LNCipedia collects long non-coding RNA sequences and annotation from different sources. In version 3.0, over 90,000 new transcripts were added More »
from biotechin.asia by Mohamad Moustafa Ali Breast cancer is one of the most divergent and heterogeneous genetic disorders that affects More »
Long non-coding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire More »
Long noncoding RNAs (lncRNAs) have been shown to play key roles in various biological processes. However, functions of most lncRNAs are poorly characterized. Here, researchers from Harbin Medical University present a framework to predict functions of lncRNAs through construction of a regulatory network between lncRNAs and protein-coding genes. Using RNA-seq data, the transcript profiles of lncRNAs and protein-coding genes are constructed. Using the Bayesian network method, a regulatory network, which implies dependency relations between lncRNAs and protein-coding genes, was built. In combining protein interaction network, highly connected coding genes linked by a given lncRNA were subsequently used to predict functions of the lncRNA through functional enrichment. Application of this method to prostate RNA-seq data showed that 762 lncRNAs in the constructed regulatory network were assigned functions. The researchers found that lncRNAs are involved in diverse biological processes, such as tissue development or embryo development (e.g., nervous system development and mesoderm development). By comparison with functions inferred using the neighboring gene-based method and functions determined using lncRNA knockdown experiments, this method can provide comparable predicted functions of lncRNAs. Overall, this method can be applied to emerging RNA-seq data, which will help researchers identify complex relations between lncRNAs and coding genes and reveal important functions of lncRNAs.
- Xiao Y, Lv Y, Zhao H, Gong Y, Hu J, Li F, Xu J, Bai J, Yu F, Li X. (2015) Predicting the Functions of Long Noncoding RNAs Using RNA-Seq Based on Bayesian Network. Biomed Res Int 2015:839590. [article]
Long non-coding RNAs (lncRNAs) have been shown to play crucial 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. For that reason, researchers from The Institute of Botany of the Chinese Academy of Sciences used total RNA-Seq to identify 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 those 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, Gene Ontology (GO) terms of genes that overlap with or are neighbors of the stress-responsive lncRNAs were analyzed. Enrichments in GO terms in biological processes such as signal transduction, energy synthesis, molecule metabolism, detoxification, transcription and translation were found. From this data, researchers conclude that the lncRNAs were 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.
Characteristics of M. truncatula lncRNAs. a The expression level of lncRNAs (log10FPKM) along the eight M. truncatula chromosomes. It comprises six concentric rings, and each corresponds to a different sample. They are control in leaves (CK-L), control in roots (CK-R), osmotic stress in leaves (OS-L), osmotic stress in roots (OS-R), salt stress in leaves (SS-L) and salt stress in roots (SS-R) from outer to inner, respectively. b Distribution of different types of lncRNAs. The intronic, intergenic and sense/antisense lncRNAs are represented by different concentric rings from outer to inner, according to the loci of lncRNAs in the genome. c Length distribution of lncRNAs. d Accumulative frequency of lncRNAs and mRNAs in two control samples. Data from other samples is shown in Additional file 1: Figure S2. e Composition of different types of lncRNAs.
T.Z. Wang, M. Liu, M.G. Zhao, R. Chen, W.H. Zhang (2015) Identification and characterization of long non-coding RNAs involved in osmotic and salt stress in Medicago truncatula using genome-wide high-throughput sequencing BMC Plant Biol. 15: 131 doi: 10.1186/s12870-015-0530-5 [article]
Recent transcriptome annotation using deep sequencing approaches have annotated a large number of long non-coding RNAs in zebrafish, a popular model organism for human diseases. These studies characterized lncRNAs in critical developmental stages as well as adult tissues. Each of the studies has uncovered a distinct set of lncRNAs, with minor overlaps. The availability of the raw RNA-Seq datasets in public domain encompassing critical developmental time-points and adult tissues provides us with a unique opportunity to understand the spatiotemporal expression patterns of lncRNAs.
Now, researchers from the CSIR-Institute of Genomics and Integrative Biology have created a catalog of lncRNAs in zebrafish, derived largely from the three annotation sets, as well as manual curation of literature to compile a total of 2,267 lncRNA transcripts in zebrafish. The lncRNAs were further classified based on the genomic context and relationship with protein coding gene neighbors into 4 categories. Analysis revealed a total of 86 intronic, 309 promoter associated, 485 overlapping and 1,386 lincRNAs. They have created a comprehensive resource which houses the annotation of lncRNAs as well as associated information including expression levels, promoter epigenetic marks, genomic variants and retroviral insertion mutants. The resource also hosts a genome browser where the datasets could be browsed in the genome context.
Availability – The resource is freely available at URL: http://genome.igib.res.in/zflncRNApedia
- Dhiman H, Kapoor S, Sivadas A, Sivasubbu S, Scaria V. (2015) zflncRNApedia: A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs. PLoS One 10(6):e0129997. [article]
from Asian Scientist
AsianScientist (Apr. 29, 2015) – A study by researchers in Duke-NUS Graduate Medical School Singapore (Duke-NUS) has shown a new way that brown fat, a potential obesity-fighting target, is regulated in the body. This finding gives researchers and weight-loss companies a possible therapeutic target for obesity.
In a Cell Metabolism article, Duke-NUS Assistant Professor Lei Sun and his team examined long non-coding ribonucleic acid (lncRNA) in adipose (fat) tissue in mice. LncRNAs have recently been recognized as important control elements for different biological functions in the body.