Fork Stalling and Template Switching As a Mechanism for Polyalanine Tract Expansion Affecting the DYC Mutant of HOXD13, a New Murine Model of Synpolydactyly

Abstract

Polyalanine expansion diseases are proposed to result from unequal crossover of sister chromatids that increases the number of repeats. In this report we suggest an alternative mechanism we put forward while we investigated a new spontaneous mutant that we named ''Dyc'' for ''Digit in Y and Carpe'' phenotype. Phenotypic analysis revealed an abnormal limb patterning similar to that of the human inherited congenital disease synpolydactyly (SPD) and to the mouse mutant model Spdh. Both human SPD and mouse Spdh mutations affect the Hoxd13 gene within a 15-residue polyalanine-encoding repeat in the first exon of the gene, leading to a dominant negative HOXD13. Genetic analysis of the Dyc mutant revealed a trinucleotide expansion in the polyalanine-encoding region of the Hoxd13 gene resulting in a 7-alanine expansion. However, unlike the Spdh mutation, this expansion cannot result from a simple duplication of a short segment. Instead, we propose the fork stalling and template switching (FosTeS) described for generation of nonrecurrent genomic rearrangements as a possible mechanism for the Dyc polyalanine extension, as well as for other polyalanine expansions described in the literature and that could not be explained by unequal crossing over.

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

“…In polyalanine expansion diseases, in which the coding trinucleotide tracts are short and often interrupted, pedigree analyses support the occurrence of both fork stalling and template switching, triggered by secondary structure formation (Fig. 5D), as well as unequal crossing-over between two normal alleles [Arai et al, 2010; Cocquempot et al, 2009; Messaed and Rouleau, 2009; Warren, 1997] (Fig. 5E).…”

Replication stress at microsatellites causes DNA double-strand breaks and break-induced replication

“…In humans, a growing cohort of neurodegenerative diseases has been attributed to DNA instability at microsatellite DNA noncanonical structures (3,4,7,(11)(12)(13)(14)(15)(16)(17)(18). Thus, replication fork barriers are believed to provoke fork stalling and template switching (FoSTeS), and microhomology-mediated break induced replication (MMBIR) (19)(20)(21)(22)(23)(24)(25)(26). The induction of gross chromosomal rearrangements (GCRs) due to FoSTeS/MMBIR has been implicated in the etiology of several developmental disorders including blepharophimosis syndrome (MIM# 110100) (23), CHARGE syndrome (MIM#214800) (27), and Pelizaeus-Merzbacher disease (MIM#312080) (28).…”

Analysis of De Novo HOXA13 Polyalanine Expansions Supports Replication Slippage Without Repair in Their Generation

“…By replication slippage, both expansions and contractions could occur, depending on whether template or nascent strand misalignment was involved [Strand et al, ; Chen et al, ; McMurray, ]. Finally, Cocquempot et al [] suggested FosTES ( Fo rk s talling and TE mplate S witching) [Lee et al, ] as the mechanism for polyalanine expansion in the Hoxd13 gene in the mouse mutant Dyc , whose structure is quite different from typical HOXA13 or HOXD13 polyalanine expansions. The authors stated that polyalanine tracts contain microhomology, symmetry, and specific sequence motifs that commonly lead to FosTES.…”