title: Analysis of histone modifications at human ribosomal DNA in liver cancer cell.
abstract: Human liver cancer is the cancer commonly seen clinically. The transcription of ribosomal DNA (rDNA) is a critical step for cells, and epigenetic marks such as post-translational histone modifications have been involved in the regulation of rDNA transcription. But less is known about the pathogenesis of the liver cancers concerning the rDNA transcription regulation. Here we aligned the ChIP-seq data of histone modification markers and CTCF to the human genome assembly which contains a single rDNA repeat in human liver cancer cell and validated their distribution with ChIP-QPCR. Human liver cancer cell possesses a higher enrichment of H3K4me1 and H3K27me3 at ~28 kb within the intergenic spacer (IGS) of rDNA and a higher enrichment of H3K4me3 and H3K27ac upstream of TSS. Furtherly, we studied whether UBF could affect histone modification markers and CTCF at rDNA in human liver cancer cell. UBF depletion leads to a decrease of gene activation mark H3K4me3 across the rDNA promoter. And other histone modification marks and CTCF were not altered after UBF depletion. Taken together, our data showed a high resolution map of histone modification marks at rDNA in human liver cancer cell and provide novel evidence to decipher chromatin-mediated regulation of rDNA in liver cancer.
authors.affiliation: Department of Medical Oncology, The People's Hospital of Shaanxi Province, Xi'an, P.R. China.
authors.forename: Feng
authors.initials: F
authors.lastname: Yu
authors.affiliation: Department of Medical Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, P.R. China.
authors.forename: Xingyong
authors.initials: X
authors.lastname: Shen
authors.affiliation: Department of Medical Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, P.R. China.
authors.forename: Li
authors.initials: L
authors.lastname: Fan
authors.affiliation: Department of Medical Oncology, Xijing Hospital, The Fourth Military Medical University, Xi'an, P.R. China.
authors.forename: Zhaocai
authors.initials: Z
authors.lastname: Yu
mesh_terms: D015153:Blotting, Western; D000076246:CCCTC-Binding Factor; D047369:Chromatin Immunoprecipitation; D004275:DNA, Ribosomal / Q000235:genetics / Q000378:metabolism*; D015972:Gene Expression Regulation, Neoplastic; D056945:Hep G2 Cells; D042421:Histone Code; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D008113:Liver Neoplasms / Q000235:genetics / Q000378:metabolism / Q000473:pathology; D008239:Lysine / Q000378:metabolism; D008745:Methylation; D035463:Pol1 Transcription Initiation Complex Proteins / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic / Q000235:genetics; D011499:Protein Processing, Post-Translational; D034622:RNA Interference; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction
chemical_list: D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D004275:DNA, Ribosomal; D006657:Histones; D035463:Pol1 Transcription Initiation Complex Proteins; D012097:Repressor Proteins; C063844:transcription factor UBF; D008239:Lysine