Appendix 1—key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Strain, strain background (Saccharomyces cerevisiae) | S288C derivatives | This paper; Fred Winston (Harvard Medical School) Winston et al., 1995 |
See Supplementary file 2. Yeast strains | |
| Strain, strain background (Saccharomyces cerevisiae) | 972 h- | Fred Winston (Harvard Medical School) |
FWP10 | spike-in control |
| Strain, strain background (Saccharomyces cerevisiae) | NRRL Y-1140 | Nathan Clark (University of Utah) |
spike-in control | |
| Genetic reagent, (Kluyveromyces lactis) |
KLLA0D16170 g-3XFLAG::
NAT |
Jin et al., 2017 | YSC193 | spike-in control |
| Recombinant DNA reagent | SHIMA plasmid library | Nakanishi et al., 2008 | recombinant histone mutant library | |
| Sequence-based reagent | PCR primers | This paper | See Supplementary file 1. Oligonucleo-tides | |
| Sequence-based reagent | histone superbinder (SB) sequence | Wang et al., 2011 | ||
| Recombinant DNA reagent | pMPY-3xHA plasmid | Schneider et al., 1995 | Plasmid vector used for SB-URA3-SB construct | |
| Recombinant DNA reagent | TOPO TA plasmid containing SB sequence | Hainer et al., 2015 | Source of SB DNA for construction of SB-URA3-SB construct | |
| Recombinant DNA reagent | SB-URA3-SB plasmid | This study | KB1479 | Used to generate yeast strains with integrated SB |
| Gene (Saccharomyces cerevisiae) | hht2-HHF2 or HHT2-hhf2 | Nakanishi et al., 2008 | ||
| Antibody | α-H3 (rabbit polyclonal) | Tomson et al., 2011 | western analysis (1:15,000) | |
| Antibody | α-H3 K36me3(rabbit polyclonal) | Abcam | ab9050 | western analysis (1:1000) |
| Antibody | α-HA (mouse monoclonal) | Roche | 12CA5 | western analysis (1:3000) |
| Antibody | α-G6PDH (rabbit) | Sigma-Aldrich | A9521 | western analysis (1:20,000) |
| Antibody | α-H3 K56ac (rabbit) | Paul Kaufman (UMass Medical School) |
western analysis (1:5000) | |
| Antibody | α-rabbit IgG-HRP | GE Healthcare | NA934 | western analysis (1:5000) |
| Antibody | α-mouse IgG-HRP | GE Healthcare | NA931 | western analysis (1:5000) |
| Commercial assay or kit | Pico Plus chemilumine-scence substrate | Thermo Fisher | #34580 | |
| Antibody | α-FLAG M2 affinity gel (mouse monoclonal) | Sigma-Aldrich | A2220 | 30 µL α-FLAG beads per 700 µL chromatin (ChIP) |
| Antibody | α-H2A (rabbit polyclonal) | ActiveMotif | #39235 | 1 µL α-H2A per 700 µL chromatin (ChIP) |
| Ather | Protein A conjugated to sepharose beads | GE Healthcare | GE17-5280-01 | 30 µL per chromatin IP |
| Commercial assay or kit | QIAquick PCR purification kit | Qiagen | #28106 | |
| Commercial assay or kit | NEBNext Ultra II library kit for Illumina | New England Biolabs | E7645 | |
| Commercial assay or kit | NEBNext Ultra II sequencing indexes | New England Biolabs | E7335, E7500, E7710 | |
| Commercial assay or kit | SoLo RNA-seq library preparation kit | TECAN | 0516–32 | |
| Commercial assay or kit | Maxima 2X SYBR Master Mix | Thermo Fisher | K0221 | |
| Commercial assay or kit | TURBO DNA-free kit | Invitrogen | AM1907 | |
| Commercial assay or kit | RiboPure Yeast RNA extraction kit | Ambion | AM1926 | |
| Commercial assay or kit | MTSEA Biotin-XX | Biotium | #90066 | |
| Commercial assay or kit | Streptavidin beads | Invitrogen | #65001 | |
| Commercial assay or kit | MinElute columns | Qiagen | #74204 | |
| Commercial assay or kit | QuikChange II kit | Agilent | #200523 | |
| Peptide, recombinant protein | Micrococcal nuclease | Thermo Fisher | #88216 | |
| Sequence-based reagent | [α-32P]dATP and [α-32P]dTTP |
PerkinElmer | used to generate Northern probes | |
| Other | S. cerevisiae reference genome | Ensembl | R64-1-1 | |
| Other | S. pombe reference genome | Ensembl | EF2 | |
| Other | K. lactis reference genome | Ensembl | ASM251v1 | |
| Software, algorithm | HISAT2 | Kim et al., 2015 | ||
| Software, algorithm | SAMtools | Li et al., 2009 | ||
| Software, algorithm | RSubread featureCounts | Liao et al., 2014 | ||
| Software, algorithm | deepTools2 | Ramírez et al., 2014; Ramírez et al., 2016 | ||
| Software, algorithm | R Studio | RStudio Team, 2016 | ||
| Software, algorithm | DANPOS2 | Chen et al., 2013 | ||
| Software, algorithm | wigToBigWig UCSC utility | Kent et al., 2010 | ||
| Software, algorithm | BEDtools | Quinlan, 2014; Quinlan and Hall, 2010 |