Enroth et al. BMC Cancer 2011, 11:450 http://www.biomedcentral.com/1471-2407/11/450 one patient, showed transitions in the chromatin states that would suggest major functional consequences (i.e. from normal H3K4me3 to tumor H3K27me3 or vice verse). This resembles the results obtained after genetic mutation analysis of all coding sequences in CRC patients, where very few mutations are frequently shared between patients [49]. These observations suggest that in a given CRC patient, there could be a few major alterations (genetic and/or epigenetic) that can be cru- cial for tumorogenesis e.g. key components that could disturb the WNT-pathway such as silencing of the APC gene and activation of the b-catenin gene or up-regula- tion of repressors of tumor suppressing genes found in patient 1. These few major and likely causative alterations could, however, have major impacts on global gene expression programs and chromatin states. Our observations sug- gest that H3K4me3 genes, typically active in normal colon, become “hyperactivated” in CRC. Since many of these genes are involved in basic cellular processes, their increased expression could merely be the result of higher metabolic demands and proliferation rates in tumor cells [50]. Mechanistically, a good candidate to mediate this “hyperactivation” response is SMYD3, a H3K4 methyltransferase frequently over-expressed in CRC and with oncogenic function [7]. On the other hand, H3K27me3 genes are already silent or lowly expressed in normal colon mucosa, and seemed to become “hypersilenced” in CRC. Down-regulation of H3K27me3 genes could be explained by polycomb-pre- marking of cancer-specific DNA hypermethylation [13,51] and subsequent loss of H3K27me3 and reduced epigenetic plasticity [12]. Due to tumor heterogeneity between different CRC patients, it is not expected that all normal colon H3K27me3 genes will loose the mark and become hypermethylated in a given tumor, which could explain why even genes that kept H3K27me3 state in our two patients seem to be hypersilenced when con- sidering larger patient cohorts. Finally, silencing of genes showing specific gain of H3K27me3 in tumors has been also reported in prostate cancer [10,11]. Mechanis- tically, the silencing of all these H3K27me3 gene groups may involve EZH2, which is frequently over-expressed in CRC and other cancer types [9] and is able to interact with and recruit DNA methyltransferases [52]. Another important aspect of the work is the evalua- tion of how well cell lines may represent the chromatin states of normal or tumor tissues. According to our data, for H3K27me3, which is important in determining cellular identity [53], cell lines could give a misleading picture of chromatin states in tissues they are supposed to represent. Such discrepancy seemed to increase depending on the differentiation grade of the cell line, Page 10 of 13 suggesting that low-grade cell lines could offer better cellular models than high grade poorly differentiated cell lines when studying chromatin states. Furthermore, our results and previous observations suggest that such alterations in H3K27me3 states can arise due to a com- bination of polycomb-premarking of DNA hypermethy- lation, subsequent lost of H3K27me3 and exacerbated DNA hypermethylation due to in vitro culture [12-14,51]. One such example is the polycomb binding profiles that were previously generated for the CRC cell line SW480 and used as a model of differentiated cells. As compared to ESCs, SW480 polycomb (H3K27me3) tar- gets were not enriched in developmental related pro- cesses [24]. Here, and previously [13], we have shown that H3K27me3 marked genes, both in normal and tumor colon tissues, are largely enriched in developmen- tal processes, and in fact, they significantly overlapped with ESC H3K27me3 targets. Therefore, we wanted to investigate how well CRC cell lines represent the chro- matin states of colon tissue samples (Table 2). This might be expected since many H3K4me3 genes corre- spond to housekeeping genes typically active in any given cell type. On the other hand, when considering H3K27me3 gene groups, the overlaps between normal and tumor samples were quite high (40-60%), while somewhat lower for HT29 (20-30%), but as described above, H3K27me3 target genes in this cell line were still largely related to developmental processes. Moreover, the fact that the HT29 H3K27me3 profile, as compared to SW480, shows higher overlap with tissues and is enriched in developmental processes, can be explained by the fact that HT29 is a low grade CRC cell line (grade II), while SW480 is a high grade (grade III-IV), poorly differentiated and highly abnormal CRC cell line. Conclusion In this work we generated the first coupled normal- tumor histone modification profiles in CRC, one of the cancer types with highest incidence in developed coun- tries, that should provide a valuable resource for future chromatin studies with CRC and/or gastrointestinal focus. By studying histone modification profiles we show that it is possible to get new insights into the epigenetic process and discover new biomarkers for cancer. Two such candidates discovered here are the PTGER2 and KLF7 genes. The former gained H3K37me3 in tumor in both our patients and the latter changed its modification status from H3K4me3 to H3K27me3 in both patients thus changing from activated to repressed state. PTGER2 has previously been implicated in CRC but further research will be needed to clarify the role of KLF7.