title: Altered promoter nucleosome positioning is an early event in gene silencing.
abstract: Gene silencing in cancer frequently involves hypermethylation and dense nucleosome occupancy across promoter regions. How a promoter transitions to this silent state is unclear. Using colorectal adenomas, we investigated nucleosome positioning, DNA methylation, and gene expression in the early stages of gene silencing. Genome-wide gene expression correlated with highly positioned nucleosomes upstream and downstream of a nucleosome-depleted transcription start site (TSS). Hypermethylated promoters displayed increased nucleosome occupancy, specifically at the TSS. We investigated 2 genes, CDH1 and CDKN2B, which were silenced in adenomas but lacked promoter hypermethylation. Instead, silencing correlated with loss of nucleosomes from the -2 position upstream of the TSS relative to normal mucosa. In contrast, permanent CDH1 silencing in carcinoma cells was characterized by promoter hypermethylation and dense nucleosome occupancy. Our findings suggest that silenced genes transition through an intermediary stage involving altered promoter nucleosome positioning, before permanent silencing by hypermethylation and dense nucleosome occupancy.
authors.affiliation: a Adult Cancer Program; Lowy Cancer Research Center and Prince of Wales Clinical School; UNSW ; Sydney , Australia.
authors.forename: Luke B
authors.initials: LB
authors.lastname: Hesson
authors.forename: Mathew A
authors.initials: MA
authors.lastname: Sloane
authors.forename: Jason Wh
authors.initials: JW
authors.lastname: Wong
authors.forename: Andrea C
authors.initials: AC
authors.lastname: Nunez
authors.forename: Sameer
authors.initials: S
authors.lastname: Srivastava
authors.forename: Benedict
authors.initials: B
authors.lastname: Ng
authors.forename: Nicholas J
authors.initials: NJ
authors.lastname: Hawkins
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Bourke
authors.forename: Robyn L
authors.initials: RL
authors.lastname: Ward
mesh_terms: D000236:Adenoma / Q000235:genetics; D000368:Aged; D015703:Antigens, CD; D015820:Cadherins / Q000235:genetics; D045744:Cell Line, Tumor; D015179:Colorectal Neoplasms / Q000235:genetics; D050762:Cyclin-Dependent Kinase Inhibitor p15 / Q000235:genetics; D019175:DNA Methylation; D044127:Epigenesis, Genetic; D005260:Female; D020868:Gene Silencing; D006801:Humans; D008297:Male; D008875:Middle Aged; D009707:Nucleosomes / Q000235:genetics*; D011401:Promoter Regions, Genetic; D024363:Transcription Initiation Site
chemical_list: D015703:Antigens, CD; C513384:CDH1 protein, human; C493966:CDKN2B protein, human; D015820:Cadherins; D050762:Cyclin-Dependent Kinase Inhibitor p15; D009707:Nucleosomes
keywords: DNA methylation; Gene silencing; TSS, transcription start site; NDR, nucleosome depleted region; CGI, CpG island; CRC, colorectal carcinoma; NOMe-Seq, nucleosome occupancy and methylome sequencing; MBD-Seq, Methyl-CpG binding domain (MBD) protein DNA enrichment and sequencing; MNase-Seq,; cancer; hypermethylation; nucleosome