Developmental transitions in Arabidopsis are regulated by antisense RNAs resulting from bidirectionally transcribed genes

Abstract

Transcription terminators are DNA elements located at the 3' end of genes that ensure efficient cleavage of nascent RNA generating the 3' end of mRNA, as well as facilitating disengagement of elongating DNA-dependent RNA polymerase II. Surprisingly, terminators are also a potent source of antisense transcription. We have recently described an Arabidopsis antisense transcript originating from the 3' end of a master regulator of Arabidopsis thaliana seed dormancy DOG1. In this review, we discuss the broader implications of our discovery in light of recent developments in yeast and Arabidopsis. We show that, surprisingly, the key features of terminators that give rise to antisense transcription are preserved between Arabidopsis and yeast, suggesting a conserved mechanism. We also compare our discovery to known antisense-based regulatory mechanisms, highlighting the link between antisense-based gene expression regulation and major developmental transitions in plants.

Antisense transcription‐dependent chromatin signature modulates sense transcript dynamics

“…Being able to modulate transcription and transcript dynamics by manipulating the activity of a chromatin modifying enzyme strongly supports antisense transcription modulating the chromatin structure in the vicinity of promoters and this in turn affecting transcription and transcript fate. Pervasive transcription is not limited to the antisense strand of genes as studied here, but is also abundant at enhancer elements, at the 3′ ends of genes and throughout gene‐rich regions of many different genomes including plants, yeast, fungi, flies and worms (Ni et al , ; Kwak et al , ; Andersson et al , ; Nojima et al , ; Booth et al , ; Krzyczmonik et al , ; Ietswaart et al , ). In some cell types, non‐coding transcripts could facilitate RNAi‐mediated degradation of the sense transcripts which might make uncovering the associations we have found in budding yeast, which lacks an RNAi system, more challenging.…”

Antisense transcription represses Arabidopsis seed dormancy QTL DOG 1 to regulate drought tolerance

“…The molecular mechanism of asDOG1 ‐mediated DOG1 suppression is currently not clear. Importantly, the DOG1 locus is devoid of DNA methylation, small RNA or high H3K9me2, suggesting that the molecular mechanism may not involve RNA interference but may be based on cis ‐acting mechanisms linked more directly to antisense transcription .…”

Extensive nuclear reprogramming and endoreduplication in mature leaf during floral induction

“…From transcriptional and chromatin-based mechanisms, to alternative splicing and post-translational regulation, numerous regulatory levels participate to the control of the floral transition [9, 11–15] and its main actors, which have been gathered in the Flowering-Interactive Database (FLOR-ID) [16]. Besides protein regulators involved in developmental transitions, an increasing number of studies have highlighted the regulatory functions of long non-coding RNAs (lncRNAs) [17, 18]. In response to vernalization, the lncRNAs COLDAIR , COLDWRAP , COOLAIR , and Antisense Long participate to the fine regulation of the key MADS-box floral repressor FLOWERING LOCUS C (FLC) via modifications of FLC chromatin environment [19–23].…”