GSM989336 Yeast_cell NA GSE40255 BY4741_WT BY4741 (MATa) DNase sacCer3 The libraries for Dnase-seq were sequenced on 1 lane for 100 cycles with an Illumina HiSeq2000 and TruSeq SBS sequencing kits version 3. Basecalls were performed with Casava1.8 (pipeline 1.9). wild_type_DNase-seq bd_0_1_2_4_sc3 GSM989336_BY4741_wild_type_DHS_peak.bed.gz GSM1516434 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_0 bw_0_1_2_4_sc3 GSM1516434_h3k27ac_tp1_0.bw GSM1516433 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_4 bw_0_1_2_4_sc3 GSM1516433_h3k27ac_tp2_4.bw GSM1516432 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_8 bw_0_1_2_4_sc3 GSM1516432_h3k27ac_tp3_8.bw GSM1516431 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_15 bw_0_1_2_4_sc3 GSM1516431_h3k27ac_tp4_15.bw GSM1516430 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_30 bw_0_1_2_4_sc3 GSM1516430_h3k27ac_tp5_30.bw GSM1516429 Yeast_cell NA GSE61888 BY4741 H3K27ac ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k27ac_60 bw_0_1_2_4_sc3 GSM1516429_h3k27ac_tp6_60.bw GSM1516464 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_0 bw_0_1_2_4_sc3 GSM1516464_h3k4me_tp1_0.bw GSM1516463 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_4 bw_0_1_2_4_sc3 GSM1516463_h3k4me_tp2_4.bw GSM1516462 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_8 bw_0_1_2_4_sc3 GSM1516462_h3k4me_tp3_8.bw GSM1516461 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_15 bw_0_1_2_4_sc3 GSM1516461_h3k4me_tp4_15.bw GSM1516460 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_30 bw_0_1_2_4_sc3 GSM1516460_h3k4me_tp5_30.bw GSM1516459 Yeast_cell NA GSE61888 BY4741 H3K4me1 ChIP-Seq sacCer3 library-strategy: MNase-ChIP-Seq h3k4me_60 bw_0_1_2_4_sc3 GSM1516459_h3k4me_tp6_60.bw GSM3639832 Yeast_cell NA GSE127843 WT_H3K4me1 MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 1.8.4 WT_H3K4me1-2 bw_0_1_2_4_sc3 GSM3639832_WT_H3K4me1-2.bw GSM3639831 Yeast_cell NA GSE127843 WT_H3K4me1 MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 1.8.4 WT_H3K4me1-1 bw_0_1_2_4_sc3 GSM3639831_WT_H3K4me1-1.bw GSM3639809 Yeast_cell NA GSE127843 WT_H3K4me1 MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 1.8.4 WT_H3K4me1-B bw_0_1_2_4_sc3 GSM3639809_WT_H3K4me1-B.bw GSM3639808 Yeast_cell NA GSE127843 WT_H3K4me1 MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 1.8.4 WT_H3K4me1-A bw_0_1_2_4_sc3 GSM3639808_WT_H3K4me1-A.bw GSM3639799 Yeast_cell NA GSE127843 S. cerevisiae WT+WT S. pombe MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 2.17.1.14 WT_AR2_spk_me1-RC07-32 bd_0_1_2_6_sc3 UsingSRR GSM3639798 Yeast_cell NA GSE127843 S. cerevisiae WT+WT S. pombe MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 2.17.1.14 WT_AR2_spk_me1-RC07-31 bd_0_1_2_6_sc3 UsingSRR GSM3639797 Yeast_cell NA GSE127843 S. cerevisiae WT+WT S. pombe MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 2.17.1.14 WT_DS1_spk_me1-RC07-30 bd_0_1_2_6_sc3 UsingSRR GSM3639796 Yeast_cell NA GSE127843 S. cerevisiae WT+WT S. pombe MGD353-13D H3K4me1 ChIP-Seq sacCer3 bcl2fastq 2.17.1.14 WT_DS1_spk_me1-RC07-29 bd_0_1_2_6_sc3 UsingSRR GSM2350621 Yeast_cell NA GSE88877 wild type W303 DNase sacCer3 Quality control: fastQC (0.10.1) Hsp82D15 bd_0_1_2_4_sc3 GSM2350621_Hsp82D15_mapped.hot.bed.gz GSM2062108 Yeast_cell NA GSE77945 POLII_WT_2 POLR2A ChIP-Seq sacCer3 Reads were mapped on sacCer3 build using bowtie version 0.12.8. POLII_WT_2 bw_0_1_2_4_sc3 GSM2062108_HI.2404.002.Index_1.wt-N_R1.fastq.gz.sacCer3.bw GSM2062107 Yeast_cell NA GSE77945 POLII_WT_1 POLR2A ChIP-Seq sacCer3 Reads were mapped on sacCer3 build using bowtie version 0.12.8. POLII_WT_1 bw_0_1_2_4_sc3 GSM2062107_HI.2404.002.Index_7.wt-M_R1.fastq.gz.sacCer3.bw GSM2700702 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt6B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700701 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt6A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700700 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt5B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700699 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt5A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700698 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt4B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700697 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt4A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700696 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt3B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700695 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt3A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700694 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt2B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700693 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt2A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700692 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt1B_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2700691 Yeast_cell NA GSE101290 yeast ATAC-Seq sacCer3 Reads were aligned using Bowtie2. Duplicate reads were removed using Picard tools and replicates were combined for analysis.ATAC-seq signal in promoters was quantified as the number of fragments mapping to the window 400bp upstream to 100bp downstream from the TSS. NucleoATAC and chromVAR were used to assess promoter accessibility and nucleosome positioning resectively. wt1A_ATAC-seq bd_0_1_2_6_sc3 UsingSRR GSM2459880 Yeast_cell NA GSE93190 Saccharomyces cerevisiae_HHY168 HHY168 POLR2A ChIP-Seq sacCer3 map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 . WT_plusrap_Rbp1_2 bw_0_1_2_4_sc3 GSM2459880_WT_plusRap_Rpb1_2.bigwig GSM2459879 Yeast_cell NA GSE93190 Saccharomyces cerevisiae_HHY168 HHY168 POLR2A ChIP-Seq sacCer3 map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 . WT_minusrap_Rbp1_2 bw_0_1_2_4_sc3 GSM2459879_WT_minusRap_Rpb1_2.bigwig GSM2183256 Yeast_cell NA GSE93190 Saccharomyces cerevisiae_HHY168 HHY168 POLR2A ChIP-Seq sacCer3 map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 . WT_plusrap_Rpb1 bw_0_1_2_4_sc3 GSM2183256_WT_plusrap_Rpb1.bigwig GSM2183255 Yeast_cell NA GSE93190 Saccharomyces cerevisiae_HHY168 HHY168 POLR2A ChIP-Seq sacCer3 map using Bowtie in Galaxy (Penn State). Mapping parameters: trim 11 bases from left, -n 2, -e 70, -l 28, -v -1, -k 1, -m -1 . WT_minusrap_Rpb1 bw_0_1_2_4_sc3 GSM2183255_WT_minusrap_Rpb1.bigwig GSM781946 Yeast_cell NA GSE31466 Yeast cell W303 POLR2A ChIP-Seq sacCer2 Raw sequencing data were first processed by the built-in Illumina analysis pipeline. Prior to the actual sequence mapping, reads were parsed according to the 4-bp index, and barcodes were then removed. Those reads lacking an intact index were discarded. The remaining bases were aligned against the S. cerevisiae S288c reference genome version 2 (SGD/UCSC sacCer2, June 2008) by the ELAND algorithm (Illumina). The peak scoring algorithm PeakSeq (Rozowsky et al., Nat Biotech (2009)) was used to identify statistically significant binding sites, changing only the following parameters to account for the compact S. cerevisiae genome: window size of 10 kb during the normalization step and bin size of 1 kb during the linear regression step (PeakSeqOutput files, with Q-value < 0.05). ChIP-Seq data from epitope-tagged strains were scored against ChIP-Seq data from their matching untagged strains. In both cases, anti-Myc antibodies were used during ChIP. Scoring reference sets were created by pooling uniquely-mapping reads from biological replicates of untagged control strains. As a reference sample marking open chromatin (Auerbach et al., PNAS (2009)), two lists of Sono-Seq significant regions were generated, obtained after scoring against either anti-Myc or anti-HA control sets. To uncover Centromere-like Regions (CLRs), we took a conservative, stringent approach to minimize false positives lacking functional significance or failing qPCR validation. For each biological replicate of a particular kinetochore component, only putative binding regions with Q-value < 10-5 were considered (Target bed files). Several other criteria were then applied. First, binding sites called in two biological replicates from Cse4, Mif2, Ndc10 and Ndc80 ChIP-Seq data, in either a Cse4 overexpression strain or in a wild-type strain, were overlapped with maxgap=150 (maximum gap between non-overlapping peaks). Next, to identify a binding region as a CLR, 1) all four kinetochore proteins must be present at the putative site given the q-value threshold; and 2), for proteins in direct contact with DNA, mean PeakSeq ratios between both replicates at a particular target site should be above 2.00 for open chromatin marker Cse4 (same for PolII and Sono-Seq regions), and 1.50 for direct DNA binders Mif2 and Ndc10. Several other filters were used to distinguish between lower confidence regions and higher confidence regions for subsequent functional analyses, including comparison of PeakSeq experimental reads and PeakSeq background reads between CLRs and CENs, inspection of normalized signal tracks (good tagged/untagged signal ratio and low background in the appropriate untagged control desired), binding over a highly PolII-occupied ORF, and presence in a HOT region. Regions that passed those criteria and filters were termed CLRs (Centromere-Like Regions). Other binding sites that did not pass the aforementioned filters were referred to as LCNCRs (for low-confidence, negative control regions). Yeast PolII ChIP-Seq bd_0_1_2_6_sc3 UsingSRR GSM941006 Yeast_cell NA GSE38384 Yeast cells, wild-type, Rpb1 ChIP W303 wild-type POLR2A ChIP-Seq Base-calling was performed using Illumina CASAVA pipeline and standard parameters. WT2 RNA Polymerase II ChIP bd_0_1_2_6_sc3 UsingSRR GSM941005 Yeast_cell NA GSE38384 Yeast cells, wild-type, Rpb1 ChIP W303 wild-type POLR2A ChIP-Seq Base-calling was performed using Illumina CASAVA pipeline and standard parameters. WT1 RNA Polymerase II ChIP bd_0_1_2_6_sc3 UsingSRR GSM3040132 Yeast_cell NA GSE111815 WT Rep3 ATAC S288C ATAC-Seq sacCer3 RNA-seq: Raw reads that contain Illumina adapter sequence were filtered by TagDust (v1.12) at an FDR threshold of 0.001. Reads were then aligned to the sacCer3 genome using Bowtie (v1.1.2) using options: -m 1, --seed=123, and --nomaqround. Samtools (v0.1.9) and bedtools (v2.25.0) were used for post-alignment data conversions. Gene counts were calculated using HTSeq (v0.6.1) and the sacCer3 sgdGene table from UCSC Genome Browser. GO terms were generated using DAVID (v6.8). WT Rep3 ATAC bw_0_1_2_4_sc3 GSM3040132_wt3_sequence.shifted.exactcut.bw GSM3040131 Yeast_cell NA GSE111815 WT Rep2 ATAC S288C ATAC-Seq sacCer3 RNA-seq: Raw reads that contain Illumina adapter sequence were filtered by TagDust (v1.12) at an FDR threshold of 0.001. Reads were then aligned to the sacCer3 genome using Bowtie (v1.1.2) using options: -m 1, --seed=123, and --nomaqround. Samtools (v0.1.9) and bedtools (v2.25.0) were used for post-alignment data conversions. Gene counts were calculated using HTSeq (v0.6.1) and the sacCer3 sgdGene table from UCSC Genome Browser. GO terms were generated using DAVID (v6.8). WT Rep2 ATAC bw_0_1_2_4_sc3 GSM3040131_wt2_sequence.shifted.exactcut.bw GSM3040130 Yeast_cell NA GSE111815 WT Rep1 ATAC S288C ATAC-Seq sacCer3 RNA-seq: Raw reads that contain Illumina adapter sequence were filtered by TagDust (v1.12) at an FDR threshold of 0.001. Reads were then aligned to the sacCer3 genome using Bowtie (v1.1.2) using options: -m 1, --seed=123, and --nomaqround. Samtools (v0.1.9) and bedtools (v2.25.0) were used for post-alignment data conversions. Gene counts were calculated using HTSeq (v0.6.1) and the sacCer3 sgdGene table from UCSC Genome Browser. GO terms were generated using DAVID (v6.8). WT Rep1 ATAC bw_0_1_2_4_sc3 GSM3040130_wt1_sequence.shifted.exactcut.bw GSM2837729 Yeast_cell NA GSE106450 S.cerevisiae cells homemade; prepared by Lee Lab ChIP-Seq sacCer3 The quality of fastq files were checked by fastqc and trimmed by trim_galore MYC_WT bd_0_1_2_6_sc3 UsingSRR GSM2813908 Yeast_cell NA GSE95356 exponential growing culture YF336 Ser5P ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(RPB1) SER5P ChIP-Seq bg_0_1_2_4_sc3 GSM2813908_wt_RPB1_ser5_2.bedgraph.gz GSM2813907 Yeast_cell NA GSE95356 exponential growing culture YF336 Ser2P ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(RPB1) SER2P ChIP-Seq bg_0_1_2_4_sc3 GSM2813907_wt_RPB1_ser2_2.bedgraph.gz GSM2507921 Yeast_cell NA GSE95356 exponential growing culture YSB3345 a-Rpb4 ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(pSET1) RPB4 ChIP-Seq rep2 bg_0_1_2_4_sc3 GSM2507921_wt_pSET1_RPB4_rep2.bedGraph.gz GSM2507920 Yeast_cell NA GSE95356 exponential growing culture YSB3345 a-Rpb3 ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(pSET1) RPB3 ChIP-Seq rep2 bg_0_1_2_4_sc3 GSM2507920_wt_pSET1_RPB3_rep2.bedGraph.gz GSM2507919 Yeast_cell NA GSE95356 exponential growing culture YSB3345 a-Rpb4 ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(pSET1) RPB4 ChIP-Seq rep1 bg_0_1_2_4_sc3 GSM2507919_wt_pSET1_RPB4_rep1.bedGraph.gz GSM2507918 Yeast_cell NA GSE95356 exponential growing culture YSB3345 a-Rpb3 ChIP-Seq sacCer3 Raw fastq files were demultiplexed using Sabre (https://github.com/najoshi/sabre) allowing one mismatch in the barcode. wt(pSET1) RPB3 ChIP-Seq rep1 bg_0_1_2_4_sc3 GSM2507918_wt_pSET1_RPB3_rep1.bedGraph.gz GSM2320251 Yeast_cell NA GSE87060 ChIP for Wild type input rep4 SK1 Hop1 ChIP-Seq SacCer3 Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome. Wild type anti-Hop1 rep2 bd_0_1_2_6_sc3 UsingSRR GSM2320250 Yeast_cell NA GSE87060 ChIP for Wild type input rep3 SK1 Hop1 ChIP-Seq SacCer3 Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome. Wild type anti-Hop1 rep1 bd_0_1_2_6_sc3 UsingSRR GSM2320249 Yeast_cell NA GSE87060 ChIP for Wild type input rep2 SK1 Red1 ChIP-Seq SacCer3 Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome. Wild type anti-Red1 rep2 bd_0_1_2_6_sc3 UsingSRR GSM2320248 Yeast_cell NA GSE87060 ChIP for Wild type input rep1 SK1 Red1 ChIP-Seq SacCer3 Sequencing reads were mapped to SacCer3 using Bowtie (http://bowtie-bio.sourceforge.net/index.shtml). The one condition adjusted was to only collect information about reads that mapped to a single position in the genome. Wild type anti-Red1 rep1 bd_0_1_2_6_sc3 UsingSRR GSM2088330 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Pcf11-ChIP 2 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Pcf11-ChIP 2 bd_0_1_2_6_sc3 UsingSRR GSM2088329 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Pcf11-ChIP 1 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Pcf11-ChIP 1 bd_0_1_2_6_sc3 UsingSRR GSM2088324 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rtt103-ChIP 2 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rtt103-ChIP 2 bd_0_1_2_6_sc3 UsingSRR GSM2088323 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rtt103-ChIP 1 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rtt103-ChIP 1 bd_0_1_2_6_sc3 UsingSRR GSM2088318 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rai1-ChIP 2 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rai1-ChIP 2 bd_0_1_2_6_sc3 UsingSRR GSM2088317 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rai1-ChIP 1 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rai1-ChIP 1 bd_0_1_2_6_sc3 UsingSRR GSM2088312 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rat1-ChIP 2 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rat1-ChIP 2 bd_0_1_2_6_sc3 UsingSRR GSM2088311 Yeast_cell NA GSE79222 Yeast cell extract BY4741 Rat1-ChIP 1 ChIP-Seq sacCer3 PAR-CLIP: Adapter sequences are first trimmed from the raw sequencing files. The quality filter then discards all reads containing unidentified nucleotides (N), Phreds scores below 30, reads shorter than 15 nucleotides (nt), or reads that are flagged by Illumina¡¯s internal chastity filter. Quality-trimmed reads are aligned to the S. cerevisiae genome (sacCer3, version 64.2.1) using the short read aligner Bowtie (version 1.1.1) with a maximum of one mismatch and taking unique matches only (options: -q -p 4 -S -sam -nohead -v 1 -e 70 -l 28 -y -a -m 1 -best -strata -phred33 -quals). The resulting SAM files are then converted into BAM and PileUp files using SAMTools. Rat1-ChIP 1 bd_0_1_2_6_sc3 UsingSRR GSM1700704 Yeast_cell NA GSE69400 WT_Rpb3_IP YPE458 (wild type) Rpb3 ChIP-Seq SacCer3 Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings. WT_Rpb3_IP_B bg_0_1_2_4_sc3 GSM1700704_WT_Rpb3_IP_B.bedGraph.gz GSM1700703 Yeast_cell NA GSE69400 WT_Rpb3_IP YPE458 (wild type) Rpb3 ChIP-Seq SacCer3 Sequencing data was aligned to the yeast genome (SacCer3) using Bowtie2 with default settings. WT_Rpb3_IP_A bg_0_1_2_4_sc3 GSM1700703_WT_Rpb3_IP_A.bedGraph.gz