43 research outputs found

    Increased ss-motif similiarity within miRNA families.

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    <p>The panels show the average number of common ss-motif among members of each miRNA family (arrow), compared to a distribution of average pre-miRNAs (repeated 1000 times). A. The miRNA gene family mir-515 (26 members; 172 common ss-motifs). B. The miRNA gene family mir-154 (17 members; 118 common ss-motifs). C. The miRNA gene family let-7 (8 members; 428 common ss-motifs).</p

    Comparison between Mirident and previously published software/algorithms.

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    1<p>Original training data.</p>2<p>“Th” indicates “Threshold”.</p><p>All the models were tested on the same data set of 124 pre-miRNAs and 124 non-pre-miRNA hairpins.</p

    Sequence-structure motif characteristics.

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    <p>Light hues (pink, light green) indicates the positive and negative randomly selected sequences (RSS). Darker hues (red, green) indicates the actual ss-motifs derived from the positive (pre-miRNA) and negative (CDS hairpin) training sets. A. Combinations of nucleotide and structural information in the ss-motifs. The figure shows occurrence of structural information relative to positions with specific nucleotide information. “Comb” denotes occurrences of specific nucleotide and structural information combined at the same position (<i>e.g.</i>, “A<sub>L</sub>”, “C<sub>D</sub>”, etc). “Up neighb” and “Dw neighb” denote occurrences of specific nucleotide notation combined with specific structural notations at the nearest upstream or downstream neighbouring position (<i>e.g.</i>, “N<sub>L</sub>A<sub>S</sub>” etc, and “A<sub>S</sub>N<sub>L</sub>” etc), respectively. B. Distribution of “L”, “R” and “D” denotes “left”, “right” and absence of (notation of) intramolecular interactions, respectively.</p

    Mirident performance.

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    <p>A. Effect of increasing number of ss-motifs on miRNA prediction accurracy. Note: The X-axis is discontinuous above 1500 motifs (dashed line). B. The ROC curve of Mirident (red line) trained with 1300 ss-motifs. The Area Under Curve (AUC) is 0.99. Results for other methods are shown for comparison.</p

    Expression of the reporter gene was detected by RT-PCR using DNase I digested RNA extracted from transgenic worms as template

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    For the negative controls (RNA-PCR) RT-PCR was performed using the same template without adding reverse transcriptase.<p><b>Copyright information:</b></p><p>Taken from "analysis of noncoding RNA promoter motifs"</p><p>http://www.biomedcentral.com/1471-2199/9/71</p><p>BMC Molecular Biology 2008;9():71-71.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527325.</p><p></p

    (A) The H/ACA snoRNA locus CeN55 is located in an intron of the protein coding gene D1046

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    1. Tiling array probe signal intensities indicate that the UM2 sequence upstream of snoRNA CeN55 might also be expressed (red box). (B) Model of RACE amplification of the putative UM2-snoRNA dicistronic fragments. 3AD is a 3'end adaptor ligated to the ncRNAs; 3RT is the primer complementary to 3AD, primer_UM2 located in the region of UM2. The RACE analysis was performed by reverse transcription using the 3RT as primer followed by PCR with primers primer_UM2 and 3RT. (C) Gel analysis of the RACE fragments.<p><b>Copyright information:</b></p><p>Taken from "analysis of noncoding RNA promoter motifs"</p><p>http://www.biomedcentral.com/1471-2199/9/71</p><p>BMC Molecular Biology 2008;9():71-71.</p><p>Published online 5 Aug 2008</p><p>PMCID:PMC2527325.</p><p></p

    GADD45A Inhibits Autophagy Through Regulating the Interaction Between BECN1 and PIK3C3

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    <div><p></p><p>GADD45A is a TP53-regulated and DNA damage-inducible tumor suppressor protein, which regulates cell cycle arrest, apoptosis, DNA repair, inhibits tumor growth and angiogenesis. However, the function of GADD45A in autophagy remains unknown. In this report, we demonstrate that GADD45A plays an important role in regulating the process of autophagy. GADD45A is able to decrease LC3-II expression and numbers of autophagosomes in mouse tissues and different cancer cell lines. Using bafilomycin A<sub>1</sub> treatment, we have observed that GADD45A regulates autophagosome initiation. Likely, GADD45A inhibition of autophagy is through its influence on the interaction between BECN1 and PIK3C3. Immunoprecipitation and GST affinity isolation assays exhibit that GADD45A directly interacts with BECN1, and in turn dissociates the BECN1-PIK3C3 complex. Furthermore, we have mapped the 71 to 81 amino acids of the GADD45A protein that are necessary for the GADD45A interaction with BECN1. Knockdown of BECN1 can abolish autophagy alterations induced by GADD45A. Taken together, these findings provide the novel evidence that GADD45A inhibits autophagy via impairing the BECN1-PIK3C3 complex formation.</p></div

    Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in -2

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    <p><b>Copyright information:</b></p><p>Taken from "Systematic identification of non-coding RNA 2,2,7-trimethylguanosine cap structures in "</p><p>http://www.biomedcentral.com/1471-2199/8/86</p><p>BMC Molecular Biology 2007;8():86-86.</p><p>Published online 29 Sep 2007</p><p>PMCID:PMC2200864.</p><p></p>erase II (Pol II) or III (Pol III), those located in introns with no evident upstream motifs (Intronic), and those with intergenic loci with no distinct upstream motifs (Other). The numbers of TMG-capped and non-TMG-capped ncRNAs were shown for each group
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