On the sequence-directed nature of human gene mutation: the role of genomic architecture and the local DNA sequence environment in mediating gene mutations underlying human inherited disease

Abstract

Different types of human gene mutation may vary in size, from structural variants (SVs) to single base-pair substitutions, but what they all have in common is that their nature, size and location are often determined either by specific characteristics of the local DNA sequence environment or by higher order features of the genomic architecture. The human genome is now recognized to contain "pervasive architectural flaws" in that certain DNA sequences are inherently mutation prone by virtue of their base composition, sequence repetitivity and/or epigenetic modification. Here, we explore how the nature, location and frequency of different types of mutation causing inherited disease are shaped in large part, and often in remarkably predictable ways, by the local DNA sequence environment. The mutability of a given gene or genomic region may also be influenced indirectly by a variety of noncanonical (non-B) secondary structures whose formation is facilitated by the underlying DNA sequence. Since these non-B DNA structures can interfere with subsequent DNA replication and repair and may serve to increase mutation frequencies in generalized fashion (i.e., both in the context of subtle mutations and SVs), they have the potential to serve as a unifying concept in studies of mutational mechanisms underlying human inherited disease.

Figure 1

Mutational mechanisms leading to gross genomic rearrangements (structural variants) including copy number variations. Non-homologous end joining (NHEJ) comprises two sub-pathways, classical or canonical NHEJ (C-NHEJ) and alternative NHEJ (A-NHEJ). In practice, some clinically observed mutations represent the end result of an untraceable in vivo mutational process and can often be explained by two or even three different mechanisms. Hence, it is often not possible to distinguish a break-induced replication (BIR) event from a non-allelic homologous recombination (NAHR) event, a microhomology-mediated BIR (MMBIR) event from a serial replication slippage (SRS) or fork stalling and template switch (FoSTeS) event, and a NHEJ event (where microhomology-mediated) from a ‘microhomology-mediated replication-dependent recombination (MMRDR) event. By contrast, mutations resulting from telomere healing or L1 retrotransposition can usually be unequivocally attributed owing to the presence of signature sequences. DSB, double-strand break; GC, gene conversion; RC, replication fork; RS, replication slippage; SRS, serial replication slippage; SSA, single-strand annealing.

Figure 2

Contribution of mutational mechanisms to the formation of structural variants (SVs) <5kb according to Kidd et al. [2010]. The contraction or expansion of variable number of tandem repeats (VNTRs) accounts for ~3% of the detected SVs.

Figure 3

Schematic representation of the different types of cytogenetically defined terminal deletions in terms of end stabilization. Whereas blocks indicate telomeres, filled circles indicate centromeres. In type A, the captured telomere and associated sequence are highlighted in blue. In type B, an internal portion of the chromosome (sequence highlighted in red in the normal chromosome) is deleted. In type C, the de novo telomere is highlighted in purple. In the box, two different mechanisms of end stabilization for terminal deletions associated with inverted duplications (indicated by facing arrows) are illustrated; the use of colour is consistent with the scheme used for types A and C.

Figure 4

Non-B DNA. Types and ribbon models of the most common non-B DNA conformations formed by repetitive DNA motifs, followed by the general sequence requirements for each structure and examples of DNA sequences (redrawn from Bacolla et al., 2004). Y, pyrimidine (C or T); R, purine (A or G). It should however be noted that, for Z-DNA at least, one strand must contain alternating G residues; x and y, any intervening sequence separating the repeats by typically 0-5 nt [Cer et al., 2011].

Figure 5

Models for microsatellite repeat expansion. Panel A. Strand slippage during DNA replication. A microsatellite repeat sequence (black and grey segments) and the associated DNA polymerase complexes (protein complexes are not shown for reasons of clarity) may transiently dissociate from the template strand and form an intra-strand hairpin stabilized by Watson-Crick and non-Watson-Crick (such as T:T) pairs with backward slippage between the repeats. The hairpin may be incorporated into genomic DNA during the next round of DNA synthesis (not shown), yielding an expansion. Panel B. Replication-independent expansion in quiescent oocytes. A base lesion (black bulge) is cleaved by base excision repair (see McMurray, 2010 for details) and the ensuing 3′-OH terminus is extended by DNA polymerase beta, displacing the DNA strand ahead of it. The displaced single-strand forms large hairpin structures, which are resistant to FEN1 cleavage and are stabilized by mismatch repair proteins (MSH2/MSH3). Further DNA ligation leaves long hairpin structures, which are subsequently incorporated into DNA (not shown) by cleavage and synthesis on the complementary strand. Panel C. Fork stalling and restart. A hairpin structure on the template for lagging strand DNA synthesis blocks replication. Replication restarts through fork-reversal (chicken-foot structure) which in the process yields a second hairpin on the newly synthesized leading strand that will subsequently be incorporated into chromosomal DNA, leading to expansion (see Mirkin, 2007 for details). Panel D. Fork stalling and template switching. After fork stalling (see Panel C), strand switching occurs, whereby the 3′-end of the growing leading strand copies microsatellite repeats from the newly synthesized lagging strand, yielding an expansion. It should be noted that large and small hairpins are not distinguished in the Figure. Panel E. Unequal crossing-over between normal alleles. Alleles a and b contain polymorphic alanine-encoding repeats (white squares, GCA; black squares, GCG; and grey squares, GCC) that can anneal in an out-of phase manner during crossover, resulting in an expanded allele and a smaller allele (not shown).