Understanding all the RNA molecules in a cell is essential for discovering how genes are regulated and how cells respond to their environment. Most single-cell RNA sequencing methods only capture polyadenylated RNAs, which represent just a portion of the transcriptome. That means many important RNA molecules, such as histone RNAs and enhancer RNAs, are often missed.

Researchers at the National University of Singapore have developed a new tool called scComplete-seq. This technique builds on existing droplet-based single-cell RNA sequencing platforms but expands their capabilities to capture both polyadenylated and nonpolyadenylated RNAs. This approach provides a more complete picture of cellular RNA content at single-cell resolution.

The team tested scComplete-seq on cancer cells and peripheral blood mononuclear cells (PBMCs). They successfully identified short and long nonpolyadenylated RNAs, revealing how these overlooked molecules change in response to different stimuli. Importantly, they also linked specific transcriptomic shifts to biological processes and enhancer activity, highlighting how this method can uncover hidden layers of gene regulation.

Because scComplete-seq is compatible with high-throughput platforms, it could be widely adopted in studies of development, disease, and immune responses where fine-scale RNA dynamics matter.

Availability – The R code to reproduce the analyses in the figures is available from the Zenodo repository (https://doi.org/10.5281/zenodo.15751322).