DNA methyltransferases are complementary in maintaining DNA methylation in embryonic stem cells

Area of Science:

• Epigenetics
• Genomics
• Molecular Biology

Background:

• Genomic imprinting is crucial for mammalian development, regulated by DNA methylation at imprinting control regions (ICRs).
• ZFP57 and ZFP445 are known to maintain genomic imprinting in mouse embryos.
• The precise mechanisms of DNA methylation maintenance at ICRs, particularly in the absence of ZFP57, require further elucidation.

Purpose of the Study:

• To investigate the roles of DNA methyltransferases (DNMTs) in maintaining DNA methylation at ICRs in mouse embryonic stem (ES) cells.
• To determine if TET proteins are involved in preventing DNA methylation loss at ICRs in ZFP57-deficient cells.
• To elucidate the complementary roles of DNMT1, DNMT3A, and DNMT3B in maintaining DNA methylation across the genome.

Main Methods:

• Generation of ZFP57-mutant mouse ES cell lines.
• Generation of ES cell clones lacking three major DNA methyltransferases (DNMT1, DNMT3A, DNMT3B).
• DNA methylation analysis at imprinting control regions (ICRs), repeats, and genic regions using allelic analysis.

Main Results:

• DNA methylation was lost at most examined ICRs in ZFP57 mutant ES cells, a loss not prevented by eliminating TET proteins.
• DNMT3A and DNMT3B were essential for DNA methylation at a subset of ICRs, while DNMT1 maintained methylation at most known ICRs.
• Germline-derived DNA methylation was lost at examined ICRs in DNMT-deficient cells, with DNMT1, DNMT3A, and DNMT3B all required for maintaining DNA methylation at various genomic sequences.

Conclusions:

• Three DNA methyltransferases (DNMT1, DNMT3A, DNMT3B) play complementary roles in maintaining DNA methylation in mouse ES cells.
• DNA methylation at ICRs is primarily maintained through the ZFP57-dependent pathway, involving multiple DNMTs.
• DNMTs are essential for maintaining DNA methylation at repeats, genic regions, and other genomic sequences, in addition to ICRs.