Methylation of class II transactivator gene promoter IV is not associated with susceptibility to Multiple Sclerosis
Multiple sclerosis (MS) is a complex trait in which alleles at or near the class II loci HLA-DRB1 and HLA-DQB1 contribute significantly to genetic risk. The MHC class II transactivator (MHC2TA) is the master controller of expression of class II genes, and methylation of the promoter of this gene has been previously been shown to alter its function. In this study we sought to assess whether or not methylation of the MHC2TA promoter pIV could contribute to MS disease aetiology.
In DNA from peripheral blood mononuclear cells from a sample of 50 monozygotic disease discordant MS twins the MHC2TA promoter IV was sequenced and analysed by methylation specific PCR.
No methylation or sequence variation of the MHC2TA promoter pIV was found.
The results of this study cannot support the notion that methylation of the pIV promoter of MHC2TA contributes to MS disease risk, although tissue and timing specific epigenetic modifications cannot be ruled out.
KeywordsMultiple Sclerosis Twin Pair Monozygotic Twin Multiple Sclerosis Disease Multiple Sclerosis Risk
Genetic-epidemiological studies indicate unequivocally that there is a genetic influence on susceptibility to Multiple Sclerosis (MS) . The only consistent genetic association with MS in Northern Europeans had been with extended MHC haplotypes especially those containing HLA-DRB1*1501 . Recently, the interleukin 7 receptor (IL7R) and interleukin 2 receptor (IL2R) genes have been shown to be additional MS susceptibility loci [2, 3]. However, any effect of IL7R or IL2R is small and it is clear that the MHC is the key MS susceptibility locus .
The MS MHC class II association has been fine mapped to the extended haplotype HLA-DQA1*0102-DQB1*0602-DRB1*1501-DRB5*0101 . Intense linkage disequilibrium within the MHC has prevented the exact susceptibility locus from being conclusively identified. Analysis of the MHC region with a large number of markers as well as classical typing show evidence for the involvement of the class II region only [6, 7]. However, the paradigm is more complex than one in which the HLA-DRB1*15 allele acts solely to increase MS risk. Our previous investigations have shown that HLA-DRB1*15 and HLA-DRB1*17 bearing haplotypes increase risk of MS, and HLA-DRB1*14 and HLA-DRB1*11 bearing haplotypes are protective [8, 9]. Additionally, HLA-DRB1*10, DRB1*01 and DRB1*08 interact with HLA-DRB1*15 to influence disease risk [8, 9].
Given the unequivocal MHC class II association with MS, the amount and cellular distribution of class II molecules may therefore be important factors in determining susceptibility to the disease. MHC class II molecule expression is regulated primarily through a transcriptional co-activator termed MHC2TA . MHC2TA functions as a non-DNA-binding co-activator that coordinates multiple events that are required for the activation of transcription including the recruitment of transcription factors and phosphorylation of RNA Polymerase II . The highly regulated pattern of expression of the gene encoding MHC2TA dictates where, when and to what level MHC class II genes are expressed . Transcription of the gene encoding MHC2TA is controlled by a large regulatory region that contains three independent promoters (pI, pIII and pIV) . The promoter pIV is essential for driving MHC2TA expression in cells that are sensitive to interferon-γ, and it has been shown that methylation of CpG dinucleotides in this promoter region can influence the expression of MHC2TA and thus MHC class II molecules .
Given a contentious association of MHC2TA polymorphisms with susceptibility to MS [13, 14], we sought to assess whether or not methylation of the MHC2TA pIV promoter could contribute to MS aetiology using a cohort of monozygotic discordant twins, potentially ideal for entangling genetic and epigenetic contributions to disease susceptibility.
All subjects used in the study were ascertained through the ongoing Canadian Collaborative Project on the Genetic Susceptibility to MS (CCPGSMS), for which the methodology has been previously described [15, 16]. Each participating centre of the CCPGSMS obtained ethical approval (as set out in the Helsinki Declaration) from the relevant institutional review board, and the entire project was reviewed and approved by the University of British Columbia. Blood was obtained with appropriate consent.
Clinical details of MS patients
Sample Size (n)
Mean age of onset (years)
% Relapsing Remitting MS
CpG Dinucleotide Prediction
The sequence of the pIV promoter from the NCBI Build 36.1 reference sequence was analysed to identify CpG islands that could be methylated. The methodology for this is described in .
Sequencing of promoter pIV
Primer sequences used for sequencing
Bisulfite treatment and Methylation Specific PCR
Primer sequences used for methylation specific PCR
Multiple sclerosis is unambiguously associated with the MHC class II region  and this locus exerts the strongest genetic effect on the risk of developing the disease . MHC2TA is the master regulator of MHC class II gene expression and therefore variability at the MHC2TA gene could conceivably influence susceptibility to MS.
In this investigation we studied the sequence variability of the pIV promoter of the MHC2TA gene and found no variation. This is in agreement with previous studies and this conservation may be a result of the importance of this promoter to gene function.
The only known epigenetic modification of DNA in mammals is methylation of cytosine at position C5 in CpG dinucleotides . DNA methylation affects transcription directly, by influencing the binding of specific transcription factors, and indirectly, by recruiting methyl-CpG-binding proteins and their associated chromatin remodeling activities. It has been shown that methylation of the pIV promoter can influence MHC2TA expression. Monozygotic twins share a common genotype. However, genetically identical twin pairs exhibit differences in susceptibility to many diseases, including MS, where the monozygotic twin concordance rate at its highest does not exceed 30% . There are several possible explanations for these observations, one of these being the existence of epigenetic differences. In this study, we used a cohort of monozygotic MS discordant twins to examine whether methylation differences of the MHC2TA promoter could explain differences in susceptibility to disease. We did not detect methylation of CpG dinucleotides in the pIV promoter in any of our samples, either MS affected or not. Although this study argues against a role of methylation of MHC2TA in MS disease pathogenesis, it must be remembered that whilst genomic information is uniform among the different cells of a complex organism, the epigenome varies from tissue to tissue, controlling the differential expression of genes and providing specific identity to each cell type. Hence, by looking solely at peripheral blood mononuclear cells we may have missed tissue specific methylation of the MHC2TA promoter. Furthermore, a recent study which compared global and locus specific methylation patterns in monozygotic twins, showed that although indistinguishable in early life, epigenetic profiles of monozygotic twins change with age  and hence for an adult onset disease with susceptibility determined early in life [23, 24] timing of any epigenetic changes may be crucial, and our study may not have been able to detect methylation of MHC2TA at an early age that has since decayed. Additionally, we may have missed low level methylation patterns and it would be necessary to examine every CpG dinucleotide of MHC2TA to be confident that an association between methylation and disease had not been missed just because the wrong markers had been typed.
In summary, although our results do not completely rule out the possibility of an association between methylation of MHC2TA and MS we believe that our data is sufficient to exclude a major effect of methylation of this gene in MS pathology.
This work was funded by the Multiple Sclerosis Society of the United Kingdom. SVR is funded by the Medical Research Council of the United Kingdom. The authors would like to thank all patients who generously participated in this study and physicians participating in the CCPGSMS. Experiments performed for this investigation comply with current guidelines and ethics. The sponsor of the study had no role in study design, data collection, data analysis, data interpretation, or writing of the report. The corresponding author had full access to all the data in the study and final responsibility for the decision to submit for publication.
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