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Large-Scale Profiling of Protein Methylation

ABSTRACT: Develop a novel de-glyco-assisted methylation site identification (DOMAIN) strategy which enables straightforward, fast, and reproducible analysis of protein methylation in a proteome-wide manner. Combining multidimensional fractionation and multiprotease digestion, our method enabled the identification of 573 methylated forms in 270 proteins, including 311 new methylation forms, in A549 cells. Combining this technique with stable isotope labeling quantitative proteomics and RNA interference, we determined the differential regulation of several putative methylated sites that are related to the protein arginine N-methyltransferase 3 (PRMT3). Collectively, our integrated proteomics workflow for comprehensive mapping of methylation sites enables a better understanding of protein methylation, while providing a rapid and effective approach for global protein methylation analysis in biomedical research.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Hepatocyte

SUBMITTER: Min Ma

LAB HEAD: Lingjun Li

PROVIDER: PXD014574 | Pride | 2019-07-18

REPOSITORIES: Pride

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Project description:DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs. Keywords: DNA methylation profiling by massively parallel sequencing Keywords: Epigenetics Targeted examination of DNA methylation in two human cell types by combining array capture and bisulfite sequencing. In addition, this study examined two histone marks in the breast tumor cell line MDA-MB-231.

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Large-Scale Profiling of Protein Methylation

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