Figure 2. Parental-Specific Histone Modifications.

(A–J) Maternal chromosome.

(A) Map (40 kb) showing maternal expression of Igf2r and Air. Arrow, Igf2r transcription; gray lollipop, silent Air transcription start 28 kb downstream of Igf2r. Black boxes above line, CpG islands at the Igf2r and Air promoters. Black bars below line, single-copy regions analyzed by ChIP-PCR. 1–12, primer pairs to assay 11.6 kb of the Air promoter region. 13–24, primer pairs to assay 12.7 kb of the Igf2r promoter region (Table S4, see note on primer pair 7). Gray boxes with roman numerals, DHS sites. DHSIX is absent from the maternal chromosome, DHSXII is unique to the maternal chromosome. (B) Typical Input-PCR in MEFB1 cells containing only the maternal Igf2r cluster.

(C–E) ChIP-PCR using antibodies against H3K4me3, H3K4me2, and H3K9Ac in MEFB1 cells. For H3K4me3, weak reproducible bands were amplified by primer 7–8 downstream of the Air transcription start marked by primer pair 6.

(F–J) ChIP-PCR using antibodies against H3K9me3, H4K20me3, H4K20me1, H3K27me3, and H3K27me1 in MEFB1 cells. One microliter of 1:100 dilution of Input or 1 μl ChIP DNA was amplified per PCR, two to four biological replicas of each ChIP-PCR were performed, and representative images are shown. M, size marker.

(K–T) Paternal chromosome.

(K) Map (40 kb) showing paternal expression of Igf2r and Air. Details in Figure 2A. Arrow, Air transcription; gray lollipop, silent Igf2r transcription start 28 kb downstream of Air. DHSIX is unique to the paternal chromosome, DHSXII is absent from the paternal chromosome.

(L) Typical Input-PCR in MEFF cells containing only the paternal Igf2r cluster. Primer pairs 5 and 6 corresponding to DHSIX generally showed reduced Input signal on the paternal chromosome.

(M–O) ChIP-PCR in MEFF cells using antibodies against H3K4me3, H3K4me2, H3K9Ac.

(P–T) ChIP-PCR in MEFF cells using antibodies against H3K9me3, H4K20me3, H4K20me1, H3K27me3, H3K27me1.