Search Results for: incrna

Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen

lncRNA

The tumor microenvironment is a crucial determinant in tumor progression. Interstitial extracellular matrix (ECM), such as type I collagen (Col-1), is aberrantly enriched in the tumor microenvironment and promotes tumor progression. Long intergenic non-coding RNAs (lincRNA) are a new family of regulatory RNAs that modulate fundamental cellular processes via diverse mechanisms.

Researchers at Tulane University School of Medicine investigated whether the expression of lincRNAs was regulated by the tumor promoting Col-1. In a three-dimensional organotypic culture model using the reconstituted basement membrane ECM Matrigel (rBM 3-D), supplementation of Col-1 disrupted acini, a differentiation feature of well-differentiated lung adenocarcinoma cells, and concurrently induced the expression of a tumor-promoting lincRNA, HOX transcript antisense RNA (HOTAIR). Induction of HOTAIR by Col-1 was diminished by a neutralizing antibody against the Col-1 receptor alpha2beta1 integrin. Col-1 activates the expression of a reporter gene controlled by the human HOTAIR promoter. Moreover the expression of HOTAIR and Col-1 was concurrently up-regulated in human non-small cell lung cancer.

These findings indicate that tumor-promoting Col-1 up-regulates the expression of HOTAIR in NSCLC cells. These initial results warrant further investigation of HOTAIR and other lincRNA genes in lung tumorigenesis.

  • Zhuang Y, Wang X, Nguyen HT, Zhuo Y, Cui X, Fewell C, Flemington EK, Shan B. (2013) Induction of long intergenic non-coding RNA HOTAIR in lung cancer cells by type I collagen. J Hematol Oncol 6(1), 35. [Epub ahead of print]. [article]

Incoming search terms:

  • EGF induction of noncoding RNA
  • hotair lincRNA
  • lincRNA hotair mechanism

Featured long non-coding RNA – HOXA-AS2

HOXA-AS2 lncRNA

HOXA cluster antisense RNA 2 (HOXA-AS2) is a long non-coding RNA located between the HOXA3 and HOXA4 genes in the HOXA cluster. Its transcript is expressed in NB4 promyelocytic leukemia cells and human peripheral blood neutrophils, and expression is increased in NB4 cells treated with all trans retinoic acid (ATRA). Knockdown of HOXA-AS2 expression by transduced shRNA decreases the number of viable cells and increases the proportion of apoptotic cells, measured by annexin V binding and by activity and cleavage of caspases-3, -8, and -9. The increase in death of HOXA-AS2 knockdown cells was accompanied by an elevated TNF-related apoptosis-inducing ligand (TRAIL) levels, but ATRA-induced NB4 cells treated with TRAIL did show an increase in HOXA-AS2 expression. These results demonstrate that ATRA induction of HOXA-AS2 suppresses ATRA-induced apoptosis, possibly through a TRAIL-mediated pathway. HOXA-AS2-mediated negative regulation thus contributes to the fine-tuning of apoptosis during ATRA-induced myeloid differentiation in NB4 cells.

  • Zhao H, Zhang X, Frazão JB, Condino-Neto A, Newburger PE. (2013) HOX antisense lincRNA HOXA-AS2 is an apoptosis repressor in all trans retinoic acid treated NB4 promyelocytic leukemia cells. J Cell Biochem [Epub ahead of print]. [abstract]

Featured New Product – The SmartChip Human LncRNA1 Panel

Wafergen BiosystemsThe field of lncRNA research is in the midst of a rapid discovery phase, but that doesn’t mean your reagents have to be“experimental”. In collaboration with Biogazelle, we’ve designed SmartChip Human lncRNA-1 Panels to maximize your investigation of lncRNA expression. They contain over 1700 triplicate, predispensed PCR assays that have been extensively validated and annotated. In addition, we’ve ensured that the lncRNA assays in this SmartChip Panel are both compliant with the Minimum Information for Publication of Quantitative Real-Time PCR Experiments (MIQE) guidelines, and curated against the latest versions of genomic databases.

Wafergen BiosystemsTo understand lncRNA expression levels across a wide variety of well-characterized biological samples and simultaneously validate the the SmartChip Human lncRNA Panel, we profiled lncRNA expression in the NCI-60 cell lines. These are a set of 59 human, cancer cell-lines derived from diverse tissues, such as brain, blood, bone marrow, breast, colon, kidney, lung, ovary, prostate, and skin. As can be seen in figure below, the resulting heatmap shows that 97% of the 1700 lncRNA assayed are expressed reproducibly in at least one of the cell lines. A snapshot of the tissue-specificity, that appears to be a hallmark of lncRNA expression, was confirmed with well-characterized HULC and GOMAFU lncRNAs.

SmartChip Human lncRNA Panel – Product Note

The SmartChip Human lncRNA1 Panel is ideal for profiling the new and important area of ‘dark matter’ RNA. Simply prepare your sample, and load it into the SmartChip Panel already containing optimized real-time PCR assays in quadruplicate for each of the over 1700 assays with 10 known assays which have stable expression and can be consider ‘endogenous’ controls, and 5 exogenous RT-PCR controls; and reap high-quality results.

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Evolutionarily conserved long intergenic non-coding RNAs in the eye

lncRNA of the eye

The discovery that the mammalian transcriptome encodes thousands of long intergenic non-coding (linc) RNA transcripts, together with recent evidence that lincRNAs can regulate protein-coding genes, has added a new level of complexity to cellular transcriptional/translational regulation. Indeed several reports now link mutations in lincRNAs to heritable human disorders.

Here researchers from the Cleveland Clinic identified a subset of lincRNAs in terminally differentiated adult human retinal neurons based on their sequence conservation across species. RNA sequencing of eye tissue from several mammalian species with varied rod/cone photoreceptor content identified 18 lincRNAs that were highly conserved across these species. Sixteen of the 18 were conserved in human retinal tissue with 14 of these also conserved in the macular region. A subset of lincRNAs exhibited restricted tissue expression profiles in mice, with preferential expression in the retina. Mouse models with different populations of retinal cells as well as in situ hybridization provided evidence that these lincRNAs localized to specific retinal compartments, most notably to the photoreceptor neuronal layer. Computational genomic loci and promoter region analyses provided a basis for regulated expression of these conserved lincRNAs in retinal post-mitotic neurons. This combined approach identified several lincRNAs that could be critical for retinal and visual maintenance in adults.

  • Mustafi D, Kevany BM, Bai X, Maeda T, Sears JE, Khalil AM, Palczewski K. (2013) Evolutionarily conserved long intergenic non-coding RNAs in the eye. Hum Mol Genet [Epub ahead of print]. [abstract]

Incoming search terms:

  • lncrna database eyes
  • The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

Systematic study of human long intergenic non-coding RNAs and their impact on cancer

lincRNAs

The functional impact of several long intergenic non-coding RNAs (lincRNAs) has been characterized in previous studies. However, it is difficult to identify lincRNAs on a large-scale and to ascertain their functions or predict their structures in laboratory experiments because of the diversity, lack of knowledge and specificity of expression of lincRNAs. Furthermore, although there are a few well-characterized examples of lincRNAs associated with cancers, these are just the tip of the iceberg owing to the complexity of cancer.

Here, by combining RNA-Seq data from several kinds of human cell lines with chromatin-state maps and human expressed sequence tags, researchers at Jilin University, China successfully identified more than 3000 human lincRNAs, most of which were novel. Subsequently, they predicted the functions of 105 lincRNAs based on a coding-non-coding gene co-expression network. Finally, they propose a genetic mediator and key regulator model to unveil the subtle relationships between lincRNAs and lung cancer. Twelve lincRNAs may be principal players in lung tumorigenesis.

lincRNAsThe present study combines large-scale identification and functional prediction of human lincRNAs, and is a pioneering work in characterizing cancer-associated lincRNAs by bioinformatics.

  • Sun L, Luo H, Liao Q, Bu D, Zhao G, Liu C, Liu Y, Zhao Y. (2013) Systematic study of human long intergenic non-coding RNAs and their impact on cancer. Sci China Life Sci [Epub ahead of print]. [abstract]

Incoming search terms:

  • linc rna
  • non examples of genes
  • IGF1 lncRNA enhancer
  • Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network