Tag Archives: lncrna
A wiki-style database hopes to serve as an online encyclopedia of lncRNA by and for the scientific community.
Scientists have set up a long non-coding RNA (lncRNA) database aimed at harnessing the collective knowledge of the scientific community. This study has been published in Nucleic Acids Research.
LncRNAs are RNAs that do not code for proteins but are nonetheless actively transcribed in human genome. In recent years, it has been recognized that they perform significant roles in a large variety of biological processes. The dysregulation of lncRNA expression is highly correlated with human cancer, neurological disorders, and many other human diseases.
Long noncoding RNAs (lncRNAs) do not code for proteins but function as RNAs. Because the functions of an RNA rely on either its sequence or secondary structure, lncRNAs should be folded at least as strongly as messenger RNAs (mRNAs), which serve as messengers for translation and are generally thought to lack secondary structure-dependent RNA-level functions. Contrary to this prediction, analysis of genome-wide experimental data of human RNA folding reveals that lncRNAs are substantially less folded than mRNAs even after the control of expression level and GC%, although both lncRNAs and mRNAs are more strongly folded than expected by chance. In contrast to mRNAs, lncRNAs show neither the positive correlation between folding strength and expression level nor the negative correlation between folding strength and evolutionary rate. These and other results support that, while RNA folding undoubtedly plays a role in RNA biology, it is also important in translation and/or protein biology.
- Yang J, Zhang J. (2014) Human long noncoding RNAs are substantially less folded than messenger RNAs. Mol Biol Evol [Epub ahead of print]. [abstract]
Long noncoding RNAs (lncRNAs) have been widely regarded as crucial regulators in various biological processes involved in carcinogenesis. However, the comprehensive lncRNA expression signature in colorectal cancer remains fully unknown. Researchers at Nanjing Medical University performed a high throughput microarray assay to detect lncRNA expression profile in three paired human colorectal cancer tissues and their adjacent normal tissues. Additional 90 paired colorectal samples were collected to verify differently expression levels of two selected lncRNAs using q-RT-PCR assay. Bioinformatic approaches were performed to explore into the functions of these differently expressed lncRNAs.
Microarray assay showed a series of lncRNAs were differently expressed in colorectal cancer. Two of the lncRNAs, HOTAIR and a novel lncRNA, lncRNA-422 were confirmed in more samples (P=0.015 for HOTAIR and P=0.027 for lncRNA-422, respectively). GSEA indicated that gene sets most correlated with them were those named up-regulated in KRAS-over, down-regulated in JAK2-knockout, down-regulated in PDGF-over and down-regulated in TBK1-knockout, all of which were cancer-related. Subsequently, GO analyses of most significantly correlated coding genes of HOTAIR and lncRNA-422 showed that these two lncRNAs may participate in carcinogenesis by regulating protein coding genes involved in special biological process relevant to cancer.
This study demonstrated that different lncRNA expression patterns were involved in colorectal cancer. Besides, HOTAIR and lncRNA-422 were identified to participate in colorectal cancer. Further studies into biological mechanisms of differently expressed lncRNAs identified in this study will help to provide new perspective in colorectal cancer pathogenesis.
- Xue Y, Ma G, Gu D, Zhu L, Hua Q, Du M, Chu H, Tong N, Chen J, Zhang Z, Wang M. (2014) Genome-wide analysis of long noncoding RNA signature in human colorectal cancer. Gene [Epub ahead of print]. [abstract]
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|Tuesday, October 14, 2014|
|University of Virginia School of Medicine, Charlottesville, EUA|
SEMINAR | 14 OCTOBER | 12:00 | MAIN AUDITORIUM
Small and long noncoding RNAs in control of cell proliferation and differentiation
Anindya Dutta, University of Virginia School of Medicine, Charlottesville, EUA
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.
Expression 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]