Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development

A wide variety of functional regulatory non-coding RNAs (ncRNAs) have been identified as essential regulators of plant growth and development. Depending on their category, ncRNAs are not only involved in modulating target gene expression at the transcriptional and post-transcriptional levels but also are involved in processes like RNA splicing and RNA-directed DNA methylation. To fulfill their molecular roles properly, ncRNAs must be precisely processed by multiprotein complexes. In the case of small RNAs, DICER-LIKE (DCL) proteins play critical roles in the production of mature molecules. Land plant genomes contain at least four distinct classes of DCL family proteins (DCL1-DCL4), of which DCL1, DCL3 and DCL4 are also present in the genomes of bryophytes, indicating the early divergence of these genes. The liverwort Marchantia polymorpha has become an attractive model species for investigating the evolutionary history of regulatory ncRNAs and proteins that are responsible for ncRNA biogenesis. Recent studies on Marchantia have started to uncover the similarities and differences in ncRNA production and function between the basal lineage of bryophytes and other land plants. In this review, we summarize findings on the essential role of regulatory ncRNAs in Marchantia development. We provide a comprehensive overview of conserved ncRNA-target modules among M. polymorpha, the moss Physcomitrium patens and the dicot Arabidopsis thaliana, as well as Marchantia-specific modules. Based on functional studies and data from the literature, we propose new connections between regulatory pathways involved in Marchantia's vegetative and reproductive development and emphasize the need for further functional studies to understand the molecular mechanisms that control ncRNA-directed developmental processes.

Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs

Long noncoding RNAs (lncRNAs) are a large and diverse class of genes in eukaryotic genomes that contribute to a variety of regulatory processes. Functionally characterized lncRNAs play critical roles in plants, ranging from regulating flowering to controlling lateral root formation. However, findings from the past decade have revealed that thousands of lncRNAs are present in plant transcriptomes, and characterization has lagged far behind identification. In this setting, distinguishing function from noise is challenging. However, the plant community has been at the forefront of discovery in lncRNA biology, providing many functional and mechanistic insights that have increased our understanding of this gene class. In this review, we examine the key discoveries and insights made in plant lncRNA biology over the past two and a half decades. We describe how discoveries made in the pregenomics era have informed efforts to identify and functionally characterize lncRNAs in the subsequent decades. We provide an overview of the functional archetypes into which characterized plant lncRNAs fit and speculate on new avenues of research that may uncover yet more archetypes. Finally, this review discusses the challenges facing the field and some exciting new molecular and computational approaches that may help inform lncRNA comparative and functional analyses.

Genome-wide analysis of long non-coding RNAs under diel light exhibits role in floral development and the circadian clock in Arabidopsis thaliana

The circadian clock is regulated by signaling networks that enhance a plant's ability to coordinate internal events with the external environment. In this study, we examine the rhythmic expression of long non-coding RNAs (lncRNAs) using multiple transcriptomes of Arabidopsis thaliana in the diel light cycle and integrated this information to have a better understanding of the functions of lncRNAs in regulating the circadian clock. We identified 968, 1050, and 998 lncRNAs at 8 h light, 16 h light and 8 h dark conditions, respectively. Among these, 423, 486, and 417 lncRNAs were uniquely present at 8 h light, 16 h light, and 8 h dark, respectively, whereas 334 lncRNAs were common under the three conditions. The specificity of identified lncRNAs under different light conditions was verified using qRT-PCR. The identified lncRNAs were less GC-rich and expressed at a significantly lower level than the mRNAs of protein-coding genes. In addition, we identified enriched motifs in lncRNA transcribing regions that were associated with light-responsive genes (SORLREP and SORLIP), flower development (AGAMOUS), and circadian clock (CCA1) under all three light conditions. We identified 10 and 12 different lncRNAs targeting different miRNAs with perfect and interrupted complementarity (endogenous target mimic). These predicted lncRNA-interacting miRNAs govern the function of a set of genes involved in the developmental process, reproductive structure development, gene silencing and transcription regulation. We demonstrated that the lncRNA transcribing regions were enriched for epigenetic marks such as H3.3, H3K4me2, H3K4me3, H4K16ac, H3K36ac, H3K56ac and depleted for heterochromatic (H3K9me2 and H3K27me1) and repressive (H3K27me3) histone modifications. Further, we found that hypermethylated genomic regions negatively correlated with lncRNA transcribing regions. Overall, our study showed that lncRNAs expressed corresponding to the diel light cycle are implicated in regulating the circadian rhythm and governing the developmental stage-specific growth.

Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana

Long non-coding RNAs (lncRNAs) are a prominent class of eukaryotic regulatory genes. Despite the numerous available transcriptomic datasets, the annotation of plant lncRNAs remains based on dated annotations that have been historically carried over. We present a substantially improved annotation of Arabidopsis thaliana lncRNAs, generated by integrating 224 transcriptomes in multiple tissues, conditions, and developmental stages. We annotate 6764 lncRNA genes, including 3772 that are novel. We characterize their tissue expression patterns and find 1425 lncRNAs are co-expressed with coding genes, with enriched functional categories such as chloroplast organization, photosynthesis, RNA regulation, transcription, and root development. This improved transcription-guided annotation constitutes a valuable resource for studying lncRNAs and the biological processes they may regulate.

Role of lncRNAs in cis- and trans-regulatory responses to salt in Populus trichocarpa

Long non-coding RNAs (lncRNAs) are emerging as versatile regulators in diverse biological processes. However, little is known about their cis- and trans-regulatory contributions in gene expression under salt stress. Using 27 RNA-seq data sets from Populus trichocarpa leaves, stems and roots, we identified 2988 high-confidence lncRNAs, including 1183 salt-induced differentially expressed lncRNAs. Among them, 301 lncRNAs have potential for positively affecting their neighboring genes, predominantly in a cis-regulatory manner rather than by co-transcription. Additionally, a co-expression network identified six striking salt-associated modules with a total of 5639 genes, including 426 lncRNAs, and in these lncRNA sequences, the DNA/RNA binding motifs are enriched. This suggests that lncRNAs might contribute to distant gene expression of the salt-associated modules in a trans-regulatory manner. Moreover, we found 30 lncRNAs that have potential to simultaneously cis- and trans-regulate salt-responsive homologous genes, and Ptlinc-NAC72, significantly induced under long-term salt stress, was selected for validating its regulation of the expression and functional roles of the homologs PtNAC72.A and PtNAC72.B (PtNAC72.A/B). The transient transformation of Ptlinc-NAC72 and a dual-luciferase assay of Ptlinc-NAC72 and PtNAC72.A/B promoters confirmed that Ptlinc-NAC72 can directly upregulate PtNAC72.A/B expression, and a presence/absence assay was further conducted to show that the regulation is probably mediated by Ptlinc-NAC72 recognizing the tandem elements (GAAAAA) in the PtNAC72.A/B 5' untranslated region (5'-UTR). Finally, the overexpression of Ptlinc-NAC72 produces a hypersensitive phenotype under salt stress. Altogether, our results shed light on the cis- and trans-regulation of gene expression by lncRNAs in Populus and provides an example of long-term salt-induced Ptlinc-NAC72 that could be used to mitigate growth costs by conferring plant resilience to salt stress.

Noncoding RNAs in Medicinal Plants and their Regulatory Roles in Bioactive Compound Production

BACKGROUND

Noncoding RNAs (ncRNAs), such as microRNAs (miRNAs), small interfering RNAs (siRNAs) and long noncoding RNAs (lncRNAs), play significant regulatory roles in plant development and secondary metabolism and are involved in plant response to biotic and abiotic stresses. They have been intensively studied in model systems and crops for approximately two decades and massive amount of information have been obtained. However, for medicinal plants, ncRNAs, particularly their regulatory roles in bioactive compound biosynthesis, are just emerging as a hot research field.

OBJECTIVE

This review aims to summarize current knowledge on herbal ncRNAs and their regulatory roles in bioactive compound production.

RESULTS

So far, scientists have identified thousands of miRNA candidates from over 50 medicinal plant species and 11794 lncRNAs from Salvia miltiorrhiza, Panax ginseng, and Digitalis purpurea. Among them, more than 30 miRNAs and five lncRNAs have been predicted to regulate bioactive compound production.

CONCLUSION

The regulation may achieve through various regulatory modules and pathways, such as the miR397-LAC module, the miR12112-PPO module, the miR156-SPL module, the miR828-MYB module, the miR858-MYB module, and other siRNA and lncRNA regulatory pathways. Further functional analysis of herbal ncRNAs will provide useful information for quality and quantity improvement of medicinal plants.

Plant Long Noncoding RNAs: New Players in the Field of Post-Transcriptional Regulations

The first reference to the "C-value paradox" reported an apparent imbalance between organismal genome size and morphological complexity. Since then, next-generation sequencing has revolutionized genomic research and revealed that eukaryotic transcriptomes contain a large fraction of non-protein-coding components. Eukaryotic genomes are pervasively transcribed and noncoding regions give rise to a plethora of noncoding RNAs with undeniable biological functions. Among them, long noncoding RNAs (lncRNAs) seem to represent a new layer of gene expression regulation, participating in a wide range of molecular mechanisms at the transcriptional and post-transcriptional levels. In addition to their role in epigenetic regulation, plant lncRNAs have been associated with the degradation of complementary RNAs, the regulation of alternative splicing, protein sub-cellular localization, the promotion of translation and protein post-translational modifications. In this review, we report and integrate numerous and complex mechanisms through which long noncoding transcripts regulate post-transcriptional gene expression in plants.

LncRNA-599547 contributes the inductive property of dermal papilla cells in cashmere goat through miR-15b-5p/Wnt10b axis

The lncRNA-599547 (619-nt in length) is identified in secondary hair follicle (SHF) of cashmere goat, but its functional roles in regulating the inductive property of dermal papilla cells (DPCs) remains unknown. We found that lncRNA-599547 had significantly higher expression in dermal papilla of cashmere goat SHF at anagen than its counterpart at telogen. The overexpression of lncRNA-599547 led to a significant increase of ALP and LEF1 expression in DPCs (p < 0.05), whereas, the siLncRNA-1 mediated silencing of lncRNA-599547 significantly down-regulated the expression of ALP and LEF1 in DPCs (p < 0.05). Based on biotin-labeled RNA pull-down assay, we found that lncRNA-599547 directly interacted with chi-miR-15b-5p in DPCs. Based on both overexpression and silencing analysis of lncRNA-599547, our results indicate that lncRNA-599547 promotes the expression of Wnt10b in DPCs but without modulating its promoter methylation level. Using the mRNA-3'UTR fragments of goat Wnt10b containing the predicted binding sites of chi-miR-15b-5p in Dual-luciferase Reporter Assays, we show that lncRNA-599547 modulates the expression of Wnt10b at the chi-miR-15b-5p mediated post-transcriptional level. Taken together, our results indicate that lncRNA-599547 sponges miR-15b-5p to positively regulate the expression of Wnt10 gene, and thereby contributes the inductive property of DPCs in cashmere goat.

Long non-coding RNAs in the alkaline stress response in sugar beet (Beta vulgaris L.)

BACKGROUND

Long noncoding RNAs (lncRNAs) play crucial roles in regulating numerous biological processes in which complicated mechanisms are involved. Nonetheless, little is known about the number, features, sequences, and possible effects of lncRNAs on plant responses to alkaline stress.

RESULTS

Leaf samples collected based on the control Beta vulgaris L., as well as those under short-term and long-term alkaline treatments, were subjected to high-throughput RNA sequencing, through which a total of 8535 lncRNAs with reliable expression were detected. Of these lncRNAs, 102 and 49 lncRNA expression profiles were altered after short- and long-term alkaline stress, respectively. Moreover, 7 lncRNAs were recognized as precursors to 17 previously identified miRNAs. Four lncRNAs responsive to alkaline stress were estimated as targets for 8 miRNAs. Moreover, computational analysis predicted 4318 potential target genes as lncRNAs responsive to alkaline stress. Analysis of functional annotations showed that the abovementioned possible target genes were involved in various bioprocesses, such as kinase activity, structural constituents of ribosomes, the ribonucleoprotein complex and protein metabolic processes. Association analysis provided convincing proof of the interplay of specific candidate target genes with lncRNAs.

CONCLUSION

LncRNAs likely exert vital roles during the regulation of the alkaline stress response and adaptation in plants through interaction with protein-coding genes. The findings of this study contribute to comprehensively examining lncRNAs in Beta vulgaris L. and shed more light on the possible roles and modulating interplays of lncRNAs responsive to alkaline stress, thereby laying a certain basis for functional analyses of these types of Beta vulgaris L. lncRNAs in the future.

The Genome-Wide Analysis of RALF-Like Genes in Strawberry (Wild and Cultivated) and Five Other Plant Species (Rosaceae)

The rapid alkalinization factor (RALF) gene family is essential for the plant growth and development. However, there is little known about these genes among Rosaceae species. Here, we identify 124 RALF-like genes from seven Rosaceae species, and 39 genes from Arabidopsis, totally 163 genes, divided into four clades according to the phylogenetic analysis, which includes 45 mature RALF genes from Rosaceae species. The YISY motif and RRXL cleavage site are typical features of true RALF genes, but some variants were detected in our study, such as YISP, YIST, NISY, YINY, YIGY, YVGY, FIGY, YIAY, and RRVM. Motif1 is widely distributed among all the clades. According to screening of cis-regulatory elements, GO annotation, expression sequence tags (EST), RNA-seq, and RT-qPCR, we reported that 24 RALF genes coding mature proteins related to tissue development, fungal infection, and hormone response. Purifying selection may play an important role in the evolutionary process of RALF-like genes among Rosaceae species according to the result from ka/ks. The tandem duplication event just occurs in four gene pairs (Fv-RALF9 and Fv-RALF10, Md-RALF7 and Md-RALF8, Pm-RALF2 and Pm-RALF8, and Pp-RALF11 and Pp-RALF14) from four Rosaceae species. Our research provides a wide overview of RALF-like genes in seven Rosaceae species involved in identification, classification, structure, expression, and evolution analysis.

Transcriptome-wide identification and functional investigation of the RDR2- and DCL3-dependent small RNAs encoded by long non-coding RNAs in Arabidopsis thaliana

The involvement of the long non-coding RNAs (lncRNAs) in small RNA (sRNA)-related pathways remains elusive. Taking advantage of the public sRNA sequencing data, we searched for RNA-dependent RNA polymerase 2 (RDR2)- and Dicer-like 3 (DCL3)-dependent sRNAs generated from the lncRNAs of Arabidopsis thaliana. First, 55,162 sRNAs were identified to be RDR2- and DCL3-dependent. These sRNAs were then mapped onto the lncRNAs. As a result, a total of 26,643 sRNAs found their loci on 3,834 lncRNAs, and 29,388 sRNAs found their loci on 4,174 reverse complementary (RC) sequences of the lncRNAs. To support the formation of the double-stranded precursors for sRNA generation, double-stranded RNA sequencing (dsRNA-seq) reads were mapped onto the sense and antisense strands of the lncRNAs with RDR2- and DCL3-dependent sRNA loci. As a result, 1,075 regions longer than 100 nt were identified to be covered by dsRNA-seq reads on 390 sense strands of the lncRNAs, and 1,352 regions were identified on 544 RC strands. Besides, 2,238 out of 3,211 dsRNA-seq read-covered sRNA loci were supported by degradome sequencing data on the sense strands of the lncRNAs. Interestingly, dozens of dsRNA-seq read-covered regions with AGO4-associated sRNA loci showed site-specific chromatin modification patterns. Thus, some of the lncRNAs were integrated into the RDR2- and DCL3-dependent sRNA biogenesis pathway. Moreover, our results indicated that the site-specific chromatin modifications mediated by the AGO4-associated sRNAs might play a regulatory role on the transcription activity of the lncRNA genes.

LncRNA-000133 from secondary hair follicle of Cashmere goat: identification, regulatory network and its effects on inductive property of dermal papilla cells

Long noncoding RNAs (lncRNAs), a class of non-protein conding RNAs > 200 nt in length, were thought to play critical roles in regulating the expression of protein-coding genes. Here, we identified and characterized a novel lncRNA-000133 from the secondary hair follicle (SHF) of cashmere goat with its ceRNA network analysis, as well as, its potential effects on inductive property of dermal papilla cells were evaluated through overexpression analysis. Expression analysis indicated that lncRNA-000133 had a significantly higher expression at anagen than that at telogen in SHF of Cashmere goat, suggesting that lncRNA-000133 might be involved in the reconstruction of SHF with the formation and growth of cashmere fiber. Taken together with methylation analysis, we showed that 5' regulatory region methylation of the lncRNA-000133 gene might be involved in its expression suppression in SHF of Cashmere goat. The ceRNA regulatory network showed that a rich and complex regulatory relationship between lncRNA-000133 and related miRNAs with their target genes. The overexpression of lncRNA-000133 led to a significant increasing in the relative expression of ET-1, SCF, ALP and LEF1 in dermal papilla cells suggesting that lncRNA-000133 appears to contribute the inductive property of dermal papilla cells.

An Overview of Methodologies in Studying lncRNAs in the High-Throughput Era: When Acronyms ATTACK!

The discovery of pervasive transcription in eukaryotic genomes provided one of many surprising (and perhaps most surprising) findings of the genomic era and led to the uncovering of a large number of previously unstudied transcriptional events. This pervasive transcription leads to the production of large numbers of noncoding RNAs (ncRNAs) and thus opened the window to study these diverse, abundant transcripts of unclear relevance and unknown function. Since that discovery, recent advances in high-throughput sequencing technologies have identified a large collection of ncRNAs, from microRNAs to long noncoding RNAs (lncRNAs). Subsequent discoveries have shown that many lncRNAs play important roles in various eukaryotic processes; these discoveries have profoundly altered our understanding of the regulation of eukaryotic gene expression. Although the identification of ncRNAs has become a standard experimental approach, the functional characterization of these diverse ncRNAs remains a major challenge. In this chapter, we highlight recent progress in the methods to identify lncRNAs and the techniques to study the molecular function of these lncRNAs and the application of these techniques to the study of plant lncRNAs.

Identification and molecular analysis of a lncRNA-HOTAIR transcript from secondary hair follicle of cashmere goat reveal integrated regulatory network with the expression regulated potentially by its promoter methylation

The HOTAIR transcript is transcribed from the antisense strand within the HOXC gene cluster, and it is thought to play a role in regulating the inductive capacity of dermal papilla cells during the reconstruction of hair-follicle. In the current investigation, we firstly isolated and characterized a lncRNA-HOTAIR transcript from the secondary hair follicle of cashmere goat. Also, we analyzed its transcriptional pattern and methylation level of HOTAIR gene promoter in secondary hair follicle of cashmere goat during anagen and telogen stages. Nucleotide composition analysis indicated that the contents of Adenine (A) and Thymine (T) are higher than that of Guanine (G) and Cytosine (C) in lncRNA-HOTAIR transcript of cashmere goat with the highest frequency distribution of AG nucleotide pair (8.06%). The regulatory network analysis showed a directly or indirectly complex regulatory relationships between lncRNA-HOTAIR of cashmere goat and its potential target molecules: miRNAs, mRNAs and proteins. Also, we showed that lncRNA-HOTAIR was properly transcribed at both anagen and telogen stages of secondary hair follicle of cashmere goat with the anagen being significantly higher than telogen in its expression, which suggest that lncRNA-HOTAIR transcript might be involved in the reconstruction of secondary hair follicle with the formation and growth of cashmere fiber. Taken together with methylation analysis of HOTAIR gene promoter, our data suggest that the promoter methylation of HOTAIR gene most likely is involved in its transcriptional suppression in secondary hair follicle of cashmere goat.

Draft genome sequence of first monocot-halophytic species Oryza coarctata reveals stress-specific genes

Oryza coarctata (KKLL; 2n = 4x = 48, 665 Mb) also known as Porteresia coarctata is an extreme halophyte species of genus Oryza. Using Illumina and Nanopore reads, we achieved the assembled genome size of 569.9 Mb, accounting 85.69% of the estimated genome size with N50 of 1.85 Mb and 19.89% repetitive region. We also found 230,968 simple sequence repeats (SSRs) and 5,512 non-coding RNAs (ncRNAs). The functional annotation of predicted 33,627 protein-coding genes and 4,916 transcription factors revealed that high salinity adaptation of this species is due to the exclusive or excessive presence of stress-specific genes as compared to rice. We have identified 8 homologs to salt-tolerant SOS1 genes, one of the three main components of salt overly sensitive (SOS) signal pathway. On the other hand, the phylogenetic analysis of the assembled chloroplast (134.75 kb) and mitochondrial genome (491.06 kb) favours the conservative nature of these organelle genomes within Oryza taxon.

Genome-Wide Identification and Characterization of Long Non-Coding RNA in Wheat Roots in Response to Ca2+ Channel Blocker

It remains unclear whether plant lncRNAs are responsive to Ca²⁺-channel blocking. When using the Ca²⁺-channel blocker, LaCl₃, to treat germinated wheat seeds for 24 h, we found that both root length and mitosis were inhibited in the LaCl₃-treated groups. The effect of the Ca²⁺-channel blocker was verified in three ways: a [Ca²⁺]_cyt decrease detected using Fluo-3/AM staining, a decrease in the Ca content measured using inductively coupled plasma mass spectrometry, and an inhibition of Ca²⁺ influx detected using Non-invasive Micro-test Technology. Genome-wide high throughput RNA-seq and bioinformatical methods were used to identify lncRNAs, and found 177 differentially expressed lncRNAs that might be in responsive to Ca²⁺-channel blocking. Among these, 108 were up-regulated and 69 were down-regulated. The validity of identified lncRNAs data from RNA-seq was verified using qPCR. GO and KEGG analysis indicated that a number of lncRNAs might be involved in diverse biological processes upon Ca²⁺-channel blocking. Further GO analysis showed that 23 lncRNAs might play roles as transcription factor (TF); Moreover, eight lncRNAs might participate in cell cycle regulation, and their relative expressions were detected using qPCR. This study also provides diverse data on wheat lncRNAs that can deepen our understanding of the function and regulatory mechanism of Ca²⁺-channel blocking in plants.

LncRNAs in Secondary Hair Follicle of Cashmere Goat: Identification, Expression, and Their Regulatory Network in Wnt Signaling Pathway

Long noncoding RNAs (lncRNAs) are a novel class of eukaryotic transcripts. They are thought to act as a critical regulator of protein-coding gene expression. Herein, we identified and characterized 13 putative lncRNAs from the expressed sequence tags from secondary hair follicle of Cashmere goat. Furthermore, we investigated their transcriptional pattern in secondary hair follicle of Liaoning Cashmere goat during telogen and anagen phases. Also, we generated intracellular regulatory networks of upregulated lncRNAs at anagen in Wnt signaling pathway based on bioinformatics analysis. The relative expression of six putative lncRNAs (lncRNA-599618, -599556, -599554, -599547, -599531, and -599509) at the anagen phase is significantly higher than that at telogen. Compared with anagen, the relative expression of four putative lncRNAs (lncRNA-599528, -599518, -599511, and -599497) was found to be significantly upregulated at telogen phase. The network generated showed that a rich and complex regulatory relationship of the putative lncRNAs and related miRNAs with their target genes in Wnt signaling pathway. Our results from the present study provided a foundation for further elucidating the functional and regulatory mechanisms of these putative lncRNAs in the development of secondary hair follicle and cashmere fiber growth of Cashmere goat.

Functions of long intergenic non-coding (linc) RNAs in plants

Whole transcriptome analyses in many organisms have revealed that most transcribed RNAs do not encode proteins. These non-coding RNAs likely contribute to the regulation of gene expression during the development of multicellular organisms. In eukaryotes, the roles of small RNAs, one class of non-coding RNAs, in transcriptional and post-transcriptional regulation have been well characterized. However, the functions of a second class of non-coding RNAs, long intergenic noncoding (linc) RNAs, are relatively unknown, especially in plants. Recent advances in RNA-seq and tiling microarray technologies have revealed the presence of many lincRNAs across plant species. This review focuses on the functions of lincRNAs that have been recently reported in plants. One of the most well characterized functions of lincRNAs is to epigenetically regulate gene expression by recruiting proteins for chromosome modification to specific loci. Second, lincRNAs are known to inhibit the physical interaction between microRNAs (miRNAs) and their target mRNAs thus controling protein levels of the target mRNAs. Lastly, lincRNAs control alternative splicing by binding and sequestering the proteins required for alternative splicing.

Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing

BACKGROUND

Long non-coding RNAs (lncRNAs) have been shown to play crucially regulatory roles in diverse biological processes involving complex mechanisms. However, information regarding the number, sequences, characteristics and potential functions of lncRNAs in plants is so far overly limited.

RESULTS

Using high-throughput sequencing and bioinformatics analysis, we identified a total of 23,324 putative lncRNAs from control, osmotic stress- and salt stress-treated leaf and root samples of Medicago truncatula, a model legume species. Out of these lncRNAs, 7,863 and 5,561 lncRNAs were identified from osmotic stress-treated leaf and root samples, respectively. While, 7,361 and 7,874 lncRNAs were identified from salt stress-treated leaf and root samples, respectively. To reveal their potential functions, we analyzed Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found.

CONCLUSIONS

LncRNAs are likely involved in regulating plant's responses and adaptation to osmotic and salt stresses in complex regulatory networks with protein-coding genes. These findings are of importance for our understanding of the potential roles of lncRNAs in responses of plants in general and M. truncatula in particular to abiotic stresses.

Identification and characterization of mRNA-like noncoding RNAs in Salvia miltiorrhiza

Identification and characterization of 5,446 mlncRNAs from Salvia miltiorrhiza showed that the majority of identified mlncRNAs were stress responsive, providing a framework for elucidating mlncRNA functions in S. miltiorrhiza. mRNA-like noncoding RNAs (mlncRNAs) are transcribed by RNA polymerase II and are polyadenylated, capped and spliced. They play important roles in plant development and defense responses. However, there is no information available for mlncRNAs in Salvia miltiorrhiza Bunge, the first Chinese medicinal material entering the international market. To perform a transcriptome-wide identification of S. miltiorrhiza mlncRNAs, we assembled over 8 million RNA-seq reads from GenBank database and 5,624 ESTs from PlantGDB into 44422 unigenes. Using a computational identification pipeline, we identified 5446 S. miltiorrhiza mlncRNA candidates from the assembled unigenes. Of the 5446 mlncRNAs, 2 are primary transcripts of conserved miRNAs, and 2030 can be grouped into 470 families with at least two members in a family. Quantitative real-time PCR analysis of mlncRNAs with at least 900 nt showed that the majority were differentially expressed in roots, stems, leaves and flowers and responsive to methyl jasmonate (MeJA) treatment in S. miltiorrhiza. Analysis of published RNA-seq data showed that a total of 3,044 mlncRNAs were expressed in hairy roots of S. miltiorrhiza and the expression of 1,904 of the 3,044 mlncRNAs was altered by yeast extract and Ag(+) treatment. The results indicate that the majority of mlncRNAs are involved in plant response to stress. This study provides a framework for understanding the roles of mlncRNAs in S. miltiorrhiza.

Long noncoding RNA transcriptome of plants

Since their discovery more than two decades ago, animal long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes. Recently, a large number of lncRNAs have also been identified in higher plants, and here, we review their identification, classification and known regulatory functions in various developmental events and stress responses. Knowledge gained from a deeper understanding of this special group of noncoding RNAs may lead to biotechnological improvement of crops. Some possible examples in this direction are discussed.

Identification of mRNA-like non-coding RNAs and validation of a mighty one named MAR in Panax ginseng

Increasing evidence suggests that long non-coding RNAs (lncRNAs) play significant roles in plants. However, little is known about lncRNAs in Panax ginseng C. A. Meyer, an economically significant medicinal plant species. A total of 3,688 mRNA-like non-coding RNAs (mlncRNAs), a class of lncRNAs, were identified in P. ginseng. Approximately 40% of the identified mlncRNAs were processed into small RNAs, implying their regulatory roles via small RNA-mediated mechanisms. Eleven miRNA-generating mlncRNAs also produced siRNAs, suggesting the coordinated production of miRNAs and siRNAs in P. ginseng. The mlncRNA-derived small RNAs might be 21-, 22-, or 24-nt phased and could be generated from both or only one strand of mlncRNAs, or from super long hairpin structures. A full-length mlncRNA, termed MAR (multiple-function-associated mlncRNA), was cloned. It generated the most abundant siRNAs. The MAR siRNAs were predominantly 24-nt and some of them were distributed in a phased pattern. A total of 228 targets were predicted for 71 MAR siRNAs. Degradome sequencing validated 68 predicted targets involved in diverse metabolic pathways, suggesting the significance of MAR in P. ginseng. Consistently, MAR was detected in all tissues analyzed and responded to methyl jasmonate (MeJA) treatment. It sheds light on the function of mlncRNAs in plants.

Genome-wide identification and characterization of long intergenic non-coding RNAs in Ganoderma lucidum

Ganoderma lucidum is a white-rot fungus best-known for its medicinal activities. We have previously sequenced its genome and annotated the protein coding genes. However, long non-coding RNAs in G. lucidum genome have not been analyzed. In this study, we have identified and characterized long intergenic non-coding RNAs (lincRNA) in G. lucidum systematically. We developed a computational pipeline, which was used to analyze RNA-Seq data derived from G. lucidum samples collected from three developmental stages. A total of 402 lincRNA candidates were identified, with an average length of 609 bp. Analysis of their adjacent protein-coding genes (apcGenes) revealed that 46 apcGenes belong to the pathways of triterpenoid biosynthesis and lignin degradation, or families of cytochrome P450, mating type B genes, and carbohydrate-active enzymes. To determine if lincRNAs and these apcGenes have any interactions, the corresponding pairs of lincRNAs and apcGenes were analyzed in detail. We developed a modified 3' RACE method to analyze the transcriptional direction of a transcript. Among the 46 lincRNAs, 37 were found unidirectionally transcribed, and 9 were found bidirectionally transcribed. The expression profiles of 16 of these 37 lincRNAs were found to be highly correlated with those of the apcGenes across the three developmental stages. Among them, 11 are positively correlated (r>0.8) and 5 are negatively correlated (r<-0.8). The co-localization and co-expression of lincRNAs and those apcGenes playing important functions is consistent with the notion that lincRNAs might be important regulators for cellular processes. In summary, this represents the very first study to identify and characterize lincRNAs in the genomes of basidiomycetes. The results obtained here have laid the foundation for study of potential lincRNA-mediated expression regulation of genes in G. lucidum.

Genome-wide discovery and characterization of maize long non-coding RNAs

BACKGROUND

Long non-coding RNAs (lncRNAs) are transcripts that are 200 bp or longer, do not encode proteins, and potentially play important roles in eukaryotic gene regulation. However, the number, characteristics and expression inheritance pattern of lncRNAs in maize are still largely unknown.

RESULTS

By exploiting available public EST databases, maize whole genome sequence annotation and RNA-seq datasets from 30 different experiments, we identified 20,163 putative lncRNAs. Of these lncRNAs, more than 90% are predicted to be the precursors of small RNAs, while 1,704 are considered to be high-confidence lncRNAs. High confidence lncRNAs have an average transcript length of 463 bp and genes encoding them contain fewer exons than annotated genes. By analyzing the expression pattern of these lncRNAs in 13 distinct tissues and 105 maize recombinant inbred lines, we show that more than 50% of the high confidence lncRNAs are expressed in a tissue-specific manner, a result that is supported by epigenetic marks. Intriguingly, the inheritance of lncRNA expression patterns in 105 recombinant inbred lines reveals apparent transgressive segregation, and maize lncRNAs are less affected by cis- than by trans-genetic factors.

CONCLUSIONS

We integrate all available transcriptomic datasets to identify a comprehensive set of maize lncRNAs, provide a unique annotation resource of the maize genome and a genome-wide characterization of maize lncRNAs, and explore the genetic control of their expression using expression quantitative trait locus mapping.

Long noncoding RNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana

Short noncoding RNAs have been demonstrated to play important roles in regulation of gene expression and stress responses, but the repertoire and functions of long noncoding RNAs (lncRNAs) remain largely unexplored, particularly in plants. To explore the role of lncRNAs in disease resistance, we used a strand-specific RNA-sequencing approach to identify lncRNAs responsive to Fusarium oxysporum infection in Arabidopsis thaliana. Antisense transcription was found in c. 20% of the annotated A. thaliana genes. Several noncoding natural antisense transcripts responsive to F. oxysporum infection were found in genes implicated in disease defense. While the majority of the novel transcriptionally active regions (TARs) were adjacent to annotated genes and could be an extension of the annotated transcripts, 159 novel intergenic TARs, including 20 F. oxysporum-responsive lncTARs, were identified. Ten F. oxysporum-induced lncTARs were functionally characterized using T-DNA insertion or RNA-interference knockdown lines, and five were demonstrated to be related to disease development. Promoter analysis suggests that some of the F. oxysporum-induced lncTARs are direct targets of transcription factor(s) responsive to pathogen attack. Our results demonstrated that strand-specific RNA sequencing is a powerful tool for uncovering hidden levels of transcriptome and that IncRNAs are important components of the antifungal networks in A. thaliana.

Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea

Abstract

Conclusions

Through comprehensive transcriptome analysis, we not only identified 29 novel gene families potentially involved in the biosynthesis of cardiac glycosides but also characterized a large number of mlncRNAs. Our results suggest the importance of mlncRNAs in secondary metabolism and stress response in D. purpurea.

Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing

BACKGROUND

Biotic and abiotic stresses, such as powdery mildew infection and high temperature, are important limiting factors for yield and grain quality in wheat production. Emerging evidences suggest that long non-protein coding RNAs (npcRNAs) are developmentally regulated and play roles in development and stress responses of plants. However, identification of long npcRNAs is limited to a few plant species, such as Arabidopsis, rice and maize, no systematic identification of long npcRNAs and their responses to abiotic and biotic stresses is reported in wheat.

RESULTS

In this study, by using computational analysis and experimental approach we identified 125 putative wheat stress responsive long npcRNAs, which are not conserved among plant species. Among them, some were precursors of small RNAs such as microRNAs and siRNAs, two long npcRNAs were identified as signal recognition particle (SRP) 7S RNA variants, and three were characterized as U3 snoRNAs. We found that wheat long npcRNAs showed tissue dependent expression patterns and were responsive to powdery mildew infection and heat stress.

CONCLUSION

Our results indicated that diverse sets of wheat long npcRNAs were responsive to powdery mildew infection and heat stress, and could function in wheat responses to both biotic and abiotic stresses, which provided a starting point to understand their functions and regulatory mechanisms in the future.

Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes

Background

MicroRNAs (miRNAs) and trans-acting small-interfering RNAs (tasi-RNAs) are small (20–22 nt long) RNAs (smRNAs) generated from hairpin secondary structures or antisense transcripts, respectively, that regulate gene expression by Watson-Crick pairing to a target mRNA and altering expression by mechanisms related to RNA interference. The high sequence homology of plant miRNAs to their targets has been the mainstay of miRNA prediction algorithms, which are limited in their predictive power for other kingdoms because miRNA complementarity is less conserved yet transitive processes (production of antisense smRNAs) are active in eukaryotes. We hypothesize that antisense transcription and associated smRNAs are biomarkers which can be computationally modeled for gene discovery.

Principal Findings

We explored rice (Oryza sativa) sense and antisense gene expression in publicly available whole genome tiling array transcriptome data and sequenced smRNA libraries (as well as C. elegans) and found evidence of transitivity of MIRNA genes similar to that found in Arabidopsis. Statistical analysis of antisense transcript abundances, presence of antisense ESTs, and association with smRNAs suggests several hundred Arabidopsis ‘orphan’ hypothetical genes are non-coding RNAs. Consistent with this hypothesis, we found novel Arabidopsis homologues of some MIRNA genes on the antisense strand of previously annotated protein-coding genes. A Support Vector Machine (SVM) was applied using thermodynamic energy of binding plus novel expression features of sense/antisense transcription topology and siRNA abundances to build a prediction model of miRNA targets. The SVM when trained on targets could predict the “ancient” (deeply conserved) class of validated Arabidopsis MIRNA genes with an accuracy of 84%, and 76% for “new” rapidly-evolving MIRNA genes.

Conclusions

Antisense and smRNA expression features and computational methods may identify novel MIRNA genes and other non-coding RNAs in plants and potentially other kingdoms, which can provide insight into antisense transcription, miRNA evolution, and post-transcriptional gene regulation.

Functional genomics using RIKEN Arabidopsis thaliana full-length cDNAs

Full-length cDNAs are essential for the correct annotation of genomic sequences as well as for the functional analysis of genes and their products. We have isolated about 240,000 RIKEN Arabidopsis full-length (RAFL) cDNA clones. These clones were clustered into about 17,000 non-redundant cDNA groups, i.e., about 60% of all Arabidopsis predicted genes. The sequence information of the RAFL cDNAs is useful for promoter analysis, and for the correct annotation of predicted transcriptional units and gene products. We prepared cDNA microarrays containing independent full-length cDNA groups and studied the expression profiles of genes under various stress- and hormone-treatment conditions, and in various mutants and transgenic plants. These expression profiling studies have shown the expression levels of many genes as a detailed snapshot describing the state of a biological system in planta under various conditions. We have applied RAFL cDNAs to the functional analysis of proteins using the full-length cDNA over-expressing (FOX) gene hunting system and the wheat germ cell-free protein synthesis system. The RAFL cDNA collection was also used for determination of the domain structure of proteins by NMR. In this review, we summarize the present state and perspectives of functional genomics using RAFL cDNAs.

Computational prediction of novel non-coding RNAs in Arabidopsis thaliana

Background

Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using tiling arrays in organisms such as human and Arabidopsis have revealed a great number of transcripts, a large portion of which have little or no capability to encode proteins. This unexpected finding suggests that the currently known repertoire of ncRNAs may only represent a small fraction of ncRNAs of the organisms. Thus, efficient and effective prediction of ncRNAs has become an important task in bioinformatics in recent years. Among the available computational methods, the comparative genomic approach seems to be the most powerful to detect ncRNAs. The recent completion of the sequencing of several major plant genomes has made the approach possible for plants.

Results

We have developed a pipeline to predict novel ncRNAs in the Arabidopsis (Arabidopsis thaliana) genome. It starts by comparing the expressed intergenic regions of Arabidopsis as provided in two whole-genome high-density oligo-probe arrays from the literature with the intergenic nucleotide sequences of all completely sequenced plant genomes including rice (Oryza sativa), poplar (Populus trichocarpa), grape (Vitis vinifera), and papaya (Carica papaya). By using multiple sequence alignment, a popular ncRNA prediction program (RNAz), wet-bench experimental validation, protein-coding potential analysis, and stringent screening against various ncRNA databases, the pipeline resulted in 16 families of novel ncRNAs (with a total of 21 ncRNAs).

Conclusion

In this paper, we undertake a genome-wide search for novel ncRNAs in the genome of Arabidopsis by a comparative genomics approach. The identified novel ncRNAs are evolutionarily conserved between Arabidopsis and other recently sequenced plants, and may conduct interesting novel biological functions.

Zm401, a short-open reading-frame mRNA or noncoding RNA, is essential for tapetum and microspore development and can regulate the floret formation in maize

In flowering plants, pollen formation depends on the differentiation and interaction of two cell types in the anther: the reproductive cells, called microsporocytes, and somatic cells that form the tapetum. Previously, we cloned a pollen specific gene, zm401, from a cDNA library generated from the mature pollen of Zea mays. Expression of partial cDNA of zm401 in maize and ectopic expression of zm401 in tobacco suggested it may play a role in anther development. Here we present the expression and functional characterization of this pollen specific gene in maize. Zm401 is expressed primarily in the anthers (tapetal cells as well as microspores) in a developmentally regulated manner. That is, it is expressed from floret forming stage, increasing in concentration up to mature pollen. Knockdown of zm401 significantly affected the expression of ZmMADS2, MZm3-3, and ZmC5, critical genes for pollen development; led to aberrant development of the microspore and tapetum, and finally male-sterility. Zm401 possesses highly conserved sequences and evolutionary conserved stable RNA secondary structure in monocotyledon. These data show that zm401 could be one of the key growth regulators in anther development, and functions as a short-open reading-frame mRNA (sORF mRNA) and/or noncoding RNA (ncRNA).

Finding noncoding RNA transcripts from low abundance expressed sequence tags

It has been proved that noncoding RNA (ncRNA) genes are much more numerous than expected. However, it remains a difficult task to identify ncRNAs with either computational algorithms or biological experiments. Recent reports have suggested that ncRNAs may also appear in the expressed sequence tags (EST's) database. Nevertheless, intergenic ESTs have received little attention and are poorly annotated owing to their low abundance. Here, we have developed a computational strategy for discovering ncRNA genes from human ESTs. We first collected ESTs that are located in the intergenic regions and do not have detailed annotations. The intergenic regions were divided into non-overlapping 50-nt windows and PhastCons scores obtained from the UCSC database were assigned to these windows. We kept conserved windows that had PhastCons scores of over 0.8 and that had at least three supporting ESTs to act as seeds. Each cluster of ESTs corresponding to the seeds was assembled into a long contig. We used two criteria to screen for ncRNA transcripts from these contigs: the first was that the longest predicted open reading frame was less than 300 nt and the second was that the likely Pol-II promoters exist within 2,000 nt upstream or downstream of the contigs. As a result, 118 novel ncRNA genes were identified from human low abundance ESTs. Of seven randomly selected candidates, six were transcribed in human 2BS cells as shown by RT-PCR. Our work proves that the EST is a 'hidden treasure' for detecting novel ncRNA genes.

Diamonds in the rough: mRNA-like non-coding RNAs

Non-coding RNAs are increasingly being identified as crucial regulators of gene expression and other cellular functions in plants. Experimental and computational methods have revealed the existence of mRNA-like non-coding RNAs (mlncRNAs), a class of non-coding RNAs that, in plants, are associated with tissue-specific expression, development and the phosphate-starvation response. Although their mechanisms of action are largely unknown, one can speculate that mlncRNAs act through secondary structures or specific sequences that bind to proteins or metabolites, or that have catalytic activity. This review summarizes the computational methods developed to identify candidate mlncRNAs, and the current experimental evidence regarding the function of several known mlncRNAs.

Expression and functional analyses of microRNA417 in Arabidopsis thaliana under stress conditions

MicroRNAs (miRNAs) are 20-25 nucleotides-long RNA transcripts that are capable of suppressing target gene expression by either mRNA cleavage or translational repression. Although many recent reports propose that miRNAs play diverse roles in growth, development, morphogenesis, and stress responses of plants, the biological roles of many miRNAs remain to be verified. Here, we investigated stress-responsive expression patterns and functional roles of miRNA417 in seed germination and seedling growth of Arabidopsis thaliana under various abiotic stress conditions. miRNA417 was expressed constantly throughout the entire growth stages and ubiquitously in all organs including stems, roots, leaves, and flowers. The expression of miRNA417 was regulated by salt stress, dehydration stress, or abscisic acid treatment. To examine the biological roles of miRNA417 in stress responses, the transgenic Arabidopsis plants that constitutively overexpress miRNA417 under the control of cauliflower mosaic virus 35S promoter were generated, and their phenotypes were analyzed under stress conditions. Results showed that seed germination of the transgenic plants was retarded compared with the wild-type plants in the presence of high salt or abscisic acid. These results imply that miRNA417 plays a role as a negative regulator of seed germination in Arabidopsis plants under salt stress conditions.

MicroRNAs in loblolly pine (Pinus taeda L.) and their association with fusiform rust gall development

MicroRNAs (miRNAs) are endogenous small RNAs that can have large-scale regulatory effects on development and on stress responses in plants. The endemic rust fungus Cronartium quercuum f. sp. fusiforme causes fusiform rust disease in pines, resulting in the development of spindle-shaped galls (cankers) on branches or stems. This disease is the most destructive disease of pines in the southern USA. To test whether miRNAs play roles in fusiform rust gall development, we cloned and identified 26 miRNAs from stem xylem of loblolly pine (Pinus taeda), which belong to four conserved and seven loblolly pine-specific miRNA families. Forty-three targets for nine of these 11 families were experimentally validated in vivo. Sequence analysis suggested that the target cleavage site may be determined not only by the miRNA sequence but also by the target sequence. Members of three loblolly pine-specific miRNA families target a large number of non-protein coding transcripts, and one of these families could also initiate secondary phased production from its target of a putative trans-acting short interfering RNA (ta-siRNA). Expression of 10 of these 11 miRNA families was significantly repressed in the galled stem. PCR-based transcript quantification showed complex expression patterns of these miRNAs and their targets in the galled tissues and in tissues surrounding the gall. We further predict 82 plant disease-related transcripts that may also response to miRNA regulation in pine. These results reveal a new genetic basis for host-pathogen interactions in the development of fusiform rust gall.

The role of microRNAs in sensing nutrient stress

Recent studies have demonstrated the novel functions of microRNAs (miRNAs) in regulating plant adaptive responses to nutrient stresses. Plant miRNAs usually down-regulate the abundance of their target mRNAs by post-transcriptional cleavage. miR395 and miR399 are up-regulated during sulphate and phosphate (Pi) deficiency, respectively. miR395 participates in sulphate assimilation and allocation via adjusting the expression of ATP sulphurylase (APS) and a sulphate transporter (AtSULTR2;1). Up-regulation of miR399 results in the down-regulation of UBC24 encoding a ubiquitin-conjugating E2 enzyme. Plants overexpressing miR399 or are defective in UBC24display Pi toxicity because of increased Pi uptake, enhanced root-to-shoot translocation and retention of Pi in the old leaves. This observation suggests that the miR399-mediated regulation of UBC24 expression is critical in Pi homeostasis. Moreover, the existence and conservation of miR395 and miR399 and their target genes among many plant species reveals the evolutionary importance of these miRNA-mediated nutrient stress responses.

Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts

Messenger RNAs that do not contain a long open reading frame (ORF) or non-protein-coding RNAs (npcRNAs) are an emerging novel class of transcripts. Their functions may involve the RNA molecule itself and/or short ORF-encoded peptides. npcRNA genes are difficult to identify using standard gene prediction programs that rely on the presence of relatively long ORFs. Here, we used detailed bioinformatic analyses of expressed sequence tag/cDNA databases to detect a restricted set of npcRNAs in the Arabidopsis (Arabidopsis thaliana) genome and further characterized these transcripts using a combination of bioinformatic and molecular approaches. Compositional analyses revealed strong nucleotide strand asymmetries in the npcRNAs, as well as a biased GC content, suggesting the existence of functional constraints on these RNAs. Thirteen of these transcripts display tissue-specific expression patterns, and three are regulated in conditions affecting root architecture. The npcRNA 78 gene contains the miR162 sequence in an alternative intron and corresponds to the MIR162a locus. Although DICER-LIKE 1 (DCL1) mRNA is known to be regulated by miR162-guided cleavage, its level does not change in a mir162a mutant. Alternative splicing of npcRNA 78 leads to several transcript isoforms, which all accumulate in a dcl1 mutant. This suggests that npcRNA 78 is a genuine substrate of DCL1 and that splicing of this microRNA primary transcript and miR162 processing are competitive nuclear events. Our results provide new insights into Arabidopsis npcRNA biology and the potential roles of these genes.

Analysis of the cDNAs of hypothetical genes on Arabidopsis chromosome 2 reveals numerous transcript variants

In the fully sequenced Arabidopsis (Arabidopsis thaliana) genome, many gene models are annotated as "hypothetical protein," whose gene structures are predicted solely by computer algorithms with no support from either expressed sequence matches from Arabidopsis, or nucleic acid or protein homologs from other species. In order to confirm their existence and predicted gene structures, a high-throughput method of rapid amplification of cDNA ends (RACE) was used to obtain their cDNA sequences from 11 cDNA populations. Primers from all of the 797 hypothetical genes on chromosome 2 were designed, and, through 5' and 3' RACE, clones from 506 genes were sequenced and cDNA sequences from 399 target genes were recovered. The cDNA sequences were obtained by assembling their 5' and 3' RACE polymerase chain reaction products. These sequences revealed that (1) the structures of 151 hypothetical genes were different from their predictions; (2) 116 hypothetical genes had alternatively spliced transcripts and 187 genes displayed polyadenylation sites; and (3) there were transcripts arising from both strands, from the strand opposite to that of the prediction and possible dicistronic transcripts. Promoters from five randomly chosen hypothetical genes (At2g02540, At2g31270, At2g33640, At2g35550, and At2g36340) were cloned into report constructs, and their expressions are tissue or development stage specific. Our results indicate at least 50% of hypothetical genes on chromosome 2 are expressed in the cDNA populations with about 38% of the gene structures differing from their predictions. Thus, by using this targeted approach, high-throughput RACE, we revealed numerous transcripts including many uncharacterized variants from these hypothetical genes.

Identification of new small non-coding RNAs from tobacco and Arabidopsis

Small non-coding RNAs (ncRNAs) have typically been searched in fully sequenced genomes using one of two approaches-experimental or computational. We developed a mixed method, using both types of information, which has the advantage of applying bio-computing methods to actually expressed sequences. Our method allowed the identification of new small ncRNAs in Arabidopsis thaliana and in the unfinished genome of Nicotiana tabacum. We constructed a N. tabacum cDNA library from small RNAs ranging from 20 to 30 nucleotides (nt). The sequences from 73 unique clones were compared to the A. thaliana genome and to all plant sequences using a pattern-matching approach (program Patbank). Thus, we selected 15 clones from the library corresponding mostly to A. thaliana or N. tabacum non-coding sequences. By Northern blot analyses, we confirmed the presence of most RNA candidates in Arabidopsis and in Nicotiana sylvestris with a size range of 21-100 nt. To gain more insight into the possible genesis of 21-24 nt sequences, stable folding of sRNAs with their flanking regions were predicted with the software MIRFOLD dedicated to the folding of microRNAs (miRNA). Stable hairpins structures were observed for some putative miRNAs.

Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster

Analysis of EST and cDNA collections from a number of metazoan species has identified genes encoding long polyadenylated transcripts that do not contain ORFs of lengths typical for protein-encoding mRNAs. Noncoding functions of such polyadenylated transcripts have been elucidated in only a few examples. The corresponding genes neither contain hallmark sequence motifs nor appear to have been conserved across phyla. Thus, it is impossible to systematically identify new members of this class of gene by using sequence homology and traditional gene-finding algorithms that depend on protein-coding potential. Consequently, even their approximate number has not been established for any metazoan genome. We curated polyadenylated transcripts with limited protein-coding capacity from intergenic regions of the Drosophila melanogaster genome. We used RT-PCR assays, hybridization to RNA blots and whole-mount embryos, and computational analyses to characterize candidate transcripts. We verify the structures and expression of 17 distinct, likely non-protein-coding polyadenylated transcripts. We show that the expression of many of these transcripts is conserved in other Drosophila species, indicating that they have important biological functions.

Complete reannotation of the Arabidopsis genome: methods, tools, protocols and the final release

Background

Since the initial publication of its complete genome sequence, Arabidopsis thaliana has become more important than ever as a model for plant research. However, the initial genome annotation was submitted by multiple centers using inconsistent methods, making the data difficult to use for many applications.

Results

Over the course of three years, TIGR has completed its effort to standardize the structural and functional annotation of the Arabidopsis genome. Using both manual and automated methods, Arabidopsis gene structures were refined and gene products were renamed and assigned to Gene Ontology categories. We present an overview of the methods employed, tools developed, and protocols followed, summarizing the contents of each data release with special emphasis on our final annotation release (version 5).

Conclusion

Over the entire period, several thousand new genes and pseudogenes were added to the annotation. Approximately one third of the originally annotated gene models were significantly refined yielding improved gene structure annotations, and every protein-coding gene was manually inspected and classified using Gene Ontology terms.

Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis

The efficacy of using Serial Analysis of Gene Expression (SAGE) to analyze the transcriptome of the model dicotyledonous plant Arabidopsis was assessed. We describe an iterative tag-to-gene matching process that exploits the availability of the whole genome sequence of Arabidopsis. The expression patterns of 98% of the annotated Arabidopsis genes could theoretically be evaluated through SAGE and using an iterative matching process 79% could be identified by a tag found at a unique site in the genome. A total of 145,170 reliable experimental tags from two Arabidopsis leaf tissue SAGE libraries were analyzed, of which 29,632 were distinct. The majority (93%) of the 12,988 experimental tags observed greater than once could be matched within the Arabidopsis genome. However, only 78% were matched to a single locus within the genome, reflecting the complexities associated with working in a highly duplicated genome. In addition to a comprehensive assessment of gene expression in Arabidopsis leaf tissue, we describe evidence of transcription from pseudo-genes as well as evidence of alternative mRNA processing and anti-sense transcription. This collection of experimental SAGE tags could be exploited to assist in the on-going annotation of the Arabidopsis genome.

Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing

Large-scale sequencing of short mRNA-derived tags can establish the qualitative and quantitative characteristics of a complex transcriptome. We sequenced 12,304,362 tags from five diverse libraries of Arabidopsis thaliana using massively parallel signature sequencing (MPSS). A total of 48,572 distinct signatures, each representing a different transcript, were expressed at significant levels. These signatures were compared to the annotation of the A. thaliana genomic sequence; in the five libraries, this comparison yielded between 17,353 and 18,361 genes with sense expression, and between 5,487 and 8,729 genes with antisense expression. An additional 6,691 MPSS signatures mapped to unannotated regions of the genome. Expression was demonstrated for 1,168 genes for which expression data were previously unknown. Alternative polyadenylation was observed for more than 25% of A. thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts.

Isolation and characterization of a novel rice gene encoding a putative insect-inducible protein homologous to wheat Wir1

A full-length cDNA, designated BpHi008A, was cloned representing a rice (Oryza sativa) mRNA that accumulates after brown planthopper (BPH) Nilapar vata lugens Stål feeding. The cDNA encodes a putative 82 amino acid protein (BpHi008A) exhibiting about 37% amino acid sequence identity to Wir1 family of proteins that are encoded by pathogen-induced transcripts in wheat. Like Wir1 proteins, it consists of a hydrophobic N-terminal half and a hydrophilic C-terminal half relatively rich in glycine and proline. These proteins are predicted to be integrated into the membrane, with the C-terminus being extracytoplastic. Genomic Southern analysis indicated that the BpHi008A gene was present as a single-copy sequence in the rice genome. Temporal and spatial studies showed that BpHi008A were systemically induced in rice when 2nd and 3rd-instars were feeding. The BpHi008A transcripts level was also increased in seedlings damaged by mechanical wounding. These data indicated that BphHi008A was implicated in the response of rice plants to BPH feeding and wounding.

SAGE analysis of transcriptome responses in Arabidopsis roots exposed to 2,4,6-trinitrotoluene

Serial analysis of gene expression was used to profile transcript levels in Arabidopsis roots and assess their responses to 2,4,6-trinitrotoluene (TNT) exposure. SAGE libraries representing control and TNT-exposed seedling root transcripts were constructed, and each was sequenced to a depth of roughly 32,000 tags. More than 19,000 unique tags were identified overall. The second most highly induced tag (27-fold increase) represented a glutathione S-transferase. Cytochrome P450 enzymes, as well as an ABC transporter and a probable nitroreductase, were highly induced by TNT exposure. Analyses also revealed an oxidative stress response upon TNT exposure. Although some increases were anticipated in light of current models for xenobiotic metabolism in plants, evidence for unsuspected conjugation pathways was also noted. Identifying transcriptome-level responses to TNT exposure will better define the metabolic pathways plants use to detoxify this xenobiotic compound, which should help improve phytoremediation strategies directed at TNT and other nitroaromatic compounds.

Functional genomics of wood quality and properties

Genomics promises to enrich the investigations of biology and biochemistry. Current advancements in genomics have major implications for genetic improvement in animals, plants, and microorganisms, and for our understanding of cell growth, development, differentiation, and communication. Significant progress has been made in the understanding of plant genomics in recent years, and the area continues to progress rapidly. Functional genomics offers enormous potential to tree improvement and the understanding of gene expression in this area of science worldwide. In this review we focus on functional genomics of wood quality and properties in trees, mainly based on progresses made in genomics study of Pinus and Populus. The aims of this review are to summarize the current status of functional genomics including: (1) Gene discovery; (2) EST and genomic sequencing; (3) From EST to functional genomics; (4) Approaches to functional analysis; (5) Engineering lignin biosynthesis; (6) Modification of cell wall biogenesis; and (7) Molecular modelling. Functional genomics has been greatly invested worldwide and will be important in identifying candidate genes whose function is critical to all aspects of plant growth, development, differentiation, and defense. Forest biotechnology industry will significantly benefit from the advent of functional genomics of wood quality and properties.