**4.3. Precursor lncRNA**

the field of bioinformatics for high-throughput RNA-seq data. The data of identified lncRNAs in plants is timely submitted to the different databases [29]. A pipeline with multiple filters has been designed for the assembly and identification of high confidence lncRNAs in **Figure 1** [30, 31]. The present status of most of the identified lncRNAs in different plant species are

The biotypes of lncRNAs were identified with respect to their genomic localization, and were mainly categorized into intergenic, intronic, sense, antisense, and bidirectional lncRNAs. As the term suggest, the intergenic lncRNA are transcribed from the region amid two genes, while introns are the source of intronic lncRNA [45]. The sense and antisense lncRNAs are derived from overlapping region of exons on the sense and antisense strands, respectively [18], when the transcription of lncRNA is initiated in the juxtaposition of adjacent mRNA on

The dramatic change, in the past years about the knowledge of lncRNA in gene regulation mechanisms, has exponentially raised with high-throughput RNA-seq data. In plants, the studies are limited to small scale in comparison to animals, but the available reports sug-

Target mimicry is a mechanism of lncRNA for regulating the functions of miRNAs. They inhibit the interaction between the miRNA and their respective targets by binding to the target of miRNA via partial complementary sequence [46]. The novel mechanism of target mimicry was first discovered in *Arabidopsis*. In addition, *phosphate Starvation 1* (*IPS1*) was the first lncRNA identified as endogenous target mimic (eTM) of miR399 involved in phosphate homeostasis [46]. During phosphate starvation, the expression of miR399 is induced in companion cells and phloem [47]. Subsequently, the expression of *PHO2* gene, a target of miR399, is repressed [47–50]. This gene encodes UBC24 (E2 ubiquitin conjugase-related enzyme) and the reduction in its expression leads to the increased expression of *Pht1;8* and *Pht1;9* (phosphate transporter genes) in roots [47, 48]. Later, a similar mechanism was discovered in ani-

mals and humans suggesting target mimicry as the prevalent phenomenon [51, 52].

The lncRNAs are known to regulate gene expression through epigenetic changes. These epigenetic changes may result in alteration of gene expression in plants. Vernalization is the most common phenomenon of lncRNA mediated epigenetic regulation in plants. In *Arabidopsis*, FLOWERING LOCUS C (FLC) gene is the principal regulator of vernalization process and regulates the flowering time [53]. The expression of this gene is regulated by *COOLAIR* and

mentioned in **Table 1**.

116 Next Generation Plant Breeding

**3.2. Classification of lncRNAs**

complementary strand, termed as bidirectional lncRNA [45].

gested their different mechanisms as following.

*COLDAIR* lncRNAs through histone modifications [54].

**4.1. lncRNA as target mimics of miRNA**

**4.2. Histone modification**

**4. Molecular mechanisms of the functioning of lncRNAs**

lncRNAs constitute an important class of riboregulators by acting as a precursor in the synthesis of shorter ncRNAs, such as miRNAs and siRNAs. In this mechanism, some lncRNAs are processed to shorter ncRNAs or may directly act as a precursor [55]. The genes of primary miRNA transcripts (pri-miRNA) encoding miRNAs are transcribed by RNA polymerase II [56]. In plants, miRNA constitutes the modest portion in small regulatory ncRNA pool due to the presence of other complex small regulatory ncRNAs. In addition, they have plant-specific RNA polymerase IV/V involved in the transcription of siRNAs and endogenous siRNAs [57]. For example, in *Triticum aestivum*, 19 lncRNAs were predicted as a precursor of 28 miRNAs [31]. In *Arabidopsis*, the 24-nt sequence of several siRNAs were matched with five lncRNAs (npc34, npc351, npc375, npc520, and npc523), which was considered as potential precursor lncRNAs. The mapping of siRNAs on both the strands of lncRNAs also strengthened the findings [58].
