Methods

High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing

lncrna

Accurate annotation of genes and their transcripts is a foundation of genomics, but currently no annotation technique combines throughput and accuracy. As a result, reference gene collections remain incomplete-many gene models are fragmentary, and thousands more remain uncataloged, particularly for long noncoding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture Long Seq (CLS), which combines ...

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A large shRNA library approach for identification of lncRNAs

lncrna

The mammalian cell cycle is a complex and tightly controlled event. Myriads of different control mechanisms are involved in its regulation. Long non-coding RNAs (lncRNA) have emerged as important regulators of many cellular processes including cellular proliferation. However, a more global and unbiased approach to identify lncRNAs with importance for cell proliferation is missing. Here, researchers from Hannover Medical School ...

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UClncR – Ultrafast and comprehensive long non-coding RNA detection from RNA-Seq

lncrna

Long non-coding RNA (lncRNA) is a large class of gene transcripts with regulatory functions discovered in recent years. Many more are expected to be revealed with accumulation of RNA-seq data from diverse types of normal and diseased tissues. However, discovering novel lncRNAs and accurately quantifying known lncRNAs is not trivial from massive RNA-seq data. Researchers at the Mayo Clinic have ...

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Fusing multiple protein-protein similarity networks can effectively boost the performance of predicting lncRNA-protein interactions

lncrna

Long non-coding RNA (lncRNA) plays important roles in many biological and pathological processes, including transcriptional regulation and gene regulation. As lncRNA interacts with multiple proteins, predicting lncRNA-protein interactions (lncRPIs) is an important way to study the functions of lncRNA. Up to now, there have been a few works that exploit protein-protein interactions (PPIs) to help the prediction of new lncRPIs. ...

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EPLMI – large-scale lncRNA-miRNA interaction profiling

lncrna

The interaction of miRNA and lncRNA is known to be important for gene regulations. However, not many computational approaches have been developed to analyse known interactions and predict the unknown ones. Given that there are now more evidences that suggest that lncRNA-miRNA interactions are closely related to their relative expression levels in the form of a titration mechanism, researchers from ...

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A Support Vector Machine based method to distinguish long non-coding RNAs from protein coding transcripts

lncRNA

In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed when analyzing this data is distinguishing between long non-coding RNAs (lncRNAs) and protein coding transcripts (PCTs). Thus, we present a Support Vector Machine (SVM) ...

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Analysis of lncRNA-Protein Interactions by RNA-Protein Pull-Down Assays and RNA Immunoprecipitation (RIP)

lncrna

Long noncoding RNAs (lncRNAs) have important roles in shaping chromatin by targeting chromatin-modifying enzymes to distinct genomic sites. This section covers two methods to analyze lncRNA-protein interactions. The RNA-protein pull-down assays use either bead-bound proteins to capture in vitro transcripts, or immobilized synthetic RNAs to bind proteins from cell lysates. In the RNA immunoprecipitation (RIP) assay, endogenous RNAs are co-immunoprecipitated ...

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BRWLDA – bi-random walks for predicting lncRNA-disease associations

lncrna

Increasing efforts have been done to figure out the association between lncRNAs and complex diseases. Many computational models construct various lncRNA similarity networks, disease similarity networks, along with known lncRNA-disease associations to infer novel associations. However, most of them neglect the structural difference between lncRNAs network and diseases network, hierarchical relationships between diseases and pattern of newly discovered associations. In ...

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Discriminating cirRNAs from other lncRNAs using a hierarchical extreme learning machine (H-ELM) algorithm

lncRNA

As non-coding RNAs, circular RNAs (cirRNAs) and long non-coding RNAs (lncRNAs) have attracted an increasing amount of attention. They have been confirmed to participate in many biological processes, including playing roles in transcriptional regulation, regulating protein-coding genes, and binding to RNA-associated proteins. Until now, the differences between these two types of non-coding RNAs have not been fully uncovered. It is ...

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Microarray expression profiling of long non-coding RNAs in epithelial ovarian cancer

lncRNA

Although numerous long non-coding RNAs (lncRNAs) have been identified to be important in human cancer, their potential regulatory roles in epithelial tumorigenesis and tumor progression in ovarian cancer remain unclear. Researchers from Nanjing Medical University set out to investigate lncRNAs that were differentially expressed (DE) in epithelial ovarian cancer and to explore their potential functions. The lncRNA profiles in five pairs ...

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