LncRNA-Seq Related Studies in Rice

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What is Long non-coding RNAs ?

  • Long non-coding RNAs (long ncRNAs, lncRNA) are non-protein coding transcripts longer than 200 nucleotides. This somewhat arbitrary limit distinguishes long ncRNAs from small regulatory RNAs such as microRNAs (miRNAs), short interfering RNAs (siRNAs), Piwi-interacting RNAs (piRNAs), small nucleolar RNAs (snoRNAs), and other short RNAs. It is generally believed that lncRNAs, RNA molecules longer than 200 nucleotides, belong to a group of RNAs with broad biogenesis, and that these molecules are always capped and polyadenylated[1][2].
  • Figure 1 describes the differences in the structure and sequence between mRNA and lncRNA. Namely, the mRNA primary coding sequence (CDS) plays a significant role in the translation, while lncRNAs regulate target gene target gene expression through the interactions between their higher-order structures and major partner proteins[2].

Figure 1. Differences in the structure and sequence between mRNA and lncRNA. [2]

  • Initially, lncRNAs were considered “transcriptional noise” without any biological function. However, thousands of reports in recent years have demonstrated that lncRNAs, which interact with DNA, RNA molecules, and transcription factors, participate in various biological processes, designated such as DNA methylation, histone modification, and chromatin remodeling, resulting in the downregulation or overexpression of target genes. Broadly, lncRNAs can be considered as a large and diverse collection of polyadenylated or nonpolyadenylated transcripts with low protein-coding potential[2].

Types of lncRNAs identified in plants

  • Figures 2 describes the types of lncRNAs identified in plants. lncRNAs can be classified according to their position of transcription with respect to the protein coding genes (black bricks). Long intergenic RNAs are transcribed between the protein coding genes while intronic lncRNAs are transcribed within the introns of the protein coding genes. Sense and antisense lncRNAs are transcribed from the sense and antisense strand of protein coding genes, re- spectively. Gray brick represents the putative plant enhancers, which have not been fully characterized in plants[3].

Figure 2. Types of lncRNAs identified in plants.[3]

LncRNA biogenesis

  • As PolII polyadenylated products, lncRNAs are decorated with a 5'-cap and polyadenylated at the 3'-end in animals and plants(Guttman et al., 2009; Liu et al., 2012). The transcription of some lncRNA genes requires specific transcription factors, mediator complex, histone modification complex and transcription elongation factor complex (Di et al., 2014; Guttman et al.,2009; Heo and Sung, 2011; Kim et al., 2011; Wang et al., 2014e).
  • Around 40–50% of lncRNA genes contain introns (Liu et al.,2012; Managadze et al., 2011; Ulitsky and Bartel, 2013; Wang et al., 2014a). In Arabidopsis, we found that the cap-binding proteins, CPB20 and CBP80, and their associated protein SERRATE regulate the biogenesis of ~20% lincRNAs (Liu et al., 2012). Mutant plants with deficiency in one of these proteins accumulate the unspliced lncRNA primary transcripts (Laubinger et al., 2008; Liu et al., 2012). Introns for some lincRNAs may have regulatory functions in transcription (Chung et al., 2006; Rose, 2002), RNA nuclear export (Akua and Shaul, 2013; Valencia et al., 2008) and suppression of RNA silencing pathway (Christie et al., 2011).

Figure 3 Xist repetitive element functions during X-chromosome inactivation. A-repeat, which contains two long stem-loop structures, is involved in PRC2 binding, while C-repeat binds YY1, assisting Xist-PRC2 complex in targeting the specific sites on Xi, and inducing histone H3 lysine K27 trimethylation (H3K27me3) and X-linked gene silencing

The function of LncRNA

  • LncRNAs can regulate gene expression on multiple levels via a number of complex mechanisms. They can function in either cis or in trans by sequence complemen- tarity or homology with RNAs or DNA, and/or by structure, forming molecular frames and scaffolds for assembly of macromolecular complexes. Most of the studied lncRNAs function in regulation of gene expression at the transcriptional level; however, some lncRNAs have been reported to regulate gene expression posttranscrip- tionally in a variety of ways.
  • On the simplest level, lncRNAs can serve as decoys that prevent the access of regulatory proteins to DNA or RNA by mimicking their targets. Some Arabidopsis lncRNAs interact with microRNAs (miRNAs) as competitors and function as miRNA target mimics, similarly to animal miRNA sponges. For example, the IPS1 lncRNA acts as a non-cleavable competitor for PHO2 mRNA, as miR399 targets the PHO2 mRNA for degradation [31]. Many endogenous miRNA target mimics have also been pre- dicted by bioinformatics approaches and the function of some has been experimentally confirmed in Arabidopsis [32]. The decoy Arabidopsis lncRNA ASCO regulates plant root development by binding to the regulators of alternative splicing, nuclear speckle RNA-binding pro- teins, and hijacking them to change the patterns of alternative splicing to produce alternative splice isoform.

Projects List

Project Title Species Published years Academic Journal RiceWiki Project ID
A long noncoding RNA regulates photoperiod-sensitive male sterility, an essential component of hybrid rice Oryza sativa L. ssp. Japnoica 2012 Proceedings of the National Academy of Sciences IC4R001-lncRNA-2012-22308482
Genome-wide screening and functional analysis identify a large number of long noncoding RNAs involved in the sexual reproduction of rice Oryza sativa L. ssp. Japnoica 2014 Genome Biology IC4R002-lncRNA-2014-25517485
RNA-Seq Analysis of Rice Roots Reveals the Involvement of Post-Transcriptional Regulation in Response to Cadmium Stress Oryza sativa L. ssp. Japnoica 2015 Frontiers in Plant Science IC4R003-lncRNA-2015-26734039
Functional analysis of long intergenic non-coding RNAs in phosphate-starved rice using competing endogenous RNA network Oryza sativa L. ssp. Japnoica 2016 Scientific Reports IC4R004-lncRNA-2016-26860696
Novel drought-responsive regulatory coding and non-coding transcripts from Oryza Sativa L. Oryza Sativa L 2016 Genes & Genomics IC4R005-lncRNA-2016-19769571
Analysis of non-coding transcriptome in rice and maize uncovers roles of conserved lncRNAs associated with agriculture traits Oryza sativa 2015 Plant Journal IC4R006-lncRNA-2015-26387578
Genome-wide identification of long noncoding RNA genes and their potential association with fecundity and virulence in rice brown planthopper, Nilaparvata lugens Oryza sativa 2015 BMC Genomics IC4R007-lncRNA-2015-26437919


  1. https://en.wikipedia.org/wiki/Long_non-coding_RNA
  2. 2.0 2.1 2.2 2.3 Li, Rui, Hongliang Zhu, and Yunbo Luo. "Understanding the Functions of Long Non-Coding RNAs through Their Higher-Order Structures." International journal of molecular sciences 17.5 (2016): 702.
  3. 3.0 3.1 Shafiq, Sarfraz, Jingrui Li, and Qianwen Sun. "Functions of plants long non-coding RNAs." Biochimica et Biophysica Acta (BBA)-Gene Regulatory Mechanisms 1859.1 (2016): 155-162.