Search Results for: long noncoding rna expression
MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures
Long noncoding RNAs (lncRNAs) regulate gene expression by association with chromatin, but how they target chromatin remains poorly understood. Researchers from the University of Gothenburg have used chromatin RNA immunoprecipitation-coupled high-throughput sequencing to identify 276 lncRNAs enriched in repressive chromatin from breast cancer cells.
Using one of the chromatin-interacting lncRNAs, MEG3, they explored the mechanisms by which lncRNAs target chromatin. They show that MEG3 and EZH2 share common target genes, including the TGF-β pathway genes. Genome-wide mapping of MEG3 binding sites reveals that MEG3 modulates the activity of TGF-β genes by binding to distal regulatory elements. MEG3 binding sites have GA-rich sequences, which guide MEG3 to the chromatin through RNA-DNA triplex formation. The researchers have found that RNA-DNA triplex structures are widespread and are present over the MEG3 binding sites associated with the TGF-β pathway genes. These findings suggest that RNA-DNA triplex formation could be a general characteristic of target gene recognition by the chromatin-interacting lncRNAs.
- Mondal T, Subhash S, Vaid R, Enroth S, Uday S, Reinius B, Mitra S, Mohammed A, James AR, Hoberg E, Moustakas A, Gyllensten U, Jones SJ, Gustafsson CM, Sims AH, Westerlund F, Gorab E, Kanduri C. (2015) MEG3 long noncoding RNA regulates the TGF-β pathway genes through formation of RNA-DNA triplex structures. Nat Commun 6:7743. [article]
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Agilent Collaborates with Ghent University to Incorporate LNCipedia Content to Human v3 Gene Expression Microarray
SANTA CLARA, Calif.–(BUSINESS WIRE)–Agilent Technologies Inc. (NYSE:A) today announced updates to its SurePrint gene expression microarrays for messenger RNA profiling applications for human, mouse and rat models. The updates improve coding and noncoding content, which will provide up-to-date tools for researchers to investigate expression patterns on a highly accessible platform.
“Through the high performance and quantitative concordance of our gene expression microarrays, along with our RNA-Seq and target-enrichment products, we enable researchers to smoothly transition between microarray screening applications and deeper next-generation sequencing discovery.”
Agilent developed the updates to its flagship SurePrint G3 Human v3 gene expression microarray in collaboration with Ghent University for complete coverage of the LNCipedia 2.1 database to assay high-confidence, long noncoding RNA (lncRNA) transcripts.
Ahmad M. Khalil, PhD, knew the odds were against him — as in thousands upon thousands to one.
Yet he and his team never wavered from their quest to identify the parts of the body responsible for revving up one of the most aggressive forms of breast cancer, HER2+. This month in Breast Cancer Research and Treatment, Khalil and his colleagues at Case Western Reserve University proved the power of persistence; from a pool of more than 30,000 possibilities, they found 38 genes and molecules that most likely trigger HER2+ cancer cells to spread.
By narrowing what was once an overwhelming range of potential culprits to a relatively manageable number, Khalil and his team dramatically increased the chances of identifying successful treatment approaches to this particularly pernicious form of breast cancer. The HER2+ subtype accounts for approximately 20 to 30 percent of early-stage breast cancer diagnoses, which are estimated to be more than 200,000 new breast cancer diagnoses each year in this country, leading to approximately 40,000 deaths annually. Several cancer chemotherapy drugs do work well at early stages of the disease — destroying 95 to 98 percent of the cancer cells in HER2+ tumors.
Researchers from the Garvan Institute of Medical Research compared quantitative RT-PCR (qRT-PCR), RNA-seq and capture sequencing (CaptureSeq) in terms of their ability to assemble and quantify long noncoding RNAs and novel coding exons across 20 human tissues. CaptureSeq was superior for the detection and quantification of genes with low expression, showed little technical variation and accurately measured differential expression. This approach expands and refines previous annotations and simultaneously generates an expression atlas.
- Clark MB, Mercer TR, Bussotti G, Leonardi T, Haynes KR, Crawford J, Brunck ME, Cao KA, Thomas GP, Chen WY, Taft RJ, Nielsen LK, Enright AJ, Mattick JS, Dinger ME. (2015) Quantitative gene profiling of long noncoding RNAs with targeted RNA sequencing. Nat Methods [Epub ahead of print]. [abstract]