Fig. 6

Nucleosome profile and transcriptome change in 6mA defective Tetrahymena. a Fuzziness of genome-wide nucleosome profile in wild-type (WT1, WT2) and methyltransferase knockout (NP61, NP62, NP71, NP72) cells. Fuzziness is defined as the deviation of nucleosome positions within each unit and is calculated by software DANPOS [32]. Two biological replicates for KO cells were constructed. NP61 and NP62 are two technical replicates for one cell strain, and NP71 and NP72 are two technical replicates for another cell strain. The smaller score represents better well-phased nucleosomes. b Clustering analysis of transcriptome for WT (WT61/WT62 and WT71/WT72 are two wild-type strains; each strain contains two technical replicates) and KO (NP61/NP62 and NP71/NP72 are two KO strains; each strain contains two technical replicates) cells. WT and KO cells are distinctly separated with a large difference. c Scheme for the model that 6mA stabilizes gene expression. In WT, 6mA is positioned to constrain nucleosome positioning which regulates gene expression. In KO, the level of 6mA significantly reduced. Nucleosomes lacking of 6mA constraints tend to be fuzzier which leads to larger transcriptional fluctuation