DNA modifications repaired by base excision repair are epigenetic.

Area of Science:

• Molecular Biology
• Epigenetics
• DNA Repair

Background:

• CREB (cAMP response element-binding protein) regulates approximately 25% of the mammalian transcriptome.
• Modifications to CREB binding sites can significantly impact transcription initiation.
• The base excision repair (BER) pathway is crucial for maintaining DNA integrity.

Purpose of the Study:

• To investigate how DNA lesions repaired by the BER pathway affect CREB binding to its consensus (CRE) sequence.
• To determine if BER pathway intermediates function as epigenetic modifiers influencing transcription factor binding.

Main Methods:

• Electrophoretic mobility shift assays (EMSA) were used to measure binding affinity (Kd) of purified human CREB to modified and wild-type CRE oligonucleotides.
• Site-directed mutagenesis and chemical modifications were employed to introduce specific alterations and lesions within the CRE sequence.

Main Results:

• DNA modifications within the CRE sequence, particularly at guanine residues, altered CREB binding affinity by up to two orders of magnitude.
• Cytosine methylation or guanine oxidation at specific sites diminished CREB binding.
• A G/U mispair within a CpG context enhanced CREB binding.
• BER pathway intermediates at certain guanine residues reduced CREB binding, while oxidation outside a CpG islet had no effect.
• Only UpG modifications enhanced DNA.CREB dimer formation.

Conclusions:

• DNA lesions processed by the BER pathway can epigenetically modulate CREB binding to its DNA recognition site.
• These findings suggest a novel mechanism by which DNA repair processes influence gene transcription regulation.
• BER pathway substrates may act as dynamic epigenetic marks controlling transcription factor interactions.