Tag Archives: lncrna

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.


  • 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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  • non-coding rna review
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Upcoming Seminar – Long noncoding RNA: transcription noise or biological modulator? A view from studies in embryonic stem cells

Dr. Xiaohua Shen, Associate Professor
Tsinghua University, Beijing, China
Wednesday, June 25, 2014 – 11:00am
CCBR Red Room
Pervasive transcription in mammalian genome produces thousands of long noncoding RNA (lncRNA) transcripts. It has been hypothesized that lncRNAs as versatile modulators regulate diverse aspects of biology. However, their biological significance remains skeptical due to healthy concerns of subtle phenotypic differences caused by technical variation of knockdown. Despite a clear need to completely inactivate lncRNA function, targeted deletion of lncRNAs is still lacking in culture. Here, we systematically deleted multiple lncRNA loci (up to 217 kb) in embryonic stem cells (ESCs) by CRISPR/Cas9 system. Homozygous deletion mutants could be generated with high efficiency (up to 19%) in a short period of time (< 2 weeks). We have further characterized a lncRNA located ~40 kb from an ultraconserved, developmentally regulated gene cluster. We propose this lncRNA functions in cis to regulate its neighboring gene transcription and in trans to orchestrate ESC differentiation. Despite of recent burst of interest in lncRNAs, our knowledge is still limited to a handful of them. Thousands of lncRNAs await for functional characterization. While focusing on biology of individual lncRNA genes, we have tried to categorize lncRNA and reveal their function in groups. I will talk about our recent progress on one lncRNA catalogue in regulating transcription and developmental processes.
Dr. Zhaolei Zhang, Associate Professor, The Donnelly Centre

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  • lnc rna neighboring gene cis and trans
  • zhaolei zhang faculty candidate

The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs


Our genome contains tens of thousands of long noncoding RNAs (lncRNAs), many of which are likely to have genetic regulatory functions. It has been proposed that lncRNA are organized into combinations of discrete functional domains, but the nature of these and their identification remain elusive. One class of sequence elements that is enriched in lncRNA is represented by transposable elements (TEs), repetitive mobile genetic sequences that have contributed widely to genome evolution through a process termed exaptation.

Here, researchers link these two concepts by proposing that exonic TEs act as RNA domains that are essential for lncRNA function. They term such elements Repeat Insertion Domains of LncRNAs (RIDLs). A growing number of RIDLs have been experimentally defined, where TE-derived fragments of lncRNA act as RNA-, DNA-, and protein-binding domains. The researchers propose that these reflect a more general phenomenon of exaptation during lncRNA evolution, where inserted TE sequences are repurposed as recognition sites for both protein and nucleic acids. they discuss a series of genomic screens that may be used in the future to systematically discover RIDLs. The RIDL hypothesis has the potential to explain how functional evolution can keep pace with the rapid gene evolution observed in lncRNA. More practically, TE maps may in the future be used to predict lncRNA function.

  • Johnson R, Guigó R. (2014) The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA [Epub ahead of print]. [article]

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  • transposable elements lncrna switserland

Simultaneous RT-qPCR Measurement of 1718 Long Non-Coding RNAs


Pieter Mestdagh, Barbara D’haene, Jan Hellemans and Jo Vandesompele

Currently, expression and function of lncRNAs during human disease and development is largely unexplored. Few platforms are available that allow sensitive and specific high-throughput lncRNA expression profiling.

Study concludes, among other things, that lncRNA expression profiling of 60 cancer cell lines representing 9 different tumour entities reveals cancer-specific lncRNA expression profiles.

Role of the lncRNA-p53 regulatory network in cancer


Advances in functional genomics have led to discovery of a large group of previous uncharacterized long non-coding RNAs (lncRNAs). Emerging evidence indicates that lncRNAs may serve as master gene regulators through various mechanisms. Dysregulation of lncRNAs is often associated with a variety of human diseases including cancer. Of significant interest, recent studies suggest that lncRNAs participate in the p53 tumor suppressor regulatory network. In this review, the authors discuss how lncRNAs serve as p53 regulators or p53 effectors. Further characterization of these p53-associated lncRNAs in cancer will provide a better understanding of lncRNA-mediated gene regulation in the p53 pathway. As a result, lncRNAs may prove to be valuable biomarkers for cancer diagnosis or potential targets for cancer therapy.

  • Zhang A, Xu M, Mo YY. (2014) Role of the lncRNA-p53 regulatory network in cancer. J Mol Cell Biol [Epub ahead of print]. [article]

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  • central dogma and noncoding RNA
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  • Role of the lncRNA-p53 regulatory network incancer