NascentStrandSequencing

Nascent strand sequencing is a molecular biology technique used to study newly synthesized RNA molecules directly within a cell. It allows researchers to capture and analyze RNA that is actively being transcribed from DNA, providing insights into gene expression dynamics and regulatory mechanisms. The process typically involves a short labeling period where cells are exposed to modified nucleotides that are incorporated into newly forming RNA strands. These modified nucleotides act as a tag.

Following the labeling, the RNA is extracted from the cells. The key step in nascent strand sequencing is the selective isolation of the labeled RNA molecules from the total RNA pool. This is often achieved using affinity purification methods that target the modified nucleotides. Once isolated, the labeled RNA is converted into a cDNA library, which is then sequenced using high-throughput sequencing technologies.

The resulting sequence data provides information about the location and abundance of nascent RNA transcripts. This allows for the study of transcription rates, the identification of actively transcribed regions of the genome, and the detection of transcriptional bursting. Nascent strand sequencing is particularly valuable for understanding transient gene expression changes, the effects of stimuli on transcription, and the kinetics of RNA synthesis. It complements other RNA analysis techniques like RNA sequencing (RNA-seq) by focusing specifically on newly produced transcripts rather than all RNA present.