lncRNAdb: a reference database for long noncoding RNAs

Amaral, Paulo; Clark, Michael B.; Gascoigne, Dennis K.; Dinger, Marcel E.; Mattick, John S.

doi:10.1093/nar/gkq1138

Cited by 529 publications

(401 citation statements)

References 64 publications

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“…In practice, however, researchers studying human lincRNAs are faced with an excessive set of noncoding transcripts of varying or unknown reliability that may not be well defined (Khalil et al 2009) and have little or no expression data (Harrow et al 2006), or with very small sets of experimentally validated ones (Amaral et al 2010). Transcripts in current annotations of the human transcriptome from the GENCODE/HAVANA (Harrow et al 2006) or the University of California at Santa Cruz (UCSC) Genome Browser (Hsu et al 2006) are valuable resources, but it is hard to evaluate their biological characteristics in the absence of expression levels and further processing.…”

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confidence: 99%

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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Large intergenic noncoding RNAs (lincRNAs) are emerging as key regulators of diverse cellular processes. Determining the function of individual lincRNAs remains a challenge. Recent advances in RNA sequencing (RNA-seq) and computational methods allow for an unprecedented analysis of such transcripts. Here, we present an integrative approach to define a reference catalog of >8000 human lincRNAs. Our catalog unifies previously existing annotation sources with transcripts we assembled from RNA-seq data collected from~4 billion RNA-seq reads across 24 tissues and cell types. We characterize each lincRNA by a panorama of >30 properties, including sequence, structural, transcriptional, and orthology features. We found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that lincRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. We distinguish an additional subset of transcripts that have high evolutionary conservation but may include short ORFs and may serve as either lincRNAs or small peptides. Our integrated, comprehensive, yet conservative reference catalog of human lincRNAs reveals the global properties of lincRNAs and will facilitate experimental studies and further functional classification of these genes.

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mentioning

confidence: 99%

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

Cabili¹,

Trapnell²,

Goff³

et al. 2011

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“…For these newly identified long ncRNAs (lncRNAs), we also calculated their coding potential scores using CPC [30]. In addition, experimentally identified lncRNAs in budding yeast were manually collected from lncRNAdb (http://www.lncrnadb.org) [31].…”

Section: Assembly Of Novel Ncrna Transcripts Bound By Rbpsmentioning

confidence: 99%

“…We curated 15 lncRNAs recently identified in yeast [31]. Six of them exhibit RBP binding signals in the gPAR-CLIP data (Table S5 in Supporting Information).…”

Section: Novel Lncrnas Bound By Rbpsmentioning

confidence: 99%

Global signatures of protein binding on structured RNAs in Saccharomyces cerevisiae

Yang

Umetsu

2013

Sci. China Life Sci.

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Protein binding is essential to the transport, decay and regulation of almost all RNA molecules. However, the structural preference of protein binding on RNAs and their cellular functions and dynamics upon changing environmental conditions are poorly understood. Here, we integrated various high-throughput data and introduced a computational framework to describe the global interactions between RNA binding proteins (RBPs) and structured RNAs in yeast at single-nucleotide resolution. We found that on average, in terms of percent total lengths, ~15% of mRNA untranslated regions (UTRs), ~37% of canonical non-coding RNAs (ncRNAs) and ~11% of long ncRNAs (lncRNAs) are bound by proteins. The RBP binding sites, in general, tend to occur at single-stranded loops, with evolutionarily conserved signatures, and often facilitate a specific RNA structure conformation in vivo. We found that four nucleotide modifications of tRNA are significantly associated with RBP binding. We also identified various structural motifs bound by RBPs in the UTRs of mRNAs, associated with localization, degradation and stress responses. Moreover, we identified >200 novel lncRNAs bound by RBPs, and about half of them contain conserved secondary structures. We present the first ensemble pattern of RBP binding sites in the structured non-coding regions of a eukaryotic genome, emphasizing their structural context and cellular functions. . Many mRNAs are regulated by one or more RBPs as co-regulators. In Saccharomyces cerevisiae, there are approximately 600 annotated and predicted RBPs, but relatively few of them have been systematically studied to determine their regulatory targets [5]. In addition to mRNAs, numerous non-coding RNAs (ncRNAs) are targets of RBPs [6,7]. Previous studies revealed that RNAs were regulated by many RBPs post-transcriptionally [8]. It is widely accepted that altering the expression of RBPs will change cellular physiology profoundly. Studies using animal models have revealed that RBPs are involved in many human diseases, such as neurologic disorders and cancers [9]. Although the mechanisms that confer the specificity of RBP-RNA interaction are poorly understood, it is clear that this specificity is determined by both the primary sequence and secondary structure of the target RNA [10,11]. The secondary structures recognized by some RBPs are known. For example, the SAM domain of the yeast post-transcriptional regulator Vts1p recognizes the shape of the SRE of the RNA ligand [12].Currently, the most direct and powerful approach to profiling RBP-RNA interactions is UV crosslinking and immunoprecipitation (CLIP) of RNA-protein complexes,

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“…Users need to keep in mind that the data set size required for such an approach to produce meaningful results is quite high (in the order of tens, if not hundreds, of samples). NONCODE, 21 lncRNAdb 22 and NRED 23 are reference databases for ncRNAs and related expression information. Long-noncoding RNAs have been mostly regarded as chromatin-associated, and thus transcription-related, factors.…”

Section: Resourcesmentioning

confidence: 99%

“…Available databases are focused mainly on UTRs annotation, 12,13 RBP-target interactions, 14,15 ncRNAs, [16][17][18][19][20][21][22][23][24] of which miRNAtarget interactions are the greater part, [16][17][18][19][20] with a limited number of resources focusing on lncRNAs, 22,23 and cis-elements. [25][26][27][28][29][30] Furthermore, a small number of resources integrating different data types is available.…”

mentioning

confidence: 99%