Tag Archives: lncrna

Gastric juice long noncoding RNA used as a tumor marker for screening gastric cancer

Long noncoding RNAs (lncRNAs) play a crucial role in tumorigenesis. However, the value of lncRNAs in the diagnosis of gastric cancer remains unknown. To identify whether lncRNA-AA174084 is a potential marker for the early diagnosis of gastric cancer (GC), the authors investigated its levels in tissues, blood, and gastric juices from patients with various stage of gastric tumorigenesis.

Total RNA in 860 specimens from patients and healthy controls was extracted. Levels of AA174084 in 134 paired GC tissues, 127 gastric mucosal tissues, 335 plasma samples, and 130 gastric juice samples at each stage of gastric tumorigenesis were measured using real-time reverse transcriptase-polymerase chain reaction analysis. The potential association between AA174084 levels and patients’ clinicopathologic features were analyzed. A receiver operating characteristic (ROC) curve was constructed for differentiating GC patients from controls.

lncRNAExpression levels of AA174084 were down-regulated significantly in 95 of 134 GC tissues (71%) compared with the levels in paired, adjacent, normal tissues (P < .001). AA174084 levels had significant, negative correlations with age (P = .031), Borrmann type (P = .016), and perineural invasion (P = .032). Plasma AA174084 levels in patients with GC dropped markedly on day 15 after surgery compared with preoperative levels (P < .001) and were associated with invasion (P = .049) and lymphatic metastasis (P = .042). AA174084 levels in gastric juice from patients with GC were significantly higher than the levels in normal mucosa or in patients with minimal gastritis, gastric ulcers, and atrophic gastritis (P < .001). The area under ROC was up to 0.848 (P < .001).

The authors conclude that AA174084 may have potential as marker for the early diagnosis of GC.

  • Shao Y, Ye M, Jiang X, Sun W, Ding X, Liu Z, Ye G, Zhang X, Xiao B, Guo J. (2014) Gastric juice long noncoding RNA used as a tumor marker for screening gastric cancer. Cancer [Epub ahead of print]. [abstract]

Non-Coding RNA and Evolution of Complexity

lncRNA

Non-coding DNA in genomes increases in concert with the increase in developmental complexity in evolution, and is consonant with the important regulatory roles identified for the many classes of non-coding RNAs transcribed from more than 85 % of the DNA regarded as ‘junk’ not so long ago Dr Mae-Wan Ho

A vast RNA underworld exposed

It wasn’t so long ago that most people still believed DNA carries the instructions for making an organism, while RNA simply copies out (transcribes) the instructions (by complementary base pairing) that are then translated into protein via a genetic code, in which different triplets of bases (codons) specify one of twenty amino acids plus start and stop signals. The proteins are the real workhorses in this hierarchy, with the DNA akin to the Holy Scripture – ‘Book of Life’ the Central Dogma – faithfully copied and transmitted by scribes (RNA), to be interpreted and implemented by the faithful (proteins).

But soon after the human genome sequence was announced, it became clear that RNA plays a much more substantive, central role than previously thought.

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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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Upcoming Seminar – Long noncoding RNA: transcription noise or biological modulator? A view from studies in embryonic stem cells

lncRNA
Dr. Xiaohua Shen, Associate Professor
Tsinghua University, Beijing, China
Wednesday, June 25, 2014 – 11:00am
CCBR Red Room
Abstract:
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.
Host:
Dr. Zhaolei Zhang, Associate Professor, The Donnelly Centre

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

lncRNA

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