Abnormal DNA methylation and deoxycytosine-deoxyguanine content in nucleosomes from lymphocytes undergoing apoptosis

Systemic lupus erythematosus (SLE) is characterized by an accelerated apopt osis of peripheral lymphocytes and an impairment of the clearance of apopto tic cells, Since changes in DNA methylation and in deoxycytosine and deoxyg uanine (GC) content have been shown to enhance the potential of DNA to acti vate murine and human B lymphocytes, we tested the capacity of lymphocytes undergoing apoptosis (under conditions that mimic the deletion of self-reac tive cells after antigen receptor engagement) to generate nucleosomes with a particular base composition. Using two cell culture systems and four apop tosis triggers, we found an increase of deoxymethylcytosine in fragmented c hromosomal DNA of apoptotic B and T lymphocytes. However, this increase was not associated with modulation of DNA (cytosine-5) methyltransferase, the enzyme that methylates eukaryotic DNA, which suggests that the changes in D NA methylation patterns are not linked to the process of de novo DNA methyl ation during cell death. In addition, we could not detect a unique methylat ion pattern in highly repetitive Alu sequences present in the human genome of SLE subjects, as compared with controls, However, the abnormal DNA methy lation of apoptotic nucleosomes was associated with an unusual pattern of n uclease-resistant, GC-rich regions in these DNA fragments. We propose that the combination of an accelerated apoptosis with a defect in the clearance of apoptotic cells results in release of increased amounts of nucleosomes w ith abnormally methylated, GC-rich DNA and provides an autologous stimulati on that could bypass tolerance to self in systemic autoimmune diseases. The se findings support the concept that the structure and dynamics of nucleoso mes are critical in determining their immunogenicity in SLE.