Single-cell polyadenylation site mapping reveals 3' isoform choice variability.

Area of Science:

• Molecular Biology
• Developmental Biology
• Genomics

Background:

• Cell-to-cell variability in gene expression is crucial for development and stem cell maintenance.
• While gene expression levels are well-studied, mRNA 3' untranslated region (UTR) polyadenylation isoform choice remains underexplored.
• Understanding 3' isoform variation in homogeneous cell populations is key to deciphering gene regulation.

Purpose of the Study:

• To investigate genome-wide polyadenylation site usage at the single-cell level in mouse embryonic and neural stem cells.
• To explore the variability of 3' isoform usage within genetically and developmentally similar cell populations.
• To analyze single-cell isoform data using a novel statistical framework.

Main Methods:

• Developed and utilized a novel single-cell transcriptomic method, BATSeq, for genome-wide polyadenylation site quantification.
• Applied the BATBayes statistical framework to analyze single-cell isoform data.
• Confirmed findings using RNA Fluorescence In Situ Hybridization (FISH) data.

Main Results:

• Cellular developmental state globally influences polyadenylation isoform usage.
• Significant cell-to-cell variation in 3' isoform choice exists even among cells in the same developmental state.
• This observed variation exceeds random chance, indicating a biological regulatory mechanism.

Conclusions:

• Single-cell 3' isoform usage exhibits variability beyond global developmental programming.
• This heterogeneity in polyadenylation site choice has implications for functional cell-to-cell differences.
• Understanding this variability can aid in resolving distinct cell populations and their functions.