Have a look at the polycomb (Pc) group of genes. They are well studied and have been shown to be the target of methylation. Since Pc genes repress a battery of segmentation genes, defects in silencing of Pc genes often results in visible segmentation defects which are easy to spot.

Regulation of Polycomb group genes Psc and Su(z)2 in Drosophila melanogaster.

Park SY, Schwartz YB, Kahn TG, Asker D, Pirrotta V.

Mech Dev. 2012 Jan-Feb;128(11-12):536-47. doi: 10.1016/j.mod.2012.01.004. Epub 2012 Jan 24.

PMID: 22289633 [PubMed - indexed for MEDLINE]

H3K27me3 is the histone mark for Polycomb proteins. So, the Hox genes, specially PREd is the best characterized upstream region for PcG binding.

The H3K4me3 is associated with Trithorax proteins. Look up where Ash1 etc bind.

If you're looking for PREs (binding sites for various members of the polycomb family) these guys have developed a prediction software which has mapped the binding sites.

http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

The cavalli lab have also done ChIPseq experiments to map where the various family members bind at 4-12hr old embryos.

http://cav-ouranos.igh.cnrs.fr/viewer-0.3_public/index.php

H3K4me3 is generally located at transcription start sites of transcribed genes (though is sometimes found at inactive promoters as well). Whatever your source material is, see if there's expression data available and assay H3K4me3 at the promoters of transcribed genes.

Check out this paper from the Pirrotta lab, http://www.nature.com/ng/journal/v38/n6/full/ng1817.html, for H3K27me3 binding sites (done in a derivative of the S2 cell line).

Polycomb where else!

Thanks for your suggestions

H3K27Me3 mark is enriched in polycomb regulated genes. H3K9Me3 mark is enriched in heterochromatin protein (HP1) regulated genes.

We analyzed H3K4me3 genome wide in drosophila:

"dKDM5/LID regulates H3K4me3 dynamics at the transcription-start site (TSS) of actively transcribed developmental genes"; Nucleic Acids Research, Volume 40, Issue 19, 9493-9505