Sometimes it takes a special kind of guy to get the job done and when the job is to keep imprinted genes differentially methylated, that guy is DNMT1. An international group of researchers led by Jacquetta Trasler in Canada set out to exploit this fact in order to identify yet unknown imprinted genomic sequences.
Several studies have shown that re-expression of Dnmt1 in ES cells lacking the enzyme led to recovery of DNA methylation levels at non-imprinted loci but not at the germ-line differentially methylated domains (gDMDs) of imprinted genes. Encouraged by these findings McGraw et al. used a mouse ES cell line harbouring a tetracycline-controllable Dnmt1 locus (Dnmttet/tet) to identify novel gDMD-like sequences that escape DNA methylation recovery after transient depletion of Dnmt1.
Here is what they found:
- DNA methylation at non-imprinted sequences such as repetitive elements recovered after transient Dnmt1 depletion.
- Transient Dnmt1 depletion lead to a permanent loss of DNA methylation at known imprinted gene gDMDs.
- Restriction landmark genome scanning (RLGS) revealed the existence of gDMDs outside of imprinted loci (non-imprinted DMDs).
- Reduced representation bisulfite sequencing (RRBS) further showed that non-imprinted DMDs are enriched at intergenic regions and overlapped with or were found in close proximity to LINE elements.
- Non-imprinted DMDs that mapped to genic regions related to disorders such as cancer and autistic disorder.
The researchers then confirm their results using a mouse model in which absence of the oocyte-specific DNMT1o isoform causes a transient loss of DNMT1 activity in the 8-cell stage embryo. From this they conclude that non-imprinted gDMDs might represent novel developmental marks with imprinted-like behaviors, which require stage specific de novo methylation and continued and uninterrupted DNMT1 activity in order to be accurately inherited.