LncRBase V.2: an updated resource for multispecies lncRNAs and ClinicLSNP hosting genetic variants in lncRNAs for cancer patients

Abstract

The recent discovery of long non-coding RNA as a regulatory molecule in the cellular system has altered the concept of the functional aptitude of the genome. Since our publication of the first version of LncRBase in 2014, there has been an enormous increase in the number of annotated lncRNAs of multiple species other than Human and Mouse. LncRBase V.2 hosts information of 549,648 lncRNAs corresponding to six additional species besides Human and Mouse, viz. Rat, Fruitfly, Zebrafish, Chicken, Cow and C. elegans. It provides additional distinct features such as (i) Transcription Factor Binding Site (TFBS) in the lncRNA promoter region, (ii) sub-cellular localization pattern of lncRNAs (iii) lnc-pri-miRNAs (iv) Possible small open reading frames (sORFs) within lncRNA. (v) Manually curated information of interacting target molecules and disease association of lncRNA genes (vi) Distribution of lncRNAs across multiple tissues of all species. Moreover, we have hosted ClinicLSNP within LncRBase V.2. ClinicLSNP has a comprehensive catalogue of lncRNA variants present within breast, ovarian, and cervical cancer inferred from 561 RNA-Seq data corresponding to these cancers. Further, we have checked whether these lncRNA variants overlap with (i)Repeat elements,(ii)CGI, (iii)TFBS within lncRNA loci (iv)SNP localization in trait-associated Linkage Disequilibrium(LD) region, (v)predicted the potentially pathogenic variants and (vi)effect of SNP on lncRNA secondary structure. Overall, LncRBaseV.2 is a user-friendly database to survey, search and retrieve information about multi-species lncRNAs. Further, ClinicLSNP will serve as a useful resource for cancer specific lncRNA variants and their related information. The database is freely accessible and available at http://dibresources.jcbose.ac.in/zhumur/lncrbase2/.

piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species

“…piRNA clusters overlapping with lncRNAs : We have studied the distribution of piRNA clusters within the lncRNA loci obtained from LncRBase V.2 [ 57 ]. As mentioned earlier, in the first point of this result section, we observed a significant overlap of piRNA clusters with the intergenic lncRNAs (Supplementary Figure SF5A) which are transcribed from in between two gene loci.…”

“…Normal tissue and disease specific small and long RNA sequencing data has been obtained from NCBI Gene Expression Omnibus (GEO) [ 84 ]. LncRNA information has been retrieved from LncRBase V.2 [ 57 ].…”

“…piRNA Target prediction : piRNA target pairs have been predicted between up regulated piRNAs and downregulated lncRNAs and mRNAs and vice versa. miRanda [ 40 ] has been used for predicting piRNA targets within lncRNAs (sequences obtained from LncRBase V.2 [ 57 ]) and 3 / UTR region of mRNAs (sequences downloaded from UCSC [ 41 ]). The target score and energy threshold are 170 and −20 kcal/mol respectively [ 88 ].…”

Long non‑coding RNA UCA1 enhances cervical cancer cell proliferation and invasion by regulating microRNA‑299‑3p expression

“…LncBase Predicted v.2 software ( 46 ) was used to predict the potential binding sites between UCA1 and miR-299-3p.…”

A Novel Regulatory Player in the Innate Immune System: Long Non-Coding RNAs

“…Long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides and lacking protein-coding potential, represent the largest group of noncoding RNAs transcribed from the genome [4]. In the most recent LncRBase V.2 database release, 241,562 and 178,336 lncRNA transcripts were defined from the human and mouse genomes, respectively [5]. Advances in high-throughput technologies led to rapidly growing data accumulation in the identification of characteristics and functions of lncRNAs, which greatly expanded our understanding of the intricate and intriguing lncRNA biology.…”