Search Results for: long noncoding rna expression

Long Noncoding RNA Regulating Apoptosis Discovered

from Genetic Engineering News

Scientists from the University of São Paulo (USP) have identified an RNA molecule known as INXS that, although containing no instructions for the production of a protein, modulates the action of an important gene that impacts apoptosis.

According to Sergio Verjovski-Almeida, Ph.D., professor at the USP Chemistry Institute, INXS expression is generally diminished in cancer cells, and methods that are capable of stimulating the production of this noncoding RNA can be used to treat tumors. In experiments on mice, the USP scientists were able to effect a 10-fold reduction in the volume of subcutaneous malignant tumors by administering local injections of a plasmid containing INXS.

The team’s findings (“Long noncoding RNA INXS is a critical mediator of BCL-XS induced apoptosis”) were published in Nucleic Acids Research.

The group headed by Dr. Verjovski-Almeida at USP has been investigating the regulatory role of so-called intronic nonprotein-coding genes—those found in the same region of the genome as a coding gene but on the opposite DNA strand. INXS, for example, is an RNA expressed on the opposite strand of a gene coding for  the BCL-X protein.

“We were studying several protein-coding genes involved in cell death in search of evidence that one of them was regulated by intronic noncoding RNA. That was when we found the gene for BCL-X, which is located on chromosome 20,” he explained.

(read more…)

 

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]

Arraystar to launch Mouse LncRNA Expression Microarray V3.0

lncRNAArraystar is going to launch Arraystar Mouse LncRNA Expression Microarray V3.0! This array is designed for the global profiling of mouse long noncoding RNAs (LncRNAs). In order to detect LncRNAs comprehensively and reliably, we updated the repertoire of LncRNAs represented on the previous Microarray V2.0.
The Arraystar Mouse LncRNA Expression Microarray V3.0 contains the following four important changes from V2.0:
1. Updated and stringent LncRNA collection. The public databases we used as the sources of our LncRNAs have been updated since the release of our V2.0 LncRNA Expression microarrays in early 2011. These databases include NCBI Refseq, UCSC Known Gene 6.0, Ensembl 38.71, Fantom3, RNAdb 2.0, and NRED. In addition, the array contains LincRNA transcripts recently identified by several laboratories and not contained in the public databases. Most importantly, we developed a stringent computational approach to identify LncRNAs from these updated databases and publications, resulting in a more reliable LncRNA collection. (read more…)

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  • microarray
  • non coding rna ucsc
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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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lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA

database

Long noncoding RNA (lncRNA) influences post-transcriptional regulation by interfering with the microRNA (miRNA) pathways, acting as competing endogenous RNA (ceRNA). These lncRNAs have miRNA responsive elements (MRE) in them, and control endogenous miRNAs available for binding with their target mRNAs, thus reducing the repression of these mRNAs.

lnCeDB provides a database of human lncRNAs (from GENCODE 19 version) that can potentially act as ceRNAs. The putative mRNA targets of human miRNAs and the targets mapped to AGO clipped regions are collected from TargetScan and StarBase respectively. The lncRNA targets of human miRNAs (up to GENCODE 11) are downloaded from miRCode database. miRNA targets on the rest of the GENCODE 19 lncRNAs are predicted by our algorithm for finding seed-matched target sites. These putative miRNA-lncRNA interactions are mapped to the Ago interacting regions within lncRNAs. To find out the likelihood of an lncRNA-mRNA pair for actually being ceRNA we take recourse to two methods. First, a ceRNA score is calculated from the ratio of the number of shared MREs between the pair with the total number of MREs of the individual candidate gene. Second, the P-value for each ceRNA pair is determined by hypergeometric test using the number of shared miRNAs between the ceRNA pair against the number of miRNAs interacting with the individual RNAs. Typically, in a pair of RNAs being targeted by common miRNA(s), there should be a correlation of expression so that the increase in level of one ceRNA results in the increased level of the other ceRNA. Near-equimolar concentration of the competing RNAs is associated with more profound ceRNA effect. In lnCeDB one can not only browse for lncRNA-mRNA pairs having common targeting miRNAs, but also compare the expression of the pair in 22 human tissues to estimate the chances of the pair for actually being ceRNAs.

Availability: Downloadable freely from http://gyanxet-beta.com/lncedb/.

Das S, Ghosal S, Sen R, Chakrabarti J (2014) lnCeDB: Database of Human Long Noncoding RNA Acting as Competing Endogenous RNA. PLoS ONE 9(6): e98965. [article]