Anti h3k18ac

ChIP was performed as previously described [45 (link)] with a few modifications. Cells were grown in YPD at 30°C to OD₆₆₀ of 0.7. Cells were lysed using Matrix D beads in a FastPrep homogenizer (MP Biomedicals) at maximum four times for 60 seconds, then sonicated to an average fragment size of 300 bp using a Bioruptor Plus (Diagenode) and clarified by centrifugation. Chromatin was immunoprecipitated using anti-H3K18ac (Millipore; catalog no. 07–354) pre-bound to Protein G Dynabeads (ThermoFisher; catalog no. 10004D) and washed 3 times in FA buffer with 150 mM NaCl then 2 times in FA buffer with 500 mM NaCl. DNA was eluted in TE with 1% SDS, cross-links were reversed by incubating overnight at 65°C, treated with 0.2mg/ml RNAse A (VWR; catalog no. E866) for 2 hours at 37°C, then extracted with phenol:chloroform:isoamylalchol and ethanol precipitated. DNA was resuspended in TE and analyzed by real-time quantitative PCR using iTaq Universal SYBR Green Supermix (BioRad; catalog no. 1725121). Ct values were determined using a CFX96 real-time detection system (BioRad).

ChIP-seq assays were performed on the fourth leaves of 4-week-old tomato plantsaccording to Bio-protocol of Ramirez-Prado et al.^{69 (link)} using 3ug of anti-H3K27me1 (Millipore, 07–448), anti-H3K9ac (Millipore, 07–352), anti-H3K14ac (Millipore, 07–353), anti-H3K18ac (Millipore, 07–354), anti-H3K27ac (Abcam, ab4729), anti-H3K4me3 (Millipore, 07–473), and anti-RNAPII (Abcam, ab26721) antibodies. ChIP-seq libraries were prepared from 10 ng of DNA using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. Two independent biological replicates were generated for each time point of heat stress. DNA libraries were checked for quality and quantified using a 2100 Bioanalyzer (Agilent) and subjected to 1 × 75 bp high-throughput sequencing by NextSeq 500 (Illumina).

Amino acids were purchased from Novabiochem of EMD Millipore (Darmstadt, Germany) and Chem-Impex (Wood Dale, IL). Anti-histone H3 (Abcam Cat# ab1791, RRID:AB_302613), anti-H3K4me2 (Abcam Cat# ab32356, RRID:AB_732924) and anti-H3K9ac (Abcam Cat# ab32129, RRID:AB_732920) antibodies and BHC80 were purchased from Abcam (Cambridge, MA). Anti-H3K14ac (Millipore Cat# 07–353, RRID:AB_310545) and anti-H3K18ac (Millipore Cat# 07–354, RRID:AB_441945) antibodies were purchased from EMD Millipore (Burlington, MA). HRP-linked anti-rabbit antibody (Cell Signaling Technology Cat# 7074, RRID:AB_2099233) was purchased from Cell Signaling Technology (Danvers, MA). HEK293F cell line (RRID:CVCL_6642) was purchased from Thermo Fisher Scientific (Waltham, MA) and shown to be negative for mycoplasma. His-FLAG-HDAC1 and Fluorogenic HDAC1 assay kit was purchased from BPS Bioscience (San Diego, CA).