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Abstract
SummaryWidespread antisense long noncoding RNA (lncRNA) overlap with many protein-coding genes in mammals and emanate from gene promoter, enhancer, and termination regions. However, their origin and biological purpose remain unclear. We show that these antisense lncRNA can be generated by R-loops that form when nascent transcript invades the DNA duplex behind elongating RNA polymerase II (Pol II). Biochemically, R-loops act as intrinsic Pol II promoters to induce de novo RNA synthesis. Furthermore, their removal across the human genome by RNase H1 overexpression causes the selective reduction of antisense transcription. Consequently, we predict that R-loops act to facilitate the synthesis of many gene proximal antisense lncRNA. Not only are R-loops widely associated with DNA damage and repair, but we now show that they have the capacity to promote de novo transcript synthesis that may have aided the evolution of gene regulation.
Highlights
A surprising feature of the mammalian genome is that only a small fraction directly encodes protein sequence
These extra long noncoding RNA transcripts include long intergenic noncoding RNA as well as enhancer RNA that initiate bi-directionally from numerous transcriptional enhancers that form a network of interactions with the promoters of protein-coding genes (Kim et al, 2010; Kowalczyk et al, 2012)
The human b-actin gene terminator, which is prone to form R-loop structures (Skourti-Stathaki et al, 2014), was placed within S. cerevisiae URA3 genic sequence, and this was inserted into a circular plasmid
Summary
A surprising feature of the mammalian genome is that only a small fraction directly encodes protein sequence. Almost all single-copy genomic DNA has the capacity to be transcribed at least in some cell types, even though only a minor fraction of these transcripts correspond to functional pre-mRNA sequence (Kapranov et al, 2007; Pelechano and Steinmetz, 2013; Schlackow et al, 2017) These extra long noncoding RNA (lncRNA) transcripts include long intergenic noncoding RNA (lincRNA) as well as enhancer RNA (eRNA) that initiate bi-directionally from numerous transcriptional enhancers that form a network of interactions with the promoters of protein-coding genes (Kim et al, 2010; Kowalczyk et al, 2012). It is the nature and origin of these AS transcripts that is the focus of our present study
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