MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures

Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. Researchers More »

LncRNA Regulator Of Brown Fat Identified

from Asian Scientist AsianScientist (Apr. 29, 2015) – A study by researchers in Duke-NUS Graduate Medical School Singapore (Duke-NUS) has More »

An update on LNCipedia – a database for annotated human lncRNA sequences

LNCipedia collects long non-coding RNA sequences and annotation from different sources. In version 3.0, over 90,000 new transcripts were added More »

Unveiling a new factor that helps breast cancer cells to tolerate drugs

from biotechin.asia by Mohamad Moustafa Ali Breast cancer is one of the most divergent and heterogeneous genetic disorders that affects More »

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 »

 

Database

zflncRNApedia – A Comprehensive Online Resource for Zebrafish Long Non-Coding RNAs

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.

rna-seq

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]

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  • Database|lncRNABlog

An update on LNCipedia – a database for annotated human lncRNA sequences

lncRNA

LNCipedia collects long non-coding RNA sequences and annotation from different sources. In version 3.0, over 90,000 new transcripts were added to the database. 6917 of these transcripts were obtained from RefSeq by filtering for accession prefix (NR_) and size (200bp). This filtering strategy however, does not confine to long non-coding RNAs and also yields transcripts associated with protein coding genes. Transcripts with incomplete open reading frames that are subject to nonsense-mediated mRNA decay for instance are also annotated with accession prefix NR_. These transcripts are generally not considered as true lncRNAs and typically exhibit a high coding potential score when assessed by PhyloCSF. The authors therefore chose to exclude these transcripts from the database and confine their analysis to the RefSeq subset with keyword biomol_ncrna_lncrna as suggested by RefSeq’s Dr. Kimm D. Pruit. This change is reflected in LNCipedia.org update 3.1 and this corrigendum serves to elucidate the discrepancies in the article caused by this update. (read more…)

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]

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  • lnc rna

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]

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  • A Micropeptide Encoded by a Putative Long Noncoding RNA Regulates Muscle Per
  • 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.