Genome-wide maps of chromatin state in drug sensitive and resistance Lewis lung carcinoma isograft mouse model. Mus musculus

We investigated histone modifications in regulation of gene expression using chromatin immunoprecipitation (ChIP) sequencing in samples from drug-sensitive vs. resistant murine lung cancer isografts. Histone modification fluctuation was analyzed in both genome wide scale and individual genes. The data showed that both chromatin status of gene promoter and transcription profile were altered by drug-resistance. Promoter activity of most low CG promoter (LCP) and high CG promoter (HCP) related genes were increased in drug resistant samples. These LCP genes were enriched in hematopoietic cell differentiation and angiogenesis-related pathways. In contrast, the HCP genes were prone to tumorigenesis, like the p53 pathway. Further analysis revealed that the key regulators during hematopoietic cell development in the thymus branch and bone marrow branch were regulated in opposite ways, which may contribute to blood cell differentiation. Overall design: LLC-R and LLC-NR cells were subcutaneously inoculated into the right flanks of C57BL/6J mice to allow tumor isografts to grow to an approximate size of 500 mm3 and then tumor isograft tissues were dissected and used for further study. Tissue sections of each isograft were prepared and formaldehyde was then inactivated. Tissue homogenate were then harvested for extraction of nuclei and digested with micrococcal nuclease. Each of different histone modification antibodies (i.e. H3K4me3,H3K27me3,H3K36me3,H3K9ac) were used to immunoprecipitate the above RNase-digested chromatin.The resulted DNA fragments were sequenced using an Illumina HiSeq instrument.