Downstream-of-gene (DoG) RNAs are RNA transcripts that arise downstream of ~10% of host genes and are continuous with their upstream RNAs [1]. DoGs are defined as having a minimal length of 5 kb beyond the polyadenylation signal (PAS) at transcription end site (TES), with maximal length up to 200 kb in mammalian cells [1]. Due to their extended lengths, DoGs often overlap with other downstream transcription units referred to as read-in genes (Fig. 1) [2, 3].

Figure 1. Under normal conditions, the gene that produces normal mRNA and is free of read-in transcription. Cellular stresses can induce the production of “Downstream-of-Gene” transcripts (DoGs). Some of them can extend the transcription further into its downstream gene referred to as “read-in” gene[2, 3]. After synthesis, many DoGs remain close to their sites of transcription, whereas others are released into the nucleoplasm[1, 4]. Both polyadenylated and un-polyadenylated DoGs have been detected at similar levels [5]. Abbreviations: TSS, transcription start-site; TES, transcript end-site.

Molecular features of DoGs

DoGs arise due to read-through transcription. This process occurs when the 3'-end termination of nascent mRNAs is inefficient, leading to the continuation of transcription beyond the normal end of a gene [6]. DoGs are characterized by three distinct features (Fig. 1)[7]: (1) Their transcription initiates at the promoter of a protein-coding host gene. The production of DoGs does not involve de novo transcription initiation from an independent transcription start site (TSS). (2) They extend in a continuous manner for a minimum of 5 kilobases beyond the 3' terminal polyadenylation signal (PAS) of the host gene. (3) They are predominantly nuclear-localized and are likely to be chromatin-associated. Notably, DoG production is independent of the transcriptional activity of the host gene, and their regulatory mechanisms are distinct and uncoupled.

Biogenesis of DoGs

Normal transcription termination requires multiple coordinated events, including slowing down, pausing, and dislodging of the RNA polymerase RNAPII and 3′end cleavage of the RNA transcript. Perturbations in any of these steps can impact on the transcription termination and lead to transcription read-through (Fig.2). Cellular stresses, e.g. osmotic stress[5], heat shock[8], viral infection[3, 9], or cancer-inducing mutations, can all promote aberrant transcription termination. Under the stressed conditions, many genes fail to terminate transcription properly and favor read-through transcription due to failure to recognize PAS or dysfunction of factors for transcript cleavage and polyadenylation. In addition, DoG-producing genes often have distinctive chromatin features that predispose them to read-through transcription[3], for example, enriched histone marks (e.g., H3K36me3 and H3K79me2) that favor transcription elongation[10] or weaker polyadenylation signals (PAS).

Figure 2. Regulation of transcription termination by the factors, mechanisms, or cellular conditions that promote (Top) or impair (Bottom) RNAPII transcription termination. Transcription termination defects caused by cellular stress, viral infection, cancer, and senescence can result in read-through transcription and DoG production.

 

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References
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