Principal Investigator Mary-Lou Pardue
We conclude that these events are more complex than the relatively regular small-scale sequence loss (50-100 nt per fly generation) that several groups have measured on broken chromosomes, a loss consistent with that expected from the well-known end replication problem (failure to replicate the terminal primer on the lagging strand each time a chromosome is replicated). In contrast, enabled by our discovery that the telomeric retrotransposons have innovative ways to add expendable sequence to their 5’ ends, we did quantitative analysis of complete elements in telomere arrays that revealed that they undergo small scale stochastic end erosion after replication. The added expendable sequence serves to buffer the terminal element from end erosion. Furthermore, all complete elements in those telomeres had been capped by a new transposition (that replaced them as the extreme end of the array) before erosion removed all of the non-essential sequence. They thus retain all of their essential sequence. This buffering appears to be effective because complete elements are overrepresented in the telomere arrays.
Small scale erosion is not the only cause of sequence loss from telomere arrays. The 5’ truncated partial elements in the arrays have a quantitative loss distribution which provides evidence of large scale terminal loss. Thus, our analyses allow us to postulate the existence of a complex process that maintains telomere length homeostasis while providing a supply of transposition-competent elements. The small scale erosion, seen at the 5’ end of complete elements removes very few nucleotides compared to those added by transposition of a new element whose length is 6kb-13kb. This presents a problem for maintaining telomere length homeostasis. The large scale terminal loss revealed by the 5’truncated elements provides a solution. We suggest that telomere length is restored by occasional terminal deletions that remove part, or sometimes all, of the telomere array, followed by rebuilding of the array to the required length. Rapid rebuilding would help explain another unexpected finding of our study: elements deep in the array should have been there for a long time without selection for function but all appear to have undecayed sequence. Terminal deletions would remove decayed elements and rebuilding an array would of necessity add transposition-competent elements.