Is Rna Found In Animals Or Plants

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

Youhuang Bai,

Youhuang Bai is a PhD student in Ming Chen'south laboratory in Zhejiang University. His research focuses on integrated approaches for identification of long noncoding RNA in plants and in silico analysis of noncoding RNA-mediated regulatory networks.

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Abstract

A recent highlight of genomics research has been the discovery of many families of transcripts which have office but do not code for proteins. An important grouping is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. Nosotros review progress in agreement the biogenesis and regulatory mechanisms of lncRNAs. We describe various computational and high throughput technologies for identifying and studying lncRNAs. We hash out the current knowledge of functional elements embedded in lncRNAs as well as insights into the lncRNA-based regulatory network in animals. We also describe genome-wide studies of large amount of lncRNAs in plants, equally well every bit knowledge of selected establish lncRNAs with a focus on biotic/abiotic stress-responsive lncRNAs.

INTRODUCTION

The majority of DNA in the man genome is transcribed but only a minor proportion (up to 2%) is covered past sequences known to code for proteins. The bulk of the human genome is not 'junk' DNA simply instead exerts a pivotal effect on the regulation of genes [i, 2]. Pervasive transcription appears to be prevalent in different genomes ranging from animals to plants. The bang-up mass of transcripts from unexpected regions, such every bit introns and intergenic parts of the genome, is not known to office as templates for protein synthesis and is termed noncoding RNAs (ncRNAs). Many different types of ncRNAs have been identified, including microRNAs (miRNAs), modest interfering RNAs (siRNAs), small nucleolar RNAs, transfer RNAs, ribosomal RNAs and long noncoding RNAs (lncRNAs).

The wide range of different types of lncRNAs is irresolute our previous noesis about gene concepts. Co-ordinate to their proximity to protein-coding genes in the genome, lncRNAs can be mainly grouped into the post-obit iii categories: (i) intergenic lncRNA (lincRNA) without any overlap with other loci, (ii) long intronic overlap that overlaps with intronic region of whatsoever other loci, and (iii) antisense exonic lncRNA that overlaps with exon(due south) of other loci on the opposite strand [3].

In addition to Pol I–III, there are two structurally and functionally singled-out establish-specific RNA polymerases (Political leader IV and V). In Arabidopsis thaliana two lncRNAs—AtR8 and AtR18, transcribed by RNA polymerase Three (Pol Three), were identified by efficient in vitro transcription in tobacco nuclear extracts [4]. Other studies have revealed that a subset of lncRNAs are the product of Political leader Iv and/or Pol V [5, 6]. Pol V-dependent long intergenic ncRNAs can be detectable by reverse transcription-PCR (RT-PCR) [vii].

Many lncRNAs have been establish to be natural antisense transcripts (NATs), a group of endogenous RNA molecules containing sequences that are complementary to other transcripts [8, nine]. NATs tin can be grouped into ii categories, cis-NATs and trans-NATs. Cis-NAT pairs are transcribed at the aforementioned genomic locus from opposite Deoxyribonucleic acid strands, whereas trans-NAT pairs are transcribed from different loci and are partially complementary. Although underlying mechanisms are largely unknown, the fact that the fraction of antisense transcripts is quite large, and do not encode for proteins, suggests that NATs play important regulatory roles in many aspects of gene regulation, including genomic imprinting, transcriptional interference, RNA masking, RNA editing, RNA interference (RNAi) and translational regulation [nine–11].

Several genome-wide studies have identified lncRNAs expressed in many organisms (including homo, mouse, zebrafish and Drosophila melanogaster) [12–sixteen]. Here, we review the striking progress in understanding the biological affect of lncRNAs. We draw the computational and high throughput technologies for identifying and studying lncRNAs, as well as the current knowledge of the functional elements embedded in lncRNAs, and the lncRNA-based regulatory networks. Furthermore, nosotros review and summarize the knowledge about the large amount of lncRNAs in plants, draw selected plant lncRNAs functional studies with a particular emphasis on biotic/abiotic stress-responsive lncRNAs.

GENOME-Broad STUDIES OF lncRNAS

Recent advances in engineering such equally tiling arrays and deep sequencing take led to the discovery of many classes of ncRNAs. Re-notation of microarrays by bioinformatics approaches has also led to the identification of novel lncRNAs in human and mouse [17]. Assay of RNA-seq and ChIP-seq data provides further data about unexpected transcripts without poly peptide-coding potential [13, 18].

Bear witness for functional roles of lncRNAs

At that place has been a surge in studies establishing the diverse impacts of lncRNAs [seven–10]. Although many lncRNAs have been identified by unlike computational and experimental methods, there are all-encompassing debates about their function in the cell [19, 20]. Roughly half of the lncRNA candidates that were recently shown to exist required for maintenance of pluripotency comprise regions with high translation efficiency, comparable to protein-coding genes [21, 22]. Only none of lncRNA candidates was shown to have clear translation efficiency or codon bias according to proposed standards past Guttman et al. [23].

The evolutionary rate of poly peptide-coding genes shows a universal negative correlation with expression: highly expressed genes are, on average, more conserved during evolution than genes with lower expression levels [24]. It has too been establish that the universal dependency between development and expression holds truthful for lincRNA genes and is comparable in magnitude to the anticorrelation detected for protein-coding genes. Sphinx is a newly evolved lncRNA involved in the regulation of male courtship beliefs of Drosophila melanogaster [25]. Information technology has been reported that the sphinx gene was formed by the insertion of a retroposed sequence of the ATP synthase F-chain gene from chromosome 2 into the 102F region of chromosome 4, recruiting sequences upstream to course a new exon and intron [26]. The rate of evolution for this young gene sphinx is significantly to a higher place neutral expectations, suggesting rapid adaptive evolution.

It is worthy to notation that a specific kind of DNA fragments, termed equally ultra-conserved elements (UCEs), are located in longer than 200 bp noncoding regions. These UCEs are absolutely conserved between orthologous regions of the human, rat and mouse genomes [27]. Despite often being noncoding Dna, the UCEs have been found to be transcriptionally agile and are proposed to be involved in diverse biological processes.

Sequence limerick of lncRNAs

Several methods take been used to distinguish between protein-coding and noncoding sequences. At that place is low GC content in lncRNAs compared with protein-coding transcripts [eighteen]. By analyzing 204 lncRNAs in the functional lncRNA database, researchers have revealed significant similarities between the lncRNAs and the iii′-untranslated regions (three′-UTRs) of mRNAs both in structural features and in sequence composition [28].

Some of the earliest bioinformatics assay employed BLAST to search ortholog of all three frame translated peptides deduced from novel transcripts [29, 30]. Coding Potential Computer is a support vector machine (SVM)-based method, using information on open up reading frame (ORF) and ortholog relationships to known protein-coding transcripts [31]. This computational identification mainly depends on the process of BLAST which searches the well-nigh likely coding region against comprehensive database of known proteins, such as Swiss-Prot and nonredundant database. It is therefore usually very time-consuming process for the prediction of hundreds of thousands of sequences in a genome-wide manner. To overcome such disadvantages, additional tools attempt to evaluate the coding potential of genomic areas by analyzing simply the master sequence. iSeeRNA employed x features related to conservation, ORF and nucleotide sequence-based information to carve up intergenic lncRNAs from protein-coding transcripts [32]. Coding-Potential Cess Tool (CPAT) uses a logistic regression model, built with features extracted from ORF and hexamer usage bias [33]. Both iSeeRNA and CPAT let users to submit sequences and receive the prediction results about instantly. In addition, Coding–NonCoding Alphabetize (CNCI) software was developed to effectively distinguish between protein-coding and noncoding sequences contained of known annotations using codon usage frequency information by profiling adjoining nucleotide triplets (Ant), as well as data on ORF [34]. Firstly, an Ant matrix was built by analyzing the usage frequency of ANT in coding sequences and ncRNA sequences. So, sequence-score of each transcript in six reading frames was calculated based on the Ant score matrix. Finally, the sequence-score, combined with other data on the sequences, was utilized to build an SVM model to distinguish poly peptide-coding sequences from the noncoding sequences. In vertebrates, prediction of coding potential heavily relies on evolutionary signatures produced from multiple sequence alignment, equally in 'phylogenetic codon commutation frequencies' (PhyloCSF) and RNAcode softwares [35, 36].

Functional elements embedded in lncRNAs

More and more researchers have recognized the pivotal regulatory role of lncRNA. However much less is known about the regulatory elements in lncRNAs compared with protein-coding genes. Until at present, three types of chemical element have been described.

miRNA binding site

A muscle-specific lncRNA linc-MD1 interacts with ii miRNAs (miR-133 and miR-135) to regulate the expression of MAML1 and MEF2C (Figure 1A), which encode two transcription factors that actuate muscle-specific gene expression [37]. LincRNA-p21 is targeted past miRNA let-7, and associated with RNA-binding protein (RBP) HuR, leads to the instability [38]. And then Rck promotes the clan of lincRNA-p21 with CTNNB1 and JUNB mRNAs, repressing their HuR-dependent translation activation through a machinery that includes reduced polysome sizes.

Figure 1:

lncRNA-mediated regulatory network. (A) Linc-MD1 sponges miR-133 and miR-135 to regulate the expression of MAML1 and MEF2C transcription factors that activate musculus-specific factor expression. (B) The lncRNA lincRNA-p21 coordinates expression of HuR-associated mRNA in HuR-dependant manner. In the presence of HuR, lincRNA-p21 is unstable through the recruitment of let-vii/Ago2, whereas in the absenteeism of HuR, lincRNA-p21 is stable and accumulates. Thus, the association of lincRNA-p21 with other HuR-associated CTNNB1 and JUNB mRNAs leads to their translation. (A colour version of this figure is available online at: http://bfg.oxfordjournals.org)

Transposable element

Antisense Uchl1 (FANTOM2 clone number: 6430596G22) is a 5′ head-to-head antisense lncRNA of the Uchl1 gene, which encodes a neuron-restricted protein associated with Parkinson's disease and Alzheimer'due south illness. Antisense Uchl1-mediated upwards-regulation of UCHL1 expression at a post-transcriptional level requires the repetitive sequence SINEB2 instead of the side by side Alu chemical element [39]. Antisense Uchl1 localization tin can exist regulated by the mTOR pathway, and its cytoplasmic level correlates with the expression of UCHL1 protein.

Highly structured motif

The 3′-ends of lncRNAs MALAT1 and the MEN β are protected from 3′–5′ exonucleases by highly conserved U- and A-rich motif which are predicted to form an triple helical structures [40, 41]. This triple helix structure strongly promotes both RNA stability and translation, despite the absence of a poly(A) tail.

lncRNA–poly peptide and lncRNA–chromatin interactions

High-throughput identification of RNA–Dna and RNA–protein interactions has facilitated the progress for exploring the mechanisms governing ncRNA–chromatin interactions. Ribonucleoprotein (RNP) immunoprecipitation followed by high-throughput sequencing (RIP-seq) has recently been adult to discover RNA transcripts that interact with a specific protein or protein complex. Co-immunoprecipitation of lncRNAs involves immunoprecipitation of a protein from cross-linked prison cell lysate followed by reverse-cantankerous-linking, isolation, and deep sequencing of RNAs, leading to the identification of all lncRNAs that are associated with a specific poly peptide complex [42]. By using a modified RIP-seq method without cross-linking, two analyses have identified that vast numbers of lncRNAs are capable of straight associating with several chromatin-modifying complexes including PRC2, CoREST and SMCX [43, 44].

Simon D et al. had adult Nautical chart (capture hybridization analysis of RNA targets), a hybridization-based purification strategy that can exist used to map the genomic binding sites for endogenous RNAs, which is analogous to chromatin immunoprecipitation (ChIP) for proteins [45]. CHART is a new technique to purify lncRNAs together with their targets (proteins and DNA fragments), in lodge to determine the genome-wide localization of a specific lncRNA in chromatin as well equally the protein content by Western blot analysis. CHART was successfully applied to lncRNAs of unlike lengths from human and fruit fly. At the same time, Chu et al. had adult chromatin isolation past RNA purification to let loftier-throughput discovery of DNA–RNA–protein interactions. In this method, specific lncRNAs bound with protein(s) and Deoxyribonucleic acid sequences are retrieved by tiling oligonucleotides, and followed by high throughput sequencing [46].

Localization

A method termed every bit 'combined knockdown and localization analysis' has been recently adult [47]. lncRNAs can be targeted past designed endoribonuclease prepared siRNAs (esiRNAs), which have been proven to be especially suitable for RNAi screening as they efficiently deplete the target transcript without causing prominent off-target effects owing to their inherent complex pools of siRNAs. Simultaneously, specific riboprobes are generated to make up one's mind lncRNAs localization in cells. Hundreds of mouse lncRNAs were experimentally studied and about eighty% probes have detected diverse localization patterns at varying expression levels for different lncRNAs, suggesting so diverse roles of lncRNAs in unlike biological processes [47].

Databases

Databases providing information on lncRNAs can exist divided into four types, co-ordinate to their information content: sequence, expression, regulation and association. These databases (i.e. Rfam, fRNAdb, NONCODE) contain various kinds of ncRNAs, including a large corporeality of lncRNAs [48, 49]. In improver to these broad RNA warehouses, many lncRNA specific databases are emerging for different sources since the last two years. The lncRNAdb is a database providing comprehensive annotations of 194 eukaryotic lncRNAs, and their biological functions take been experimentally verified [50]. Recently, the Functional LncRNA Database has been published, containing 204 well-studied lncRNAs and their splicing variants manually culled from the literatures [28]. A public repository Noncoding RNA Expression Database provides gene expression information for thousands of long ncRNAs in human being and mouse [51]. PLncDB contains comprehensive data related to Arabidopsis lncRNAs, such as genomic information, expression profiles, siRNA data and associated epigenetic markers [52].

The lncRNA regulation mediated by the miRNAs and transcription factors is being studied. The miRcode database offers a map of putative miRNA target sites in the long noncoding transcriptome, as well as protein-coding genes by using the TargetScan program [53]. In the 2013 database issue of Nucleic Acids Research, an integrated database ChIPbase was published to provide transcription factor binding maps and data on transcriptional regulations of coding genes and ncRNAs derived from hundreds of Bit-Seq data sets [54]. In the same result, some other paper descripted the LncRNADisease database, containing more than 480 lncRNA-disease related entries and 475 lncRNA interaction entries, covering 208 lncRNAs and 166 diseases derived from ∼500 publications [55]. The interaction between few well-studied lncRNAs (such as XIST, H19) and other molecules is available from the NPInter database [56].

lncRNA-MEDIATED REGULATORY NETWORK

The emerging picture of transcriptional and post-transcriptional regulation is that an extremely rich landscape of diverse RNAs is transcribed by a large fraction of the genome in a spatiotemporally dependent manner. The regulation of lncRNA may be similar to that of protein-coding transcripts, which is highly regulated by pocket-sized ncRNAs, such as miRNA. At the same time, there are NAT annotation databases in both human and found genomes [57, 58]. By combining the information of miRNA-target relationship and of NAT regulation between mRNA and lncRNA transcripts, a comprehensive RNA regulatory network can exist obtained, providing convincing testify for the being of a layer of lncRNA-based regulation of gene expression.

lncRNAs play pivotal roles in transcriptional and post-transcriptional regulation and the influence among RBPs, lncRNAs and miRNAs is beginning to emerge [38]. RBP HuR is good example of a node in the lncRNA-based regulatory network. HuR associates with many mRNAs, which tin can influence cell proliferation, survival, carcinogenesis and stress-/immune-responses [59, 60]. In the presence of HuR, lincRNA-p21 is unstable through the recruitment of let-7/Ago2 (Effigy 1B). HuR promotes the translation of targets CTNNB1 and JUNB mRNAs past favoring their association with polysomes. In the absence of HuR, lincRNA-p21 is stable and accumulates, and Rck promotes the clan of lincRNA-p21 with CTNNB1 and JUNB mRNAs, repressing their translation through a machinery that includes reduced polysome sizes (Figure 1B). Therefore HuR-dependent translation requires rapid degradation of lincRNA-p21 in order to prevent the recruitment of translation repressors onto target mRNAs. Similar regulation mechanisms may affect other mRNAs whose translation is increased by HuR [61].

Figure 2:

Schematic representation of machinery of different kinds of lncRNAs in plants. (A) Antisense of PHO1;two regulates the expression of the sense of PHO1;2 transcript in phosphate-deficient condition. (B) The lncRNA COLDAIR is transcribed from the intronic region of FLC locus, and functions to recruit PRC2 to induce histone modifications at the FLC locus, reducing the level of FLC expression. (C) LDMAR regulates the transcription of itself by producing an lncRNA. LDMAR is normally expressed in NK58N, whereas the C-to-Thousand mutation contradistinct the secondary construction of LDMAR and leads to DNA methylation of the promoter region through the RdDM pathway in NK58S.

Both HuR and lincMD1 are involved in musculus differentiation and are under the repressive control of miR-133. Legnini et al. identified HuR as another component of the lincMD1-regulated circuitry, which binds linc-MD1 and protects it from Drosha cleavage at the expense of miR-133b biogenesis [62]. Thus, these findings help to point out an established positive feed forward control among miRNA, lncRNA and products of mRNA.

GENOME-Broad IDENTIFICATION OF lncRNA IN PLANTS

It has been reported that thousands of distinct noncoding regions result in transcription units in Arabidopsis [63, 64]. There are more 6000 intergenic lncRNAs and 37 238 sense–antisense transcript pairs in Arabidopsis discovered from analyzing tiling assortment, other expression arrays and RNA-seq [65, 66]. These results showed that nearly 70% of Arabidopsis protein-coding genomic loci retain antisense transcripts with no coding potential. Expression profiling of antisense transcripts indicates that organ-specific or condition-specific lncRNAs are under specific regulation, suggesting that they are non generated past spurious transcriptional noise [66].

A computational method was developed to place endogenous miRNA target mimic sites within long intergenic noncoding gene for 20 conserved miRNAs in Arabidopsis and rice [67]. Using strand-specific RNA sequencing, Vocal et al. applied a method based on model comparing (NASTI-seq) to identify cis-NAT pairs, which lead to an increase in the number of known cis-NAT pairs in Arabidopsis by more than threescore% [68].

Intermediate-size ncRNAs (im-ncRNAs) are divers as RNA transcripts with a length ranging from l to 300 nt. They are particularly difficult to study experimentally due to their stable secondary structures, lack of a poly (A), and depression efficiency of reverse transcription. In A. thaliana, assay of 521 novel im-ncRNAs has shown that these im-ncRNAs are independently regulated components and mostly evolutionary divergent. Similarly, by 454 deep sequencing, 754 novel im-ncRNAs were identified in Oryza sativa [69]. The chromosome location of im-ncRNAs is without strand bias and chromosome bias.

Transcriptome assay of early developing maize seed has identified more than 1000 lncRNA candidates. Most 45% of the lncRNAs showed to a higher place 2-fold expression alter between embryo and endosperm, indicating that a part of these candidate lncRNAs are tissue-preferentially expressed [70]. Global patterns of allelic factor expression in developing maize endosperms from reciprocal crosses between inbreds B73 and Mo17 revealed that 38 lncRNAs expressed in the endosperm likewise every bit more than than 179 poly peptide-coding genes are imprinted [71]. Very recently, Li et al. integrated RNA-seq datasets from thirty unlike experiments to identify 1704 high-confidence lncRNAs and revealed that maize lncRNAs are less affected by cis- than by trans-genetic factors by expression quantitative locus mapping [72].

Transcriptome reconstruction by RNA sequencing in foxtail millet has identified more than 500 lncRNAs [73] and demonstrated sequence features similar to those observed for lncRNA in animals. An increasing amount of papers seek to place the novel intergenic transcribed region and antisense transcription by using RNA sequencing technology in plants [74, 75].

EXAMPLES OF lncRNA FUNCTIONS IN PLANTS

In comparison to animals, the studies of lncRNA in plants are just showtime to emerge. Several lncRNAs have been identified by the genome-wide screens of cDNA libraries, tiling arrays and RNA-seq data in plants (for more details see side by side section below) [65, 76–78].

PHO1 plays an important role in phosphate homeostasis of establish [79]. Although Os-PHO1;ii is likely the functional ortholog of At-PHO1, an interesting characteristic distinguishing all three rice PHO1 genes from their Arabidopsis homologs is the presence of cis-NATs associated with all of them [80]. NAT of Bone-PHO1;2 increased its expression in phosphate-deficient condition and leads to an increase of PHO1;2 poly peptide concentration without changes of the levels of expression, sequence, or nuclear consign of PHO1;2 mRNA [81]. Polysome profiles revealed that both the sense PHO1;two and the antisense NAT shifted toward the translationally active polysomes, leading to new insights into how lncRNA enhances protein expression independently of mRNA level (Effigy 2A).

Another lncRNA, called IPS1, is induced upon phosphate starvation and accumulates into the roots and shoots in plants. IPS1 has complementarity to miR-399, but contains a mismatched loop that renders it uncleavable when miR-399 binds. lncRNA IPS1 is not broken but instead sequesters miR-399, leading to increased expression of miR-399 targets including PHO2 transcript [82]. This miracle in plants is called 'miRNA mimic', which is too found in mammalian genomes. These transcripts are named as 'competing endogenous RNA' [83, 84].

A third example, the lncRNA COLDAIR (Common cold ASSISTED INTRONIC NONCODING RNA), is related to vernalization. Vernalization is an environmentally induced epigenetic switch, during which winter common cold triggers epigenetic silencing of floral repressors and thus provides competence to bloom in spring. In Arabidopsis, wintertime cold triggers enrichment of histone modification H3K27me3 at chromatin of the floral repressor, FLOWERING LOCUS C (FLC), and results in the epigenetically stable repression of FLC [85]. This epigenetic change is mediated by an evolutionarily conserved repressive complex, polycomb repressive circuitous 2 (PRC2). In A. thaliana, the long intronic ncRNA COLDAIR was identified to confer vernalization-mediated epigenetic repression by physically associating with a component of PRC2 and targets PRC2 to FLC [86] (Figure 2B).

It is well known that photoperiod- and temperature-sensitive genic male sterile lines (PGMS and TGMS) have made a dandy contribution to two-line hybrid breeding in rice since 1990s. Recently, Ding et al. have identified that PGMS in rice is regulated past a lncRNA of 1236 bases, termed as long-day-specific male-fertility-associated RNA (LDMAR), which is required for normal pollen development of plants nether long-day conditions [87]. Meanwhile, Zhou et al. have independently revealed that a P/TMS12-ane locus encodes a unique ncRNA, which generates a 21 nt pocket-sized RNA osa-smR5864w (Figure 2C), conferring PGMS in the japonica rice line Nongken 58S (NK58S) and TGMS in the indica rice line Peiai 64S [88]. Although these 2 publications have independently identified two unlike ncRNA molecules, both researches reported that a C-to-G nucleotide transversion took place at position 22258571 of chromosome 12 in the primitive male sterility trait. Though contempo papers provide a starting bespeak for figuring out how lncRNA is responsible for the male fertility regulation, their precise mechanisms are still unclear. So in this regard, it is virtually likely that the primary transcript LDMAR may be processed kickoff into the 136 nt intermediate forerunner and then into osa-smR5864w [89]. It is suggested that the RNA-directed DNA methylation (RdDM) is involved in regulating photoperiod-sensitive male sterility in rice. A spontaneous mutation causing a single nucleotide polymorphism (SNP) between the wild-blazon and mutant alters the secondary structure of LDMAR. Moreover, many homo SNPs located on lncRNAs are institute to be associated with prostate cancer hazard [xc]. The SNP density in regions of lncRNA was similar to that in protein-coding regions, simply they were less polymorphic than surrounding regions. It was also reported that SNP in lncRNA Igf2as associates with increased muscle damage (strength loss and soreness) later on eccentric exercise, similar to SNPs institute in poly peptide-coding gene IGF2 [91].

It is suggested that some lncRNA sequences are precursors to short ncRNA in human and other genomes. By analyzing the total length cDNA library of A. thaliana, 76 novel lncRNAs were identified, with ix non-protein coding RNAs (npcRNAs) representing precursors of singled-out type of small-scale RNA, such as miRNA, tasiRNA and 24 nt siRNA [77, 78]. RT-PCR analysis demonstrated that npc83, the miR869a forerunner, overaccumulates in dcl4 mutant, suggesting that miR869a is a young miRNA factor [78].

lncRNA CsM10 was isolated in Cucumis sativus and showed differential expression patterns in dissimilar tissues, developmental stages and photoperiods. In maize, the putative lncRNA Zm401 is expressed specifically in pollen. Genetic studies show a role for Zm401 in regulating the expression of critical genes necessary for pollen development including MZm3-3 (up-regulated), ZmMADS2 and ZmC5 (down-regulated). The lncRNA Enod40 directed the re-localization of MtRBP1 (Medicago truncatula RBP ane) from the nucleus to cytoplasmic granules during specific stages of legume (M. truncatula) root nodule organogenesis.

It must also be noted that viroids are a class of sub-viral plant-pathogenic lncRNAs, composed of a single-stranded, circular molecule with a size in the range of 246–400 nt. Because viroids need to subvert the pathways regulating the lncRNA compartmentalization after host entry, understanding the machinery of the viroids compartmentalization may provide insights into the traffic of both foreign and endogenous lncRNA into different organelles in cell.

lncRNAs are also present in telomerase which is an RNP reverse transcriptase. Telomerase contains two essential lncRNA subunits TER1 and TER2 that are essential for telomere repeat synthesis in A. thaliana. TER1 is required for telomere maintenance and provides the major template for telomerase [92], whereas TER2 is assembled in singled-out RNP complex to modulate telomerase in response to DNA damage [93].

RESPONES TO BIOTIC/ABIOTIC STRESSES

Increasing evidence points to the fact that lncRNAs play of import roles in the regulation of gene expression within biotic/abiotic stress responses. As mentioned higher up, COLDAIR expression is induced past exposure to a cold exposure environment. Besides, the Pol 3-transcribed lncRNA AtR8 is conserved amidst Arabidopsis and Brassicaceae and expression of AtR8 responds negatively to hypoxic stress [4]. Another example TER2 is a Deoxyribonucleic acid damage-induced lncRNA that works in concert with the TER1 to promote genome integrity in Arabidopsis [93].

In Arabidopsis, more than than a thousand intergenic lncRNAs accept been plant to be significantly altered after drought, cold, loftier-common salt and/or abscisic acid treatments. Treatment by elf18 (EF-Tu), which triggers pathogen-associated molecular pattern responses, could also increase the expression level of one of the representative stress responsive lincRNAs [65]. It was reported that abiotic stress altered the accumulation of 22 npcRNAs amid the 76 npcRNAs identified through genome-wide analysis of full-length cDNAs [78].

In rice, mining of strand-specific RNA-seq data identified thousands of antisense transcripts, including 84, 74 and 128 cis-NAT pairs related with drought, salt and cold stresses, respectively [94]. A reference annotation-based transcript assembly was generated using RNA-seq coupled with a comprehensive time-course experiment, identifying 438 unannotated loci that were differentially expressed under Pi starvation. Several new loci encode pocket-size proteins with no homology to known proteins and are enriched in the nonpolysomal fraction, suggesting that these phosphate-responsive transcripts are likely to be ncRNA [95].

Twenty Fusarium oxysporum-responsive lncRNAs, from 159 novel intergenic transcriptional regions, were identified using a strand-specific RNA sequencing approach in Arabidopsis [96]. Co-induction of multiple neighboring protein-coding genes and lncRNAs suggested that some fungal-responsive promoter elements may contribute to regulation of mRNA and F. oxysporum-responsive lncRNA during the transcriptomic changes in response to F. oxysporum infection [96].

Drought-regulated expression patterns were shown in two distinct NATs of Si003758m (a homolog of Arabidopsis SAG21, involving oxidative stress tolerance) and Si038715m (a hydroxyproline-rich glycoprotein family unit protein, involving the process of defense force response to pathogen attack) [97]. Another written report identified 125 putative stress (powdery mildew infection and estrus stress) responsive lncRNAs in wheat [98].

CONCLUSIONS

Even though sustained efforts have been made to characterize lncRNAs by Sanger sequencing, histone marker ChIP-seq, or (non)strand-specific RNA-seq, the electric current annotation of lncRNAs is likely to be far from complete, specially in plants. Emerging functions for lncRNAs are their contribution to diverse transcriptional and postal service-transcriptional gene regulation, epigenetic regulation, and response to different environmental conditions, such as biotic/abiotic stresses. In the future, more discoveries will probably get in across the identification of new mechanisms of lncRNAs that regulate gene expression during developmental and differentiation processes, and will likely continue to aggrandize knowledge near the biological significance of lncRNA in a more comprehensive style.

The complex system of lncRNA loci and protein-coding genes on chromosomes leads to the sophisticated transcriptional regulation of both lncRNA and mRNA in RNA regulatory networks with some specific modules enriched for dissimilar biological function. At the same fourth dimension, one main regulatory role of lncRNA is that they tin can exist miRNA sponge, considering they contain unlike miRNA binding sites. Combined with the known relationship betwixt protein-coding transcripts, the lncRNA-mediated RNA regulatory network covers the near of import biological processes. Therefore, information technology is important to predict the functional relevance of lncRNAs from the comprehensive genome-scale network of lncRNA-mediated interactions.

lncRNAs play widespread roles in transcriptional and post-transcriptional gene regulation, epigenetic regulation, and response to different environmental stress in diverse species.
Adjacent generation sequencing, combined with avant-garde computational methods, provides powerful capabilities for identifying lncRNAs and inferring their functions in a genome-wide way.
Constructing and mining the lncRNA-mediated regulatory networks in both animals and plants facilitates a more comprehensive agreement of lncRNAs functions.

Acknowledgements

The authors give thanks Dr Christian Klukas, Guy J. Baudoux and Zeeshan Gillani for critical reading of the manuscript. They also give thanks the anonymous reviewer for many valuable suggestions to improve this manuscript.

FUNDING

This piece of work was supported by the National Natural Sciences Foundation of Prc (No. 31371328, 30971743), National Science and Technology Project of China (No. 2008AA10Z125, 2009DFA32030), the Fundamental Enquiry Funds for the Central Universities, and the Program for Innovative Research Team in University.

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Source: https://academic.oup.com/bfg/article/14/2/91/256862

Posted by: vazquezbence1954.blogspot.com

Is Rna Found In Animals Or Plants

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

Abstract

INTRODUCTION

GENOME-Broad STUDIES OF lncRNAS

Bear witness for functional roles of lncRNAs

Sequence limerick of lncRNAs

Functional elements embedded in lncRNAs

miRNA binding site

Transposable element

Highly structured motif

lncRNA–poly peptide and lncRNA–chromatin interactions

Localization

Databases

lncRNA-MEDIATED REGULATORY NETWORK

GENOME-Broad IDENTIFICATION OF lncRNA IN PLANTS

EXAMPLES OF lncRNA FUNCTIONS IN PLANTS

RESPONES TO BIOTIC/ABIOTIC STRESSES

CONCLUSIONS

Acknowledgements

FUNDING

References

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