**5. Conclusions**

sequence was shared with its counterpart in sorghum. In maize, one of most important crop species, genome-wide identification of differentially expressed lncRNAs during drought conditions led to the identification of 567 upregulated and 97 downregulated lncRNAs, among them 538 particles were considered to be novel. Moreover, 8 lncRNAs molecules were homologous to the miRNA precursors, 62 were classified as both shRNA and siRNA precur‐

In the best known model plant, *Arabidopsis thaliana*, genome-wide characterization of lncRNAs was performed as well. A correlated expression of lncRNAs with its epigenetic and structural features in response to four stresses (heat, cold, drought, and salt) has been described [140]. The authors identified 245 polyadenylated and 58 nonpolyadenylated lncRNAs that are differentially expressed under stress stimuli, and most of the selected candidates were further validated by qRT-PCR. From experiments on Arabidopsis came best studied cases of plant lncRNAs functions such as: *COLDAIR, COOLAIR, At4/IPS1, npc48,* and *npc536* [141–145].

One of best described mechanism of lncRNAs action is lncRNA transcript IPS1 (Induced by Phosphate Starvation 1). IPS1 can interact with miRNA as a competitor and function as miRNA target mimics, which resembles the miRNA sponges from animal systems. Maintaining the phosphate balance is a complicated mechanism in plants, regulated, among others, by miR399 as described in Paragraph 2.1. Low activity of PHO2, ruled by mRNA cleavage mediated by miR399, causes the elevation of phosphate uptake by increasing the expression of two root phosphate transporters. Phosphate starvation also increases the level of IPS1 transcript that has a 23-nt conserved domain, partially complementary to miR399 with 3-nt mismatch overlapping with the miR399-mediated cleavage site. As a non-cleavable product, IPS1 competes with PHO2 and can therefore weaken the miR399-mediated repression of PHO2 [142]. The miRNA sponge strategy is used in the therapy of human diseases and similar processes in plants (target mimic) and can be a very useful tool in plant research as well as in agricultural applications. As mentioned before, in Arabidopsis to date about 20 putative target mimicry events were predicted, which suggest the potential role of this mechanism in other

Another model organism, *Saccharomyces cerevisiae*, allows researchers to define and clarify a large number of new and unexpected roles of lncRNAs, such as promoting the timing of gene expression [147], cell cycle regulation during stress conditions [148], or local reduction of histone density and chromatin remodeling in response to glucose starvation [149]. Upon osmostress in yeast, hundreds of stress-responsive genes are induced by the stress-activated protein kinase (SAPK) p38/Hog1. Whole-genome tiling arrays were used to identify a set of Hog1-induced lncRNAs. One of the genes expressing a Hog1-dependent lncRNA in antisense orientation is CDC28, the cyclin-dependent kinase 1 (CDK1) that controls the cell cycle in yeast. Cdc28 lncRNA mediates the establishment of gene looping and the relocalization of Hog1 and RSC from the 3' UTR to the +1 nucleosome to induce CDC28 expression. The increase in expression level of Cdc28 makes cells able to re-enter the cell cycle more efficiently after stress conditions occur. This may represent a more general mechanism to prime the expression of

sors, and 279 were classified as siRNA precursors [139].

168 Abiotic and Biotic Stress in Plants - Recent Advances and Future Perspectives

pathways than the maintenance of phosphate homeostasis [146].

genes needed after stresses [148].

The rapidly growing human population is constantly stressing agro-ecosystems. In 2007, a FAO (Food and Agriculture Organization of the United Nations) report stated that only about 3.5% of the global agricultural area is not affected by any of the environmental stresses. Since recent advances in biotechnology and molecular biology have dramatically changed our understanding of gene expression regulation and responses of plants to abiotic stresses, we are now armed in new tools that could help us fight various stress conditions and improve the growth and yield of crops and other industrially important species. Our journey in the small RNA world has begun in the past century, in the 90s, with the discovery of RNA interference pathway, followed by siRNAs and their role in DNA methylation and chromatin modifica‐ tions. Consequently, new and relatively surprising small RNA groups (tRNA-derived small RNAs, snoRNA-derived small RNAs, mRNA-derived small RNAs) have been discovered and slowly but surely their role in cells and in the adaptation to various environmental conditions is being established. Concurrently, thousands of lncRNAs have already been identified and thousands of them are still waiting to be discovered in different organisms, tissues, or in response to different stimuli. With the advent of new high-throughput techniques, it became easier and much faster to collect a vast amount of different types of molecular data. The analysis of such a high amount of data and understanding of mutual correlations and relationships between genes, their roles, and small RNAs is now a challenge that researchers and scientists must face. Nevertheless, we believe that by combining new methodologies with the help of bioinformatic approaches and wet lab experiments, we can shed light on a genomic "dark matter" and start to appreciate important physiological roles of various types of non-protein coding RNAs, as well as their potential applications.
