Methods

Lncident – A Tool for Rapid Identification of Long Noncoding RNAs

lncrna

More and more studies have demonstrated that long noncoding RNAs (lncRNAs) play critical roles in diversity of biological process and are also associated with various types of disease. How to rapidly identify lncRNAs and messenger RNA is the fundamental step to uncover the function of lncRNAs identification. Researchers at Jilin University have devloped a novel method for rapid identification of ...

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IntNetLncSim – an integrative network analysis method to infer human lncRNA functional similarity

Increasing evidence indicated that long non-coding RNAs (lncRNAs) were involved in various biological processes and complex diseases by communicating with mRNAs/miRNAs each other. Exploiting interactions between lncRNAs and mRNA/miRNAs to lncRNA functional similarity (LFS) is an effective method to explore function of lncRNAs and predict novel lncRNA-disease associations. Researchers from Harbin Medical University have proposed an integrative framework, IntNetLncSim, to ...

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Researchers develop new CRISPR sgRNA design tool, demonstrate efficient CRISPR deletion of an enhancer and exonic fragment of the lncRNA MALAT1

lncRNA

CRISPR-Cas9 technology can be used to engineer precise genomic deletions with pairs of single guide RNAs (sgRNAs). This approach has been widely adopted for diverse applications, from disease modelling of individual loci, to parallelized loss-of-function screens of thousands of regulatory elements. However, no solution has been presented for the unique bioinformatic design requirements of CRISPR deletion. Researchers from the Centre for ...

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Bioinformatics for Novel Long Intergenic Noncoding RNA (lincRNA) Identification

lncRNA

Long intergenic noncoding RNAs (lincRNAs) , which are larger than 200 nucleotides and transcribed from the intergenic regions of protein coding genes, have been shown by accumulating findings to be widely expressed and extensively functional in many cellular processes. Nevertheless, given their cell/tissue-specificity, there is a need of identifying novel lincRNAs in a given system. To fulfill this purpose, researchers ...

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New tool predicts the interaction of proteins and RNA

CRG Researchers developed Global Score, a method that allows, for the first time, to predict protein interactions with long non-coding RNAs. This algorithm helps scientists prioritize binding partners for experimental validation, which will contribute to our understanding of the role of long non-coding RNAs in normal cell function and in disease. Far from just reading the information contained in the ...

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High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing (CLS)

lncrna

Accurate annotations of genes and their transcripts is a foundation of genomics, but no annotation technique presently combines throughput and accuracy. As a result, current reference gene collections remain far from complete: many genes models are fragmentary, while thousands more remain uncatalogued, particularly for long non coding RNAs (lncRNAs). To accelerate lncRNA annotation, the GENCODE consortium has developed RNA Capture ...

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ExInAtor – driver lncRNA discovery using mutational patterns in tumour DNA

lncRNA

Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such “driver lncRNAs” are known. Until now, they have been discovered through changes in expression, leading to problems in distinguishing between causative roles and passenger effects. Researchers at the CRG – Barcelona Institute of Science and Technology have developed a different ...

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FEELnc – a tool for long non-coding RNA annotation

lncRNA

Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, researchers from University Rennes1 present FEELnc (FlExible Extraction of ...

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LncPriCNet – Global Prioritizing Disease Candidate lncRNAs via a Multi-level Composite Network

lncRNA

LncRNAs play pivotal roles in many important biological processes, but research on the functions of lncRNAs in human disease is still in its infancy. Therefore, it is urgent to prioritize lncRNAs that are potentially associated with diseases. Researchers from the Shanghai Jiao Tong University have developed a novel algorithm, LncPriCNet, that uses a multi-level composite network to prioritize candidate lncRNAs ...

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Comparing Machine Learning Based Tools for Long Noncoding Transcripts Discrimination

lncRNA

Long noncoding RNA (lncRNA) is a kind of noncoding RNA with length more than 200 nucleotides, which aroused interest of people in recent years. Lots of studies have confirmed that human genome contains many thousands of lncRNAs which exert great influence over some critical regulators of cellular process. With the advent of high-throughput sequencing technologies, a great quantity of sequences ...

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