Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells.

Nat Biotechnol 2009 Apr 29;27(4):361-8. Epub 2009 Mar 29.

Department of Genetics, Harvard Medical School, Cambridge, MA, USA.

Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed approximately 10,000 bisulfite padlock probes to profile approximately 7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for approximately 1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions.

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.1533DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566772PMC
April 2009
23 Reads

Publication Analysis

Top Keywords

gene-body methylation
12
highly expressed
8
methylation highly
8
expressed genes
8
methylation
6
existing expression
4
chromatin immunoprecipitation
4
expression chromatin
4
advantage existing
4
targets takes
4
takes advantage
4
immunoprecipitation data
4
enabled observe
4
promoter methylation
4
methylation high
4
low promoter
4
pattern low
4
choice targets
4
observe pattern
4
data enabled
4

References

(Supplied by CrossRef)

MM Suzuki et al.
Nat. Rev. Genet. 2008

MG Goll et al.
Annu. Rev. Biochem. 2005

AP Feinberg et al.
Nat. Rev. Cancer 2004

YH Jiang et al.
Annu. Rev. Genomics Hum. Genet. 2004

SJ Clark et al.
Nucleic Acids Res. 1994

AP Bird et al.
J. Mol. Biol. 1978

I Keshet et al.
Nat. Genet. 2006

SH Cross et al.
Nat. Genet. 1994

TA Rauch et al.
Proc. Natl. Acad. Sci. USA 2009

A Hellman et al.
Science 2007

B Khulan et al.
Genome Res. 2006

Similar Publications