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Mapping and elucidating the function of modified bases in DNA

Nature Reviews Chemistry volume 1, Article number: 0069 (2017) Cite this article

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An Erratum to this article was published on 11 October 2017

Abstract

Chemically modified bases exist naturally in genomic DNA. Research into these bases has been invigorated by the discovery of several modified bases in the mammalian genome, in particular 5-methylcytosine and its oxidized derivatives, such as 5-(hydroxymethyl)cytosine and 5-formylcytosine, as well as the enzymes that form and process them, such as the DNA methyltransferases and the ten-eleven translocation enzymes. In this Review, we provide an overview of natural modified bases that have been reported in DNA, our current knowledge of their roles, and the techniques that have enabled us to probe their functions. Analytical methods have been invaluable in helping to advance this field. For example, chemical and enzymatic methods have provided the means to detect and decode modified bases, giving rise to an expanding array of sequencing approaches. Advanced liquid chromatography and tandem mass spectrometry have provided the means to detect and quantify modified bases with very high sensitivity, increasing the prospect of discovering unknown modifications. It is already evident that natural modified DNA bases and their associated enzymology are of fundamental importance to normal biology and to disease. The next decade promises to yield more insights, discoveries and applications from this burgeoning field of research.

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Figure 1: Watson–Crick base pairing and DNA grooves.
Figure 2: Overview of modified DNA bases.
Figure 3: The active demethylation pathway.
Figure 4: Methods for sequencing modified cytosine bases.

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Acknowledgements

The Balasubramanian laboratory is supported by core funding from Cancer Research UK (C14303/A17197). S.B. is a senior investigator of the Wellcome Trust (Grant No. 099232/z/12/z).

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Authors and Affiliations

  1. Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK

    Eun-Ang Raiber, Robyn Hardisty, Pieter van Delft & Shankar Balasubramanian

  2. Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK

    Shankar Balasubramanian

  3. School of Clinical Medicine, University of Cambridge, Hills Road, Cambridge, CB2 0SP, UK

    Shankar Balasubramanian

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  1. Eun-Ang Raiber
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  2. Robyn Hardisty
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  3. Pieter van Delft
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  4. Shankar Balasubramanian
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All authors contributed equally to all aspects of this article.

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Correspondence to Shankar Balasubramanian.

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PowerPoint slides

Glossary

Transcription factors

Proteins that bind to a specific DNA sequence to control the transcription of the genetic information from DNA to RNA.

Restriction methylation

DNA methylation that protects bacteria from restriction endonuclease enzymes, providing a defence mechanism against invasion by bacteriophages and viruses.

Promoters

Regions of DNA that are located near to transcription start sites and control transcription initiation.

Retrotransposons

Genetic elements that are transcribed into RNA, then reverse-transcribed back into DNA and inserted into the genome.

Genomic imprinting

An epigenetic marking of one copy of the gene (from the mother or father) that ensures gene expression in a parent-of-origin-specific manner.

Transposon silencing

Gene silencing of transposons by epigenetic mechanisms, including DNA methylation and the effect of small non-coding RNAs, which prevents transcription and ensures genome stability.

Histone modifications

Post-translational chemical modifications of amino acid residues on a histone.

Chromatin-remodelling proteins

Proteins that control access to the genetic information by either inducing histone modifications or using energy to alter histone–DNA interactions.

CpG islands

(CGIs). Regions with high cytosine-phosphate-guanine (CpG) dinucleotide density.

Pluripotent stem cells

Cells that can differentiate into any other tissue of the body.

Enhancer regions

Regulatory regions of the genome that are marked by histone modifications and enhance the transcription of their associated genes when bound to transcription factors.

Base excision repair

(BER). A cellular mechanism that removes small base lesions, caused by mismatched or modified DNA bases, from the DNA.

Histone octamer

An eight-protein complex of two histone H2A–H2B dimers and two histone H3–H4 dimers that together form the core of the nucleosome.

B cells

A type of white blood cell that is fundamental to the adaptive immune system.

Class-switch recombination

A process whereby B cells rearrange parts of the immunoglobulin heavy chain locus to generate antibodies with different properties.

Telomeric regions

Repetitive nucleotide sequences that protect the ends of chromosomes.

Repetitive elements

Sequences that occur multiple times throughout the genome.

RNA polymerase II

An enzyme that catalyses the transcription of DNA to RNA.

Transfer RNA

An adaptor RNA and amino acid carrier that helps to decode mRNA for translation into the synthesis of proteins.

Restriction endonucleases

Enzymes that cut DNA at endogenous phosphodiester bonds.

β-Elimination

DNA cleavage at the phosphodiester bond resulting in the elimination of the 3′-phosphate residue.

δ-Elimination

DNA cleavage at the phosphodiester bond resulting in the elimination of the 5′-phosphate residue.

Clustered regularly interspaced short palindromic repeats (CRISPR) systems

Genome-editing systems, such as CRISPR–Cas9, that rely on a bacterial virus-defence mechanism involving repetitive DNA sequences that contain snippets of viral DNA. By manipulating CRISPR systems, DNA can be cut at a desired location, allowing genes to be removed or added.

Transcription activator-like effectors

(TALEs). Proteins that can be programmed to target specific DNA sequences in the genome.

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Raiber, EA., Hardisty, R., van Delft, P. et al. Mapping and elucidating the function of modified bases in DNA. Nat Rev Chem 1, 0069 (2017). https://doi.org/10.1038/s41570-017-0069

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