A research team led by scientists at the National Institutes of Health’s National Human Genome Research Institute (NHGRI) has developed an advanced technique that offers an exceptionally detailed view of how RNA levels change in cells over time. The team used the new method to examine the cellular dynamics of RNA molecules following two distinct cellular stresses. This approach, called scSLAM-IsoSeq, provides essential information for researchers studying fundamental cellular processes and human diseases caused by abnormal RNA regulation such as cancer and developmental disorders.

The team of scientists, led by Bing Ren, PhD, scientific director of the NHGRI Center for Computational and Functional Genomics and a Howard Hughes Medical Institute investigator, published their findings today (September 22, 2022) in the journal Nature.

“The new technique makes it possible to simultaneously analyze RNA dynamics and features such as gene regulatory regions and RNA modifications, which is an exciting advancement for researchers,” said Ren.

RNA molecules are essential for life; they play a pivotal role in many biological processes, including protein synthesis, cell signaling, and gene regulation. The levels and activity of RNA molecules must be tightly controlled within a cell to maintain cellular homeostasis.

In 2014, Ren’s team invented a method called single-cell RNA-seq (scRNA-seq), a powerful tool that offers comprehensive information about the levels, functions, and characteristics of RNA molecules in individual cells. scRNA-seq has since become a widely used technology that has advanced researchers’ understanding of the complexities of cellular biology.

“Single-cell RNA-seq revolutionized the field by providing a snapshot of individual cells at a specific time point,” said co-first author Jingjing Li, PhD, a senior research fellow in Ren’s lab. “With the new approach, we can study not just a static picture, but also a dynamic movie of how RNA changes in response to cellular events or genetic perturbations, giving us unprecedented insights into the intricate regulatory mechanisms of gene expression.”

The researchers created the scSLAM-IsoSeq technique by building on two previously existing methods: scSLAM-seq, which measures the synthesis rate of RNA molecules in individual cells; and Iso-seq, which can capture various forms of RNA molecules (isoforms). The resulting technique, scSLAM-IsoSeq, provides highly detailed information about the dynamics and features of individual RNA molecules, including the rate of RNA production and breakdown, alternative splicing patterns, and modifications.

To demonstrate the capabilities of scSLAM-IsoSeq, the NHGRI researchers analyzed RNA dynamics and features in two different cellular stress conditions: heat shock and treatment with the drug thapsigargin, both known to induce a cellular stress response. They studied these cellular responses in two different cell types: mouse embryonic stem cells and human induced pluripotent stem cells. This research enabled the team to reveal novel insights into how RNA molecules respond to a changing environment. For instance, they found that RNA isoforms play essential roles in the cellular stress response, suggesting their potential as therapeutic targets for diseases arising from cellular stress.

“We believe this new technique will be transformative for RNA biology and will pave the way for future studies on RNA regulation, cellular reprogramming, and disease mechanisms,” said co-first author Jianan Ma, PhD, also a senior research fellow in Ren’s lab.

The researchers plan to further improve scSLAM-IsoSeq and make it more accessible to the wider scientific community to spur new discoveries in RNA biology and human diseases.