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Alterations of 5-hydroxymethylcytosine in human cancers.

Mariani CJ, Madzo J, Moen EL, Yesilkanal A, Godley LA - Cancers (Basel) (2013)

Bottom Line: Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA.With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC.Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

View Article: PubMed Central - PubMed

Affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC 2115, Chicago, IL 60637, USA. lgodley@medicine.bsd.uchicago.edu.

ABSTRACT
Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

No MeSH data available.


Related in: MedlinePlus

Techniques used to distinguish modified cytosine species at single base resolution. (A) In traditional bisulfite sequencing, bisulfite converts cytosine to uracil (yellow circles), which is then sequenced as a thymine (green circles), whereas 5-mC and 5-hmC remain unchanged. (B) In oxidative bisulfite sequencing, an additional oxidative step is included before bisulfite treatment that converts 5-hmC to 5-fC. 5-fC is then converted to uracil on bisulfite treatment so that both cytosine and 5-hmC are read as thymines during sequencing of oxidative-bisulfite treated DNA. (C) Finally, in Tet-assisted bisulfite sequencing (TAB-Seq), all 5-hmC residues are conjugated to glucose (small red circle). This protects them from oxidation during treatment with Tet, which converts all modified cytosines, except 5-hmC, to 5-caC. On bisulfite treatment, only glucose conjugated 5-hmC residues are protected from deamination and are read as cytosines during sequencing.
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cancers-05-00786-f004: Techniques used to distinguish modified cytosine species at single base resolution. (A) In traditional bisulfite sequencing, bisulfite converts cytosine to uracil (yellow circles), which is then sequenced as a thymine (green circles), whereas 5-mC and 5-hmC remain unchanged. (B) In oxidative bisulfite sequencing, an additional oxidative step is included before bisulfite treatment that converts 5-hmC to 5-fC. 5-fC is then converted to uracil on bisulfite treatment so that both cytosine and 5-hmC are read as thymines during sequencing of oxidative-bisulfite treated DNA. (C) Finally, in Tet-assisted bisulfite sequencing (TAB-Seq), all 5-hmC residues are conjugated to glucose (small red circle). This protects them from oxidation during treatment with Tet, which converts all modified cytosines, except 5-hmC, to 5-caC. On bisulfite treatment, only glucose conjugated 5-hmC residues are protected from deamination and are read as cytosines during sequencing.

Mentions: Three techniques have been developed to identify 5-hmC at single base resolution within the genome. The first technique, referred to as oxidative bisulfite sequencing, adds an oxidative step before traditional bisulfite treatment of gDNA. In this step, DNA is treated with potassium perruthenate (KRuO4), which oxidizes 5-hmC into 5-fC. On treatment with bisulfite, 5-fC (like cytosine) is converted to uracil, which is then PCR amplified and sequenced as thymine. By performing oxidative bisulfite sequencing in parallel with traditional bisulfite sequencing, the location of 5-hmC can be inferred by finding residues converted to thymine in oxidative-bisulfite sequencing, but not in traditional bisulfite sequencing (Figure 4) [49].


Alterations of 5-hydroxymethylcytosine in human cancers.

Mariani CJ, Madzo J, Moen EL, Yesilkanal A, Godley LA - Cancers (Basel) (2013)

Techniques used to distinguish modified cytosine species at single base resolution. (A) In traditional bisulfite sequencing, bisulfite converts cytosine to uracil (yellow circles), which is then sequenced as a thymine (green circles), whereas 5-mC and 5-hmC remain unchanged. (B) In oxidative bisulfite sequencing, an additional oxidative step is included before bisulfite treatment that converts 5-hmC to 5-fC. 5-fC is then converted to uracil on bisulfite treatment so that both cytosine and 5-hmC are read as thymines during sequencing of oxidative-bisulfite treated DNA. (C) Finally, in Tet-assisted bisulfite sequencing (TAB-Seq), all 5-hmC residues are conjugated to glucose (small red circle). This protects them from oxidation during treatment with Tet, which converts all modified cytosines, except 5-hmC, to 5-caC. On bisulfite treatment, only glucose conjugated 5-hmC residues are protected from deamination and are read as cytosines during sequencing.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3795365&req=5

cancers-05-00786-f004: Techniques used to distinguish modified cytosine species at single base resolution. (A) In traditional bisulfite sequencing, bisulfite converts cytosine to uracil (yellow circles), which is then sequenced as a thymine (green circles), whereas 5-mC and 5-hmC remain unchanged. (B) In oxidative bisulfite sequencing, an additional oxidative step is included before bisulfite treatment that converts 5-hmC to 5-fC. 5-fC is then converted to uracil on bisulfite treatment so that both cytosine and 5-hmC are read as thymines during sequencing of oxidative-bisulfite treated DNA. (C) Finally, in Tet-assisted bisulfite sequencing (TAB-Seq), all 5-hmC residues are conjugated to glucose (small red circle). This protects them from oxidation during treatment with Tet, which converts all modified cytosines, except 5-hmC, to 5-caC. On bisulfite treatment, only glucose conjugated 5-hmC residues are protected from deamination and are read as cytosines during sequencing.
Mentions: Three techniques have been developed to identify 5-hmC at single base resolution within the genome. The first technique, referred to as oxidative bisulfite sequencing, adds an oxidative step before traditional bisulfite treatment of gDNA. In this step, DNA is treated with potassium perruthenate (KRuO4), which oxidizes 5-hmC into 5-fC. On treatment with bisulfite, 5-fC (like cytosine) is converted to uracil, which is then PCR amplified and sequenced as thymine. By performing oxidative bisulfite sequencing in parallel with traditional bisulfite sequencing, the location of 5-hmC can be inferred by finding residues converted to thymine in oxidative-bisulfite sequencing, but not in traditional bisulfite sequencing (Figure 4) [49].

Bottom Line: Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA.With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC.Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

View Article: PubMed Central - PubMed

Affiliation: Section of Hematology/Oncology, Department of Medicine, The University of Chicago, 5841 S. Maryland Ave., MC 2115, Chicago, IL 60637, USA. lgodley@medicine.bsd.uchicago.edu.

ABSTRACT
Prior to 2009, 5-methylcytosine (5-mC) was thought to be the only biologically significant cytosine modification in mammalian DNA. With the discovery of the TET enzymes, which convert 5-methylcytosine (5-mC) to 5-hydroxymethylcytosine (5-hmC), however, intense interest has emerged in determining the biological function of 5-hmC. Here, we review the techniques used to study 5-hmC and evidence that alterations to 5-hmC physiology play a functional role in the molecular pathogenesis of human cancers.

No MeSH data available.


Related in: MedlinePlus