LEGEND:
* indicates terminal nucleosome, i.e., the last nucleosome in the genic region of each gene.
? indicates ambiguity because the midpoint distance between a sample nucleosome and its assigned parent nucleosome is greater than 80 bp.
ORF, RNA, DNA features are collected from SGD 9-15-2006.
TN: transposable element, LTR: long terminal repeat, including Ty1, Ty2, Ty3, Ty4, Ty5, Ty1-5'LTR, Ty1-3'LTR, Ty2-5'LTR, Ty2-3'LTR, Ty3-5'LTR, Ty3-3'LTR, Ty4-5'LTR, Ty4-3'LTR, retroTN: retrotransposon, including Ty1-1, Ty1-2, Ty1-2, Ty1-3, Ty1-4, Ty1-5, Ty2-1, Ty2-2, Ty2-3, Ty3-1, Ty4-1, Ty5-1, Telomere includes telomeric_repeat, X_element_combinatorial_repeats, X_element_core_sequence, Y'_element.
anti-sense and new transcript are collected from: Miura F, Kawaguchi N, Sese J, et al. (2006) A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. PNAS, 103:17846-17851.
CUT and SUT are collected from: Xu Z, Wei W, Gagneur J, et al. (2009) Bidirectional promoters generate pervasive transcription in yeast. Nature, 457:1033-1037.
Refence: Refence nucleosomes derived from the six sets of bulk nucleosomes from wild-type yeast (H3/H4 from track WT-454, nucleosomes from track WT-Affy, normal from track HS, Wild Type from track isw2, track 454_All, and track SOLiD). Light gray indicates nucleosomes in NFRs; darkgray indicates nucleosomes in NDRs; black indicates nucleosomal singlets or arrays. (Read the paper for the definition of NFR, NDR, nucleosomal singlet and array.)
WT-454: both H34 and H2A.Z nucleosomes from Wild-Type yeast (strain BY4741) were produced by ChIP-sequencing technology (454 sequencer). H34 (H3 and H4, i.e., dataset 1) nucleosomes refer to: Mavrich TN, Ioshikhes IP, Venters BJ, et al. (2008) A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Research, 18(7):1073-83.
H2A.Z nucleosomes refer to: Albert I, Mavrich TN, Tomsho LP, et al. (2007) Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature, 446(7135):572-6.
454_All (dataset 2): bulk nucleosomes from wild-type yeast (strain BY4741) were produced by ChIP-sequencing technology (454 sequencer). Details refer to: Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Computational Biology, 4(11):e1000216.
SOLiD (dataset 3): bulk nucleosomes from wild-type yeast (strain BY4741) were produced by ChIP-sequencing technology (SOLiD).
Solexa norm~HS (norm is dataset 4): bulk nucleosomes from wild-type yeast (strain S288C) under normal condition and heatshock treatment were produced by ChIP-sequencing technology (Solexa sequencer). Details refer to: Shivaswamy S, Bhinge A, Zhao Y et al. (2008) Dynamic Remodeling of Individual Nucleosomes Across a Eukaryotic Genome in Response to Transcriptional Perturbation PLoS Biol, 18;6(3):e65.
Affy WT~isw2 (WT is dataset 5): bulk nucleosomes from Wild-Type and isw2-deletion yeast (strain S288C) were produced by Tiling array technology (Affymetrix). In brief, nucleosomal DNA was harvested by MNase and exonuclease III digestion. The wild-type fragmented (~50 bp) nucleosomal DNA was used as treatment. The wild-type full-length (~150 bp) nucleosomal DNA was used as control. A signal intensity ratio of treatment probes to control probles was calculated. The average signal from all the +1 nucleosomes were taken out as the idealized nucleosome signals. The genome-wide nucleosome positions were futher determined by iteratively fitting the idealized nucleosome signal to the data set. Such that, the tiling array probes were grouped into nucleosomal probes and linker probes. For the nucleosome positioning in isw2 deletion mutant yeast, the isw2-deletion fragmented nucleosomal DNA was used as treatment. The isw2-deletion full-length nucleosomal DNA was used as control. Isw2 is an ATP-dependent chromatin remodelling enzyme. Details refer to: Whitehouse I, Rando OJ, Delrow J, Tsukiyama T (2007) Chromatin remodelling at promoters suppresses antisense transcription. Nature, 450(7172):1031-5.
WT-Affy (dataset 6): bulk nucleosomes from Wild-Type yeast (strain BY4741) were produced by Tiling array technology (Affymetrix). In brief, MNase-digested DNA was used as treatment. Genomic DNA fragmented by nuclease was used as control. A signal intensity ratio of treatment probes to control probles was calculated. An HMM (Hidden Markov Model) was trained by serveral well-characterized nucleosome location data to obtain optimal parameters that were further applied to classify tiling array probes as nucleosome state and liker state. Details refer to: Lee W, Tillo D, Bray N, et al. (2007) A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet, 38(10):1210-5.
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