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Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters

Abstract

Mammalian transcriptomes are complex and formed by extensive promoter activity. In addition, gene promoters are largely divergent and initiate transcription of reverse-oriented promoter upstream transcripts (PROMPTs). Although PROMPTs are commonly terminated early, influenced by polyadenylation sites, promoters often cluster so that the divergent activity of one might impact another. Here we found that the distance between promoters strongly correlates with the expression, stability and length of their associated PROMPTs. Adjacent promoters driving divergent mRNA transcription support PROMPT formation, but owing to polyadenylation site constraints, these transcripts tend to spread into the neighboring mRNA on the same strand. This mechanism to derive new alternative mRNA transcription start sites (TSSs) is also evident at closely spaced promoters supporting convergent mRNA transcription. We suggest that basic building blocks of divergently transcribed core promoter pairs, in combination with the wealth of TSSs in mammalian genomes, provide a framework with which evolution shapes transcriptomes.

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Figure 1: A general building block for transcription initiation.
Figure 2: Common organization of divergent RNA-RNA TSS pairs.
Figure 3: PROMPT generation and properties between divergent mRNA TSSs.
Figure 4: Organization of TSS pairs forming NAT and nNAT constellations.
Figure 5: Properties of NATs and nNATs.
Figure 6: PROMPT properties in convergent constellations.
Figure 7: Models for PROMPT and alternative TSS generation in bidirectional constellations.

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Gene Expression Omnibus

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Gene Expression Omnibus

Sequence Read Archive

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Acknowledgements

Work in the T.H.J. laboratory was supported by the European Research Council (ERC) (grant 339953) as well as the Danish National Research Foundation (grant DNRF58), the Lundbeck Foundation and the Novo Nordisk Foundation. Work in the A.S. laboratory was supported by grants from the Lundbeck Foundation, the Novo Nordisk-Foundation and the Innovation Fund Denmark. J.H. was supported by a Boehringer-Ingelheim PhD fellowship. R.A. was supported by ERC grant 638273. Work in the L.M.S. laboratory was supported by the Deutsche Forschungsgemeinschaft (grant 1422/3-1). A.A.P. was supported by a Jane Coffin Childs postdoctoral fellowship. We thank the European Molecular Biology Laboratory Genomics Core Facility for technical support.

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Authors

Contributions

Y.C. analyzed the data. A.A.P. performed exploratory computational analyses for divergent mRNAs. M.L. performed exploratory computational analyses for convergent loci constellations. N.M. and V.P. produced the TIF-seq libraries. A.I.J. processed TIF-seq reads. J.H. conducted RT-qPCR validations. R.A. assisted with enhancer definitions, co-guidance of analyses and interpretation of results. L.M.S. supervised A.I.J. and V.P.. Y.C. and A.S. produced images. T.H.J. and A.S. conceived and supervised the project. Y.C., T.H.J. and A.S. wrote the paper. All authors read and approved of the manuscript.

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Correspondence to Torben Heick Jensen or Albin Sandelin.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–5, Supplementary Tables 1–2 and Supplementary Note 1 (PDF 20121 kb)

Supplementary Dataset 1

Genomic coordinates for analyzed regions. (XLSX 388 kb)

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Chen, Y., Pai, A., Herudek, J. et al. Principles for RNA metabolism and alternative transcription initiation within closely spaced promoters. Nat Genet 48, 984–994 (2016). https://doi.org/10.1038/ng.3616

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