title: Identical sets of methylated and nonmethylated genes in Ciona intestinalis sperm and muscle cells.
abstract: BACKGROUND
  The discovery of gene body methylation, which refers to DNA methylation within gene coding region, suggests an as yet unknown role of DNA methylation at actively transcribed genes. In invertebrates, gene bodies are the primary targets of DNA methylation, and only a subset of expressed genes is modified.
  
  
  RESULTS
  Here we investigate the tissue variability of both the global levels and distribution of 5-methylcytosine (5mC) in the sea squirt Ciona intestinalis. We find that global 5mC content of early developmental embryos is high, but is strikingly reduced in body wall tissues. We chose sperm and adult muscle cells, with high and reduced levels of global 5mC respectively, for genome-wide analysis of 5mC targets. By means of CXXC-affinity purification followed by deep sequencing (CAP-seq), and genome-wide bisulfite sequencing (BS-seq), we designated body-methylated and unmethylated genes in each tissue. Surprisingly, body-methylated and unmethylated gene groups are identical in the sperm and muscle cells. Our analysis of microarray expression data shows that gene body methylation is associated with broad expression throughout development. Moreover, transgenic analysis reveals contrasting gene body methylation at an identical gene-promoter combination when integrated at different genomic sites.
  
  
  CONCLUSIONS
  We conclude that gene body methylation is not a direct regulator of tissue specific gene expression in C. intestinalis. Our findings reveal constant targeting of gene body methylation irrespective of cell type, and they emphasize a correlation between gene body methylation and ubiquitously expressed genes. Our transgenic experiments suggest that the promoter does not determine the methylation status of the associated gene body.
authors.forename: Miho M
authors.initials: MM
authors.lastname: Suzuki
authors.forename: Akiko
authors.initials: A
authors.lastname: Yoshinari
authors.forename: Madoka
authors.initials: M
authors.lastname: Obara
authors.forename: Shohei
authors.initials: S
authors.lastname: Takuno
authors.forename: Shuji
authors.initials: S
authors.lastname: Shigenobu
authors.forename: Yasunori
authors.initials: Y
authors.lastname: Sasakura
authors.forename: Alastair Rw
authors.initials: AR
authors.lastname: Kerr
authors.forename: Shaun
authors.initials: S
authors.lastname: Webb
authors.forename: Adrian
authors.initials: A
authors.lastname: Bird
authors.forename: Atsuo
authors.initials: A
authors.lastname: Nakayama