Transcriptional termination in mammals: Stopping the RNA polymerase II juggernaut

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Science  10 Jun 2016:
Vol. 352, Issue 6291, aad9926
DOI: 10.1126/science.aad9926

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An end to gene transcription

Much attention has been focused on regulating the start of gene transcription. But transcription must also be terminated, and the mechanisms are only now being defined in detail in eukaryotes. Proudfoot reviews how termination happens for RNA polymerase II genes, mainly in mammals, covering the various steps that can lead to messenger RNA (mRNA) 3′ end formation and how they can be regulated. Termination can occur at various positions throughout the gene, forming the wild-type mRNA, preventing the synthesis of aberrant mRNAs, or generating alternative mRNAs with different regulatory or coding properties.

Science, this issue p. 10.1126/science.aad9926

Structured Abstract


Genes correspond to single transcription units, starting from the promoter and ending at the terminator. Terminating gene transcription is directly coupled to mRNA processing, which occurs cotranscriptionally. When RNA polymerase II (Pol II) reaches the gene end, it first slows down over the terminator. This is partly because 3′-end cleavage and polyadenylation (CPA) complex is recruited onto Pol II when poly(A) signals appear in the nascent transcript. This nascent transcript will often invade the DNA duplex to form an R-loop structure, which induces further polymerase slowdown. During this time, CPA releases mRNA from chromatin into eventual cytoplasmic translation. Pol II continues to transcribe its DNA template after mRNA release. However, this is short-lived, as an exonuclease (Xrn2) degrades the transcript from its 5′ end. When this molecular torpedo catches up with Pol II, then conformational shockwaves are transmitted into its active site, which releases Pol II from the DNA template. Pol II is then free to restart transcription on another gene promoter.


The above process of Pol II termination appears surprisingly complex, but provides unanticipated layers of gene regulation. First, most protein-coding genes generate multiple mRNAs of different lengths caused by the use of alternative poly(A) sites (APA), which in turn is dictated by gene termination. Alternative mRNAs with shorter or longer 3′-untranslated region (3′UTR) sequences possess different sequence codes for how long to survive or where in the cell to translate their proteins. Second, termination of transcription is employed as a quality-control mechanism. Transcription errors occur either because the DNA template is damaged or because the RNA is mis-synthesized and induce premature termination before reaching the gene end. These truncated transcripts are rapidly degraded and, if Pol II becomes arrested on the DNA template, then it is degraded in situ by the proteasome to allow subsequent rounds of transcription.

Recent studies reveal that cellular stress such as osmotic or heat shock, as well as viral infection or cancer-inducing mutations, can all promote aberrant termination. Under these varied conditions, many genes fail to terminate transcription. The resulting extensive readthrough transcription can cause massive deregulation of downstream gene expression.


Many questions remain about the mechanism and regulation of transcriptional termination. Exactly how degradation of the transcript by Xrn2 together with CPA and various helicases promotes Pol II termination remains poorly understood. Structural changes occurring within Pol II to promote this effect are currently unknown. Their resolution will need new technology, such as cryo–electron microscopy.

The regulation of APA to generate mRNA with different 3′UTRs is similarly poorly understood. Although changes in CPA factor levels or in the transcription process itself can affect APA, dominant factors and mechanisms used in biology to achieve this regulation remain enigmatic. The easy perturbation of termination resulting in readthrough transcripts appears to be at odds with the elaborate mechanisms in place to stop the Pol II juggernaut. It is evident that the field of Pol II termination has many surprises in store for future research into this fascinating process.

Mechanism of RNA polymerase II (Pol II) termination over the 3′ end of a protein-coding gene.

Two alternative poly(A) signals are shown placed within a blue background that indicates the terminal region of the gene transcript ending in the termination region. The inset depicts key players in the termination mechanism, including the Xrn2 torpedo, SETX helicase, and the CPA complex associated with the nearby Pol II carboxyl-terminal domain. The released mature mRNA is shown. Also indicated is the R-loop structure, which induces Pol II pausing along with specific chromatin modifications positioned on the downstream DNA. Cellular stress induces transcriptional readthrough, often invading the downstream gene as shown by the red background. [Figure created by Hannah Mischo]


Terminating transcription is a highly intricate process for mammalian protein-coding genes. First, the chromatin template slows down transcription at the gene end. Then, the transcript is cleaved at the poly(A) signal to release the messenger RNA. The remaining transcript is selectively unraveled and degraded. This induces critical conformational changes in the heart of the enzyme that trigger termination. Termination can also occur at variable positions along the gene and so prevent aberrant transcript formation or intentionally make different transcripts. These may form multiple messenger RNAs with altered regulatory properties or encode different proteins. Finally, termination can be perturbed to achieve particular cellular needs or blocked in cancer or virally infected cells. In such cases, failure to terminate transcription can spell disaster for the cell.

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