Figure 2

Selective enrichment of repressive histone marks at the long interspersed nuclear element-1 (L1) and long terminal repeat (LTR) promoters. Shown is representative sequential chromatin immunoprecipitation (SeqChIP) raw data using the first chromatin immunoprecipitation (ChIP) to H2A or H2A.Z antibodies followed by the second ChIP to H3K4me2, H3K9me3, AcH4K16, H4K20me3 and HP1α antibodies. About 1% of the sonicated chromatin was set aside as total input DNA before the ChIP assays. DNA was purified following crosslink reversal and used as positive controls. Mouse IgG ChIP served as negative controls. Dilutions of 10 and 5 ng of ChIP DNA were used to determine the relative abundance of histone marks at the promoter regions of L1 and LTR retrotransposons. One-tenth of each PCR product was visualized on a 3% agarose gel. Marker, 1 kb-plus DNA marker. Top panel shows the relative enrichment of H2A.Z, H3K9me3 and HP1α as unison at the L1 promoter that includes tandem repeats of L1 monomers whereas the bottom panel shows the enrichment of H2A in the promoters of MmERV and IAP classes of LTR elements.