Differential regulation of gene expression at 27°C correlates with changes in H2A.Z enrichment. (A) Venn diagram representation of the overlap between thermo- and CIM/SIM-induced genes and genes with temperature-dependent HTA11 enrichment. Thermo- and CIM/SIM-induced genes include CIM- and/or SIM-induced genes that are up-regulated at 27°C compared to 17°C on either medium. Genes with temperature-dependent HTA11 enrichment include those that lose or gain HTA11 within the chromatin spanning their coding region plus 2 upstream nucleosomes (294 bp) in plants transferred to 27°C compared to plants maintained at 17°C. The enrichment (representation factor, hypergeometric test) of thermo- and CIM/SIM-induced genes among genes with temperature-dependent HTA11 enrichment is indicated. **P value < 0.01. ***P value < 0.001. (B) Heat map representation of the normalized ChIP-seq read density distribution for HTA11 within the chromatin spanning the coding region plus 2 upstream nucleosomes (294 bp) of all HTA11-marked genes in plants transferred to 27°C or plants maintained at 17°C. The position of the transcription start site (TSS) and transcription termination site (TTS) is marked. Line graphs show the summed HTA11 enrichment for HTA11-marked genes that are thermo-induced and up-regulated on CIM/SIM, HTA11-marked genes that are thermo-repressed and down-regulated on CIM/SIM and all other HTA11-marked genes. For the sake of clarity, only a subset of randomly chosen other HTA11-marked genes is shown in the heat maps, but the whole group is taken into account in the line graphs. (C) Line plots showing the HTA11 occupancy across the coding region of IPT1, LOG3, CUC1, CUC3, ESR2, WUS, YUC1, YUC4 and SAUR15. Data are shown for 240 min at 17°C or after transfer to 27°C. HSP70 is shown as a reference temperature-induced gene (Kumar and Wigge 2010) and PP2AA3 as a reference non-induced gene (Czechowski et al. 2005).