Introduction

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.

Publications

  1. A probabilistic generative model for quantification of DNA modifications enables analysis of demethylation pathways.
    Cite this
    Äijö T, Huang Y, Mannerström H, Chavez L, Tsagaratou A, Rao A, Lähdesmäki H, 2016-03-01 - Genome biology

Credits

  1. Tarmo Äijö
    Developer

    Present address: Simons Center for Data Analysis, Simons Foundation, United States of America

  2. Yun Huang
    Developer

    Present address: Institute of Biosciences & Technology, Texas A&M University Health Science Center, United States of America

  3. Henrik Mannerström
    Developer

    Department of Computer Science, Aalto University School of Science, Finland

  4. Lukas Chavez
    Developer

    Present address: Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Germany

  5. Ageliki Tsagaratou
    Developer

    La Jolla Institute for Allergy and Immunology, La Jolla, United States of America

  6. Anjana Rao
    Developer

    Department of Signaling and Gene Expression, La Jolla Institute for Allergy and Immunology

  7. Harri Lähdesmäki
    Investigator

    Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Finland

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Summary
AccessionBT006976
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionFinland
Submitted ByHarri Lähdesmäki