Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray

Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-based technologies for high-throughput expression profiling, they are still not routinely used in diagnostic. Microarrays, on the other hand, are more widely used for diagnostic profiling, especially for very small ncRNA (e.g., miRNAs), employing locked nucleic acid (LNA) arrays. However, LNA microarrays are quite expensive for high-throughput studies targeting longer ncRNAs, while DNA arrays do not provide satisfying results for the analysis of small RNAs. Here, we describe a mixed DNA/LNA microarray platform, where directly labeled small and longer ncRNAs are hybridized on LNA probes or custom DNA probes, respectively, enabling sensitive and specific analysis of a complex RNA population on a unique array in one single experiment. The DNA/LNA system, requiring relatively low amounts of total RNA, which complies with diagnostic references, was successfully applied to the analysis of differential ncRNA expression in mouse embryonic stem cells and adult brain cells

Prediction and preliminary validation of oncogene regulation by miRNAs-3

<p><b>Copyright information:</b></p><p>Taken from "Prediction and preliminary validation of oncogene regulation by miRNAs"</p><p>http://www.biomedcentral.com/1471-2199/8/79</p><p>BMC Molecular Biology 2007;8():79-79.</p><p>Published online 18 Sep 2007</p><p>PMCID:PMC2096627.</p><p></p>ours after transfection of HeLa cells with anti-let-7c inhibitor. RNAs and protein samples were extracted from non-transfected HeLa cells and cells transfected with the anti-let-7c and anti-miR-195 oligos, as indicated in figures. In case of the western analysis a positive control (protein extract from lymphoma cells overexpressing cMYC) was included as well

Prediction and preliminary validation of oncogene regulation by miRNAs-1

<p><b>Copyright information:</b></p><p>Taken from "Prediction and preliminary validation of oncogene regulation by miRNAs"</p><p>http://www.biomedcentral.com/1471-2199/8/79</p><p>BMC Molecular Biology 2007;8():79-79.</p><p>Published online 18 Sep 2007</p><p>PMCID:PMC2096627.</p><p></p> sites for appropriate miRNAs were inserted into EII site. Single target sites or triplets were used for and genes (for sequences see the Additional file )

Prediction and preliminary validation of oncogene regulation by miRNAs-4

<p><b>Copyright information:</b></p><p>Taken from "Prediction and preliminary validation of oncogene regulation by miRNAs"</p><p>http://www.biomedcentral.com/1471-2199/8/79</p><p>BMC Molecular Biology 2007;8():79-79.</p><p>Published online 18 Sep 2007</p><p>PMCID:PMC2096627.</p><p></p>tively. In figures (B) and (D) the predicted interaction between miRNA and the respective mutated binding site is depicted (B for , D for ). (E) microRNA 195 from the miR-15 family was predicted to be a reliable regulator for gene (see text for more details)

Prediction and preliminary validation of oncogene regulation by miRNAs-2

<p><b>Copyright information:</b></p><p>Taken from "Prediction and preliminary validation of oncogene regulation by miRNAs"</p><p>http://www.biomedcentral.com/1471-2199/8/79</p><p>BMC Molecular Biology 2007;8():79-79.</p><p>Published online 18 Sep 2007</p><p>PMCID:PMC2096627.</p><p></p>carrying a single binding site for miR-16, (B) reporter construct carrying a triple binding site for miR-16, (C) reporter constructs carrying a single binding site for let-7, (D) reporter constructs including sensors carrying the whole 3'UTRs from the gene. The luciferase activity was normalised against expression. Results are presented in % (100% – luciferase vector with no binding site, (+) control). Average from several experiments is shown (details in the text)

Prediction and preliminary validation of oncogene regulation by miRNAs-0

<p><b>Copyright information:</b></p><p>Taken from "Prediction and preliminary validation of oncogene regulation by miRNAs"</p><p>http://www.biomedcentral.com/1471-2199/8/79</p><p>BMC Molecular Biology 2007;8():79-79.</p><p>Published online 18 Sep 2007</p><p>PMCID:PMC2096627.</p><p></p>The structure selected by the filter should have full complementarity in the 5'miRNA-end, optionally a central loop/bulge and good 3' pairing with up to three mismatches