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Báo cáo y học: "ptimized design and data analysis of tag-based cytosine methylation assays"

Tuyển tập các báo cáo nghiên cứu về y học được đăng trên tạp chí y học Wertheim cung cấp cho các bạn kiến thức về ngành y đề tài: Optimized design and data analysis of tag-based cytosine methylation assays. | Suzuki et al. Genome Biology 2010 11 R36 http genomebiology.eom 2010 11 4 R36 w Genome Biology METHOD _ Open Access Optimized design and data analysis of tag-based cytosine methylation assays Masako Suzuki Qiang Jing Daniel Lia Marién Pascual Andrew McLellan and John M Greally Abstract Using the type III restriction-modification enzyme EcoP15I we isolated sequences flanking sites digested by the methylation-sensitive HpaII enzyme or its methylation-insensitive MspI isoschizomer for massively parallel sequencing. A novel data transformation allows us to normalise HpaII by MspI counts resulting in more accurate quantification of methylation at 1.8 million loci in the human genome. This HELP-tagging assay is not sensitive to sequence polymorphism or base composition and allows exploration of both CG-rich and depleted genomic contexts. Background Epigenetic mechanisms of transcriptional regulation are increasingly being studied for their potential influences in human disease pathogenesis. Much of this interest is based on the paradigm of neoplastic transformation in which epigenetic changes appear to be universal widespread throughout the genome causative of critical transcriptional changes and predictive of disease prognosis reviewed in 1 . Furthermore these epigenetic changes represent potential pharmacological targets for reversal and amelioration of the disease process 2 . Of the large number of regulatory processes referred to as epigenetic there exist numerous assays to study chromatin component distribution cytosine methylation and microRNA expression genome-wide. The chromatin components include a large number of post-translational modifications of histones variant histones DNA-binding proteins and associated complexes all tested by chromatin immunoprecipitation ChIP approaches coupled with microarray hybridization or massively parallel sequencing MPS . MicroRNAs can be identified and quantified by using microarrays and MPS while cytosine methylation can be .