Skip to main content
SpringerLink
Log in

Computational epigenetic profiling of CpG islets in MTHFR

  • Published:
Molecular Biology Reports Aims and scope Submit manuscript

Abstract

Computational epigenetics is a new area of research focused on exploring how DNA methylation patterns affect transcription factor binding that affect gene expression patterns. The aim of this study was to produce a new protocol for the detection of DNA methylation patterns using computational analysis which can be further confirmed by bisulfite PCR with serial pyrosequencing. The upstream regulatory element and pre-initiation complex relative to CpG islets within the methylenetetrahydrofolate reductase gene were determined via computational analysis and online databases. The 1,104 bp long CpG island located near to or at the alternative promoter site of methylenetetrahydrofolate reductase gene was identified. The CpG plot indicated that CpG islets A and B, within the island, contained 62 and 75 % GC content CpG ratios of 0.70 and 0.80–0.95, respectively. Further exploration of the CpG islets A and B indicates that the transcription start sites were GGC which were absent from the TATA boxes. In addition, although six PROSITE motifs were identified in CpG B, no motifs were detected in CpG A. A number of cis-regulatory elements were found in different regions within the CpGs A and B. Transcription factors were predicted to bind to CpGs A and B with varying affinities depending on the DNA methylation status. In addition, transcription factor binding may influence the expression patterns of the methylenetetrahydrofolate reductase gene by recruiting chromatin condensation inducing factors. These results have significant implications for the understanding of the architecture of transcription factor binding at CpG islets as well as DNA methylation patterns that affect chromatin structure.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

Abbreviations

TSS:

Transcription start site

MBD:

Methyl-CpG binding domain proteins

MTHFR:

Methylenetetrahydrofolate reductase

DBTSS:

Database of transcription start sites

ENCODE:

Encyclopedia of DNA elements

ChIP-seq:

Chromatin immunoprecipitation-sequencing

MRE:

Methyl-sensitive restriction enzyme

MeDIP-seq:

DNA immunoprecipitation-sequencing

H3K4me3:

H3 lysine 4 trimethylation

References

  1. Bock C, Walter J, Paulsen M, Lengauer T (2007) CpG island mapping by epigenome prediction. PLoS Comput Biol 3:e110

    Article  PubMed Central  PubMed  Google Scholar 

  2. Reed K, Poulin ML, Yan L, Parissenti AM (2010) Comparison of bisulfite sequencing PCR with pyrosequencing for measuring differences in DNA methylation. Anal Biochem 397:96–106

    Article  CAS  PubMed  Google Scholar 

  3. Ammerpohl O, Martin-Subero JI, Richter J, Vater I, Siebert R (2009) Hunting for the 5th base: techniques for analyzing DNA methylation. Biochim Biophys Acta 1790:847–862

    Article  CAS  PubMed  Google Scholar 

  4. Matouk CC, Marsden PA (2008) Epigenetic regulation of vascular endothelial gene expression. Circ Res 102:873–887

    Article  CAS  PubMed  Google Scholar 

  5. Hackenberg M, Barturen G, Carpena P, Luque-Escamilla P, Previti C, Oliver J (2010) Prediction of CpG island function: CpG clustering vs. Sliding-window methods. BMC Genomics 11:327

    Article  PubMed Central  PubMed  Google Scholar 

  6. Antequera F (2003) Structure, function and evolution of CpG island promoters. Cell Mol Life Sci 60:1647–1658

    Article  CAS  PubMed  Google Scholar 

  7. Fang F, Fan S, Zhang X, Zhang MQ (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics 22:2204–2209

    Article  CAS  PubMed  Google Scholar 

  8. Tran P, Leclerc D, Chan M, Pai A, Hiou-Tim F, Wu Q, Goyette P, Artigas C, Milos R, Rozen R (2002) Multiple transcription start sites and alternative splicing in the methylenetetrahydrofolate reductase gene result in two enzyme isoforms. Mamm Genome 13:483–492

    Article  CAS  PubMed  Google Scholar 

  9. Maron BA, Loscalzo J (2009) The treatment of hyperhomocysteinemia. Annu Rev Med 60:39–54

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  10. Vaissiere T, Hung RJ, Zaridze D, Moukeria A, Cuenin C, Fasolo V, Ferro G, Paliwal A, Hainaut P, Brennan P, Tost J, Boffetta P, Herceg Z (2009) Quantitative analysis of DNA methylation profiles in lung cancer identifies aberrant DNA methylation of specific genes and its association with gender and cancer risk factors. Cancer Res 69:243–252

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  11. Khazamipour N, Noruzinia M, Fatehmanesh P, Keyhanee M, Pujol P (2009) MTHFR promoter hypermethylation in testicular biopsies of patients with non-obstructive azoospermia: the role of epigenetics in male infertility. Hum Reprod 24:2361–2364

    Article  CAS  PubMed  Google Scholar 

  12. UCSC Genome Browser. http://genome.ucsc.edu/cgi-bin/hgTracks

  13. CpG Plot. http://www.ebi.ac.uk/Tools/emboss/cpgplot/

  14. Eukaryotic Promoter Database. http://epd.vital-it.ch/

  15. CpGcluster. http://bioinfo2.ugr.es/CpGcluster/

  16. Database of transcription start sites. http://dbtss.hgc.jp/

  17. Neural network promoter prediction. http://www.fruitfly.org/seq_tools/promoter.html

  18. MOTIF. http://www.genome.jp/tools/motif/

  19. PROMO. http://alggen.lsi.upc.es

  20. Weber M, Hellmann I, Stadler MB, Ramos L, Paabo S, Rebhan M, Schubeler D (2007) Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet 39:457–466

    Article  CAS  PubMed  Google Scholar 

  21. Zhao X, Valen E, Parker BJ, Sandelin A (2011) Systematic clustering of transcription start site landscapes. PLoS ONE 6:e23409

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  22. Maunakea AK, Nagarajan RP, Bilenky M, Ballinger TJ, D/’Souza C, Fouse SD, Johnson BE, Hong C, Nielsen C, Zhao Y, Turecki G, Delaney A, Varhol R, Thiessen N, Shchors K, Heine VM, Rowitch DH, Xing X, Fiore C, Schillebeeckx M, Jones SJM, Haussler D, Marra MA, Hirst M, Wang T, Costello JF (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature 466:253–257

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  23. Homberger A, Linnebank M, Winter C, Willenbring H, Marquardt T, Harms E, Koch HG (2000) Genomic structure and transcript variants of the human methylenetetrahydrofolate reductase gene. Eur J Hum Genet 8:725–729

    Article  CAS  PubMed  Google Scholar 

  24. Yamashita R, Wakaguri H, Sugano S, Suzuki Y, Nakai K (2010) DBTSS provides a tissue specific dynamic view of transcription start sites. Nucleic Acids Res 38:D98–D104

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  25. Hon GC, Hawkins RD, Ren B (2009) Predictive chromatin signatures in the mammalian genome. Hum Mol Genet 18:R195–R201

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  26. Jin B, Li Y, Robertson KD (2011) DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer 2:607–617

    Article  PubMed Central  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The researchers wish to thank the Griffith Health Institute and to acknowledge financial support for this work from Griffith University and RU Grant (1001/PPSP/815073). The first author was the recipient of an Endeavour Research Fellowship and a MyBrain 15 (MyPhD) scholarship.

Conflict of interest

None declared.

Author information

Authors and Affiliations

  1. Human Genome Centre, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia

    Keat Wei & Siew Hua Gan

  2. Institute of Health and Biomedical Innovation, Queensland University of Technology, Musk Ave, Kelvin Grove, QLD, 4059, Australia

    Keat Wei, Heidi Sutherland, Emily Camilleri, Larisa M. Haupt & Lyn R. Griffiths

Authors
  1. Keat Wei
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Heidi Sutherland
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Emily Camilleri
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Larisa M. Haupt
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Lyn R. Griffiths
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Siew Hua Gan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Keat Wei.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 13 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Wei, K., Sutherland, H., Camilleri, E. et al. Computational epigenetic profiling of CpG islets in MTHFR. Mol Biol Rep 41, 8285–8292 (2014). https://doi.org/10.1007/s11033-014-3729-x

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11033-014-3729-x

Keywords

Search

Navigation