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1.
Figure 4

Figure 4. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Effects on genic arrays are stronger for Hrp3-bound loci, also seen for genes without substantially changed expression levels in the hrp1Δ hrp3Δ mutant, and not stronger for loci with increased cryptic antisense transcription. (A) and (B) Data as in Figure 3B and C, respectively, but divided into Hrp3-bound (369 calls) and -unbound (3644) loci (Walfridsson et al, 2007). (C) Data as in Figure 3C, but only genes without any transcriptional changes (2570 calls). (D) Data as in Figure 3C, but only genes with upregulated cryptic antisense transcription (828 calls).

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
2.
Figure 2

Figure 2. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Histogram of transcript level changes as summarized in Table I. (A) Sense transcript levels of the indicated mutants relative to respective controls. (B) Sense and cryptic antisense transcript levels relative to wt for the indicated mutants. Red and blue dashed lines depict the 1.5 fold and 2 fold thresholds, respectively. The total number of changed transcripts (n) is indicated in the upper left corner of each panel.

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
3.
Figure 5

Figure 5. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Hrp1 and Hrp3 efficiently space nucleosomes in vitro in an ATP-dependent manner. Phage λ DNA salt dialysis chromatin was incubated with Hrp1, Hrp3 and ATP as indicated above the lanes and digested with MNase. Wedges on top of the lanes correspond to increasing concentrations of 1, 2 and 4 U/ml. ‘M' denotes 100 bp marker (New England Biolabs).

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
4.
Figure 3

Figure 3. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Hrp1 and Hrp3 together are critical for the generation of TSS-aligned genic nucleosome arrays. Overlay of TSS-aligned nucleosome occupancy profiles for 4013 genes in wt (Hu303, average of five biological replicates) and (A) hrp1Δ (Hu2239, average of two biological replicates), (B) hrp3Δ (Hu0575/EJY321, average of two biological replicates) and (C) hrp1Δ hrp3Δ (Hu2303, average two biological replicates) at 30°C. (DF) Spectral analysis as in (Lantermann et al, 2010) for the data in panels (AC), respectively. 6.2 or 6.5 nucleosomes per 1000, bp translate into a NRL of 161 or 154 bp in hrp1Δ or wt, respectively.

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
5.
Figure 1

Figure 1. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

H2A.Z, Swr1, Snf21 and Mit1 do not have a major role in nucleosome positioning around TSSs in S. pombe. Overlay of TSS-aligned nucleosome occupancy profiles for 4013 genes in (A) wt (Hu303, average of five biological replicates) and pht1Δ swr1Δ (Hu2127, average of two biological replicates) at 30°C, (B) wt (K240/Hu2261, average of two biological replicates) and snf21-ts (KYP176/Hu2262, average of two biological replicates) after 6 h at 34°C, (C) wt (as in (B)) and snf21-ts swr1Δ (Hu2314, average of two biological replicates) after 6 h at 34°C, and (D) wt (as in (A)) and mit1 (Hu1294, average of two biological replicates) at 30°C.

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
6.
Figure 6

Figure 6. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Hrp1 and Hrp3 show concentration- and ATP-dependent spacing activity in Nap1-assembly assay. (A) Phage λ DNA was mixed under physiological conditions with recombinant S. pombe histones, recombinant Nap1, purified Hrp1, Hrp3 and ATP as indicated on top of the lanes and digested with MNase (as in Figure 5). All samples were electrophoresed in the same gel, thin white lines mark horizontal rearrangement in Photoshop. (B) As panel (A) but with different Hrp1 and Hrp3 concentrations (in nM) as indicated. Samples in lanes 1, 2, 13 and 14 did not contain ATP. Lanes ‘M' as in Figure 5.

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.
7.
Figure 7

Figure 7. From: CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe.

Schematic illustrating the difference between bulk spacing and TSS-aligned genic arrays. (A) TSS-aligned regular nucleosome arrays with the same spacing and register relative to the TSS for many different genes are the basis for the NFR-array nucleosome organization observed in vivo. (B) Regions of regularly spaced nucleosomes (grey circles) at different positions relative to the TSS for different genes (and maybe also per gene in different cells) will give rise to bulk MNase ladders but not to regular genic arrays in TSS-aligned nucleosome occupancy composite plots. Note that the positions of the NFR, the −1, +1, and less so the +2 nucleosomes may remain largely unchanged.

Julia Pointner, et al. EMBO J. 2012 November 28;31(23):4388-4403.

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