Dataset Information

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development.

ABSTRACT: Non-coding RNAs constitute a major portion of the transcriptome in most of eukaryotes. Long non-coding transcripts originating from the DNA segment present between the protein coding genes are termed as long intergenic non-coding RNAs (lincRNAs). Several evidences suggest the role of lincRNAs in regulation of various biological processes. In this study, we identified a total of 2248 lincRNAs in chickpea using RNA-seq data from eight successive stages of flower development and three vegetative tissues via an optimized pipeline. Different characteristic features of lincRNAs were studied and compared with those of predicted mRNAs in chickpea. Further, we utilized a method using network propagation algorithm to reveal the putative function of lincRNAs in plants. In total, at least 79% of the identified chickpea lincRNAs were assigned with a putative function. A comprehensive expression profiling revealed differential expression patterns and tissue specificity of lincRNAs in different stages of flower development in chickpea. In addition, potential lincRNAs-miRNA interactions were explored for the predicted lincRNAs in chickpea. These findings will pave the way for understanding the role of lincRNAs in the regulatory mechanism underlying flower development in chickpea and other legumes.

SUBMITTER: Khemka N

PROVIDER: S-EPMC5024101 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature

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Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development.

Khemka Niraj N Singh Vikash Kumar VK Garg Rohini R Jain Mukesh M

Scientific reports 20160915

Non-coding RNAs constitute a major portion of the transcriptome in most of eukaryotes. Long non-coding transcripts originating from the DNA segment present between the protein coding genes are termed as long intergenic non-coding RNAs (lincRNAs). Several evidences suggest the role of lincRNAs in regulation of various biological processes. In this study, we identified a total of 2248 lincRNAs in chickpea using RNA-seq data from eight successive stages of flower development and three vegetative ti ...[more]

PMID: 27628568

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Project description:BackgroundLong non-coding RNAs (lncRNAs) are transcripts more than 200 bp in length do not encode proteins. Up to the present, it has been reported that lncRNAs play an essential role in developmental processes through their regulatory functions. However, their characteristics, expression inheritance patterns, and functions in Prunus mume are quite unidentified.ResultsIn this present study, we exposed the specific characters of pistil development process between single pistil cv 'Qingjia No.2' (QJN2) and multiple pistils cv 'Da Yu' (DY). We found that early October is the key stage for pistil differentiation. The similarity epidermis was observed between two types of pistil. We also further investigated a complete pistil development lncRNA profiles through RNA-seq in Prunus mume. 2572 unique lncRNAs and 24,648 genes mapped to Prunus mume genome, furthermore, 591 novel lncRNAs were predicted. Both unique lncRNAs and novel lncRNAs are shorter in length than the mRNAs, and the overall expression level of lncRNAs was lower than mRNAs in Prunus mume. 186 known lncRNAs, 1638 genes and 89 novel lncRNAs were identified as significant differential expressed in QJN2 compared with DY. We predicted 421 target genes of differentially expressed known lncRNAs (DEKLs) and 254 target genes of differentially expressed novel lncRNAs (DENLs). 153 miRNAs were predicted interacted with 100 DEKLs while 112 miRNAs were predicted interacted with 55 DENLs. Further analysis of the DEKLs showed that the lncRNA of XR_514690.2 down-regulated its target ppe-miR172d, and up-regulated AP2, respectively. Meanwhile, the other lncRNA of TCONS_00032517 induced cytokinin negative regulator gene A-ARR expression via repressing its target miRNA ppe-miR160a/b in DY. At the same time we found that the AP2 expression was significantly up-regulated by zeatin (ZT) treatment in flower buds. Our experiments suggest that the two lncRNAs of XR_514690.2 and TCONS_00032517 might contribute the formation of multiple pistils in Prunus mume.ConclusionThis study shows the first characterization of lncRNAs involved in pistil development and provides new indications to elucidate how lncRNAs and their targets play role in pistil differentiation and flower development in Prunus mume.

Project description:BACKGROUND:Long non-coding RNAs (lncRNAs) are key regulators of diverse cellular processes. Although a number of studies have reported the identification of bovine lncRNAs across many tissues, very little is known about the identity and characteristics of lncRNAs in bovine oocytes. METHODS:A bovine oocyte cDNA library was constructed and sequenced using the Illumina HiSeq 2000 sequencing system. The oocyte transcriptome was constructed using the ab initio assembly software Scripture and Cufflinks. The assembled transcripts were categorized to identify the novel intergenic transcripts, and the coding potential of these novel transcripts was assessed using CPAT and PhyloCSF. The resulting candidate long intergenic non-coding RNAs (lincRNAs) transcripts were further evaluated to determine if any of them contain any known protein coding domains in the Pfam database. RT-PCR was used to analyze the expression of oocyte-expressed lincRNAs in various bovine tissues. RESULTS:A total of 85 million raw reads were generated from sequencing of the bovine oocyte library. Transcriptome reconstruction resulted in the assembly of a total of 42,396 transcripts from 37,678 genomic loci. Analysis of the assembled transcripts using the step-wide pipeline resulted in the identification of 1535 oocyte lincRNAs corresponding to 1183 putative non-coding genes. A comparison of the oocyte lincRNAs with the lncRNAs reported in other bovine tissues indicated that 970 of the 1535 oocyte lincRNAs appear to be unique to bovine oocytes. RT-PCR analysis of 5 selected lincRNAs showed either specific or predominant expression of 4 lincRNAs in the fetal ovary. Functional prediction of the oocyte-expressed lincRNAs suggested their involvement in oogenesis through regulating their neighboring protein-coding genes. CONCLUSIONS:This study provides a starting point for future research aimed at understanding the roles of lncRNAs in controlling oocyte development and early embryogenesis in cattle.

Project description:Recently, large numbers of normal human tissues have been profiled for non-coding RNAs and more than fourteen thousand long intergenic non-coding RNAs (lincRNAs) are found expressed in normal human tissues. The functional roles of these normal lincRNAs (nlincRNAs) in the regulation of protein coding genes in normal and disease biology are yet to be established. Here, we have profiled two RNA-seq datasets including cancer and matched non-neoplastic tissues from 12 individuals from diverse demography for both coding genes and nlincRNAs. We find 130 nlincRNAs significantly regulated in cancer, with 127 regulated in the same direction in the two datasets. Interestingly, according to Illumina Body Map, significant numbers of these nlincRNAs display baseline null expression in normal prostate tissues but are specific to other tissues such as thyroid, kidney, liver and testis. A number of the regulated nlincRNAs share loci with coding genes, which are either co-regulated or oppositely regulated in all cancer samples studied here. For example, in all cancer samples i) the nlincRNA, TCONS_00029157, and a neighboring tumor suppressor factor, SIK1, are both down regulated; ii) several thyroid-specific nlincRNAs in the neighborhood of the thyroid-specific gene TPO, are both up-regulated; and iii) the TCONS_00010581, an isoform of HEIH, is down-regulated while the neighboring EZH2 gene is up-regulated in cancer. Several nlincRNAs from a prostate cancer associated chromosomal locus, 8q24, are up-regulated in cancer along with other known prostate cancer associated genes including PCAT-1, PVT1, and PCAT-92. We observe that there is significant bias towards up-regulation of nlincRNAs with as high as 118 out of 127 up-regulated in cancer, even though regulation of coding genes is skewed towards down-regulation. Considering that all reported cancer associated lincRNAs (clincRNAs) are biased towards up-regulation, we conclude that this bias may be functionally relevant.

Dataset Information

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development.

Publications

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development.

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