Featured long non-coding RNA – RNA-LET


In this study, researchers from Second Military Medical University, China found that the lncRNA Low Expression in Tumor (lncRNA-LET) was generally downregulated in hepatocellular carcinomas, colorectal cancers, and squamous-cell lung carcinomas. They demonstrated that hypoxia-induced histone deacetylase 3 repressed lncRNA-LET by reducing the histone acetylation-mediated modulation of the lncRNA-LET promoter region. Interestingly, the downregulation of lncRNA-LET was found to be ...

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Long noncoding RNAs – the search for function

In the late 1990s, before the publication of the human genome, John Rinn, then at Yale University, was hunting for protein genes on chromosome 22 with his graduate student adviser Michael Snyder. The only genes they found were ones that had already been discovered, but their arrays identified a steady stream of transcribed regions with no apparent purpose. These long ...

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RNA promotes metastasis in lung cancer


The vast majority – approximately 80 percent – of our DNA does not code for proteins, yet it gets transcribed into RNA. These RNA molecules are called non-coding and fulfill multiple tasks in the cell. Alongside a well-studied group of small RNAs, there is also a class of so-called long non-coding RNAs consisting of more than 200 nucleotides. Long non-coding ...

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Regulation of Mammalian Gene Dosage by Long Noncoding RNAs


Recent transcriptome studies suggest that long noncoding RNAs (lncRNAs) are key components of the mammalian genome, and their study has become a new frontier in biomedical research. In fact, lncRNAs in the mammalian genome were identified and studied at particular epigenetic loci, including imprinted loci and X-chromosome inactivation center, at least two decades ago—long before development of high throughput sequencing ...

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GraphClust – alignment-free structural clustering of local RNA secondary structures


Clustering according to sequence-structure similarity has now become a generally accepted scheme for ncRNA annotation. Its application to complete genomic sequences as well as whole transcriptomes is therefore desirable but hindered by extremely high computational costs. Now, researchers at University of Freiburg, Germany have developed a novel linear-time, alignment-free method for comparing and clustering RNAs according to sequence and structure. ...

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Paired genes in stem cells shed new light on gene organization and regulation

gene pairs

CAMBRIDGE, Mass. (February 4, 2013) – Whitehead Institute researchers have determined that DNA transcription, the process that produces messenger RNA (mRNA) templates used in protein production, also runs in the opposite direction along the DNA to create corresponding long noncoding RNAs (lncRNAs). Moreover, the mRNAs and lncRNAs are transcribed coordinately as stem cells differentiate into other cell types. This surprising ...

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Featured lncRNA – PTCSC3


Researchers at The Ohio State University describe a unique, long, intergenic, noncoding RNA gene (lincRNA) named Papillary Thyroid Carcinoma Susceptibility Candidate 3 (PTCSC3) located 3.2 kb downstream of rs944289 at 14q.13.3 and the expression of which is strictly thyroid specific. By quantitative PCR, PTCSC3 expression was strongly down-regulated (P = 2.84 × 10(-14)) in thyroid tumor tissue of 46 PTC ...

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Long noncoding RNA – an emerging paradigm of cancer research

Tumor Biology

Recent studies have demonstrated the importance of non-protein coding part of human genome in carcinogenesis and metastasis. Among numerous kinds of non-protein coding RNAs, long noncoding RNAs (lncRNAs) play a key regulatory role in cancer biology. LncRNAs are dysregulated in different kinds of cancer and the expression levels of certain lncRNAs are associated with recurrence, metastasis, and prognosis of cancer. ...

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