Why is there a higher alignment of gene antisense regions in single-cell transcriptomics?

Single-cell RNA sequencing (scRNA-seq) is a method for sequencing RNA molecules within individual cells. When analyzing scRNA-seq data, high alignment to antisense strands or antisense regions is sometimes observed. This is because:

1.Inherent Antisense Transcription:

In fact, antisense transcription is a naturally occurring process in many cells. These antisense RNAs are often functionally related to their corresponding genes and may be involved in gene regulation, expression inhibition, etc. For example, some antisense RNAs can bind to sense strand mRNA to form double-stranded structures, thereby preventing the mRNA from being translated.

2.TechnicalReasons:During the sample preparation process of scRNA-seq, template switching events may be introduced. During reverse transcription, when the RNA polymerase encounters structural obstacles or template switching, it may jump to a nearby RNA molecule, possibly leading to cDNA synthesis on the non-template strand, thereby generating antisense RNA.

3.Random Primers:

Using random primers for reverse transcription may produce cDNA of antisense RNA, which could lead to the observation of antisense region alignment in sequencing data.

4.Data Analysis Bias:

In processing scRNA-seq data, library preparation, alignment strategies, and the reference genome used can all affect alignment results. For example, when using an exhaustive reference genome that includes multiple transcripts and non-coding RNAs for alignment, more antisense region alignments may be observed.

Biotech Company - BiologicalProductsCharacterization, a leading provider of multi-omics mass spectrometry detection services

Related Services:

Single-cell sequencing