LncRNA Information
Species Arabidopsis thaliana Chromosome 3 Start site 3050989
End site 3051530 Chain plus Exon NO. 1
Assembly TAIR10 Class lincRNA NCBI accession AF236376
Ensembl N/A Sequence

Function (not disease relevant)
Methods Sample/condition Expression pattern Dysfunction type Description PMID Source
Northern blot/qRT-PCR phosphate balance up-regulated N/A Arabidopsis thaliana(AtIPS1) that is induced by Pi starvation, and studied the effect of cytokinin on its expression in response to Pi deprivation. AtIPS1 belongs to the TPSI1/Mt4 family, the members of which are induced by Pi starvation, and the RNAs of which contain only short, non-conserved open reading frames. AtIPS1 is induced by Pi starvation and expression in the root. The induction of AtIPS1 expression under Pi starvation is reversible. AtIPS1:GUS responsiveness to Pi starvationin roots is repressed by cytokinins. However, cytokinins did not repress the increase in root-hair number and length induced by Pi starvation, a response dependent on local Pi concentration rather than on whole-plant Pi status. Our results raise the possibility that cytokinins may be involved in the negative modulation of long-distance, systemically controlled Pi starvation responses, which are dependent on whole-plant Pi status. (Ana et al., 2002) The lncRNA, INDUCED BY PHOSPHATE STARVATIONA (IPS1), is a noncoding transcript that is intimately associated with the function of miRNA399. Under phosphate starvation, the expression PHO2, a target of miRNA399, is up-regulated due to increased binding and sequestering of miRNA399 by IPS1. IPS1 contains complementary sequences to the phosphate (Pi) starvation-induced miRNA399 and thus can compete with PHO2 transcripts for the binding of miRNA399. However, IPS1 is not cleaved by the miRNA because the paring with miRNA is interrupted by a mismatched loop at the expected miRNA cleavage site. (Kim et al., 2011) The effect of miR-399 on PHO2 mRNA was greatly suppressed by simultaneous IPS1 overexpression,suggesting that IPS1 antagonizes the effects of miR-399. In agreement with previous reports on the negative effect of PHO2 on shoot Pi content9-12, the shoot Pi content of IPS1-overexpressing plants was lower than that in their counterparts lacking IPS1 overexpression. And IPS1 contains a motif with sequence complementarity to the phosphate (Pi) starvation-induced miRNA miR-399,IPS1 over expression results in increased accumulation of the miR-399 target PHO2 mRNA and, concomitantly, in reduced shoot Pi content. (Franco-Zorrilla et al., 2007) Induced by Phosphate Starvation1(IPS1), which can bind to ath-miR399 with a three-nucleotide bulge between the 5'end 10th and 11th positions of ath-miR399. Such pairing abolished the cleavage effect of ath-miR399 on IPS1; thus, IPS1 can serve as a decoy for ath-miR399 to interfere with the binding of ath-miR399 to its other targets. (Wu et al., 2013) Under phosphate starvation, transcript levels of the natural target of miR399, PHO2, are increased because of the binding and sequestering of miR399 by IPS1. IPS1 contains a centrally bulged miR399-binding site (called 'target mimic’) that prevents IPS1 cleavage by miR399 and apparently inhibits recycling of the miR399 effector complex. (Brosnan et al., 2009) Induced by Phosphate Starvation 1 (IPS1) with a binding site for miR-399, a phosphate starvation-induced miRNA. However,miR-399 binding does not induce degradation of the IPS1 transcript due to mismatched nucleotides in the binding site, but rather results in sequestration of miR-399 from other target transcripts. Thus, IPS1 can effectively function as a sponge in hibiting the number of miR-399 molecules available for regulating its target PHO2 mRNA. The Arabidopsis thaliana pho2 mutant is aphosphate over-accumulator. This mutant carries a mutation in the PHO2 gene,encoding a ubiquitin-conjugating enzyme(UBC24), that leads to a reduction in full-length transcripts. In response to phosphate starvation, IPS1 RNAs are induced. The latter can sequester miR-399 resulting in stabilization and increased accumulation of PHO2 and, concomitantly, in reduced shoot phosphate content. (Kartha et al., 2014) 22104407, 17643101, 23429259, 19447594, 24523727 PLNlncRbase

Interaction target Level of interaction Type of interaction Description PMID Source
miR-399 RNA-RNA regulation The IPS1 ncRNA is poorly evolutionarily conserved except for a short motif that is highly complementary to miR-399, a miRNA that is induced in response to phosphate starvation, although the basepairing is interrupted by a mismatched loop at the expected miRNA cleavage site. This interruption in basepairing causes the IPS1 ncRNA to be noncleavable and instead allows IPS1 to sequester miR-399, resulting in increased expression of miR-399 target genes. 19571179 LncRNADisease
PHO2 RNA-RNA regulation N/A 22104407, 17643101, 23429259, 19447594, 24523727 PLNlncRbase