- A transcription start site (TSS) is the exact nucleotide position in the genome where RNA polymerase begins transcribing DNA into RNA. It marks the 5′ end of the primary RNA transcript and is a key reference point for understanding gene regulation.
- The TSS is not always fixed—many genes have multiple start sites, which can vary depending on cell type, developmental stage, or environmental conditions, leading to the production of different transcript isoforms.
- In eukaryotes, the TSS is typically located within the core promoter region, which contains sequence motifs such as the TATA box, Initiator (Inr) element, or downstream promoter elements that help position the transcription machinery. The +1 position refers to the first transcribed base, with upstream nucleotides numbered negatively (–1, –2, etc.). The majority of eukaryotic mRNAs receive a 7-methylguanosine cap shortly after initiation, which protects the RNA from degradation and is used in many TSS mapping methods.
- In prokaryotes, the TSS lies downstream of promoter elements such as the –10 (Pribnow box) and –35 regions, which are recognized by the sigma factor of RNA polymerase. The first base is usually an adenine (A) or guanine (G), although this preference is not absolute. Prokaryotic transcripts typically have a triphosphate at the 5′ end, distinguishing them from processed RNAs.
- Identifying the TSS is crucial for promoter annotation, studying transcription factor binding, and understanding how genes are differentially expressed. Variations in TSS usage can influence the length of the 5′ untranslated region (5′ UTR), affecting mRNA stability, localization, and translational efficiency. As such, precise TSS mapping is a fundamental step in transcriptomics and functional genomics.
