Gene regulation / transcription · BEGINNER LESSON
Transcription start site
A transcription start site (TSS) is the exact DNA position where RNA polymerase begins making a new RNA transcript. It is identified as a base-specific starting boundary of transcription.
What it is and what is measured
A transcription start site, or TSS, is the first DNA base copied into RNA when transcription begins. In practice, researchers measure the exact genomic position of this start point, often by genome-wide TSS mapping or prediction. In bacteria, identifying TSS helps locate promoter regions and other nearby regulatory elements; in eukaryotes, the TSS lies within the promoter where RNA polymerase II begins transcription.
[1] TSSpredator-Web: A web-application for transcription start site ... [2] A Transcription Factor-Centric View of Transcription Regulation - PMC [3] The molecular basis of transcription initiation by RNA ...
How TSS relates to transcription
A promoter is the DNA region around the TSS. In eukaryotes, RNA polymerase II does not start on its own; initiation needs a preinitiation complex (PIC), a group of general transcription factors and other proteins assembled at the promoter. The same start region is also influenced by enhancers, which are distant DNA elements that can boost transcription. In bacteria, TSS positions can reveal untranslated regions, non-coding RNAs, antisense RNAs, and orphan TSS that do not match annotated genes.
[1] TSSpredator-Web: A web-application for transcription start site ... [2] A Transcription Factor-Centric View of Transcription Regulation - PMC
Why identification is difficult
Standard RNA-seq is not enough for base-exact TSS calling because it cannot separate primary transcripts, which begin at the true start, from processed transcripts, which have degraded 5′ ends. Those processed reads can shift the signal and make the true start look less precise. Genome annotations also often list translation start sites and coding regions rather than exact transcription starts, so dedicated TSS methods are needed. Some tools classify detected sites by position relative to genes, including primary, secondary, internal, antisense, and orphan TSS.
[1] TSSpredator-Web: A web-application for transcription start site ...
Limitations and interpretation
A TSS prediction is only as good as the underlying data, thresholds, and gene annotation used for comparison. A signal near a gene may be classified differently depending on distance, strand, and whether the site is the strongest signal in a region. The sources also note that many transcription-factor binding events are not clearly regulatory in vivo, so nearby binding or signal does not automatically prove function at a TSS.
[1] TSSpredator-Web: A web-application for transcription start site ... [2] A Transcription Factor-Centric View of Transcription Regulation - PMC
SEE THE IDEA
How a TSS fits into transcription
The genomic region that includes the TSS and nearby control sequences.
The exact base where RNA synthesis begins.
In eukaryotes, a preinitiation complex helps RNA polymerase II start.
The new RNA molecule that extends away from the start site.
The promoter contains the TSS; transcription machinery assembles there and begins RNA synthesis at that exact base.
A TSS is the starting coordinate inside the promoter where transcription begins.
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Sources and further reading
This general lesson was generated from public source material. It explains a concept; it does not interpret a private paper or provide medical advice.