BiQ Analyzer HiMod: An interactive software tool for high-throughput locus-specific analysis of 5-methylcytosine and its oxidized derivatives

Nucleic Acids Research

Volumn 42, Issue W1, 2014, Pages

  Becker, Daniel ^a,b   Lutsik, Pavlo ^a   Ebert, Peter ^b   Bock, Christoph ^b,c,d   Lengauer, Thomas ^b   Walter, Jörn ^a  

^a SAARLAND UNIVERSITY   (Germany)

^b MAX PLANCK INSTITUTE FOR INFORMATICS   (Germany)

^c ERICH SCHMID INSTITUTE OF MATERIALS SCIENCE   (Austria)

^d MEDICAL UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

5 METHYLCYTOSINE;

ARTICLE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; DATA PROCESSING; DNA MODIFICATION; GENE LOCUS; NONHUMAN; OXIDATION; PRIORITY JOURNAL; QUALITY CONTROL; SEQUENCE ALIGNMENT;

5-METHYLCYTOSINE; ANIMALS; DNA; DNA METHYLATION; GENETIC LOCI; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INTERNET; MICE; OXIDATION-REDUCTION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84904805405     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku457     Document Type: Article

References (28)

1. Smith,Z.D. and Meissner,A. (2013) DNA methylation: roles in mammalian development. Nat. Rev. Genet., 14, 204-220.
2. Bergman,Y. and Cedar,H. (2013) DNA methylation dynamics in health and disease (vol 20, pg 274, 2013).Nat. Struct. Mol. Biol., 20, 1236-1236.
3. Harris,R.A., Wang,T., Coarfa,C., Nagarajan,R.P., Hong,C., Downey,S.L., Johnson,B.E., Fouse,S.D., Delaney,A., Zhao,Y. et al. (2010) Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat. Biotechnol., 28, U1097-U1194.
4. Bock,C., Tomazou,E.M., Brinkman,A.B., Mueller,F., Simmer,F., Gu,H., Jaeger,N., Gnirke,A., Stunnenberg,H.G. and Meissner,A. (2010) Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol., 28, U1106-U1196.
5. Bock,C. (2012) Analysing and interpreting DNA methylation data. Nat. Rev. Genet., 13, 705-719.
6. Branco,M.R., Ficz,G. and Reik,W. (2012) Uncovering the role of 5-hydroxymethylcytosine in the epigenome. Nat. Rev. Genet., 13, 7-13.
7. Kohli,R.M. and Zhang,Y. (2013) TET enzymes, TDG and the dynamics of DNA demethylation. Nature, 502, 472-479.
8. Huang,Y., Pastor,W.A., Shen,Y., Tahiliani,M., Liu,D.R. and Rao,A. (2010) The behaviour of 5-hydroxymethylcytosine in bisulfite sequencing. PLoS One, 5, e8888.
9. Booth,M.J., Branco,M.R., Ficz,G., Oxley,D., Krueger,F., Reik,W. and Balasubramanian,S. (2012) Quantitative sequencing of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution. Science, 336, 934-937.
10. Schuler,P. and Miller,A.K. (2012) Sequencing the sixth base (5-hydroxymethylcytosine): selective DNA oxidation enables base-pair resolution. Angew. Chem., Int. Ed. Engl., 51, 10704-10707.
11. Song,C.X., Szulwach,K.E., Dai,Q., Fu,Y., Mao,S.Q., Lin,L., Street,C., Li,Y., Poidevin,M., Wu,H. et al. (2013) Genome-wide profiling of 5-formylcytosine reveals its roles in epigenetic priming. Cell, 153, 678-691.
12. Lu,X., Song,C.X., Szulwach,K., Wang,Z., Weidenbacher,P., Jin,P. and He,C. (2013) Chemical modification-assisted bisulfite sequencing (CAB-Seq) for 5-carboxylcytosine detection in DNA. J. Am. Chem. Soc., 135, 9315-9317.
13. Kumaki,Y., Oda,M. and Okano,M. (2008) QUMA: quantification tool for methylation analysis. Nucleic Acids Res., 36, W170-W175.
14. Lutsik,P., Feuerbach,L., Arand,J., Lengauer,T., Walter,J. and Bock,C. (2011) BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res., 39, W551-W556.
15. Bock,C., Reither,S., Mikeska,T., Paulsen,M., Walter,J. and Lengauer,T. (2005) BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics, 21, 4067-4068.
16. Rohde,C., Zhang,Y., Reinhardt,R. and Jeltsch,A. (2010) BISMA-fast and accurate bisulfite sequencing data analysis of individual clones from unique and repetitive sequences. BMC Bioinformatics, 11, e230.
17. Hetzl,J., Foerster,A.M., Raidl,G. and Mittelsten Scheid,O. (2007) CyMATE: a new tool for methylation analysis of plant genomic DNA after bisulphite sequencing. Plant J., 51, 526-536.
18. Schuffler,P., Mikeska,T.,Waha,A., Lengauer,T. and Bock,C. (2009) MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol, 10, eR105.
19. Qu,J., Zhou,M., Song,Q., Hong,E.E. and Smith,A.D. (2013) MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation. Bioinformatics, 29, 2645-2646.
20. Blankenberg,D., Von Kuster,G., Coraor,N., Ananda,G., Lazarus,R., Mangan,M., Nekrutenko,A. and Taylor,J. (2010) Galaxy: a web-based genome analysis tool for experimentalists. Curr. Protoc. Mol. Biol., Chapter 19, Unit 19 10 11-21.
21. Giardine,B., Riemer,C., Hardison,R.C., Burhans,R., Elnitski,L., Shah,P., Zhang,Y., Blankenberg,D., Albert,I., Taylor,J. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
22. Goecks,J., Nekrutenko,A., Taylor,J. and Galaxy,T. (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol., 11, eR86.
23. Holland,R.C., Down,T.A., Pocock,M., Prlic,A., Huen,D., James,K., Foisy,S., Drager,A., Yates,A., Heuer,M. et al. (2008) BioJava: an open-source framework for bioinformatics. Bioinformatics, 24, 2096-2097.
24. Robinson,J.T., Thorvaldsdottir,H.,Winckler,W., Guttman,M., Lander,E.S., Getz,G. and Mesirov,J.P. (2011) Integrative genomics viewer. Nat. Biotechnol., 29, 24-26.
25. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
26. Ficz,G., Hore,T.A., Santos,F., Lee,H.J., Dean,W., Arand,J., Krueger,F., Oxley,D., Paul,Y.-L., Walter,J. et al. (2013) FGF Signaling Inhibition in ESCs Drives Rapid Genome-wide Demethylation to the Epigenetic Ground State of Pluripotency. Cell Stem Cell, 13, 351-359.
27. Arand,J., Spieler,D., Karius,T., Branco,M.R., Meilinger,D., Meissner,A., Jenuwein,T., Xu,G., Leonhardt,H.,Wolf,V. et al. (2012) In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet., 8, e1002750.
28. Hu,X., Zhang,L., Mao,S.Q., Li,Z., Chen,J., Zhang,R.R., Wu,H.P., Gao,J., Guo,F., Liu,W. et al. (2014) Tet and TDG mediate DNA demethylation essential for mesenchymal-to-epithelial transition in somatic cell reprogramming. Cell Stem Cell, 14, 512-522.