Transcriptional read-through of the long non-coding RNA SVALKA governs plant cold acclimation

Abstract

SummaryMost DNA in the genomes of higher organisms does not encode proteins, but is transcribed by RNA polymerase II (RNAPII) into long non-coding RNA (lncRNA). The biological significance of most lncRNA is largely unclear. Here, we identify a lncRNA (SVALKA) in a cold-sensitive region of the Arabidopsis genome. Mutations in SVALKA affect the timing of maximal CBF1 expression and freezing tolerance. RNAPII read-through transcription of SVALKA results in a cryptic lncRNA overlapping CBF1 on the antisense strand, termed asCBF1. asCBF1 transcription is anti-correlated with CBF1 expression. Our molecular dissection reveals that CBF1 is suppressed by RNAPII collision stemming from the SVALKA-asCBF1 lncRNA cascade. The SVK-asCBF1 cascade provides a mechanism to tightly control CBF1 expression and timing that could be exploited to maximize freezing tolerance with mitigated fitness costs. Inversion of the transcriptional direction of a lncRNA cascade relative to the genes in a co-regulated cluster provides an elegant inbuilt negative feedback for cluster expression. Our results provide a compelling example of local gene regulation by lncRNA transcription having a profound impact on the ability of plants to appropriately acclimate to suboptimal environmental conditions. not peer-reviewed) is the author/funder. All rights reserved. No reuse allowed without permission.The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/287946 doi: bioRxiv preprint first posted online Mar. 23, 2018; Main RNA Polymerase II (RNAPII) transcription in genomes results in the production of many long noncoding RNAs (lncRNAs) 1 . The functional significance of resulting lncRNA molecules is actively debated even though biological roles are identified for an increasing number of examples [2][3][4] . Expression of lncRNAs is remarkably specific to the environmental condition, tissue or cell type, arguing for roles of lncRNA in regulation [5][6][7] . In addition to functions carried out by lncRNA molecules, the process of transcribing non-coding DNA sequences can by itself be regulatory in many systems 8,9 . Non-coding DNA regions in genomes can therefore affect gene expression by different mechanisms that need to be resolved experimentally.Sessile organisms respond to changing environmental conditions with regulation of gene expression. Early events in the Arabidopsis cold response include rapid transcriptional upregulation of the intron-less C-repeat/dehydration-responsive element binding factors (CBFs) 10,11 . The CBFs are highly conserved transcription factors that promote cold tolerance in many plant species and are often arranged in a single cluster 12. CBF expression during cold exposure activates downstream COLD REGULATED (COR) genes that promote freezing tolerance by adjusting the physiological and biochemical properties of plant cell interiors [13][14][15] . Intriguingly, constitutive CBF expression increases cold-tolerance but is also associated with fitness penalties [16][17][18][19] . antisense CBF1 lncRNA (...

Advances and challenges in uncovering cold tolerance regulatory mechanisms in plants

“…Interestingly, the expression of SVALKA is increased after 4 h of cold treatment when CBF1 expression is decreased (Kindgren et al, 2018). RNA Polymerase II read-through transcription of SVALKA results in the production of asCBF1, a cryptic antisense transcript overlapping CBF1 to repress cold-induction of CBF1 gene (Kindgren et al, 2018). This study provides a new regulatory mechanism of CBF1 expression under cold stress.…”

“…A recent study reported a cold-responsive long noncoding RNA, named SVALKA, plays a role in regulating CBF1 expression. Interestingly, the expression of SVALKA is increased after 4 h of cold treatment when CBF1 expression is decreased (Kindgren et al, 2018). RNA Polymerase II read-through transcription of SVALKA results in the production of asCBF1, a cryptic antisense transcript overlapping CBF1 to repress cold-induction of CBF1 gene (Kindgren et al, 2018).…”

Organismal benefits of transcription speed control at gene boundaries

“…stands for not significant. E Image of homozygous mutant nrpb2-2 fully complemented by NRPB2 WT -FLAG (top, NRPB2 WT +/+ nrpb2-2 À/À ) and partially complemented by NRPB2 Y732F -FLAG (bottom, immunoprecipitation from plants (RNAPII-ChIP) [25,37], we analyzed nascent RNA attached to RNAPII to monitor RNAPII elongation [38]. We identified three pathogen resistance-related Toll/interleukin receptor (TIR)-type NB-LRR genes AT4G19520, AT5G41740, and AT5G41750 [39,40] that are rapidly induced by flagellin 22 treatment.…”

“…We identified three pathogen resistance-related Toll/interleukin receptor (TIR)-type NB-LRR genes AT4G19520, AT5G41740, and AT5G41750 [39,40] that are rapidly induced by flagellin 22 treatment. To monitor the "waves" of RNAPII elongation on these three genes after transcriptional induction, we performed a time course experiment during flagellin 22 treatment and determined the RNAPII signal by analyzing nascent RNA attached to RNAPII [38]. We chose NRPB2 WT -FLAG +/+ Col-0 and NRPB2 Y732F -FLAG +/+ Col-0 as material for this assay since we detected no differences in growth and immune response in this background.…”

“…Nascent RNA isolation Nascent RNA was isolated according to previously described protocol with minor changes [38]. Table EV1.…”