Chromatin-level modifications of TE-related genes. Reverse-transcribed cDNA, DNA from ChIP, and McrBC-digested genomic DNA were amplified by PCR for TE-related genes (a) with and without transcription in seedling shoots, and (b) with transcription in cultured cells but not seedling shoots. Primers corresponded to transcribed ORFs. Mock RT-PCR was performed without reverse transcriptase (w/o RT). ChIP was carried out with histone H3 anti-dimethyl lysine-4 (H3K4m) or anti-dimethyl lysine-9 (H3K9m) antibodies together with total DNA input (T) and no antibody (Mock) controls. McrPCR was performed on McrBC digested (+) and untreated (-) total genomic DNA. Actin was used as a positive control and Os10g35890, a gene of unknown function without transcription in seedlings, as a negative control. The same gray scale was used to indicate magnitude of transcription signals from microarray (Array). ChIP, chromatin immunoprecipitation; ORF, open reading frame; PCR, polymerase chain reaction; TE, transposable element.