Reverse Transcription Errors and RNA-DNA Differences at Short Tandem Repeats

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transcriptome studies traditionally focus on gene expression and isoform variation.
• Variation in transcript sequence, including RNA editing and transcription errors (RNA-DNA differences or RDDs), is understudied.
• Detecting RDDs is challenging due to reverse transcription (RT) and sequencing errors.

Purpose of the Study:

• To investigate transcript sequence variation specifically in short tandem repeats (STRs).
• To develop a method for inferring RNA-DNA difference (RDD) and reverse transcription (RT) error rates.
• To evaluate the impact of STR variation on health and disease.

Main Methods:

• Developed a maximum-likelihood estimator (MLE) to quantify RT error and RDD rates.
• Accounted for next-generation sequencing error rates in the MLE model.
• Conducted large-scale DNA and RNA sequencing experiments in a primate species.

Main Results:

• RT error rates increase exponentially with STR length and are biased toward expansions.
• RDD rates were found to be approximately one order of magnitude lower than RT error rates.
• RT error rates estimated using the MLE were consistent with results from barcoded RNA sequencing in C. elegans.

Conclusions:

• The developed MLE provides a robust method for evaluating RT error and RDD rates.
• STR nonallelic transcript variation, in addition to allelic variation, may contribute to disease phenotypes.
• The findings have significant implications for medical genomics and understanding disease-associated transcripts.