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We detected differences among cell types in broad modification regions for H3K27me3 in many of the more lengthy regions that were tiled in this array format.
(4) We detected significant and clear changes in broad modification areas for H3K27me3 and, to a lesser extent, for H3K9me3, implying that the processes creating or maintaining these broad modifications differed in activity among cell types; in one case we verified that this change in a broad modification affected gene expression.
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Do we observe differences in broad modifications among BTSC types and neural stem cells?
Here, we examine variation in broad modifications among our five cell types.
We find substantial differences among cell types in broad modifications and bivalent promoters.
In contrast, clear changes in broad modifications were much less prevalent for H3K9me3 (4 of 44) and were absent for meC and H3K4me3 (0 of 44 in each case).
To study alterations in broad modifications, we examined the longer regions represented in this microarray format (see Methods; Additional file 34).
Hence, the change in the presence of this broad region of H3K9me3 is correlated with a large difference in mRNA levels for CACNG7, suggesting that these changes in broad modifications can have transcriptional, and presumably ultimately functional, consequences.
We observed large differences among cell types in total number of H3K9me3+ positive promoters and peaks and in broad modifications (defined as >50 kb peak length) for H3K27me3 and, to a lesser extent, H3K9me3.
Unfortunately, this array format only covers a portion of the genome, hence, it will be necessary to use other methods, most likely ChIP-seq, to fully establish the prevalence of differences in broad modifications for this mark across different cell types.
We verified that a change in a broad modification affected gene expression of CACNG7.
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