Non‐B DNA Structure and Mutations Causing Human Genetic Disease

Abstract

In addition to the canonical right‐handed double helix, several noncanonical deoxyribonucleic acid (DNA) secondary structures have been characterised, including quadruplexes, triplexes, slipped/hairpins, Z‐DNA and cruciforms. The formation of these structures is mediated by repetitive sequence motifs, such as G‐rich sequences, purine/pyrimidine tracts, direct (tandem) repeats, alternating purine–pyrimidines and inverted repeats, respectively. Such repeats are abundant in the human genome and are found in association with specific classes of genes, supporting a role for them in gene regulation or protein function. Repetitive sequence motifs are also commonly found at sites of chromosomal alteration, including gross rearrangements and copy number variations (CNVs) associated with both disease and phenotypic variation. Finally, variable number tandem repeats (VNTRs) or microsatellites are present in many gene regulatory regions. Characterised by an inherent capacity to expand spontaneously, such sequences are not only known to cause >30 neurological diseases but may also contribute to human disease susceptibility. The formation of alternative non‐B DNA structures is believed to promote genomic alterations by impeding efficient DNA replication and repair.

Key Concepts:

  • The structure of DNA is polymorphic as well as its sequence; in addition to the canonical right‐handed double helix (B‐DNA), repetitive sequences can also adopt alternative (non‐B DNA) conformations such as quadruplexes, triplexes, slipped/hairpins, Z‐DNA and cruciforms.

  • Repetitive DNA sequences are found at locations within many human genes that suggest they can either affect transcription or alternatively encode homopolymeric amino acid runs that could be important for either protein–protein or protein–DNA/RNA interactions.

  • The integrity of the Y‐chromosome depends on large inverted repeats, which have the capacity to form cruciform structures that may potentiate intrachromosomal recombination.

  • Copy number variation (CNV) is a form of genetic alteration that, by involving thousands of loci in the genome, contributes to human individuality.

  • Repetitive sequences capable of forming non‐B DNA are found at sites of chromosomal breaks, CNVs and other rearrangements such as translocations and gene conversion events, which can contribute to human genetic disease.

  • The recurrent translocation t(22;11) events associated with Emanuel syndrome are mediated by cruciform structures that occur at inverted repeats.

  • Tandem repeats (microsatellites) may expand within gene sequences, contributing to more than 30 neurological diseases. Present in variable number in genes in the population, they may contribute to human disease susceptibility.

  • Experiments in model systems and bioinformatic analyses support the conclusion that repetitive sequences trigger genomic instability by adopting non‐B DNA conformations.

  • Non‐B DNA structures stimulate mutations via mechanisms that alter DNA synthesis and repair.

Keywords: non‐B DNA; microsatellites; copy number variation (CNV); triplet repeat diseases; polyglutamine expansion; translocations; DNA repair; DNA replication; double strand breaks (DSB); gene expression regulation

Figure 1.

Non‐B DNA structures formed by genomic repetitive sequences. (a) Most common non‐B DNA conformations, ribbon models of helical foldings, repetitive motifs requirement and example of sequences. Center dot, Watson–Crick hydrogen bond interactions; x,y, nucleotides in the spacer between repeats; L, lateral loop; D, diagonal loop and CR, chain reversal loop. For cruciform DNA, an extended conformation is shown. For triplex DNA, a 3′ RRY isomer is depicted in which the 3′‐half of the purine‐rich strand folds back to form the Hoogsteen‐bound third strand. For quadruplex DNA, an idealised structure is drawn to highlight the loop characteristics and the relative orientation of the syn and anti N‐glycosidic configurations. (b) RRY base triplets showing the Hoogsteen‐bound base (left). Thymine can be incorporated into RRY triplexes due to the symmetry of the carbonyl groups. (c) YRY base triplets showing the Hoogsteen‐bound pyrimidine and the stabilisation afforded by cytosine protonation. (d) G‐tetrad.

Figure 2.

Non‐B DNA‐forming repeats and genome‐wide gene expression. (a) The gene expression profile of 13 237 nonredundant annotated human (RefSeq) genes (y‐axis) was examined in 79 tissues/cancer/cell types (x‐axis) and the average values plotted for the 8124 genes that contained quadruplex‐forming repeats (filled squares) within ±500 base pairs of the main transcription start site (TSS) and the remaining genes that did not contain such elements within ±500 base pairs of the main TSS (open squares). (b) The gene expression levels for 16 146 gene probes in the 70 human tissues/cell types included in (a) was plotted as percent of data (y‐axis) falling within specific intervals of gene expression (x‐axis) for control genes (black) and for 190 genes (red) that contained triplex‐forming tetranucleotide repeats ≥72 base pairs long. With kind permission from Springer Science+Business Media (Zhao et al., ).

Figure 3.

Cruciform‐mediated chromosomal t(11;22) translocation and the Emanuel syndrome. The PATRR sequences on human chromosome 11 (green) and 22 (black) are proposed to fold into large cruciform structures at some frequency during gametogenesis and be cleaved at the single‐stranded tips, resulting in double‐strand breaks (left insets). The broken chromosomal ends (middle) join aberrantly, yielding the derivative chromosomes der(11) and der(22) (right). Occasional inheritance of der(22), in addition to a normal karyotype, is responsible for the Emanuel syndrome in the offspring.

Figure 4.

Triplet repeat expansion alters mRNA function. (a) In DM1, CTG expansion in the 3′‐UTR of the DMPK gene causes the ensuing mRNA to fold into a large and stable double‐stranded hairpin stabilised by U•U and G•C base pairs, which recruits muscleblind‐like (Drosophila) (MBNL1), a mediator of pre‐mRNA alternative splicing regulation. CUG‐hairpins also stimulate CUG RNA‐binding protein 1 (CUGBP1) hyperphosphorylation and stabilisation, which alter several events related to alternative splicing, mRNA tanslation and mRNA decay. (b) Sequestration of MBNL1 and CUGBP1 activation shift alternative splicing programs from the adult stage towards embryonic‐specific patterns, including activation of exon 5 inclusion of cardiac isoforms of TNNT2 (cTNT) during heart remodeling, exclusion of exon 11 in the insulin receptor (IR) pre‐mRNA and inclusion of stop‐containing exon in chloride channel 1 transcripts. Adapted from Lee and Cooper with kind permission by Portland Press Ltd. Copyright © the Biochemical Society.

Figure 5.

Modulators of triplet repeat expansion in mouse models of MRDs. The mismatch repair proteins Msh2 and Msh3 are required for triplet repeat instability throughout all developmental stages. DNAcytosine‐5‐methyltransferase 1 (Dnmt1) protects against expansions in an expanded CAG model in the germline. Ataxia talangiectasia and Rad3 related (Atr) protein prevent expansion in the female germline and in somatic tissues of a CGG repeat mouse model. Post‐meiotic segregation increased 2 (Pms2) and 8‐oxoguanine glycosylase (Ogg1) are selectively involved in age‐dependent somatic instability. Reproduced from Dion and Wilson with permission from Elsevier.

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Bacolla, Albino, Cooper, David N, and Vasquez, Karen M(Oct 2010) Non‐B DNA Structure and Mutations Causing Human Genetic Disease. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0022657]