By Allison Proffitt
February 3, 2010 | SINGAPORE—Researchers at the Genome Institute of Singapore and The Scripps Research Institute have shown dramatic changes in DNA methylation as stem cells differentiate and the patterns revealed could influence transcription and gene expression. The results were published on Wednesday in Genome Research.
We did genome research to understand epigenetic influences in differentiated cells, senior author Chia-Lin Wei at GIS, told Bio-IT World. “We did comprehensive mapping on three different stages of stem cells.” The group used human embryonic stem cells; human embryonic stem cells that had differentiated into skin-like cells, an intermediate stage; and fully-differentiated cells derived from human skin.
DNA methylation causes specific subunits of DNA to be chemically modified and this modification can control which areas of the genome are active and which are dormant. DNA methylation is critical to the process in which embryonic cells change from ‘pluripotent stem cells’, which have the ability to turn into hundreds of cell types, to ‘differentiated cells’, distinct types of cells that make up different parts of the body, such as the skin, hair, nerves, etc.
Wei told Bio-IT World that the results revealed intriguing new patterns in the genome. The sequencing was done with the Illumina GA2x, and represents 15x coverage for each of the three cell types.
DNA methylation helps control which areas of the genome are active and which are dormant. Wei and her colleagues found that segments of the genome are methylated or de-methylated during differentiation, and some of the changes in methylation were surprising.
The team saw promoter hypomethylation at CpG sites, which was expected, but using a whole genome approach found that global CpG methylation was higher than previously thought (55% vs. 40%). The team also found a unique pattern of CpA methylation that was greatly enriched in stem cells. As cells differentiate, there is a dramatic decrease in CpA methylation, Wei said.
The team also uncovered increased methylation of intergenic regions and gene promoters, followed by a sharp dip about 1000 bases upstream of a transcription start site and reaching a minimum immediately before the transcription site. Methylation gradually increases over the transcribed region and is then maintained at a high level. At the end of a transcription region, a second drop occurs.
Most interestingly, decreased methylation of introns and increased methylation of exons (10% higher in stem cells) were found. The increased and decreased methylation revealed what could be very telling patterns. Striking, said Wei, were “specific spikes” at the junction of introns and exons. Researchers observed a sharp spike in DNA methylation at the 5’ end and a sharp dip at the 3’ end of the intron/exon boundary.
The patterns suggest roles for DNA methylation in RNA transcription, mRNA splicing, and even gene expression. “But we haven’t grasped the entire implications,” said Wei.