Toshio Tsukiyama - Publications

Affiliations: 
University of Washington, Seattle, Seattle, WA 
Area:
Molecular Biology, Biochemistry, Cell Biology
Website:
https://sharedresources.fredhutch.org/profile/tsukiyama-toshio

71 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Cucinotta CE, Dell RH, Braceros KC, Tsukiyama T. RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry. Elife. 10. PMID 34042048 DOI: 10.7554/eLife.67033  1
2020 Poramba-Liyanage DW, Korthout T, Cucinotta CE, van Kruijsbergen I, van Welsem T, El Atmioui D, Ovaa H, Tsukiyama T, van Leeuwen F. Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes. Genome Research. PMID 32188699 DOI: 10.1101/Gr.256255.119  1
2020 Chong SY, Cutler S, Lin JJ, Tsai CH, Tsai HK, Biggins S, Tsukiyama T, Lo YC, Kao CF. H3K4 methylation at active genes mitigates transcription-replication conflicts during replication stress. Nature Communications. 11: 809. PMID 32041946 DOI: 10.1038/S41467-020-14595-4  0.32
2019 Swygert SG, Tsukiyama T. Unraveling quiescence-specific repressive chromatin domains. Current Genetics. PMID 31055637 DOI: 10.1007/S00294-019-00985-9  1
2018 Swygert SG, Kim S, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T. Condensin-Dependent Chromatin Compaction Represses Transcription Globally during Quiescence. Molecular Cell. PMID 30595435 DOI: 10.1016/J.Molcel.2018.11.020  1
2018 Spain MM, Swygert SG, Tsukiyama T. Preparation and Analysis of Saccharomyces cerevisiae Quiescent Cells. Methods in Molecular Biology (Clifton, N.J.). 1686: 125-135. PMID 29030817 DOI: 10.1007/978-1-4939-7371-2_9  1
2016 Rodriguez J, Lee L, Lynch B, Tsukiyama T. Nucleosome occupancy as a novel chromatin parameter for replication origin functions. Genome Research. PMID 27895110 DOI: 10.1101/Gr.209940.116  0.56
2016 McKnight JN, Tsukiyama T, Bowman GD. Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler. Genome Research. PMID 26993344 DOI: 10.1101/Gr.199919.115  1
2016 Alcid EA, Tsukiyama T. Systematic approaches to identify functional lncRNAs. Current Opinion in Genetics & Development. 37: 46-50. PMID 26821363 DOI: 10.1016/J.Gde.2015.12.005  1
2015 McKnight JN, Tsukiyama T. The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae. Genomics Data. 6: 245-8. PMID 26697386 DOI: 10.1016/J.Gdata.2015.10.008  1
2015 McKnight JN, Breeden LL, Tsukiyama T. A Molecular Off Switch for Transcriptional Quiescence. Cell Cycle (Georgetown, Tex.). 0. PMID 26514179 DOI: 10.1080/15384101.2015.1112618  1
2015 McKnight JN, Boerma JW, Breeden LL, Tsukiyama T. Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry. Molecular Cell. 59: 732-43. PMID 26300265 DOI: 10.1016/J.Molcel.2015.07.014  1
2015 Lee L, Rodriguez J, Tsukiyama T. Chromatin remodeling factors Isw2 and Ino80 regulate checkpoint activity and chromatin structure in S phase. Genetics. 199: 1077-91. PMID 25701287 DOI: 10.1534/Genetics.115.174730  1
2014 Bogenschutz NL, Rodriguez J, Tsukiyama T. Initiation of DNA replication from non-canonical sites on an origin-depleted chromosome. Plos One. 9: e114545. PMID 25486280 DOI: 10.1371/Journal.Pone.0114545  1
2014 Alcid EA, Tsukiyama T. ATP-dependent chromatin remodeling shapes the long noncoding RNA landscape. Genes & Development. 28: 2348-60. PMID 25367034 DOI: 10.1101/Gad.250902.114  1
2014 Rodriguez J, McKnight JN, Tsukiyama T. Genome-Wide Analysis of Nucleosome Positions, Occupancy, and Accessibility in Yeast: Nucleosome Mapping, High-Resolution Histone ChIP, and NCAM. Current Protocols in Molecular Biology / Edited by Frederick M. Ausubel ... [Et Al.]. 108: 21.28.1-21.28.16. PMID 25271716 DOI: 10.1002/0471142727.Mb2128S108  1
2013 Yadon AN, Tsukiyama T. DNA looping-dependent targeting of a chromatin remodeling factor. Cell Cycle (Georgetown, Tex.). 12: 1809-10. PMID 23708514 DOI: 10.4161/Cc.25114  1
2013 Yadon AN, Singh BN, Hampsey M, Tsukiyama T. DNA looping facilitates targeting of a chromatin remodeling enzyme. Molecular Cell. 50: 93-103. PMID 23478442 DOI: 10.1016/J.Molcel.2013.02.005  1
2013 Zentner GE, Tsukiyama T, Henikoff S. ISWI and CHD chromatin remodelers bind promoters but act in gene bodies. Plos Genetics. 9: e1003317. PMID 23468649 DOI: 10.1371/journal.pgen.1003317  1
2013 Rodriguez J, Tsukiyama T. ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress. Genes & Development. 27: 74-86. PMID 23307868 DOI: 10.1101/Gad.202978.112  1
2012 Unnikrishnan A, Akiyoshi B, Biggins S, Tsukiyama T. An efficient purification system for native minichromosome from saccharomyces cerevisiae Methods in Molecular Biology. 833: 115-123. PMID 22183591 DOI: 10.1007/978-1-61779-477-3_8  1
2011 Au TJ, Rodriguez J, Vincent JA, Tsukiyama T. ATP-dependent chromatin remodeling factors tune S phase checkpoint activity. Molecular and Cellular Biology. 31: 4454-63. PMID 21930788 DOI: 10.1128/Mcb.05931-11  1
2011 Yadon AN, Tsukiyama T. SnapShot: Chromatin remodeling: ISWI. Cell. 144: 453-453.e1. PMID 21295704 DOI: 10.1016/J.Cell.2011.01.019  1
2010 Yadon AN, Van de Mark D, Basom R, Delrow J, Whitehouse I, Tsukiyama T. Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription. Molecular and Cellular Biology. 30: 5110-22. PMID 20805356 DOI: 10.1128/Mcb.00602-10  1
2010 Unnikrishnan A, Gafken PR, Tsukiyama T. Dynamic changes in histone acetylation regulate origins of DNA replication. Nature Structural & Molecular Biology. 17: 430-7. PMID 20228802 DOI: 10.1038/Nsmb.1780  1
2010 Tsukiyama T, Bogenschutz N, Kwong T, Rodriguez J, Unnikrishnan A, Yadon A. ISWI chromatin remodeling complexes Handbook of Cell Signaling, 2/E. 3: 2357-2362. DOI: 10.1016/B978-0-12-374145-5.00283-7  1
2009 Whitehouse I, Tsukiyama T. Opening windows to the genome. Cell. 137: 400-2. PMID 19410536 DOI: 10.1016/J.Cell.2009.04.026  1
2008 Vincent JA, Kwong TJ, Tsukiyama T. ATP-dependent chromatin remodeling shapes the DNA replication landscape. Nature Structural & Molecular Biology. 15: 477-84. PMID 18408730 DOI: 10.1038/Nsmb.1419  1
2007 Whitehouse I, Rando OJ, Delrow J, Tsukiyama T. Chromatin remodelling at promoters suppresses antisense transcription. Nature. 450: 1031-5. PMID 18075583 DOI: 10.1038/Nature06391  1
2006 Kim Y, McLaughlin N, Lindstrom K, Tsukiyama T, Clark DJ. Activation of Saccharomyces cerevisiae HIS3 results in Gcn4p-dependent, SWI/SNF-dependent mobilization of nucleosomes over the entire gene. Molecular and Cellular Biology. 26: 8607-22. PMID 16982689 DOI: 10.1128/Mcb.00678-06  1
2006 Lindstrom KC, Vary JC, Parthun MR, Delrow J, Tsukiyama T. Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress-induced gene repression. Molecular and Cellular Biology. 26: 6117-29. PMID 16880522 DOI: 10.1128/Mcb.00642-06  0.56
2006 Whitehouse I, Tsukiyama T. Antagonistic forces that position nucleosomes in vivo. Nature Structural & Molecular Biology. 13: 633-40. PMID 16819518 DOI: 10.1038/Nsmb1111  1
2006 Tsukiyama T, Parkhurst S. Chromosomes and expression mechanisms Current Opinion in Genetics and Development. 16: 101-103. DOI: 10.1016/J.Gde.2006.02.016  1
2005 Fazzio TG, Gelbart ME, Tsukiyama T. Two distinct mechanisms of chromatin interaction by the Isw2 chromatin remodeling complex in vivo. Molecular and Cellular Biology. 25: 9165-74. PMID 16227570 DOI: 10.1128/Mcb.25.21.9165-9174.2005  1
2005 Bachman N, Gelbart ME, Tsukiyama T, Boeke JD. TFIIIB subunit Bdp1p is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs. Genes & Development. 19: 955-64. PMID 15833918 DOI: 10.1101/Gad.1299105  1
2005 Gelbart ME, Bachman N, Delrow J, Boeke JD, Tsukiyama T. Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant. Genes & Development. 19: 942-54. PMID 15833917 DOI: 10.1101/Gad.1298905  1
2004 McConnell AD, Gelbart ME, Tsukiyama T. Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo. Molecular and Cellular Biology. 24: 2605-13. PMID 15024052 DOI: 10.1128/Mcb.24.7.2605-2613.2004  1
2004 Vary JC, Fazzio TG, Tsukiyama T. Assembly of yeast chromatin using ISWI complexes. Methods in Enzymology. 375: 88-102. PMID 14870661 DOI: 10.1016/S0076-6879(03)75006-X  1
2003 Fazzio TG, Tsukiyama T. Chromatin remodeling in vivo: evidence for a nucleosome sliding mechanism. Molecular Cell. 12: 1333-40. PMID 14636590 DOI: 10.1016/S1097-2765(03)00436-2  1
2003 Moreau JL, Lee M, Mahachi N, Vary J, Mellor J, Tsukiyama T, Goding CR. Regulated displacement of TBP from the PHO8 promoter in vivo requires Cbf1 and the Isw1 chromatin remodeling complex. Molecular Cell. 11: 1609-20. PMID 12820973 DOI: 10.1016/S1097-2765(03)00184-9  1
2003 Vary JC, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T. Yeast Isw1p forms two separable complexes in vivo. Molecular and Cellular Biology. 23: 80-91. PMID 12482963 DOI: 10.1128/Mcb.23.1.80-91.2003  1
2002 Kassabov SR, Henry NM, Zofall M, Tsukiyama T, Bartholomew B. High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2. Molecular and Cellular Biology. 22: 7524-34. PMID 12370299 DOI: 10.1128/Mcb.22.21.7524-7534.2002  1
2002 Tsukiyama T. The in vivo functions of ATP-dependent chromatin-remodelling factors. Nature Reviews. Molecular Cell Biology. 3: 422-9. PMID 12042764 DOI: 10.1038/Nrm828  1
2002 Kooperberg C, Fazzio TG, Delrow JJ, Tsukiyama T. Improved background correction for spotted DNA microarrays. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 55-66. PMID 11911795 DOI: 10.1089/10665270252833190  1
2001 Fazzio TG, Kooperberg C, Goldmark JP, Neal C, Basom R, Delrow J, Tsukiyama T. Widespread collaboration of Isw2 and Sin3-Rpd3 chromatin remodeling complexes in transcriptional repression. Molecular and Cellular Biology. 21: 6450-60. PMID 11533234 DOI: 10.1128/Mcb.21.19.6450-6460.2001  1
2001 Gelbart ME, Rechsteiner T, Richmond TJ, Tsukiyama T. Interactions of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates. Molecular and Cellular Biology. 21: 2098-106. PMID 11238944 DOI: 10.1128/Mcb.21.6.2098-2106.2001  1
2001 Mizuguchi G, Vassilev A, Tsukiyama T, Nakatani Y, Wu C. ATP-dependent Nucleosome Remodeling and Histone Hyperacetylation Synergistically Facilitate Transcription of Chromatin Journal of Biological Chemistry. 276: 14773-14783. DOI: 10.1074/Jbc.M100125200  1
2000 Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T. The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p. Cell. 103: 423-33. PMID 11081629 DOI: 10.1016/S0092-8674(00)00134-3  1
2000 Deuring R, Fanti L, Armstrong JA, Sarte M, Papoulas O, Prestel M, Daubresse G, Verardo M, Moseley SL, Berloco M, Tsukiyama T, Wu C, Pimpinelli S, Tamkun JW. The ISWI chromatin-remodeling protein is required for gene expression and the maintenance of higher order chromatin structure in vivo. Molecular Cell. 5: 355-65. PMID 10882076 DOI: 10.1016/S1097-2765(00)80430-X  1
1999 Sandaltzopoulos R, Ossipow V, Gdula DA, Tsukiyama T, Wu C. Purification of Drosophila nucleosome remodeling factor Methods in Enzymology. 304: 757-765. PMID 10372395 DOI: 10.1016/S0076-6879(99)04046-X  1
1999 Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C. Characterization of the imitation switch subfamily of ATP-dependent chromatin-remodeling factors in Saccharomyces cerevisiae Genes and Development. 13: 686-697. PMID 10090725 DOI: 10.1101/Gad.13.6.686  1
1998 Wu C, Tsukiyama T, Gdula D, Georgel P, Martínez-Balbás M, Mizuguchi G, Ossipow V, Sandaltzopoulos R, Wang HM. ATP-dependent remodeling of chromatin Cold Spring Harbor Symposia On Quantitative Biology. 63: 525-534. PMID 10384317 DOI: 10.1101/Sqb.1998.63.525  1
1998 Gdula DA, Sandaltzopoulos R, Tsukiyama T, Ossipow V, Wu C. Inorganic pyrophosphatase is a component of the Drosophila nucleosome remodeling factor complex Genes and Development. 12: 3206-3216. PMID 9784495 DOI: 10.1101/Gad.12.20.3206  1
1998 Martínez-Balbás MA, Tsukiyama T, Gdula D, Wu C. Drosophila NURF-55, a WD repeat protein involved in histone metabolism Proceedings of the National Academy of Sciences of the United States of America. 95: 132-137. PMID 9419341 DOI: 10.1073/Pnas.95.1.132  1
1997 Mizuguchi G, Tsukiyama T, Wisniewski J, Wu C. Role of nucleosome remodeling factor NURF in transcriptional activation of chromatin Molecular Cell. 1: 141-150. PMID 9659911 DOI: 10.1016/S1097-2765(00)80015-5  1
1997 Georgel PT, Tsukiyama T, Wu C. Role of histone tails in nucleosome remodeling by Drosophila NURF Embo Journal. 16: 4717-4726. PMID 9303316 DOI: 10.1093/Emboj/16.15.4717  1
1997 Tsukiyama T, Wu C. Chromatin remodeling and transcription Current Opinion in Genetics and Development. 7: 182-191. PMID 9115421 DOI: 10.1016/S0959-437X(97)80127-X  1
1996 Tsukiyama T, Wu C. Purification of GAGA factor of Drosophila and its role in nucleosome disruption Methods in Enzymology. 274: 291-299. PMID 8902813 DOI: 10.1016/S0076-6879(96)74025-9  1
1995 Ninomiya Y, Okada M, Kotomura N, Suzuki K, Tsukiyama T, Niwa O. Genomic organization and isoforms of the mouse ELP gene Journal of Biochemistry. 118: 380-389. PMID 8543574  0.96
1995 Tsukiyama T, Daniel C, Tamkun J, Wu C. ISWI, a member of the SWI2/SNF2 ATPase family, encodes the 140 kDa subunit of the nucleosome remodeling factor. Cell. 83: 1021-6. PMID 8521502 DOI: 10.1016/0092-8674(95)90217-1  1
1995 Tsukiyama T, Wu C. Purification and properties of an ATP-dependent nucleosome remodeling factor Cell. 83: 1011-1020. PMID 8521501 DOI: 10.1016/0092-8674(95)90216-3  1
1995 Taketo M, Parker KL, Howard TA, Tsukiyama T, Wong M, Niwa O, Morton CC, Miron PM, Seldin MF. Homologs of Drosophila Fushi-Tarazu factor 1 map to mouse chromosome 2 and human chromosome 9q33. Genomics. 25: 565-7. PMID 7789992 DOI: 10.1016/0888-7543(95)80059-U  0.96
1994 Tsukiyama T, Becker PB, Wu C. ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor Nature. 367: 525-532. PMID 8107823 DOI: 10.1038/367525A0  1
1994 Morohashi KI, Iida H, Nomura M, Hatano O, Honda SI, Tsukiyama T, Niwa O, Hara T, Takakusu A, Shibata Y, Omura T. Functional difference between Ad4BP and ELP, and their distributions in steroidogenic tissues Molecular Endocrinology. 8: 643-653. PMID 8058072 DOI: 10.1210/MEND.8.5.8058072  0.96
1994 Kim SJ, Tsukiyama T, Lewis MS, Wu C. Interaction of the DNA-binding domain of Drosophila heat shock factor with its cognate DNA site: a thermodynamic analysis using analytical ultracentrifugation. Protein Science : a Publication of the Protein Society. 3: 1040-51. PMID 7920249 DOI: 10.1002/Pro.5560030706  1
1994 Becker PB, Tsukiyama T, Wu C. Chromatin assembly extracts from Drosophila embryos Methods in Cell Biology. 44: 207-223. PMID 7707953 DOI: 10.1016/S0091-679X(08)60915-2  1
1994 Kotomura N, Okada M, Ninomiya Y, Tsukiyama T, Umesono K, Evans RM, Niwa O. Repression of retinoic acid-induced transactivation by embryonal LTR binding protein Journal of Biochemistry. 116: 1309-1316. PMID 7706222 DOI: 10.1093/Oxfordjournals.Jbchem.A124680  0.96
1994 Becker PB, Tsukiyama T, Wu C. Chromatin assembly extracts from Drosophila embryos. Methods in Cell Biology. 44: 207-223. DOI: 10.5282/Ubm/Epub.7384  1
1992 Isaka M, Inoue H, Tsukiyama T, Niwa O, Hakura A. Rat cellular mutants for expression of mRNA from the long terminal repeat of murine retrovirus Virology. 189: 141-149. PMID 1604805 DOI: 10.1016/0042-6822(92)90689-M  0.96
1992 Tsukiyama T, Niwa O. Isolation of high affinity cellular targets of the embryonal LTR binding protein, an undifferentiated embryonal carcinoma cell-specific repressor of moloney leukemia virus Nucleic Acids Research. 20: 1477-1482. PMID 1579438 DOI: 10.1093/Nar/20.7.1477  0.96
1992 Tsukiyama T, Ueda H, Hirose S, Niwa O. Embryonal Long Terminal Repeat-Binding Protein Is a Murine Homolog of FTZ-F1, a Member of the Steroid Receptor Superfamily Molecular and Cellular Biology. 12: 1286-1291. PMID 1545809 DOI: 10.1128/Mcb.12.3.1286  0.96
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