Search Results for: long noncoding rna expression
The worst subtype of neuroblastoma is caused by MYCN oncogene amplification and N-Myc oncoprotein over-expression. Long noncoding RNAs (lncRNAs) are emerging as critical regulators of gene expression and tumourigenesis. While Myc oncoproteins are well-known to exert tumourigenic effects by regulating the expression of protein-coding genes and microRNAs, little is known about which lncRNAs are Myc targets and whether the Myc target lncRNAs play a role in Myc-induced oncogenesis.
Here researchers at the Children’s Cancer Institute Australia for Medical Research performed differential gene expression studies using lncRNA microarray in neuroblastoma cells after transfection with control or N-Myc-specific small interfering RNA (siRNA), and identified N-Myc target lncRNAs including the novel lncRNA linc00467, the expression and function of which were completely unknown. RT-PCR, chromatin immunoprecipitation and luciferase assays showed that N-Myc suppressed linc00467 gene expression through direct binding to the linc00467 gene promoter and reducing linc00467 promoter activity. While N-Myc suppressed the expression of RD3, the protein-coding gene immediately down-stream of linc00467 gene, through direct binding to the RD3 gene promoter and reducing RD3 promoter activity, linc00467 reduced RD3 mRNA expression. Moreover, Affymetrix microarray analysis revealed that one of genes significantly up-regulated by linc00467 siRNA was the tumour suppressor gene DKK1. Importantly, knocking-down linc00467 expression with siRNA in neuroblastoma cells reduced the number of viable cells and increased the percentage of apoptotic cells, and co-transfection with DKK1 siRNA blocked the effects. These findings therefore demonstrate that N-Myc-mediated suppression of linc00467 gene transcription counterintuitively blocks N-Myc-mediated reduction in RD3 mRNA expression, and reduces neuroblastoma cell survival by inducing DKK1 expression.
- Atmadibrata B, Liu PY, Sokolowski N, Zhang L, Wong M, et al. (2014) The Novel Long Noncoding RNA linc00467 Promotes Cell Survival but Is Down-Regulated by N-Myc. PLoS ONE 9(2): e88112.
The life cycle of Plasmodium falciparum is very complex, with an erythrocytic stage that involves the invasion of red blood cells and the survival and growth of the parasite within the host. Over the past several decades, numbers of studies have shown that proteins exported by P. falciparum to the surface of infected red blood cells play a critical role in recognition and interaction with host receptors and are thus essential for the completion of the life cycle of P. falciparum. However, little is known about long noncoding RNAs (lncRNAs).
In this study, researchers at Ningbo University, China designed a computational pipeline to identify new lncRNAs of P. falciparum from published RNA-seq data and analyzed their sequences and expression features. As a result, 164 novel lncRNAs were found. The sequences and expression features of P. falciparum lncRNAs were similar to those of humans and mice: there was a lack of sequence conservation, low expression levels, and high expression coefficient of variance and co-expression with nearby coding sequences in the genome. Next, a coding/noncoding gene co-expression network for P. falciparum was constructed to further annotate the functions of novel and known lncRNAs. In total, the functions of 69 lncRNAs, including 44 novel lncRNAs, were annotated. The main functions of the lncRNAs included metabolic processes, biosynthetic processes, regulation of biological processes, establishment of localization, catabolic processes, cellular component organization, and interspecies interactions between organisms. These results will provide clues to further the investigation of interactions between human hosts and parasites and the mechanisms of P. falciparum infection.
- Liao Q, Shen J, Liu J, Sun X, Zhao G, Chang Y, Xu L, Li X, Zhao Y, Zheng H, Zhao Y, Wu Z. (2014) Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data. Parasitol Res [Epub ahead of print]. [astract]
Incoming search terms:
- Genome-wide identification and functional annotation of Plasmodium falciparum long noncoding RNAs from RNA-seq data
Ectopic and eutopic endometrial lncRNA and messenger RNA (mRNA) expression levels were determined by microarray in four patients; quantitative reverse transcription-polymerase chain reaction validation of 10 differentially expressed lncRNAs was conducted in another 21 patients. The lncRNAs’ functions were predicted through coexpressed mRNA annotations.
A total of 948 lncRNA transcripts and 4,088 mRNA transcripts were dysregulated in ectopic endometrial tissue, compared with paired eutopic endometrial tissue. The expressions of the 10 chosen lncRNAs were validated by quantitative reverse transcription-polymerase chain reaction. Functional analysis suggests that several groups of lncRNAs may participate in biological pathways related to endometriosis by cis- and/or trans-regulation of protein-coding genes.
This study constitutes the first report of lncRNA expression patterns in human ectopic and eutopic endometrial tissue. Nearly 1,000 dysregulated lncRNA transcripts are found by microarray.
- Sun PR1, Jia SZ1, Lin H1, Leng JH2, Lang JH1.(2014) Genome-wide profiling of long noncoding ribonucleic acid expression patterns in ovarian endometriosis by microarray. Fertil Steril [Epub ahead of print]. [abstract]
Incoming search terms:
- agilent lncRNA
- methods to detect lncRNA
Although some long noncoding RNAs (lncRNAs) have been shown to regulate gene expression in cis, it remains unclear whether lncRNAs can directly regulate transcription in trans by interacting with chromatin genome-wide independently of their sites of synthesis.
Here, researchers from the University of Oxford describe the genomically local and more distal functions of Paupar, a vertebrate-conserved and central nervous system-expressed lncRNA transcribed from a locus upstream of the gene encoding the PAX6 transcription factor. Knockdown of Paupar disrupts the normal cell cycle profile of neuroblastoma cells and induces neural differentiation. Paupar acts in a transcript-dependent manner both locally, to regulate Pax6, as well as distally by binding and regulating genes on multiple chromosomes, in part through physical association with PAX6 protein. Paupar binding sites are enriched near promoters and can function as transcriptional regulatory elements whose activity is modulated by Paupar transcript levels. These findings demonstrate that a lncRNA can function in trans at transcriptional regulatory elements distinct from its site of synthesis to control large-scale transcriptional programmes.
- Vance KW, Sansom SN, Lee S, Chalei V, Kong L, Cooper SE, Oliver PL, Ponting CP. (2014) The long non-coding RNA Paupar regulates the expression of both local and distal genes. EMBO J [Epub ahead of print]. [abstract]
Incoming search terms:
- lncrna Oxford