibrotic Gene Expression Coexists with Alveolar Proteinosis
　　in Early Indium Lung.Inhal. Toxicol.28, 421-428, 2016.
46. Eitoku M, Suganuma N, and Kiyosawa H: Comparison of two types of non-adherent plate for neuronal differentiation
　　of mouse embryonic stem cells.Cytotechnology 68, 2761-2768, 2016.
45. Okui S, Ushida C, Kiyosawa H, and Kawai G: Sequence and structure analysis of a mirror tRNA located upstream
　　of the cytochrome oxidase I mRNA in mouse mitochondria. J. Biochem. 159, 341-350, 2016.
44. Noguchi S, Eitoku M, Moriya S, Kondo S, Kiyosawa H, Watanabe T, and Suganuma N: Regulation of Gene Expression
　　by Sodium Valproate in Epithelial-to-Mesenchymal Transition, Lung 193, 691-700, 2015.
43. Kiyosawa H, Okumura A, Okui S, Ushida C, and Kawai G: Secondary structure-based analysis
　　of mouse brain small RNA sequences obtained by using next-generation sequencing. Genomics 106, 122-128, 2015.
42. Machida M, Takeda K, Fujimaki S, Ikemune S, Ikemune S, Nesori S, Kiyosawa H, and Takemasa T:
　　RNA overshoot accompanies recovery of delayed plantaris muscle growth resulting from juvenile hindlimb suspension.
　　Adv. Exerc. Sports Physiol. 19, 39-46, 2013.
41. Takemasa T, Abe Y, Kumagai C, and Kiyosawa H: Possible involvement of microRNA-21
　　in skeletal muscle hypertrophy.Adv. Exerc. Sports Physiol.18, 5-15. 2012.
40. Takemasa T, Yakushiji N, Kikuchi DM, Deocaris C, Widodo, Machida M, and Kiyosawa H: Fundamental study
　　of detection of muscle hypertrophy-oriented gene doping by myostatin knock down using RNA interference.
　　J.Sports Sci.Med. 11, 294-303. 2012.
39. Kohama C, Kato H, Numata K, Hirose M, Takemasa T, Ogura A, and Kiyosawa H:
　　ES cell differentiation system recapitulates the establishment of imprinted gene expression
　　in a cell-type-specific manner. Hum. Mol. Genet. 21, 1391-1401. 2012.
38. Machida M, Takeda K, Yokono H, Ikemune S, Taniguchi Y, Kiyosawa H, and Takemasa T:
　　Reduction of ribosome biogenesis with activation of the mTOR pathway in denervated atrophic muscle.
　　J. Cell. Physiol. 227, 1569-1576. 2012.
37. Saito R, Kohno K, Okada Y, Osada Y, Numata K, Kohama C, Watanabe K, Nakaoka H, Yamamoto N, Kanai A,
　　Yasue H, Murata S, Abe K, Tomita M,Ohkohchi N, and Kiyosawa H: Comprehensive expressional analyses
　　of antisense transcripts in colon cancer tissues using artificial antisense probes.BMC Medical Genomics 4, 42, 2011.
36. Numata K, Kohama C, Abe K, and Kiyosawa H: Highly parallel SNP genotyping reveals high-resolution landscape
　　of mono-allelic Ube3a expression associated with locus-wide antisense transcription.
　　Nucleic Acids Res. 39, 2649-2657, 2011.
35. Watanabe Y, Numata K, Murata S, Osada Y, Saito R, Nakaoka H, Yamamoto N, Watanabe K, Kato H, Abe K,
　　and Kiyosawa H: Genome-wide analysis of expression modes and DNA methylation status
　　at sense-antisense transcript loci in mouse. Genomics 96, 333-341, 2010.
34. Chiba M, Kiyosawa H, Hiraiwa N, Ohkohchi N, and Yasue H:
　　Existence of Pink1 antisense RNAs in mouse and their localization. Cytogenet. Genome Res. 126, 259-270, 2009.
33. Numata K, Osada Y, Okada Y, Saito R, Hiraiwa N, Nakaoka H, Yamamoto N, Watanabe K, Okubo K, Kohama C,
　　Kanai A, Abe K, and Kiyosawa H:Identification of novel endogenous antisense transcripts
　　by DNA microarray analysis targeting complementary strand of annotated genes. BMC Genomics 10, 392, 2009.
32. Chiba M, Kubo M, Miura T, Satou T, Resaeian A, Kiyosawa H, Ohkohchi N, and Yasue H:
　　Localization of sense and antisense transcripts of Prdx2 gene in mouse tissues. Cytogenet.
　　Genome Res. 121, 222-231, 2008.
31. Okada Y, Tashiro C, Numata K, Watanabe K, Nakaoka H, Yamamoto N, Okubo K, Ikeda R, Saito R, Kanai A,
　　Abe K, Tomita M, and Kiyosawa H: Comparative expression analysis uncovers novel features
　　of endogenous antisense transcription. Hum. Mol. Genet. 17, 1631-1640, 2008.
30. Numata K, Okada Y, Saito R, Kiyosawa H, Kanai A, and Tomita M: Comparative analysis
　　of cis-encoded antisense RNAs in eukaryotes.Gene 392, 134-141, 2007.
29. Kiyosawa H, Mise N, Iwase S, Hayashizaki Y, and Abe K: Disclosing hidden transcripts:mouse natural sense-antisense
　　transcripts tend to be poly(A) negative and nuclear localized. Genome Res. 15, 463-474, 2005.
28. Kiyosawa H, Kawashima T, Silva D, Petrovsky N, Hasegawa Y, Sakai K, and Hayashizaki Y:
　　Systematic genome-wide approach to positional candidate cloning for identification of novel human disease genes.
　　Intern. Med. J. 34, 79-90, 2004.
27. Kiyosawa H, Yamanaka I, Osato N, Kondo S, RIKEN GER Group and GSL Members, and Hayashizaki Y:
　　Antisense transcripts with FANTOM2 clone set and their implications for gene regulation.
　　Genome Res. 13, 1324-1334, 2003.
26. Tojo M, Kiyosawa H, Iwatsuki K, Nakamura K, and Kaneko F: Expression of the GLI2 oncogene
　　and its isoforms in human basal cell carcinoma. Br. J. Dermatol. 148, 892-897, 2003.
25. Kiyosawa H and Abe K: Speculations on the role of natural antisense transcripts
　　in mammalian X chromosome evolution. Cytogenet. Genome Res.99, 151-156, 2002.
24. The FANTOM Consortium and The RIKEN Genome Exploration Research Group Phase I & II Team:
　　Analysis of the mouse transcriptome based on functional annotation of 60,770 full length cDNAs.
　　Nature 420, 563-573. 2002. [The FANTOM Consortium: Okazaki Y, Furuno M, Kasukawa T, Adachi J,Bono H,
　　Kondo S,Nikaido I, Osato N, Saito R, Suzuki H, Yamanaka I, Kiyosawa H, Yagi K, Tomaru Y, Hasegawa Y, Nogami A,
　　Schönbach C,Gojobori T,Baldarelli R, Hill DP, Bult C,Hume DA, Quackenbush J, Schriml LM, Kanapin A, Matsuda H,
　　Batalov S, Beisel KW, Blake JA, Bradt D, Brusic V, Chothia C, Corbani LE, Cousins S, Dalla E, Dragani TA, Fletcher CF,
　　Forrest A, Frazer KS,Gaasterland T, Gariboldi M, Gissi C, Godzik A, Gough J, Grimmond S, Gustincich S, Hirokawa N,
　　Jackson IJ,Jarvis ED,Kanai A, Kawaji H, Kawasawa Y, Kedzierski RM, King BL, Konagaya A, Kurochkin IV, Lee Y,
　　Lenhard B, Lyons PA, Maglott DR, Maltais L, Marchionni L,McKenzie L, Miki H, Nagashima T, Numata K, Okido T,
　　Pavan WJ, Pertea G, Pesole G, Petrovsky N, Pillai R,Pontius JU, Qi D, Ramachandran S, Ravasi T, Reed JC,Reed DJ,
　　Reid J, Ring BZ, Ringwald M, Sandelin A, Schneider C, Semple CAM, Setou M, Shimada K ,Sultana R, Takenaka Y,
　　Taylor MS, Teasdale RD, Tomita M, Verardo R, Wagner L, Wahlestedt C, Wang Y, Watanabe Y, Wells C, Wilming LG,
　　Wynshaw-Boris A, Yanagisawa M, Yang I, Yang L, Yuan Z, Zavolan M, Zhu Y,Zimmer A].
23. Komatsu S, Kiyosawa H, Yoshiki A, Okazaki Y, Yoshino M, Tomaru Y, Watanabe S, Muramatsu M, Kusakabe M,
　　and Hayashizaki Y: Identification of seven loci for static glucokinesis and dynamic glucokinesis in mice. Mamm.
　　Genome 13. 293-298, 2002.
22. Mizuno Y, Sotomaru Y, Katsuzawa Y, Kono T, Meguro M, Oshimura M, Kawai J, Tomaru Y, Kiyosawa H,
　　Nikaido I,Amanuma H, Hayashizaki Y, and Okazaki Y: Asb4, Ata3,
　　and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray.
　　Biochem. Biophys.Res. Commun. 290, 1499-1505, 2002.
21. Yamanaka I, Kiyosawa H, Kondo S, Saito T, Carninci P, Shinagawa A, Aizawa K, Fukuda S, Hara A, Itoh M, Kawai J,
　　Shibata K, Arakawa T, Ishii Y,and Hayashizaki Y: Mapping of 19032 mouse cDNAs on mouse chromosomes.
　　J. Struct. Funct. Genomics 2, 23-28, 2002.
20. Tojo M, Kiyosawa H, Iwatsuki K, and Kaneko F: Expression of a sonic hedgehog signal transducer,
　　hedgehog-interacting protein, by human basal cell carcinoma. Br. J. Dermatol. 146, 69-73, 2002.
19. Kondo S, Shinagawa A, Saito T, Kiyosawa H, Yamanaka I, Aizawa K, Fukuda S, Hara A, Itoh M, Kawai J, Shibata K,
　　and Hayashizaki Y: Computational analysis of full-length mouse cDNAs compared with human genome sequences.
　　Mamm. Genome 12, 673-677, 2001.
18. The RIKEN Genome Exploration Research Group Phase II Team and the FANTOM Consortium:
　　Functional annotation of a full-length mouse cDNA collection.Nature 409, 685-690, 2001.
　　 [RIKEN Genome Exploration Research Group PhaseII team: Kawai J, Shinagawa A, Shibata K, Yoshino M,
　　Itoh M, Ishii Y, Arakawa T, Hara A, Fukunishi Y, Konno H, Adachi J, Fukuda S, Aizawa K, Izawa M, Nishi K,
　　Kiyosawa H, Kondo S,Yamanaka I, Saito T].
17. Takeda J, Sato Y, Kiyosawa H, Mori T, Yokoya S, Irisawa A, Miyata M, Obara K, Fujita T, Suzuki T, Kasukawa R,
　　and Wanaka A: 　Anti-tumor immunity against CT26 colon tumor in mice immunized
　　with plasmid DNA encoding β-galactosidase fused to an envelope protein of endogenous retrovirus.
　　Cell. Immunol. 204, 11-18, 2000.
16. Wang Y, Saigoh K, Osaka H, Yamanishi T, Suh J, Kiyosawa H, Sakai Y, Wakana S, and Wada K:
　　YAC/BAC-based physical and transcript mapping around the gracile axonal dystrophy (gad) locus identifies Uchl1,
　　Pmx2b, Atp3a2, and Hip2 genes. Genomics 66, 333-336, 2000.
15. Bennett CL, Yoshioka R, Kiyosawa H, Barker DF, Fain PR, Shigeoka AO, and Chance PF: X-Linked syndrome
　　of polyendocrinopathy, immune dysfunction, and diarrhea maps to Xp11.23-Xq13.3. Am. J. Hum.
　　Genet. 66, 461-468, 2000.
14. Saigoh K, Wang Y-L, Suh J-G, Yamanishi T, Sakai Y, Kiyosawa H, Harada T, Ichihara N, Wakana S, Kikuchi T,
　　and Wada K: Intragenic deletion in the gene encoding ubiquitin carboxy-terminal hydrolase in gad mice.
　　Nat. Genet. 23, 47-51, 1999.
13. Tojo M, Mori T, Kiyosawa H, Honma Y, Tanno Y, Kanazawa K, Yokoya S, Kaneko F, and Wanaka A:
　　Expression of sonic hedgehog signal transducers, patched and smoothend, in human basal cell carcinoma.
　　Pathol. Int. 49, 687-694, 1999.
12. Honma Y, Kanazawa K, Mori T, Tanno Y, Tojo M, Kiyosawa H, Takeda J, Nikaido T, Tsukamoto T, Yokoya S,
　　and Wanaka A: Identification of a novel gene,OASIS, which encodes for a putative CREB/ATF family
　　transcription factor in the long-term cultured astrocytes and gliotic tissue.Mol. Brain Res. 69, 93-103, 1999.
11. Honma Y, Kiyosawa H, Mori T, Oguri A, Nikaido T, Kanazawa K, Tojo M, Takeda J, Tanno Y, Yokoya S, Kawabata I,
　　Ikeda H, and Wanaka A: Eos: a novel member of the Ikaros gene family expressed predominantly
　　in the developing nervous system. FEBS Letters 447, 76-80, 1999.
10. Rieben WK, Gonzales CM, Gonzales ST, Pilkington KJ, Kiyosawa H, Hughes JE, and Welker DL:
　　Dictyostelium discoideum nuclear plasmid Ddp5 is a chimera related to the Ddp1 and Ddp2 plasmid families.
　　Genetics 148, 1117-1125, 1998.
  9. Ikegami T, Ikeda H, Chance PF, Kiyosawa H, Yamamoto M, Sobue G, Ohnishi A, Tachi N, and Hayasaka K:
　　Facilitated diagnosis of CMT1A duplication in chromosome17p11.2-12: analysis with a CMT1A-REP repeat probe
　　and photostimulated luminescence imaging. Hum. Mutat. 9, 563-566, 1997.
  8. Yamamoto M, Yasuda T, Hayasaka K, Ohnishi A, Yoshikawa H, Yanagihara T, Ikegami T, Yamamoto T, Ohashi H,
　　Nishimura T, Mitsuma T, Kiyosawa H, Chance PF, and Sobue G: Locations of crossover breakpoints within
　　the CMT1A-REP repeat in Japanese patients with CMT1A and HNPP. Hum. Genet. 99, 151-154, 1997.
  7. Kiyosawa H, and Chance PF: Primate origin of the CMT1A-REP repeat and analysis of a putative
　　transposon-associated recombinational hotspot.Hum. Mol. Genet. 5, 745-753, 1996.
  6. Kiyosawa H, Lensch MW, and Chance PF: Analysis of the CMT1A-REP repeat: Mapping crossover breakpoints
　　in CMT1A and HNPP. Hum. Mol. Genet. 4, 2327-2334, 1995.
  5. Kiyosawa H, Hughes JE, and Welker DL: The replication origin position and its relationship to
　　a negative trans-acting transcription regulator encoded by Dictyostelium discoideum nuclear plasmid Ddp1.
　　Curr. Genet. 27, 479-485, 1995.
  4. Hughes JE, Kiyosawa H, and Welker DL: Plasmid maintenance functions encoded
　　on Dictyostelium discoideum nuclear plasmid Ddp1. Mol. Cell. Biol. 14, 6117-6124, 1994.
  3. Farrar NA, Kiyosawa H, Hughes JE, Welker DL, and Williams KL: Nucleotide sequence of Ddp1,
　　a high copy number nuclear plasmid of Dictyostelium discoideum. Plasmid 31, 184-195, 1994.
  2. Kiyosawa H, Hughes JE, and Welker DL: Compatible Dictyostelium mucoroides nuclear plasmids Dmp1
　　and Dmp2 both belong to the Ddp1 plasmid family.Plasmid 31, 121-130, 1994.
  1. Kiyosawa H, Hughes JE, Podgorski GJ, and Welker DL: Small circular plasmids
　　of the eukaryote Dictyostelium purpureum define two novel plasmid families. Plasmid 30, 106-118, 1993.

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