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Genome-wide analyses reveal RNA polymerase II located upstream of genes poised for rapid response upon S. cerevisiae stationary phase exit.

Radonjic M, Andrau JC, Lijnzaad P, Kemmeren P, Kockelkorn TT, van Leenen D, van Berkum NL, Holstege FC.

Mol Cell. 2005 Apr 15;18(2):171-83.


Genome-wide distribution of yeast RNA polymerase II and its control by Sen1 helicase.

Steinmetz EJ, Warren CL, Kuehner JN, Panbehi B, Ansari AZ, Brow DA.

Mol Cell. 2006 Dec 8;24(5):735-46.


Genomewide recruitment analysis of Rpb4, a subunit of polymerase II in Saccharomyces cerevisiae, reveals its involvement in transcription elongation.

Verma-Gaur J, Rao SN, Taya T, Sadhale P.

Eukaryot Cell. 2008 Jun;7(6):1009-18. doi: 10.1128/EC.00057-08. Epub 2008 Apr 25.


Genome-wide RNA polymerase II: not genes only!

Koch F, Jourquin F, Ferrier P, Andrau JC.

Trends Biochem Sci. 2008 Jun;33(6):265-73. doi: 10.1016/j.tibs.2008.04.006. Epub 2008 May 6. Review.


Genome-wide occupancy profile of mediator and the Srb8-11 module reveals interactions with coding regions.

Zhu X, Wirén M, Sinha I, Rasmussen NN, Linder T, Holmberg S, Ekwall K, Gustafsson CM.

Mol Cell. 2006 Apr 21;22(2):169-78.


Stress-dependent dynamics of global chromatin remodeling in yeast: dual role for SWI/SNF in the heat shock stress response.

Shivaswamy S, Iyer VR.

Mol Cell Biol. 2008 Apr;28(7):2221-34. doi: 10.1128/MCB.01659-07. Epub 2008 Jan 22.


Genome-wide location of the coactivator mediator: Binding without activation and transient Cdk8 interaction on DNA.

Andrau JC, van de Pasch L, Lijnzaad P, Bijma T, Koerkamp MG, van de Peppel J, Werner M, Holstege FC.

Mol Cell. 2006 Apr 21;22(2):179-92.


Differential regulation of gene expression by RNA polymerase II in response to DNA damage.

Heo JH, Jeong SJ, Seol JW, Kim HJ, Han JW, Lee HW, Cho EJ.

Biochem Biophys Res Commun. 2004 Dec 17;325(3):892-8.


Genome-wide analysis of the effects of location and number of stress response elements on gene expression in Saccharomyces cerevisiae.

Yoshikawa K, Furusawa C, Hirasawa T, Shimizu H.

J Biosci Bioeng. 2008 Nov;106(5):507-10. doi: 10.1263/jbb.106.507.


Amino acid substitutions in yeast TFIIF confer upstream shifts in transcription initiation and altered interaction with RNA polymerase II.

Ghazy MA, Brodie SA, Ammerman ML, Ziegler LM, Ponticelli AS.

Mol Cell Biol. 2004 Dec;24(24):10975-85.


The Saccharomyces cerevisiae linker histone Hho1p is essential for chromatin compaction in stationary phase and is displaced by transcription.

Schäfer G, McEvoy CR, Patterton HG.

Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14838-43. doi: 10.1073/pnas.0806337105. Epub 2008 Sep 17.


Genome-wide monitoring of wine yeast gene expression during alcoholic fermentation.

Rossignol T, Dulau L, Julien A, Blondin B.

Yeast. 2003 Dec;20(16):1369-85.


Genome-wide transcriptional changes during the lag phase of Saccharomyces cerevisiae.

Brejning J, Jespersen L, Arneborg N.

Arch Microbiol. 2003 Apr;179(4):278-94. Epub 2003 Mar 11.


Nutrient-regulated antisense and intragenic RNAs modulate a signal transduction pathway in yeast.

Nishizawa M, Komai T, Katou Y, Shirahige K, Ito T, Toh-E A.

PLoS Biol. 2008 Dec 23;6(12):2817-30. doi: 10.1371/journal.pbio.0060326.


Genomic analysis of stationary-phase and exit in Saccharomyces cerevisiae: gene expression and identification of novel essential genes.

Martinez MJ, Roy S, Archuletta AB, Wentzell PD, Anna-Arriola SS, Rodriguez AL, Aragon AD, Quiñones GA, Allen C, Werner-Washburne M.

Mol Biol Cell. 2004 Dec;15(12):5295-305. Epub 2004 Sep 29.


Genome-wide expression profile of steroid response in Saccharomyces cerevisiae.

Banerjee D, Pillai B, Karnani N, Mukhopadhyay G, Prasad R.

Biochem Biophys Res Commun. 2004 Apr 30;317(2):406-13.


Genomic analyses of transcription factor binding, histone acetylation, and gene expression reveal mechanistically distinct classes of estrogen-regulated promoters.

Kininis M, Chen BS, Diehl AG, Isaacs GD, Zhang T, Siepel AC, Clark AG, Kraus WL.

Mol Cell Biol. 2007 Jul;27(14):5090-104. Epub 2007 May 21.


Expression profiling of the bottom fermenting yeast Saccharomyces pastorianus orthologous genes using oligonucleotide microarrays.

Minato T, Yoshida S, Ishiguro T, Shimada E, Mizutani S, Kobayashi O, Yoshimoto H.

Yeast. 2009 Mar;26(3):147-65. doi: 10.1002/yea.1654.

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