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dc.contributor.authorSun, Shuying ( )
dc.contributor.authorLee, Yu Ri ( )
dc.contributor.authorEnfield, Brittany ( )
dc.date.accessioned2019-10-01T17:06:24Z
dc.date.available2019-10-01T17:06:24Z
dc.date.issued2019
dc.identifier.citationSun, S., Lee, Y. R., & Enfield, B. (2019). Hemimethylation patterns in breast cancer cell lines. Cancer Informatics, 18, pp. 1-12.en_US
dc.identifier.urihttps://digital.library.txstate.edu/handle/10877/8656
dc.description.abstractDNA methylation is an epigenetic event that involves adding a methyl group to the cytosine (C) site, especially the one that pairs with a guanine (G) site (ie, CG or CpG site), in a human genome. This event plays an important role in both cancerous and normal cell development. Previous studies often assume symmetric methylation on both DNA strands. However, asymmetric methylation, or hemimethylation (methylation that occurs only on 1 DNA strand), does exist and has been reported in several studies. Due to the limitation of previous DNA methylation sequencing technologies, researchers could only study hemimethylation on specific genes, but the overall genomic hemimethylation landscape remains relatively unexplored. With the development of advanced next-generation sequencing techniques, it is now possible to measure methylation levels on both forward and reverse strands at all CpG sites in an entire genome. Analyzing hemimethylation patterns may potentially reveal regions related to undergoing tumor growth. For our research, we first identify hemimethylated CpG sites in breast cancer cell lines using Wilcoxon signed rank tests. We then identify hemimethylation patterns by grouping consecutive hemimethylated CpG sites based on their methylation states, methylation "M" or unmethylation "U." These patterns include regular (or consecutive) hemimethylation clusters (eg, "MMM" on one strand and "UUU" on another strand) and polarity (or reverse) clusters (eg, "MU" on one strand and "UM" on another strand). Our results reveal that most hemimethylation clusters are the polarity type, and hemimethylation does occur across the entire genome with notably higher numbers in the breast cancer cell lines. The lengths or sizes of most hemimethylation clusters are very short, often less than 50 base pairs. After mapping hemimethylation clusters and sites to corresponding genes, we study the functions of these genes and find that several of the highly hemimethylated genes may influence tumor growth or suppression. These genes may also indicate a progressing transition to a new tumor stage.en_US
dc.formatText
dc.format.extent12 pages
dc.format.medium1 file (.pdf)
dc.language.isoen_USen_US
dc.publisherSageen_US
dc.sourceCancer Informatics, 2019, Vol. 18, pp. 1-12
dc.subjectMethylationen_US
dc.subjectHemimethylation
dc.subjectBioinformatics
dc.subjectBreast cancer
dc.titleHemimethylation Patterns in Breast Cancer Cell Linesen_US
txstate.documenttypeArticle
dc.identifier.doihttps://doi.org/10.1177/1176935119872959
dc.rights.licenseCreative Commons Non Commercial CC BY-NC: This article is distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 License (http://www.creativecommons.org/licenses/by-nc/4.0/) which permits non-commercial use, reproduction and distribution of the work without further permission provided the original work is attributed as specified on the SAGE and Open Access pages (https://us.sagepub.com/en-us/nam/open-access-at-sage).
txstate.departmentMathematics


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