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1.
FIGURE 3.

FIGURE 3. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Validation of microarray results by Northern blot analysis. The identity of the selected transcripts is indicated on the right. The signals from the Northern blot were normalized to 18S rRNA (not shown). These values were compared with the values measured by microarray (average of two independent profiles). Values are given as fold changes relative to the values obtained in mock treated (cont.) cells (positive values, overrepresented; negative values, underrepresented).

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
2.
FIGURE 4.

FIGURE 4. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

NMD factors regulate a common set of transcripts. (A–D) Expression profiles of RNAs at least 1.5-fold over- and underrepresented, respectively, in UPF1-depleted cells (A,B), or in UPF3-depleted cells (C,D) and detectable in all depletions. Average expression levels of two independent profiles per protein are shown. (E) Core NMD targets corresponding to transcripts at least 1.5-fold upregulated in 10 out of 12 profiles of cells depleted of NMD factors. (F) Transcripts at least 1.5-fold downregulated in 10 out of 12 profiles of cells depleted of NMDfactors. RNAs are represented as lines and colored relative to their expression levels, as indicated. Note that the lines are wider in (F). The number of mRNAs displayed per panel is indicated in italics.

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
3.
FIGURE 5.

FIGURE 5. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Core transcripts represent authentic NMD targets. (A–K) RNA samples isolated from control cells (cont.) or cells depleted of XRN1 were analyzed by Northern blot using probes complementary to the mRNAs indicated below the panels. Asterisks indicate the positions of the 3′-decay intermediates. No decay intermediates were detected for CG30035 or pgi. To detect the ago2, dcr-2, smg6 decay intermediates, poly(A)+ RNAs was isolated and analyzed on a 1.6% agarose gel. The position of RNA size markers is indicated on the left.

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
4.
FIGURE 2.

FIGURE 2. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Expression profiles of Drosophila cells depleted of NMD factors. RNAs are represented as lines and colored relative to their expression levels, as indicated. Average expression levels of two independent profiles are shown. The experiment tree was calculated using the distance option of the genespring software (Euclidian distance). Although 5379 mRNAs were detected in the 12 profiles obtained for the NMD factors, the top panel of this figure displays 4940 mRNAs, which were detectable both in the 12 profiles obtained in NMD-deficient cells and in the two profiles of THO-depleted cells. The fractions of regulated transcripts in two independent profiles for each factor are indicated underneath.

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
5.
FIGURE 1.

FIGURE 1. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Depletion of NMD factors impairs cell proliferation and leads to G2/M-cell cycle arrest. (A) Drosophila SL2 cells were treated with the indicated dsRNAs. Cell numbers were determined up to 7 d after addition of dsRNAs. (B–E) FACS analysis of asynchronously growing SL2 cells. Cells were treated with the indicated dsRNAs, stained with propidium iodide and analyzed using a flow cytometer. The table shows the proportion of cells in different phases of the cell cycle as shown in (D).

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
6.
FIGURE 7.

FIGURE 7. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

NMD regulates the expression of transcripts associated with diverse cellular processes. (A) Percentage of genes associated with the functional categories shown on the left. Black bars: 5379 detectable RNAs; cyan bars: core transcripts (184 mRNAs); blue bars: upregulated transcripts in eight out of 12 profiles obtained for NMD factors (360 mRNAs). Asterisks indicate functional categories for which the enrichment or the underrepresentation among core transcripts is significant (two asterisks, P value < 1 × 10−2, one asterisk, P value < 5 × 10−2). (B,C) Transcripts exclusively regulated in the individual knockdowns. Transcripts up- or downregulated in cells depleted of one or two NMD factors but unaffected in the other depletions.

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.
7.
FIGURE 6.

FIGURE 6. From: Nonsense-mediated mRNA decay factors act in concert to regulate common mRNA targets.

Features of NMD targets. (A) Drosophila chromosomes are represented as vertical lines. Centromeres are located at the bottom of the panel and are shown as dots. The scale bar on the left corresponds to the euchromatic sequence. Horizontal lines indicate the positions of core transcripts shown in Figure 4E ▶. The number of genes and of probe sets present in the array per chromosome is indicated below the panel. The fractions of detectable and upregulated transcripts are given in percentages. (B) Signal intensities (averages of two independent experiments) after normalization are shown in a histogram plot for all detectable transcripts in control cells (yellow bars) as well as for core transcripts in control cells (red bars) or in UPF1-depleted cells (blue bars). (C) The distribution of transcript lengths is shown for detectable and core transcripts. Numbers in brackets indicate the average length in nucleotides. (D) The distribution of intron counts per gene is shown for detectable and core transcripts. Numbers in brackets indicate the average number of introns.

JAN REHWINKEL, et al. RNA. 2005 October;11(10):1530-1544.

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