A novel hypoxic stress-responsive long non-coding RNA transcribed by RNA polymerase III in Arabidopsis

Abstract

Recently, a large number of non-coding RNAs (ncRNAs) have been found in a wide variety of organisms, but their biological functions are poorly understood, except for several tiny RNAs. To identify novel ncRNAs with essential functions in flowering plants, we focused attention on RNA polymerase III (Pol III) and its transcriptional activity, because most Pol III-transcribed RNAs contribute to key processes relating to cell activities, and have highly conserved promoter elements: upstream sequence elements, a TATA-like sequence, and a poly(T) stretch as a transcription terminator. After in silico prediction from the Arabidopsis genome, 20 novel ncRNAs candidates were obtained. AtR8 RNA (approx. 260 nt) and AtR18 RNA (approx. 160 nt) were identified by efficient in vitro transcription by Pol III in tobacco nuclear extracts. AtR8 RNA was conserved among six additional taxa of Brassicaceae, and the secondary structure of the RNA was also conserved among the orthologs. Abundant accumulation of AtR8 RNA was observed in the plant roots and cytosol of cultured cells. The RNA was not processed into a smaller fragment and no short open reading frame was included. Remarkably, expression of the AtR8 RNA responded negatively to hypoxic stress, and this regulation evidently differed from that of U6 snRNA.

Databases for lncRNAs: a comparative evaluation of emerging tools

“…Although the biogenesis of lncRNAs involves either polymerase II or polymerase III, this feature is not presently included (Dieci et al 2007;Wu et al 2012). Also, even when databases such as lncRNAdb and Noncode currently indicate subcellular location of lncRNAs extracted from literature, this type of annotation remains limited.…”

“…Owing to these diverse molecular mechanisms, lncRNAs are now known as important regulators of fundamental processes such as development, imprinting, and cell differentiation (Kretz 2013;Lee and Bartolomei 2013;Lv et al 2013). They are also involved in stress responses to heat, hypoxia, or DNA damage (Jolly et al 2004;Bertozzi et al 2011;Wu et al 2012;Place and Noonan 2013;Wan et al 2013;Yang et al 2013a;Zhang et al 2013).…”

PLNlncRbase: A resource for experimentally identified lncRNAs in plants

“…Current efforts have described several investigations with a particular focus on abiotic/biotic stress responses (factors limiting crop yield) for plant lncRNAs (Xin et al, 2011;Liu et al, 2012). For example, the Pol III-transcribed conserved lncRNA AtR8 acts negatively to hypoxic conditions in both Arabidopsis and Brassicaceae (Wu et al, 2012). Another finding is that twenty lncRNAs from 159 intergenic regions in Arabidopsis thaliana were discovered to be responsive to Fusarium oxysporum using a strand-specific RNA-sequencing method (Zhu et al, 2014).…”

Physiological and Molecular Mechanisms of Flooding Tolerance in Plants

“…AtR8 was preferentially localized to cytoplasm of root tissues. It is possible that the lnc RNA negatively regulates translation or ANPs and decrease in abundance of these RNAs upregulate translation of ANPs (Wu et al 2012 ).…”

“…Putative targets for these hypoxiaresponsive miRNA are transcription factors mainly from the MYB, NAC, Homeobox, SPL, ARF, AP2, MADS, and CCAAT-HAP2 families having important roles in plant growth and fl oral development (Moldovan et al 2009 ). Wu et al ( 2012 ) identifi ed long non-coding RNAs (lnc RNA) responsive to hypoxia stress in Arabidopsis. Abundance of lnc RNA AtR8 was decreased by hypoxic treatments and recovered upon reoxygenation.…”