Additional file 1:

Imprinted gene characterisation. Imprinted genes: this worksheet lists the imprinted genes mined for histone modification and expression status from source data of high-throughput papers; Promoter differentially methylated region (DMR) status: this worksheet details the promoter DMR status of imprinted genes used for analysis of histone modification profiles at genes with and without promoter DMRs, including references; Chromatin and expression states: this worksheet provides data extracted from six high-throughput studies for all available imprinted genes. Notably, not all imprinted genes were present in the source data files, most likely due to the high proportion of imprinted genes currently holding a predicted status in gene reference databases. If a gene was not present in one source data file the output is given as 'Gene not present'. Genes imprinted only in mice, or where imprinting status is not confirmed in humans, or where no orthologous human gene exists (*), are excluded from further human analyses. The same applies for human-specific imprinted genes (^†), which are excluded from all mouse analyses. Isoform-dependent imprinted genes (^‡) are not included in any further analyses. hESC, human embryonic stem cells; mESC, mouse embryonic stem cells; REH, human pro-B cells; mNPC, mouse neural progenitor cells; MEF, mouse embryonic fibroblasts; TSS, transcription start site; HCP, high CpG promoter; ICP, intermediate CpG promoter; LCP, low CpG promoter; MPSS, massively parallel signature sequencing.

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Additional file 2:

Histone modification enrichment at developmentally expressed and repressed imprinted genes in embryonic stem cells (ESCs). Enrichment of H3K4me3, H3K27me3, H3K9me3 and H4K20me3 at transcription start sites of developmentally expressed and repressed imprinted genes were assessed in mouse ESCs using high-throughput enrichment and expression source data from Mikkelsen et al. [50]. The presence of one particular modification at an imprinted gene does not preclude the presence of another. Developmentally expressed and developmentally repressed imprinted genes do not have significantly different epigenetic profiles for these four marks (chi-square contingency test, P = 0.525).

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Additional file 3:

Allele-specific histone modification enrichment at imprinted genes. In order to compare the results of our genome-wide analyses with allele-specific data, we have characterised previously published histone modification enrichment profiles involved in imprinting and developmental repression at imprinted genes. This data supports our findings and provides independent validation of our results.

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