Search Results for: long noncoding rna expression
A new study led by researchers at The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James) describes a novel marker that might help doctors choose the least toxic, most effective treatment for many older patients with acute myeloid leukemia (AML). AML occurs mainly in older patients and has a three-year survival rate of 5 to 15 percent.
The researchers investigated patterns of molecules called long noncoding RNAs (lncRNAs), a class of RNA molecules more than 200 nucleotide units long that are involved in regulating genes. The researchers examined the abundance, or expression, of lncRNAs in patients who were 60 years and older and who had cytogenetically normal (CN) AML.
The study is published online in the Proceedings of the National Academy of Sciences.
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]
COLUMBUS, Ohio – A new study led by researchers at The Ohio State University Comprehensive Cancer Center – Arthur G. James Cancer Hospital and Richard J. Solove Research Institute (OSUCCC – James) describes a novel marker that might help doctors choose the least toxic, most effective treatment for many older patients with acute myeloid leukemia (AML). AML occurs mainly in older patients and has a three-year survival rate of 5 to 15 percent.
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]
Incoming search terms:
LncRNA2Target – a database for differentially expressed genes after lncRNA knockdown or overexpression
Long noncoding RNAs (lncRNAs) have been emerged as critical regulators of gene expression at epigenetic, transcriptional and post-transcriptional level, yet what genes are regulated by lncRNAs remains to be characterized. To assess the effects of a specific lncRNA on gene expression, increasing researchers profiled the genome-wide or individual gene expression level changes after knocking down or overexpressing the lncRNA. However, no online repository is currently available to collect these differentially expressed genes regulated by lncRNAs.
To make it convenient for researchers to know what genes are regulated by a lncRNA or which lncRNAs regulate a given gene of interest, researchers at the Harbin Institute of Technology have developed LncRNA2Target: a comprehensive resource of differentially expressed genes after lncRNA knockdown or overexpression.
In this database system, target genes of a lncRNA are defined as the differentially expressed genes after knocking down or overexpressing the lncRNA. By reviewing all published lncRNA papers, we manually curated the differentially expressed target genes confirmed by qRT-PCR or western blot, and identified all the differential target genes from the microarray or RNA-seq data.
Availability – the LncRNA2Target database is available at: http://www.lncrna2target.org/
- Qinghua Jiang; Jixuan Wang; Xiaoliang Wu; Rui Ma; Tianjiao Zhang; Shuilin Jin; Zhijie Han; Renjie Tan; Jiajie Peng; Guiyou Liu; Yu Li; Yadong Wang. LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression. Nucleic Acids Research 2014; doi: 10.1093/nar/gku1173