A proposed reverse transcription mechanism for (CAG)n and similar expandable repeats that cause neurological and other diseases

Abstract

The mechanism of (CAG)n repeat generation, and related expandable repeat diseases in non-dividing cells, is currently understood in terms of a DNA template-based DNA repair synthesis process involving hairpin stabilized slippage, local error-prone repair via MutSβ (MSH2-MSH3) hairpin protective stabilization, then nascent strand extension by DNA polymerases-β and -δ. We advance a very similar slipped hairpin-stabilized model involving MSH2-MSH3 with two key differences: the copying template may also be the nascent pre-mRNA with the repair pathway being mediated by the Y-family error-prone enzymes DNA polymerase-η and DNA polymerase-κ acting as reverse transcriptases. We argue that both DNA-based and RNA-based mechanisms could well be activated in affected non-dividing brain cells in vivo. Here, we compare the advantages of the RNA/RT-based model proposed by us as an adjunct to previously proposed models. In brief, our model depends upon dysregulated innate and adaptive immunity cascades involving AID/APOBEC and ADAR deaminases that are known to be involved in normal locus-specific immunoglobulin somatic hypermutation, cancer progression and somatic mutations at many off-target non-immunoglobulin sites across the genome: we explain how these processes could also play an active role in repeat expansion diseases at RNA polymerase II-transcribed genes.

APOBECs orchestrate genomic and epigenomic editing across health and disease

“…Pre-mRNA hairpin loops are known to occur in TNR diseases; therefore, pre-mRNA might serve as a template for cDNA generation by RNA reverse transcription and lead to an expanded template to 'repair' the damage induced by APOBECs. Thus, it was proposed that APOBEC off-target mutagenesis drives Ig SHM-like RNA reverse transcription responses and is partially responsible for repeat expansion diseases [129]. Interestingly, TNR expansions have also been identified as a common feature of pan-cancer genome exon-sequencing data [130].…”

Unveiling Human Non-Random Genome Editing Mechanisms Activated in Response to Chronic Environmental Changes: I. Where Might These Mechanisms Come from and What Might They Have Led To?

“…The death of cells bearing inadequate protein versions and the survival of cells bearing the fittest mutation(s) able to increase protein efficiency might then determine the "selection" of the inheritable gene version(s). Indeed, a non-random mutation mechanism with similar activity has already been described in adaptive immunity during somatic hypermutation (SHM) of immunoglobulins (Igs) [9,10]. However, it would appear that known mechanisms of adaptation are unable to explain the above-mentioned observations regarding other eukaryotic genes.…”

“…Of note, under stress conditions, the mutation rate substantially increases (e.g., under SIM) and the probability of multiple adaptive mutations and saltational evolution (a sudden multimutation leap potentially leading to speciation and macroevolution) becomes more likely to occur [7]. Indeed, rapid genetic adaptations of eukaryotic organisms induced by environmental stress conditions have been widely documented and environmentally driven non-random genome variations mediated by different mechanisms (such as DNA mutagenic and/or methylating/de-methylating enzymes and/or transposable elements) have been proposed to explain some rapid biological adaptations [9][10][11][12]22,23]. However, these hypothesised mechanisms do not exhaustively describe the specific molecular links that mediate the causal relationship between environmental stress conditions and the ability to rapidly induce adaptive DNA mutations in specific genomic regions (while sparing the rest of the genome).…”

“…It is therefore difficult to explain how only random mutations could have led to the sophisticated molecular entanglements of eukaryotic cells and to the huge and expanding number of species found on Earth today. Indeed, random mutations represent a weak point in the modern synthesis of evolution, and mathematicians have predicted the existence of non-random mutation mechanisms [8] and non-random genome manipulation mechanisms have also been proposed [9][10][11][12].…”

Predicting clinical outcomes using cancer progression associated signatures

“…In this model, deamination targets are presented in C-site motifs both in the displaced ssDNA of the non-transcribed strand, and may also be accessed in the exposed ssDNA of the transcribed strand at annealed RNA:DNA hybrids assisted via the action of the RNA exosome [ 33 ]. ADAR A-site deamination targets are present in WA-motifs in the dsRNA stem loops of the nascent pre-mRNA, and in the RNA and DNA A-site moieties in the RNA:DNA hybrid, assisted by the reverse transcriptase activities of DNA Polymerase-eta (Pol η) [ 31 , 34 , 35 ]. This presumptive model is based on known deaminase targets and their role in oncogenesis, combined with the mechanisms underlying reverse transcription.…”