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Pairs of promoter pairs in a web of transcription

Nature Genetics volume 48, pages 975–976 (2016)Cite this article

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A new analysis has characterized a fundamental building block of complex transcribed loci. Constellations of core promoters can generally be reduced to pairs of divergent transcription units, where the distance between the pairs of transcription units correlates with constraints on genomic context, which in turn contribute to transcript fate.

It has increasingly been recognized that mammalian genomes can pervasively be transcribed into RNA. Protein-coding and noncoding RNAs alike may comprise multiple transcript variants that themselves are embedded in a complex web of additional transcription units. Such arrangements may include divergently transcribed RNAs—sometimes protein coding, many times not—and antisense transcripts. On page 984 of this issue, a new analysis of human transcript data from Albin Sandelin, Torben Heick Jensen and colleagues addresses the underlying relationships between groups of RNAs transcribed from proximal transcription units1. Chen et al. find that many complicated arrangements of transcripts (which they term 'constellations'), covering many classes of RNA, likely derive from simple building blocks consisting of divergently transcribed core promoter pairs. Different stabilities of divergently transcribed RNAs relate to the density of sequence elements that control transcript stability2,3. When promoters are closely spaced, the density of such sequence elements is altered; therefore, the fates of transcripts derived from closely spaced promoter groups can be altered. This is an important, unifying view for the complex transcription initiation observed throughout the human genome and provides a rationale for understanding relationships among RNAs based on repeats of a simple architecture.

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Figure 1: Transcription can originate divergently in nucleosome-free regions, which provide paired core promoters.

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  1. Craig D. Kaplan is in the Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,

    Craig D Kaplan

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  1. Craig D Kaplan
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Correspondence to Craig D Kaplan.

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Kaplan, C. Pairs of promoter pairs in a web of transcription. Nat Genet 48, 975–976 (2016). https://doi.org/10.1038/ng.3649

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