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Breeden LL, Tsukiyama T. 
Quiescence in Saccharomyces cerevisiae
PMID: 36449357 DOI: 10.1146/annurev-genet-080320-023632
Annual Rev Genet. 2022, 30: 253-278

Raman P, Rominger, MC Young JM, Molaro A, Tsukiyama T, Malik HS
Novel Classes and Evolutionary Turnover of Histone H2B Variants in the Mammalian Germline
PMID: 35099534 PMCID: PMC8857922 
Mol Biol Evol  2022 Feb 3;39(2):msac019. doi: 10.1093/molbev/msac019.


Swygert  SG , Lin D , Portillo-Ledesma S, Lin PY, Hunt  DR,  Kao CF,  Schlick T, Noble WS, Tsukiyama T.
Local chromatin fiber folding represses transcription and loop extrusion in quiescent cells
 PMID: 34734806 DOI: 10.7554/eLife.72062

Cucinotta CE, Dell RH, Braceros KCA, Tsukiyama T.
RSC primes the quiescent genome for hypertranscription upon cell cycle re-entry.
eLife 2021;10:e67033 doi: 10.7554/eLife.67033


Swygert SG, Lin D, Portillo-Ledesma S, Lin P-Y, Hunt DR, Kao C-F, Schlick T, Noble WS, Tsukiyama T.
Chromatin Fiber Folding Represses Transcription and Loop Extrusion in Quiescent Cells
 bioRxiv. 2020. doi:

Chong SY, Cutler S, Lin JJ, Tsai HK, Biggins S, Tsukiyama T, Kao CF.
H3K4 methylation at active genes metigate transcription-replication conflicts during replication stress.
Nat Comm. 2020 Feb 10;11(1): 809  

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, 2020, 4:635-646  PMCID: PMC7197482


Swygert SG, Kim S, Wu X, Fu T, Hsieh T-H, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T.
Condensin-dependent chromatin condensation represses transcription globally during quiescence.
Mol Cell 2019, 73:533-546.

Swygert SG, Tsukiyama T.
Unraveling quiescence-specific repressive chromatin domains.
Curr Genet. 2019, 65:1145-1151.


Cutler S, Lee L, Tsukiyama T
Chromatin Remodeling Factors Isw2 and Ino80 Regulate Chromatin, Replication, and Copy Number of the Saccharomyces cerevisiae Ribosomal DNA Locus
Genetics. 2018, 210: 1543-1556

Spain MM, Swygert SG, Tsukiyama T.
Preparation and analysis of Saccharomyces cerevisiae quiescent cells.
Methods Mol Biol. 2018, 1686:124-135.

Spain MM, Braceros CA, Tsukiyama T.
SWI/SNF coordinates transcriptional activation through Rpd3-mediated histone hypoacetylation during quiescence entry.
BioRxiv. 2018. doi:

Swygert SG, Wu X, Fu T, Hsieh TH, Rando OJ, Eisenman RN, Shendure J, McKnight JN, Tsukiyama T.
Condensin-dependent chromatin condensation represses transcription globally during quiescence.
bioRxiv. 2018. doi:


Rodriguez J, Lee L, Lynch B, Tsukiyama T.
Nucleosome occupancy as a novel chromatin parameter for origin functions.
Genome Res 2017, 27: 269-277.


McKnight JN, Tsukiyama T., Bowman GD.
Sequence-targeted nucleosome sliding in vivo by a hybrid Chd1 chromatin remodeler.
Genome Res 2016, 26: 693-704.

Alcid E, Tsukiyama T.
Systematic approaches to identify functional lncRNAs.
Curr Opinion Genet Dev. 2016, 37: 46-50.

Alcid EA,Tsukiyama T.
Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi.

Nat Struct Mol Biol. 2016, 23: 450–455


Alcid EA,Tsukiyama T.
Systematic approaches to identify functional lncRNAs.
Curr Opin Genet Dev, 2016 37: 46-50.

McKnight JN,  Tsukiyama T.
The conserved HDAC Rpd3 drives transcriptional quiescence in S. cerevisiae.
Genome Data. 2015  PMCID:PMC4664762

McKnight JN, Breeden LL, Tsukiyama T.
A Molecular Off Switch for Transcriptional Quiescence.
Cell cycle. 2015 PMID:26514179

Lee L, Rodriguez J, Tsukiyama T.
Chromatin remodeling factors Isw2 and Ino80 regulate checkpoint activity and chromatin structure in S phase.
Genetics. 2015 Apr;199(4):1077-91. doi: 10.1534/genetics.115.174730. Epub 2015 Feb 19.

McKnight JN, Boerma JW, Breeden LL, Tsukiyama T.
Global Promoter Targeting of a Conserved Lysine Deacetylase for Transcriptional Shutoff during Quiescence Entry.
Molecular cell. 2015, 5: 732-743


Bogenschutz N, Rodriguez J, Tsukiyama T.
Initiation of DNA Replication from Non-Canonical Sites on an Origin-Depleted Chromosome.
PLOS1 2014, 9(12): e114545.

Alcid E, Tsukiyama T
ATP-dependent chromatin remodeling shapes the long noncoding RNA transcriptome.
Genes Dev 2014, 28: 2348-2360.

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 2014,  Supplement 108, 21 8 1- 8 16.


Yadon A, Singh BN, Hampsey M, Tsukiyama T. 
DNA looping facilitates targeting of a chromatin remodeling enzyme.
Mol Cell 2013, 50: 93-103

Yadon AN, Tsukiyama T.
DNA looping-dependent targeting of a chromatin remodeling factor.
Cell Cycle. 2013, 12: 1809-10

Zentner GE, Tsukiyama T, Henikoff S. 
ISWI and CHD chromatin remodelers bind promoters but act in gene bodies.
PLoS Genet 2013 9:e1003317

Rodriguez J, Tsukiyama T.
ATR-like kinase Mec1 facilitates both chromatin accessibility at DNA replication forks and replication fork progression during replication stress.
Genes Dev 2013, 27: 74-86


Unnikrishnan A, Akiyoshi B, Biggns S, Tsukiyama T. 
An efficient purification system for native minichromosome from S. cerevisiae. Methods in Molecular Biology.
Methods in Molecular Biology 2012, 833: 115-123


Yadon A, Tsukiyama T.
SnapShot: Chromatin remodeling: ISWI.
Cell 2011, 144: 453-453

Au T, Rodriguez J, Vincent J, Tsukiyama T.
ATP-dependent chromatin remodeling factors tune S phase checkpoint activity.
Mol Cel Biol 2011, 31: 4454-63


Yadon A, 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.
Mol Cell Biol 2010, 30: 5110-5122

Unnikrishnan A, Gafken P, Tsukiyama T.
Dynamic changes in histone acetylation regulate origin of DNA replication.
Nature Struct Mol Biol 2010, 17: 430-437


Tsukiyama T, Bogenschutz N, Kwong T, Rodriguez J, Unnikrishnan A, Yadon A.
ISWI chromatin remodeling complexes.
Handbook of Cell Signaling 2009, 3: 2357-2362

Whitehouse I, Tsukiyama T.
Opening Windows to the Genome
Cell 2009, 137: 400-402


Vincent JA, Kwong T, Tsukiyama T.
ATP-dependent chromatin remodeling shapes the DNA replication landscape.
Nat Struct Mol Biol 2008, 15: 477-484


Whitehouse I, Rando OJ, Delrow J, Tsukiyama T.
Chromatin remodelling at promoters suppress antisense transcription.
Nature 2007, 450:1031-1036.


Lindstrom KC, Vary JC Jr, Parthun MR, Delrow J, Tsukiyama T.
Isw1 functions in parallel with the NuA4 and Swr1 complexes in stress- induced gene repression.
Mol Cell Biol. 2006, Aug;26 16: 6117-29.

Whitehouse I, Tsukiyama T.
Antagonistic forces that position nucleosomes in vivo.
Nat Struct Mol Biol., 2006, Jul; 13 7: 633-40.

Tsukiyama, T. and Parkhurst, S.
Chromosomes and expression mechanisms. (editorial overview).
Curr. Opin. Genet. Dev., 2006, 16: 101-103


Fazzio TG, Gelbart ME, and Tsukiyama T.
Two Distinct Mechanisms of Chromatin Interaction by the Isw2 Chromatin Remodeling Complex In Vivo.
Mol. Cell. Biol. 2005, 25: 9165-9174

Gelbart ME, Bachman N, Delrow J, Boeke JD, and Tsukiyama T.
Genome-wide identification of Isw2 chromatin-remodeling targets by localization of a catalytically inactive mutant.
Genes Dev. 2005, 19: 942-954.  Supplemental data

Bachman N, Gelbart ME, Tsukiyama T, and Boeke JD.
TFIIIB subunit of Bdp1 is required for periodic integration of the Ty1 retrotransposon and targeting of Isw2p to S. cerevisiae tDNAs.
Genes Dev. 2005, 19: 955-964.


McConnell AD, Gelbart ME, Tsukiyama T.
Histone fold protein Dls1p is required for Isw2-dependent chromatin remodeling in vivo.
Mol Cell Biol 2004, 24:2605-2613.  Supplemental data

Vary JC, Fazzio TG, Tsukiyama T
Assembly of yeast chromatin using ISWI complexes.
Meth Enzymol 2004, 375:88-102.


Fazzio TG, Tsukiyama T.
Chromatin remodeling in vivo: Evidence for a nucleosome sliding mechanism.
Mol Cell 2003, 12:1333-1340.

Moreau J-L, Lee M, Mahachi N, Vary JC Jr, Mellor J, Tsukiyama T, Goding CR.
Regulated displacement of TBP from the PHO8 promoter in vivo requires Cbf1 and the Isw1 chromatin remodeling complex.
Mol Cell 2003, 11:1609-1620.

Vary JC Jr, Gangaraju VK, Qin J, Landel CC, Kooperberg C, Bartholomew B, Tsukiyama T.
Yeast Isw1p forms two separable complexes in vivo.
Mol Cell Biol 2003, 23:80-91.   Supplemental data


Kassabov SR, Henry NM, Zofall M, Tsukiyama T, Bartholomew B.
High-resolution mapping of changes in histone-DNA contacts of nucleosomes remodeled by ISW2.
Mol Cell Biol
 2002, 22:7524-34.

Tsukiyama, T.
The in vivo functions of ATP-dependent chromatin-remodelling factors.
Nat Rev Mol Cell Biol 2002, 3:422-429.

Kooperberg C, Fazzio TG, Tsukiyama T.
Improved background correction for spotted DNA microarrays.
J. Comp Biol 2002, 9:55-66.


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.
Mol Cell Biol 2001, 21:6450-6460.
* Correction for the above paper; on page 6452 under results, the ftp site no longer in existence. Please refer to this link instead DNA micro array supplemental data

Gelbart ME, Rechsteiner T, Richmond TJ, Tsukiyama T.
Interaction of Isw2 chromatin remodeling complex with nucleosomal arrays: analyses using recombinant yeast histones and immobilized templates.
Mol Cell Biol 2001, 21:2098-2106.


Goldmark JP, Fazzio TG, Estep PW, Church GM, Tsukiyama T.
The Isw2 chromatin remodeling complex represses early meiotic genes upon recruitment by Ume6p.
Cell 2000, 103:423-433.


Tsukiyama T, Palmer J, Landel CC, Shiloach J, Wu C.
Characterization of ISWI subfamily of ATP-dependent chromatin remodeling factors in S. cerevisiae.
Genes Dev 1999, 13:686-697.