Search Results for: long non coding rna review

Review – Posttranscriptional Gene Regulation by Long Non-coding RNA

graphical_abstract

Eukaryotic cells transcribe a vast number of noncoding RNA species. Among them, long noncoding RNAs (lncRNAs) have been widely implicated in the regulation of gene transcription. However, examples of posttranscriptional gene regulation by lncRNAs are emerging. For example, through extended base-pairing, lncRNAs can stabilize or promote the translation of target mRNAs, while partial base-pairing facilitates mRNA decay or inhibits target mRNA translation. In the absence of complementarity, lncRNAs can suppress precursor mRNA splicing and translation by acting as decoys of RNA-binding proteins or microRNAs and can compete for microRNA-mediated inhibition leading to increased expression of the mRNA. Through these regulatory mechanisms, lncRNAs can elicit differentiation, proliferation, and cytoprotective programs, underscoring the rising recognition of lncRNA roles in human disease.

  • Yoon JH, Abdelmohsen K, Gorospe M. (2012) Posttranscriptional Gene Regulation by Long Noncoding RNA.  J Mol Biol [Epub ahead of print]. [abstract]

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Long Noncoding RNAs in Imprinting and X Chromosome Inactivation

The field of long noncoding RNA (lncRNA) research has been rapidly advancing in recent years. Technological advancements and deep-sequencing of the transcriptome have facilitated the identification of numerous new lncRNAs, many with unusual properties, however, the function of most of these molecules is still largely unknown. Some evidence suggests that several of these lncRNAs may regulate their own transcription in cis, and that of nearby genes, by recruiting remodeling factors to local chromatin. Notably, lncRNAs are known to exist at many imprinted gene clusters. Genomic imprinting is a complex and highly regulated process resulting in the monoallelic silencing of certain genes, based on the parent-of-origin of the allele. It is thought that lncRNAs may regulate many imprinted loci, however, the mechanism by which they exert such influence is poorly understood. This review will discuss what is known about the lncRNAs of major imprinted loci, and the roles they play in the regulation of imprinting.

lncRNA

  • Autuoro JM, Pirnie SP, Carmichael GG. (2014) Long Noncoding RNAs in Imprinting and X Chromosome Inactivation. Biomolecules 4(1):76-100. [article]

RNA regulatory networks in animals and plants: a long noncoding RNA perspective

A recent highlight of genomics research has been the discovery of many families of transcripts which have function but do not code for proteins. An important group is long noncoding RNAs (lncRNAs), which are typically longer than 200 nt, and whose members originate from thousands of loci across genomes. The authors review progress in understanding the biogenesis and regulatory mechanisms of lncRNAs. They describe diverse computational and high throughput technologies for identifying and studying lncRNAs. They discuss the current knowledge of functional elements embedded in lncRNAs as well as insights into the lncRNA-based regulatory network in animals. The authors also describe genome-wide studies of large amount of lncRNAs in plants, as well as knowledge of selected plant lncRNAs with a focus on biotic/abiotic stress-responsive lncRNAs.

lncRNA

  • Bai Y, Dai X, Harrison AP, Chen M. (2014) RNA regulatory networks in animals and plants: a long noncoding RNA perspective. Brief Funct Genomics [Epub ahead of print]. [abstract]

 

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Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease

Comprehensive analysis of the mammalian transcriptome has revealed that long non-coding RNAs (lncRNAs) may make up a large fraction of cellular transcripts. Recent years have seen a surge of studies aimed at functionally characterizing the role of lncRNAs in development and disease. In this review, the authors discuss new findings implicating lncRNAs in controlling development of the central nervous system (CNS). The evolution of the higher vertebrate brain has been accompanied by an increase in the levels and complexities of lncRNAs expressed within the developing nervous system. Although a limited number of CNS-expressed lncRNAs are now known to modulate the activity of proteins important for neuronal differentiation, the function of the vast majority of neuronal-expressed lncRNAs is still unknown. Topics of intense current interest include the mechanism by which CNS-expressed lncRNAs might function in epigenetic and transcriptional regulation during neuronal development, and how gain and loss of function of individual lncRNAs contribute to neurological diseases.

lncRNA

  • Clark BS, Blackshaw S. (2014) Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front Genet 5, 164. [article]

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Long non-coding RNAs in lung cancer: comparison of microarray and RNA-seq techniques

from the RNA-Seq Blog

PV Nazarov*, T Kaoma, A Muller, S Fritah, L Vallar

*Corresponding author: PV Nazarov
Genomics Research Unit, CRP-Sante, Luxembourg, Luxembourg

F1000Posters 2013, 4: 1446 (poster) [English] – Poster [1.22 MB]

rna-seq

Presented at:
Benelux Bioinformatics Conference 2013 , 9 – 10 Dec 2013, P82

Affiliated Society:
Benelux Bioinformatics Conference

Background / Purpose:
We compared two experimental approaches – standard microarray technology and next-generation RNA-seq for the analysis of changes in lncRNA expression profiles in NSCLC cancer tissue samples.
Main conclusion:
Generally speaking, RNA-seq technique outperforms arrays when studying lncRNAs. Cufflinks status should be taken into account together with counts or FPKM values in order to avoid misinterpreting the results.
Next steps:
Correlation between co-localized lncRNAs and mRNAs should be further investigated.
Disclosures:
No relevant competing interests disclosed.
Funding:
Luxembourg FNR CORE grant, ASTSTRO

Please note that most posters on this site present work that is preliminary in nature and has not been peer reviewed.

This poster is open access subject to the CC BY Creative Commons 3.0 License

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  • noncoding rna cancer