Quantum behavior in Short Tandem Repeats (STRs)
Upon examining a wide array of sequences related to R2R3MYBs, we encountered a phenomenon that lies well beyond the realm of any biological perspective; it somewhat resembles the principles of quantum mechanics.
Introduction
The transcription machinery responsible for producing mRNA for R2R3MYB relies on various cis-regulatory sequences. Among these is the STR (5), a short tandem repeat sequence found within the first intron of the R2R3MYB gene. In the following sections, we will focus on this specific sequence, particularly on how its length is altered.
Three examples of STRs in the Fragaria second intron of different polyTA lengths.
PacBio's Single Molecule, Real-Time (SMRT) sequencing technology produces long and highly accurate DNA reads, typically measuring in the tens of kilobases. This capability enables the detailed analysis of complex, repetitive regions. We selected SRA samples of various species that match the specified quality from: https://www.ncbi.nlm.nih.gov/.
The length variability of STRs (MYB10 TF intron) in epidermal cells of the plant Fragaria x ananassa is relatively high*. The somatic mutation rate is notably elevated within the STR borders, while it is nearly absent in the rest of the sequence. We observed similar characteristics in Arabidopsis (PAP1), Aquilegia vulgaris (MYB), Misopates (ROS1), and Silene latifolia (MYB). The accuracy of the DNA polymerase is affected by an unknown reason when copying the STR string.
It appears that all significant other factors within a plant nucleus possess somatically variable short tandem repeats (STRs).
These somatic mutations occur relatively frequently, significantly exceeding the rates of regular mutations. The changes from cell to cell can be as high as p = 0.5. Moreover, these mutations can either stabilize the string, lengthen it, or shorten it. Since the length of the string influences the activity of RNA polymerase II, understanding these mutations can provide valuable insights into the regulation of this process.
What instance is the origin of these somatic mutations?
Is it the loose fidelity of the polymerases when reaching the repeating area, or is it another event that occurs in the field of quantum mechanics? We can summarize three different behaviors of these mutations.
a) The STRs are long or short, and there is no significant variation in the strings caused by somatic mutations in the plant's tissue. (Erythranthe nasuta)
b) The strings are longer, and when somatic mutations occur along the string, they would generally delete one or two of the repeats. The STR tends to become shorter.
c) The strings are longer, but this time the somatic mutations tend to elongate the string by one or two repeats (Fragaria vesca).
We have reassessed the results of an ongoing non-stochastic mutation process. The mutation rate is very high within any short tandem repeats (STRs) and exhibits a vectorized pattern, indicating that the mutations lead to a phenotypic diversity.
Conclusions:
Without a thorough understanding of the dynamics occurring along these STRs at every replication stage in plant tissue, it is challenging to make meaningful interpretations about any evolutionary events that may be occurring. These STRs serve as significant hubs for somatic changes and their consequences. Therefore, further investigations—encompassing molecular, physical, and other approaches—are urgently needed to uncover the truth.