Genome-wide Identification Of lncRNAs Research Articles

Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705.

Long non-coding RNAs (lncRNAs) play an important role in eukaryotic cells. However, there is no report of lncRNAs in endophytic fungi Calcarisporium arbuscula. Here, in Calcarisporium arbuscula NRRL 3705, an endophytic fungus predominantly producing mycotoxins aurovertins, the genome-wide identification of lncRNAs was carried out based on RNA-Seq. Totally, 1332 lncRNAs were identified, including 1082 long intergenic noncoding RNAs, 64 long intronic noncoding RNAs and 186 long noncoding natural antisense transcripts. The average length of lncRNA and mRNA were 254 and 1102bp, respectively. LncRNAs were shorter, with fewer exons and lower expression levels. Moreover, there were 39 up-regulated lncRNAs and 10 down-regulated lncRNAs in the ΔaurA mutant, which lacks the aurovertin biosynthetic enzyme AurA. Interestingly, expression of genes related to the metabolism of linoleic acid and methane were significantly down regulated in the ΔaurA mutant. This study enriches the endophytic fungal lncRNA database and provide a basis for further research.

Transcriptome dynamics uncovers long non-coding RNAs response to salinity stress in Chenopodium quinoa

Chenopodium quinoa is a crop with outstanding tolerance to saline soil, but long non-coding RNAs (LncRNAs) expression profile driven by salt stress in quinoa has rarely been observed yet. Based on the high-quality quinoa reference genome and high-throughput RNA sequencing (RNA-seq), genome-wide identification of LncRNAs was performed, and their dynamic response under salt stress was then investigated. In total, 153,751 high-confidence LncRNAs were discovered and dispersed intensively in chromosomes. Expression profile analysis demonstrated significant differences between LncRNAs and coding RNAs. Under salt stress conditions, 4,460 differentially expressed LncRNAs were discovered, of which only 54 were differentially expressed at all the stress time points. Besides, strongly significantly correlation was observed between salt-responsive LncRNAs and their closest neighboring genes (r = 0.346, p-value < 2.2e-16). Furthermore, a weighted co-expression network was then constructed to infer the potential biological functions of LncRNAs. Seven modules were significantly correlated with salt treatments, resulting in 210 hub genes, including 22 transcription factors and 70 LncRNAs. These results indicated that LncRNAs might interact with transcription factors to respond to salinity stress. Gene ontology enrichment of the coding genes of these modules showed that they were highly related to regulating metabolic processes, biological regulation and response to stress. This study is the genome-wide analysis of the LncRNAs responding to salt stress in quinoa. The findings will provide a solid framework for further functional research of salt responsive LncRNAs, contributing to quinoa genetic improvement.

Genome wide identification of lncRNAs and circRNAs having regulatory role in fruit shelf life in health crop cucumber (Cucumis sativus L.).

Cucumber is an extremely perishable vegetable; however, under room conditions, the fruits become unfit for consumption 2–3 days after harvesting. One natural variant, DC-48 with an extended shelf-life was identified, fruits of which can be stored up to 10–15 days under room temperature. The genes involved in this economically important trait are regulated by non-coding RNAs. The study aims to identify the long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) by taking two contrasting genotypes, DC-48 and DC-83, at two different fruit developmental stages. The upper epidermis of the fruits was collected at 5 days and 10 days after pollination (DAP) for high throughput RNA sequencing. The differential expression analysis was performed to identify differentially expressed (DE) lncRNAs and circRNAs along with the network analysis of lncRNA, miRNA, circRNA, and mRNA interactions. A total of 97 DElncRNAs were identified where 18 were common under both the developmental stages (8 down regulated and 10 upregulated). Based on the back-spliced reads, 238 circRNAs were found to be distributed uniformly throughout the cucumber genomes with the highest numbers (71) in chromosome 4. The majority of the circRNAs (49%) were exonic in origin followed by inter-genic (47%) and intronic (4%) origin. The genes related to fruit firmness, namely, polygalacturonase, expansin, pectate lyase, and xyloglucan glycosyltransferase were present in the target sites and co-localized networks indicating the role of the lncRNA and circRNAs in their regulation. Genes related to fruit ripening, namely, trehalose-6-phosphate synthase, squamosa promoter binding protein, WRKY domain transcription factors, MADS box proteins, abscisic stress ripening inhibitors, and different classes of heat shock proteins (HSPs) were also found to be regulated by the identified lncRNA and circRNAs. Besides, ethylene biosynthesis and chlorophyll metabolisms were also found to be regulated by DElncRNAs and circRNAs. A total of 17 transcripts were also successfully validated through RT PCR data. These results would help the breeders to identify the complex molecular network and regulatory role of the lncRNAs and circRNAs in determining the shelf-life of cucumbers.

Genome-wide identification of lncRNAs, miRNAs, mRNAs and their regulatory networks involved in tapping panel dryness in rubber tree (Hevea brasiliensis).

Noncoding RNAs (ncRNAs) play pivotal roles in various biological processes in plants. However, the role of ncRNAs in tapping panel dryness (TPD) of rubber tree (Hevea brasiliensis Muell. Arg.) is largely unknown. Here, the whole transcriptome analyses of bark tissues from healthy and TPD trees were performed to identify differentially expressed long ncRNAs (DELs), microRNAs/miRNAs (DEMs), genes (DEGs) and their regulatory networks involved in TPD. A total of 263 DELs, 174 DEMs and 1574 DEGs were identified in the bark of TPD tree compared with that of healthy tree. Kyoto Encyclopedia of Genes and Genomes analysis revealed that most of the DEGs and targets of DELs and DEMs were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites and plant hormone signal transduction. Additionally, the majority of DEGs and DELs related to rubber biosynthesis were downregulated in TPD trees. Furthermore, 98 DEGs and 44 DELs were targeted by 54 DEMs, 190 DEGs were identified as putative targets of 56 DELs, and 2 and 44 DELs were predicted as precursors and endogenous target mimics of 2 and 6 DEMs, respectively. Based on these, the DEL-DEM-DEG regulatory network involved in TPD was constructed, and 13 hub DELs, 3 hub DEMs and 2 hub DEGs were identified. The results provide novel insights into the regulatory roles of ncRNAs underlying TPD and lay a foundation for future functional characterization of long ncRNAs, miRNAs and genes involved in TPD in rubber tree.

Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor.

Long non-coding RNAs (lncRNAs) emerge as critical regulators across a wide variety of biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs may be potentially responsible for the regulatory functions of cellular and biological progresses in the reproductive phase of V. destructor. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable parasite control.

Genome-wide identification of lncRNAs during hickory (Carya cathayensis) flowering.

Non-coding RNAs with lengths greater than 200bp are known as long non-coding RNAs (lncRNAs), and these RNAs play important role in gene regulation and plant development. However, to date, little is known regarding the role played by lncRNAs during flowering in hickory (Carya cathayensis). Here, we performed whole transcriptome RNA-sequencing of samples from hickory female and male floral buds, in which three samples (H0311PF, H0318PF, and H0402PF) represent pre-flowering, flowering, and post-flowering, respectively, while eight male samples collected from May 8th to June 13th as this time course are the key stage for male floral bud differentiation. We identified 2163 lncRNAs in hickory during flowering, containing 213 intronic, 1488 intergenic, and 462 antisense lncRNAs. We noticed that 510 and 648 lncRNAs were differentially expressed corresponding to female and male floral buds, respectively. And some of the lncRNAs were in a tightly tissue-specific or stage-specific manner. To further understand the roles of the lncRNAs, we predicted the function of the lncRNAs in cis- and trans-acting modes. The results showed that 924 lncRNAs were cis-correlated with 1536 protein-coding genes, while 1207 lncRNAs co-expressed (trans-acting) with 7432 protein-coding genes (R > 0.95 or R < - 0.95). These lncRNAs were all enriched in flower development-associated biological processes, i.e., circadian rhythm, vernalization response, response to gibberellin, inflorescence development, floral organ development, etc. To further understand the relationships between lncRNAs and floral-core genes, we build a co-expressing lncRNA-mRNA flowering network. We classified these floral genes into different pathway (photoperiod, vernalization, gibberellin, autonomous, and sucrose pathway) according to their particular functions. We found a set of lncRNAs that preferentially expressed in these pathways. The network showed that some lncRNAs (i.e., XLOC_038669, XLOC_017938) functioned in a particular flowering time pathway, while others (i.e., XLOC_011251, XLOC_04110) were involved in multiple pathway. Furthermore, some lncRNAs (i.e., XLOC_038669, XLOC_009597, and XLOC_049539) played roles in single or multiple pathways via interaction with each other. This study provides a genome-wide survey of hickory flower-related lncRNAs and will contribute to further understanding of the molecular mechanism underpinning flowering in hickory.

Genome-Wide Identification of lncRNAs During Rice Seed Development.

Rice seed is a pivotal reproductive organ that directly determines yield and quality. Long non-coding RNAs (lncRNAs) have been recognized as key regulators in plant development, but the roles of lncRNAs in rice seed development remain unclear. In this study, we performed a paired-end RNA sequencing in samples of rice pistils and seeds at three and seven days after pollination (DAP) respectively. A total of 540 lncRNAs were obtained, among which 482 lncRNAs had significantly different expression patterns during seed development. Results from semi-qPCR conducted on 15 randomly selected differentially expressed lncRNAs suggested high reliability of the transcriptomic data. RNA interference of TCONS_00023703, which is predominantly transcribed in developing seeds, significantly reduced grain length and thousand-grain weight. These results expanded the dataset of lncRNA in rice and enhanced our understanding of the biological functions of lncRNAs in rice seed development

Genome-wide identification of lncRNAs and mRNAs differentially expressed in human vascular smooth muscle cells stimulated by high phosphorus

Background Cardiovascular events are the primary cause of death for chronic kidney disease patients, which occurred via vascular calcification evolving pathogenically. Although a high level of phosphorus contributes to the induction of osteogenic differentiation of vascular smooth muscle cells (VSMCs), the role of lncRNA in this process awaits further study. Methods In this study, we systematically investigated the variation of gene expression in human VSMCs induced by high phosphorus. LncRNAs and mRNAs expression were revealed by microarray analyses of the control group and high-phosphorus (HP) group. LncRNA-mRNA co-expression network was established based on the specific lncRNA-mRNA relationships. Hierarchical clustering was used to identify a common set of regulated genes. In addition, Gene Ontology enrichment, Kyoto Gene-Encyclopedia and genomic analyses were conducted for the mRNAs differentially expressed under high phosphorus. Result RT-qPCR results confirmed that the expression of RUNX2, BMP2 and osteocalcin in HP group exhibited significant increases than in control group (p < .05). VSMC in HP group also showed higher intracellular calcium content. Volcano plots results show that 379 mRNAs and 728 lncRNAs different expressed in HP group. LncRNA-mRNA co-expression networks analysis revealed that 8 lncRNAs were the most highly connected lncRNAs. Quantitative analysis indicated that two lncRNAs were confirmed to increase significantly in the HP group. The mRNA expression of NT5E and ICAM1 were higher in group HP, while MAP3K7CL was lower than CON group (p < .05). Conclusion This study provided a working list of lncRNAs that may be relevant to osteogenic differentiation, which presents a new insights into the mechanism of vascular calcification induced by high phosphorus in VSMCs.

Genome-Wide Identification of lncRNAs and Analysis of ceRNA Networks During Tomato Resistance to Phytophthora infestans.

Our previous studies have revealed the function of long noncoding RNAs (lncRNAs) and microRNAs (miRNAs) in tomato in response to Phytophthora infestans infection. However, the interaction relationships between lncRNAs and miRNAs during tomato resistance to P. infestans infection are unknown. In this study, 9,011 lncRNAs were identified from tomato plants, including 115 upregulated and 81 downregulated lncRNAs. Among these, 148 were found to be differentially expressed and might affect the expression of 771 genes, which are composed of 887 matched lncRNA-mRNA pairs. In total, 88 lncRNAs were identified as endogenous RNAs (ceRNAs) and predicted to decoy 46 miRNAs. Degradome sequencing revealed that 11 miRNAs that were decoyed by 20 lncRNAs could target 30 genes. These lncRNAs, miRNAs, and target genes were predicted to form 10 regulatory modules. Among them, lncRNA42705/lncRNA08711, lncRNA39896, and lncRNA11265/lncRNA15816 might modulate MYB, HD-Zip, and NAC transcription factors by decoying miR159, miR166b, and miR164a-5p, respectively. Upon P. infestans infection, the expression levels of lncRNA42705 and lncRNA08711 displayed a negative correlation with the expression level of miR159 and a positive correlation with the expression levels of MYB genes. Tomato plants in which lncRNA42705 and lncRNA08711 were silenced displayed increased levels of miR159 and decreased levels of MYB, respectively. The result demonstrated that lncRNAs might function as ceRNAs to decoy miRNAs and affect their target genes in tomato plants, increasing resistance to disease.

Genome-wide identification of lncRNAs as novel prognosis biomarkers of glioma.

Glioma is the primary cancer of the central nervous system, and defining the prognosis of glioma is of great significance in the clinical. The long noncoding RNAs (lncRNAs) emerge as important regulators of pathological processes. This study aimed to identify lncRNAs which could function as potential prognosis biomarkers of glioma. Glioma RNA-seq data from TCGA and CGGA were analyzed to identify neoplasm grade associated lncRNAs by DEseq. 2R and weighted gene co-expression network analysis. Consensus module genes were analyzed in Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway to predict lncRNAs biological functions. Then neutrophil immune estimations were analyzed by Tumor Immune Estimation Resource. Transcrption factors of these lncRNAs were predicted by PROMO. Overall survival and receiver operating characteristic (ROC) analyses were applied to test the accuracy of predicted lncRNAs as the markers of prognosis. We identified four lncRNAs most correlated with both higher neoplasm grade and worse prognosis, including AC064875.2, HOTAIRM1, LINC00908, and RP11-84A19.3. Neutrophil-mediated immunity and cell adhesion junction were considered as the main biological functions of these lncRNAs. In addition, the correlation of these four lncRNAs with glioma prognosis was validated. Neutrophil immune infiltration is implicated in higher neoplasm grade and worse prognosis of glioma. AC064875.2, HOTAIRM1, LINC00908, and RP11-84A19.3 may serve as potential prognosis biomarkers of glioma.

RBPSponge: genome-wide identification of lncRNAs that sponge RBPs.

Long non-coding RNAs (lncRNAs) can act as molecular sponge or decoys for an RNA-binding protein (RBP) through their RBP-binding sites, thereby modulating the expression of all target genes of the corresponding RBP of interest. Here, we present a web tool named RBPSponge to explore lncRNAs based on their potential to act as a sponge for an RBP of interest. RBPSponge identifies the occurrences of RBP-binding sites and CLIP peaks on lncRNAs, and enables users to run statistical analyses to investigate the regulatory network between lncRNAs, RBPs and targets of RBPs. The web server is available at https://www.RBPSponge.com. Supplementary data are available at Bioinformatics online.

Genome-wide identification of lncRNAs and mRNAs differentially expressed in non-functioning pituitary adenoma and construction of an lncRNA-mRNA co-expression network.

ABSTRACTThe involvement of long non-coding RNAs (lncRNAs) during tumorigenesis is a recent emerging theme. Yet no systematic evaluation of lncRNAs has been previously reported for non-functioning pituitary adenoma (NFPA), a fairly common type of intracranial tumor. Here, we report the first genome-wide expression profile for lncRNAs and mRNAs in NFPA, using formalin-fixed and paraffin-embedded tissue specimens. Using microarray analyses, we identified 113 lncRNAs and 80 mRNAs differentially expressed in NFPA; this list includes lncRNAs previously implicated in a variety of cancers. Using real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR) we further confirmed differential expression in NFPA for ten of the 113 lncRNAs. Using these ten doubly confirmed lncRNAs, we constructed an lncRNA-mRNA co-expression network comprising of 130 specific lncRNA-mRNA co-expression relationships. In addition, we conducted GO and KEGG analyses for the 80 mRNAs differentially expressed in NFPA. Our microarray and qRT-PCR analyses provided a working list of lncRNAs that may be functionally relevant to NFPA tumorigenesis. Our co-expression network in turn connected these largely uncharacterized lncRNAs to specific mRNAs, whose roles we further elucidated via GO and KEGG analyses, thus providing specific, testable hypotheses for the functions of these lncRNAs. Together, our study laid the foundation for future investigation of the specific function and mechanism by which lncRNAs are involved in NFPA tumorigenesis.

Exploring the Secrets of Long Noncoding RNAs

High-throughput sequencing has revealed that the majority of RNAs have no capacity to encode protein. Among these non-coding transcripts, recent work has focused on the roles of long noncoding RNAs (lncRNAs) of >200 nucleotides. Although many of their attributes, such as patterns of expression, remain largely unknown, lncRNAs have key functions in transcriptional, post-transcriptional, and epigenetic gene regulation; Also, new work indicates their functions in scaffolding ribonuclear protein complexes. In plants, genome-wide identification of lncRNAs has been conducted in several species, including Zea mays, and recent research showed that lncRNAs regulate flowering time in the photoperiod pathway, and function in nodulation. In this review, we discuss the basic mechanisms by which lncRNAs regulate key cellular processes, using the large body of knowledge on animal and yeast lncRNAs to illustrate the significance of emerging work on lncRNAs in plants.