Early demethylation of non-CpG, CpC-rich, elements in the myogenin 5’-flanking region

• DOI: 10.4161/cc.9.19.13193
• Publication Date: 2010-10-07T18:33:55Z
• Authors: Andrea Fuso; Giampiero Ferraguti; Francesco Grandoni; Raffaella Ruggeri; Sigfrido Scarpa; Roberto Strom; Marco Lucarelli
• Keywords: Base Sequence; 5' Flanking Region; Molecular Sequence Data; DNA Methylation; Muscle Development; Cell Line; Mice; Gene Expression Regulation; active demethylation; non-cpg island genes; short cpc-rich elements; demethylation dynamics; non-cpg methylation; transcriptionalmodulation; transcriptional modulation; muscle differentiation; Animals; Cluster Analysis; Humans; CpG Islands; Myogenin; Muscle, Skeletal; Promoter Regions, Genetic

The dynamic changes and structural patterns of DNA methylation of genes without CpG islands are poorly characterized. The relevance of CpG to the non-CpG methylation equilibrium in transcriptional repression is unknown. In this work, we analyzed the DNA methylation pattern of the 5'-flanking of the myogenin gene, a positive regulator of muscle differentiation with no CpG island and low CpG density, in both C2C12 muscle satellite cells and embryonic muscle. Embryonic brain was studied as a non-expressing tissue. High levels of both CpG and non-CpG methylation were observed in non-expressing experimental conditions. Both CpG and non-CpG methylation rapidly dropped during muscle differentiation and myogenin transcriptional activation, with an active demethylation dynamics. Non-CpG demethylation occurred more rapidly than CpG demethylation. Demethylation spread from initially highly methylated short CpC-rich elements to a virtually unmethylated status. These short elements have a high CpC content and density, share some motifs and largely coincide with putative recognition sequences of some differentiation-related transcription factors. Our findings point to a dynamically controlled equilibrium between CpG and non-CpG active demethylation in the transcriptional control of tissue-specific genes. The short CpC-rich elements are new structural features of the methylation machinery, whose functions may include priming the complete demethylation of a transcriptionally crucial DNA region.