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1.
Figure 5.

Figure 5. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Developmental profile of the Slc16a2-Rlim region. (A) Composite (comp) and allelic (Cast, 129) ES d0 and d7 profiles, showing strong and moderate EZH2 sites across the Slc16a2-Rlim region. SNP and Indel density per 1-kb window, CpG islands and bivalent domains are shown above the epitope tracks. (B) Three potential models for spreading of EZH2.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
2.
Figure 6.

Figure 6. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Spread of H3K27me3 from EZH2 sites occurs in a distance-dependent manner. (A) EZH2 and H3K27me3 densities from d0 and d7 were binned over Chr13 and ChrX positions to obtain correlation coefficients and Z scores from a permutation-based random model. Pearson R coefficients are indicated for the correlation of strong/moderate EZH2 sites (orange values) and H3K27me3/moderate EZH2 sites (black values). A purple triangle marks the location of the Xic. (B,C) Smoothed trend lines of EZH2 (B) or H3K27me3 (C) densities at a given distance from the nearest strong site, on indicated days and chromosomes. Densities are plotted over a sliding 1-kb window with steps of 200 bp.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
3.
Figure 7.

Figure 7. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

A hierarchy of EZH2 sites, with limited EZH2 translocation and long-range H3K27me3 gradient. (A) Smoothed trend lines of EZH2 densities at a moderate (mod) site at given distances (x-axis) from the nearest strong site, on indicated days and chromosomes. (B) Smoothed trend lines of H3K27me3 densities at a moderate (mod) site at given distances (x-axis) from the nearest strong site, on indicated days and chromosomes. Color-coded triangles denote distance-at-half-maximum for each chromosomal time point. (C) Depiction of the number of moderate (mod) sites at given distances from the nearest strong site on d0 and d7 for Chr13 and ChrX. Scale: Bubble sizes represent fractions of 0.2, 0.05, and 0.02 of all mod sites. Each graphed bubble represents the median of sites in 40-kb bins. Pearson correlation coefficients (R) and Z scores (Fisher transformed) are shown. (D) Model and summary.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
4.
Figure 2.

Figure 2. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Many strong EZH2 sites are defined bivalent domains. (A) Characteristics of constant, acquired, and lost strong EZH2 sites on d0 and d7. The portion of sites overlapping CpG islands is indicated by stripes. (B) Changes in peak widths and densities (coverage per bp) for EZH2 and H3K27me3 between d0 and d7. Medians (turquoise, Chr13; orange, ChrX), 25–75 percentile (box) and 10–90 percentile (error bars) are shown. (C) Allelic skewing of strong EZH2 sites. Numbers of sites skewing to Cast (blue) or 129 (red) are shown. Those with significant skewing (P < 0.05, norm. approx. of binomial) are shown in darker blue and red. (Gray bars) Nonpolymorphic sites; (n/d), not determined. (D) Summed coverage of EZH2 and H3K27me3 at strong and moderate sites as a percentage of total chromosomal coverage on d0 and d7 (left) and as fold-change (d7/d0, right).

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
5.
Figure 4.

Figure 4. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Relationship of repetitive elements to EZH2 sites. (A) Repeat classes enriched or depleted in strong sites, ±3 kb flanking strong sites, and moderate sites are plotted by their level of enrichment (positive log2 odds ratio) or depletion (negative). Different time points and chromosomes, as marked. Bubble sizes indicate the fraction of sites (scale: 0.05, 0.2, 0.5, 1.0) containing a given repeat class (if enriched) or lacking it (if depleted). For example, LINE1 sequences are depleted across the board in most sites, hence their bubbles are large. Only statistically significant (Z > 2.5) enrichment or depletion is shown (bubble sizes smaller than 0.05 indicate insignificance). The full data are listed in Supplemental Table S2 for further reference. (B–D) Log2 odds ratios for significant (Z > 2.5) enrichment and depletion of specific repeat types at strong sites (B), flanking (±3 kb) strong sites (C), and moderate sites (D). The full data are listed in Supplemental Table S3 for further reference.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
6.
Figure 1.

Figure 1. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Allelic chromatin profiles of Xa and Xi. (A) Metagene analysis for chromatin epitopes on Chr13 and ChrX at indicated time points. Coverages were averaged over all genes (843 for Chr13, 1007 for ChrX) and scaled from the TSS to the 3′ end, E. Profiles extend 3 kb upstream of the TSS and 3 kb downstream from E. Densities were normalized to the average gene coverage over the chromosome. (B,C) Pearson correlations for pairwise comparisons between epitopes were compared to a permutation-based random model and resulting Z-scores plotted in heat maps. (B) Plots of MEF results. (C) Plots of ES d0 and d7 results. Numerical Z-scores are color-coded and scaled identically for all heat maps. (Yellow–red patches) Significant positive correlation, (blue patches) significant negative correlation. A white diagonal line separates Cast and 129 results.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.
7.
Figure 3.

Figure 3. From: Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations.

Moderate EZH2 sites are noncanonical PRC2 targets. (A) Characteristics of moderate EZH2 sites on d0 and d7. The portion of sites overlapping CpG islands is indicated by stripes. (B) Allelic skewing of moderate EZH2 sites. Numbers of sites skewing to Cast (blue) or 129 (red) are shown. Those with significant skewing (P < 0.05, norm. approx. of binomial) are shown in darker blue and red. (Gray bars) nonpolymorphic sites; (n/d) not determined. (C) Changes in EZH2 and H3K27me3 densities between d0 and d7. Medians (turquoise, Chr13; orange, ChrX), 25–75 percentile (box) and 10–90 percentile (error bars) are shown. (D) Metasite analysis for strong and moderate sites at indicated time points. Coverages were averaged over all strong (ChrX: 56, 147, 50 sites; Chr13: 79, 81, 83 sites for d0, d7, and MEFs) and moderate sites (ChrX: 1618, 4077, 1211 sites; chr13: 1241, 1041, 758 sites for d0, d7, and MEFs) and scaled from start to end. Profiles extend ±20 kb into flanks. Densities were normalized to the average site coverage over the chromosome.

Stefan F. Pinter, et al. Genome Res. 2012 October;22(10):1864-1876.

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