Abstract
Long noncoding RNAs (lncRNAs) are noncoding transcripts longer than 200 nucleotides, which show evidence of pervasive transcription and participate in a plethora of cellular regulatory processes. Although several noncoding transcripts have been functionally annotated as lncRNAs within the genome, not all have been proven to fulfill the criteria for a functional regulator and further analyses have to be done in order to include them in a functional cohort. LncRNAs are being classified and reclassified in an ongoing annotation process, and the challenge is fraught with ambiguity, as newer evidences of their biogenesis and functional implication come into light. In our effort to understand the complexity of this still enigmatic biomolecule, we have developed a new database entitled “LncRBase” where we have classified and characterized lncRNAs in human and mouse. It is an extensive resource of human and mouse lncRNA transcripts belonging to fourteen distinct subtypes, with a total of 83,201 entries for mouse and 133,361 entries for human: among these, we have newly annotated 8,507 mouse and 14,813 human non coding RNA transcripts (from UCSC and H-InvDB 8.0) as lncRNAs. We have especially considered protein coding gene loci which act as hosts for non coding transcripts. LncRBase includes different lncRNA transcript variants of protein coding genes within LncRBase. LncRBase provides information about the genomic context of different lncRNA subtypes, their interaction with small non coding RNAs (ncRNAs) viz. piwi interacting RNAs (piRNAs) and microRNAs (miRNAs) and their mode of regulation, via association with diverse other genomic elements. Adequate knowledge about genomic origin and molecular features of lncRNAs is essential to understand their functional and behavioral complexities. Overall, LncRBase provides a thorough study on various aspects of lncRNA origin and function and a user-friendly interface to search for lncRNA information. LncRBase is available at http://bicresources.jcbose.ac.in/zhumur/lncrbase.
Highlights
Once set aside as genomic ‘junk’, the non coding repertoire of the transcriptome has steadily emerged to be functionally significant guiding factors in the regulation of various biological processes impacting cellular development, differentiation, and metabolism
(7) IA, Intronic Antisense long noncoding RNAs (lncRNAs) completely overlapping with an intron in the opposite strand.(8) IO, Intron Overlapping lncRNA splice variants of a gene, contain intronic sequence.(9) PS, Pseudogene transcripts having homology to protein coding transcripts but containing disrupted coding sequence and an active homologous gene can be found at another locus.(10) SO, Sense Overlapping lncRNAs containing a coding gene in its intron on the same strand
Genomic elements, including 5/UTR exons, 3/UTR exons, CDS exons, introns (RefSeq annotations), CpG Islands (CGI) and fasta sequences of lncRNA promoter regions were downloaded from the University of Santa Cruz (UCSC) Table Browser data retrieval options. miRNA related information was downloaded from mirBase20 [59]. piwi interacting RNAs (piRNAs) sequences were downloaded from National Centre for Biotechnology Information (NCBI) [60] in fasta format
Summary
Once set aside as genomic ‘junk’, the non coding repertoire of the transcriptome has steadily emerged to be functionally significant guiding factors in the regulation of various biological processes impacting cellular development, differentiation, and metabolism. LncRNAs are transcripts longer than a somewhat arbitrary cut-off of 200 nucleotides (nts) [3,4], albeit less conserved than protein coding RNAs and have high tissue specificity [5,6,7], initially raising the doubt of being ‘transcriptional artifacts’. Tiling array studies of the human genome point out to the fact that a large fraction of the transcription machinery is employed for synthesis and maintenance of lncRNAs [8,9]. LncRNAs contribute to a plethora of cellular regulatory processes, ranging from X chromosome inactivation, genomic imprinting and chromatin modification, to telomere elongation, transcriptional activation, and nuclear trafficking [10,11]. Parallel studies on lncRNA function and expression in different cellular systems have led to the accumulation of massive amounts of experimental results, ready to be collated into comprehensive, reliable catalogs of lncRNA information
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