Figure 3

Effects of H2A.Z enrichment on gene expression. (A) Venn diagram shows H2A.Z-enriched genes that are upregulated (133 genes) and downregulated (23 genes) more than 1.5-fold with a P value of <0.05 in LD611 bladder cells. (B) Functional groups associated with the 133 genes that are enriched by H2A.Z and are upregulated in LD611 cancer cells. Biological processes are graphically depicted by P value. (C) Representative Integrative Genomics Viewer (IGV) genome browser tracks show the levels of H2A.Z near the TSS in LD611 (red) and UROtsa (blue) cells. Maximum sequencing depth over the displayed area is indicated on the right side in parentheses along with name of the genes. Different genomic coordinates and genome window size for BIRC3 (chr11:101,691,391-101,717,344; 26 kb); CCND1 (chr11:69,163,054-69,180,423; 17 kb); DDX43 (chr6:74,159,006-74,186,010; 26 kb); FADD (chr11:69,724,917-69,733,156; 8 kb); MEN1 (chr11:64,325,562-64,337,342; 11 kb); NT5E (chr6:86,214,021-86,264,228; 50 kb); POLDIP2 (chr17:23,695,786-23,710,730; 15 kb); PPFIA1 (chr11:69,792,454-69,910,255; 118 kb); STK3 (chr8:99,505,659-99,937,462; 432 kb) and YAP1 (chr11:101,484,402-101,611,364; 127 kb) are shown along with Reference Sequence (RefSeq) data. (D) LD611 and UROtsa cells were analyzed by quantitative chromatin immunoprecipitation (ChIP) using H2A.Z antibody to validate ChIP-sequencing results. Immunoprecipitated DNA was amplified by quantitative PCR (qPCR) with primers specific for the 10 genes. The primers are listed in Additional file 6: Table S5. Percent input was determined as the amount of immunoprecipitated DNA relative to input DNA. Error bars represent standard deviation of three independent experiments. (E) The RNA samples from LD611 and UROtsa cells were analyzed by quantitative reverse transcription PCR (qRT-PCR) using primers listed in Additional file 6: Table S5. Expression level was normalized to that of actin, and average and standard deviation of three independent experiments are shown.