A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

  • Tarmo Äijö Simons Center for Data Analysis (Contributor)
  • Yun-Hui Huang (Contributor)
  • Henrik Mannerström (Contributor)
  • Lukas Chavez (Contributor)
  • Ageliki Tsagaratou La Jolla Institute for Allergy and Immunology (Contributor)
  • Anjana Rao (Contributor)
  • Harri Lähdesmäki (Contributor)

Tietoaineisto

Description

Abstract We present a generative model, Lux, to quantify DNA methylation modifications from any combination of bisulfite sequencing approaches, including reduced, oxidative, TET-assisted, chemical-modification assisted, and methylase-assisted bisulfite sequencing data. Lux models all cytosine modifications (C, 5mC, 5hmC, 5fC, and 5caC) simultaneously together with experimental parameters, including bisulfite conversion and oxidation efficiencies, as well as various chemical labeling and protection steps. We show that Lux improves the quantification and comparison of cytosine modification levels and that Lux can process any oxidized methylcytosine sequencing data sets to quantify all cytosine modifications. Analysis of targeted data from Tet2-knockdown embryonic stem cells and T cells during development demonstrates DNA modification quantification at unprecedented detail, quantifies active demethylation pathways and reveals 5hmC localization in putative regulatory regions.
Koska saatavilla1 tammikuuta 2016

Tutkimustuotos

A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways

Äijö, T., Huang, Y., Mannerström, H., Chavez, L., Tsagaratou, A., Rao, A. & Lähdesmäki, H., 14 maaliskuuta 2016, julkaisussa : GENOME BIOLOGY. 17, 1, s. 1-22 49.

Tutkimustuotos: LehtiartikkeliArticleScientificvertaisarvioitu

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  • 11 Sitaatiot (Scopus)
    177 Lataukset (Pure)

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    Äijö, T. (Contributor), Huang, Y. (Contributor), Mannerström, H. (Contributor), Chavez, L. (Contributor), Tsagaratou, A. (Contributor), Rao, A. (Contributor), Lähdesmäki, H. (Contributor) (1 tammikuuta 2016). A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways10.6084/m9.figshare.c.3604346.v1