Modeling the mutational dynamics of very short tandem repeats

TL;DR

This paper develops a model for the mutational dynamics of short tandem repeats (STRs) to enable rapid phylogenetic analysis and lineage reconstruction, highlighting variability across different cell lines and potential influencing factors.

Contribution

The study introduces a new model for STR mutational dynamics at the repeat unit level, facilitating fast molecular clock estimates for lineage tracing.

Findings

STR mutational dynamics are consistent within a cell line

Dynamics vary among different cell lines

Other factors beyond caretaker gene mutations influence STR variability

Abstract

Short tandem repeats (STRs) are low-entropy regions in the genome, consisting of a short (1-6 bp) unit that is consecutively repeated multiple times. They are known for high mutational instability, due to so-called stutter-mutations, in which the number of units in the run increases or descreases. In particular, STRs with repeat unit length of 1-2 bp are prone to mutate even within several cell divisions. The extremely rapid accumulation of variation makes them interesting phylogenetic markers for retrospective single-cell lineage reconstruction. Here we model their mutational dynamics at the level of individual repeat unit type and then aggregate length variations over many STR loci with the aim of obtaining a very fast ``molecular clock''. We calibrate our model based on several datasets with known lineage structure prepared from cultured cells. We find that the mutational dynamics of STRs are reasonably consistent for a given cell line, but vary among different ones. This suggests that the dynamics are not entirely explained by mutations in caretaker genes, rather, various other factors play a role -- possibly tissue origin and differentiation state. Further data and research is necessary to asses their relative effects.