Dynamic and widespread lncRNA expression in the sponge and the origin of animal complexity

Long non-coding RNAs (lncRNAs) are important developmental regulators in bilaterian animals. A correlation has been claimed between the lncRNA repertoire More »

Featured lncRNA – PVT1

It is becoming increasingly clear that short and long noncoding RNAs critically participate in the regulation of cell growth, differentiation, More »

Researchers use RNA-Seq to show that lincRNAs can also contribute to HER2+ breast cancers

Ahmad M. Khalil, PhD, knew the odds were against him — as in thousands upon thousands to one. Yet he More »

Scientists develop a novel method to suppress malaria parasite’s virulence genes, break the code of its immune evasion

Revealed: how malaria evades the immune response by using long noncoding RNA to express one gene while silencing others Up More »

Long Noncoding RNAs in Cardiovascular Diseases

In recent years, increasing evidence suggests that noncoding RNAs play important roles in the regulation of tissue homeostasis and pathophysiological More »

 

Database

GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development

Spermatogenic failure is a major cause of male infertility, which affects millions of couples worldwide. Recent discovery of long non-coding RNAs (lncRNAs) as critical regulators in normal and disease development provides new clues for delineating the molecular regulation in male germ cell development. However, few functional lncRNAs have been characterized to date. A major limitation in studying lncRNA in male germ cell development is the absence of germ cell-specific lncRNA annotation. Current lncRNA annotations are assembled by transcriptome data from heterogeneous tissue sources; specific germ cell transcript information of various developmental stages is therefore under-represented, which may lead to biased prediction or fail to identity important germ cell-specific lncRNAs.

GermlncRNA provides the first comprehensive web-based and open-access lncRNA catalogue for three key male germ cell stages, including type A spermatogonia, pachytene spermatocytes and round spermatids. This information has been developed by integrating male germ transcriptome resources derived from RNA-Seq, tiling microarray and GermSAGE. Characterizations on lncRNA-associated regulatory features, potential coding gene and microRNA targets are also provided. Search results from GermlncRNA can be exported to Galaxy for downstream analysis or downloaded locally. Taken together, GermlncRNA offers a new avenue to better understand the role of lncRNAs and associated targets during spermatogenesis.

lncRNA

Availability – Database URL: http://germlncrna.cbiit.cuhk.edu.hk/

  • Luk AC, Gao H, Xiao S, Liao J, Wang D, Tu J, Rennert OM, Chan WY, Lee TL. (2015) GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development. Database (Oxford) bav044. [abstract]

lncRNASNP – a database of SNPs in lncRNAs and their potential functions

Long non-coding RNAs (lncRNAs) play key roles in various cellular contexts and diseases by diverse mechanisms. With the rapid growth of identified lncRNAs and disease-associated single nucleotide polymorphisms (SNPs), there is a great demand to study SNPs in lncRNAs. Aiming to provide a useful resource about lncRNA SNPs, researchers from the Huazhong University of Science and Technology systematically identified SNPs in lncRNAs and analyzed their potential impacts on lncRNA structure and function. In total, they identified 495,729 and 777,095 SNPs in more than 30,000 lncRNA transcripts in human and mouse, respectively. A large number of SNPs were predicted with the potential to impact on the miRNA-lncRNA interaction. The experimental evidence and conservation of miRNA-lncRNA interaction, as well as miRNA expressions from TCGA were also integrated to prioritize the miRNA-lncRNA interactions and SNPs on the binding sites. Furthermore, by mapping SNPs to GWAS results, they found that 142 human lncRNA SNPs are GWAS tagSNPs and 197,827 lncRNA SNPs are in the GWAS linkage disequilibrium regions. All these data for human and mouse lncRNAs were imported into lncRNASNP database, which includes two sub-databases lncRNASNP-human and lncRNASNP-mouse. The lncRNASNP database has a user-friendly interface for searching and browsing through the SNP, lncRNA and miRNA sections.

lncRNA

Availability – the lncRNASNP database is available at: http://bioinfo.life.hust.edu.cn/lncRNASNP/

  • Gong J, Liu W, Zhang J, Miao X, Guo AY. (2015) lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res 43(Database issue):D181-6. [article]

Incoming search terms:

  • LncRnaAndDiseaseDatabase|lncRNABlog
  • The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3中文版

ALDB – a domestic-animal long noncoding RNA database

The domestic-animal lncRNA database (ALDB) is the first comprehensive database with a focus on the domestic-animal lncRNAs. ALDB currently comprises 12,103 pig lincRNAs, 8,923 chicken lincRNAs, and 8,250 cow lincRNAs, which have been identified using computational pipeline in this study. Moreover, ALDB provides related useful data, such as genome-wide expression profile and animal quantitative trait loci (QTLs), that is not available in the existing lncRNA database (lncRNAdb and NONCODE), along with convenient tools, such as BLAST, GBrowse and flexible search functionalities.

lncRNA

  • Li, Aimin (2015): ALDB: a domestic-animal long noncoding RNA database. figshare.

 

Community Curated Database For LncRNA

lncRNA

A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community.

Scientists have set up a long non-coding RNA (lncRNA) database aimed at harnessing the collective knowledge of the scientific community. This study has been published in Nucleic Acids Research.

LncRNAs are RNAs that do not code for proteins but are nonetheless actively transcribed in human genome. In recent years, it has been recognized that they perform significant roles in a large variety of biological processes. The dysregulation of lncRNA expression is highly correlated with human cancer, neurological disorders, and many other human diseases.

LncRNA2Target – a database for differentially expressed genes after lncRNA knockdown or overexpression

Long noncoding RNAs (lncRNAs) have been emerged as critical regulators of gene expression at epigenetic, transcriptional and post-transcriptional level, yet what genes are regulated by lncRNAs remains to be characterized. To assess the effects of a specific lncRNA on gene expression, increasing researchers profiled the genome-wide or individual gene expression level changes after knocking down or overexpressing the lncRNA. However, no online repository is currently available to collect these differentially expressed genes regulated by lncRNAs.

To make it convenient for researchers to know what genes are regulated by a lncRNA or which lncRNAs regulate a given gene of interest, researchers at the Harbin Institute of Technology have developed LncRNA2Target: a comprehensive resource of differentially expressed genes after lncRNA knockdown or overexpression.

lncRNA

In this database system, target genes of a lncRNA are defined as the differentially expressed genes after knocking down or overexpressing the lncRNA. By reviewing all published lncRNA papers, we manually curated the differentially expressed target genes confirmed by qRT-PCR or western blot, and identified all the differential target genes from the microarray or RNA-seq data.

Availability – the LncRNA2Target database is available at: http://www.lncrna2target.org/

Incoming search terms:

  • lncrna knockdown
  • lncrna overexpression no effect