A domesticated Harbinger transposase forms a complex with HDA6 and promotes histone H3 deacetylation at genes but not TEs in Arabidopsis

In eukaryotes, histone acetylation is a major modification on histone N-terminal tails that is tightly connected to transcriptional activation. HDA6 is a histone deacetylase involved in the transcriptional regulation of genes and transposable elements (TEs) in Arabidopsis thaliana. HDA6 has been shown to participate in several complexes in plants, including a conserved SIN3 complex. Here, we uncover a novel protein complex containing HDA6, several Harbinger transposon-derived proteins (HHP1, SANT1, SANT2, SANT3, and SANT4), and MBD domain-containing proteins (MBD1, MBD2, and MBD4). We show that mutations of all four SANT genes in the sant-null mutant cause increased expression of the flowering repressors FLC, MAF4, and MAF5, resulting in a late flowering phenotype. Transcriptome deep sequencing reveals that while the SANT proteins and HDA6 regulate the expression of largely overlapping sets of genes, TE silencing is unaffected in sant-null mutants. Our global histone H3 acetylation profiling shows that SANT proteins and HDA6 modulate gene expression through deacetylation. Collectively, our findings suggest that Harbinger transposon-derived SANT domain-containing proteins are required for histone deacetylation and flowering time control in plants. For RNA-seq: three independent biological replicates of wild-type(Col-0), hhp1, mbd 1/2/4, sant1234-null and hda6 were used for RNA deep sequencing assay. Total RNA was extracted from 12-day-old Arabidopsis seedlings growing on 1/2 MS medium plates with TRIzol reagent (Invitrogen). mRNA-seq libraries were built according to the manufacturer’s protocol (NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA)) and paired-end sequenced on an Illumina NovaSeq 6000 platform. For ChIP-seq: three biological replicates of 12-day-old wild-type(Col-0), sant1234-null and hda6 seedlings growing on 1/2 MS medium plates were used for histone H3 modification ChIP-seq experiment. Sequencing libraries were generated using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® (NEB, USA) and then paired-end sequenced on Illumina NovaSeq 6000 platform. We used anti-acetylated Histone H3 antibody (Merck Millipore, 06-599). Each replicate contained two dataset: ChIP and input (to avoid background interference).