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1.
FIG. 2.

FIG. 2. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

HMGN1 binding profile at BTG2 locus. Shown are the binding profiles of HMGN1 along with CTCF, H3K27me3, H3K36me3, H3K4me3, H3K9ac, RNA Pol II, IgG, and DNase I HS sites at a 167-kb region surrounding the BTG2 gene (see Materials and Methods for details on scoring profiles). Boxes i to v, colocalization of HMGN1 with DNase I HS sites. Note that boxes i and v also contain CTCF binding sites. The IgG control does not shown any enrichment.

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.
2.
FIG. 3.

FIG. 3. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

HMGN1 binding sites and DNase I HS sites overlap. (A) The overlap between HMGN1 and DNase I HS sites in the genome. (B) DNase I HS sites that overlap HMGN1 sites are more hypersensitive and more likely to occur in promoters than DNase I HS sites that do not overlap HMGN1 sites. (C) HMGN1 sites that overlap DNase I HS sites have stronger HMGN1 signals and are more likely to occur in promoters than HMGN1 sites that do not overlap DNase I HS sites. (D) DNase I HS sites that overlap HMGN1 sites tend to be larger than those sites that do not overlap HMGN1 sites. (E) H3K4me3 is enriched at DNase I HS sites overlapping HMGN1 sites relative to DNase I HS sites that are not overlapping HMGN1 sites (see Materials and Methods for details on modification score profiles). (F) H2A.Z is enriched at DNase I HS sites overlapping HMGN1 sites relative to DNase I HS sites that are not overlapping HMGN1 sites. (G) H3K27me3 is depleted at the HMGN1 binding sites.

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.
3.
FIG. 5.

FIG. 5. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

HMGN1 is enriched at intron-exon boundaries. (A and B) HMGN1 and nucleosome profiles at the intron-exon junctions of expressed genes. (C and D) HMGN1 and nucleosome profiles at the intron-exon junctions of nonexpressed genes. In the x axis “start” denotes exon start and “end” denotes exon end regions. The numbers denote base pairs from these reference points. The “Nucleosome Score” and “HMGN1 Score” on the y axis denote the score as determined by the adjusted sense (antisense) read contributions in 5-bp windows normalized by the number of genes in each set (see Materials and Methods for details).

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.
4.
FIG. 1.

FIG. 1. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

Confirmation of HMGN1 signals obtained by ChIP-Seq. (A) Western blot showing the specificity of HMGN1 antibodies. The Coomassie blue staining shows the whole protein extract from cells, which was used for Western blotting with antibodies specific for either human HMGN1 or HMGN2. (B and C) Confirmation of HMGN1 peaks using TaqMan quantitative real-time PCR. (B) Boxes 1 to 3, HMGN1 ChIP-Seq positive regions; box 4, HMGN1 ChIP-Seq negative region. Highlighted regions were tested for HMGN1 enrichment using quantitative PCR analysis. (C) Quantitative PCR validation of ChIP-Seq results. HMGN1 binding is enriched in regions 1 to 3 compared to IgG control, whereas region 4 shows no HMGN1 enrichment.

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.
5.
FIG. 4.

FIG. 4. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

CTCF and YY1 binding sites are associated with HMGN1. (A) Nucleosome profiles along with HMGN1 and CTCF binding profiles in a segment of chromosome 5 near the SLC4A9 locus. A substantial overlap between HMGN1 and CTCF binding is observed. Lower panel, enlargement of a 500-bp region. CTCF binds to the linker region, and HMGN1 appears to bind to the nucleosome adjacent to the CTCF binding site. Tag density indicates the number of adjusted reads in 10-bp windows. (B) In CD4+ T cells CTCF binds to linker regions surrounded by well-positioned nucleosomes and displays an enrichment of HMGN1 at the binding sites. Blue and purple lines indicate nucleosome reads from sense and antisense strands, respectively. Red and green lines indicate HMGN1 reads from sense and antisense strands, respectively. rpb, reads per bp. The inferred nucleosome positions are represented as ovals. BS, CTCF binding site. (C) In CD4+ T cells, the HeLa cell-specific CTCF sites are occluded by nucleosomes and HMGN1 binding levels are low. Blue and purple lines indicate nucleosome reads from sense and antisense strands, respectively. Red and green lines indicate HMGN1 reads from sense and antisense strands, respectively. BS, CTCF binding site. (D) YY1 binds to linker regions bracketed by well-positioned nucleosomes and HMGN1 is enriched surrounding the binding sites. BS, YY1 binding site.

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.
6.
FIG. 6.

FIG. 6. From: Genomic Profiling of HMGN1 Reveals an Association with Chromatin at Regulatory Regions .

HMGN1 marks promoters of active genes. (A) Distribution of HMGN1 binding sites in CD4+ T cells. The distribution of “Random” peaks is shown as a control. “Upstream” and “Downstream” regions are defined as 2 kb upstream of the TSS and 2 kb downstream of the transcription end site, respectively. 5′ and 3′ UTR, Exon, and Intron coordinates were obtained from UCSC Gene coordinates. Only internal (not first or last) exons were considered. “Intergenic” regions were classified as all regions not within 2 kb of an annotated gene. (B) HMGN1 binding profiles across the gene bodies of expressed and nonexpressed genes. The x axis scale between the transcription start (TxStart) and end (TxEnd) sites denotes the percentage of gene body length. The y axis indicates the normalized read count per base pair (nrpb). (C) HMGN1 binding is significantly enriched at the promoter of the CD4 gene, which is expressed in CD4+ T cells. The “Tag density” indicates the number of adjusted reads aligning in 10-bp windows. (D) The MyoD gene, which is silent in CD4+ T cells, is devoid of HMGN1 binding. (E) Nucleosome position signals of the genes expressed in CD4+ T cells plotted with the HMGN1 signals. Gray and black dashed lines indicate the HMGN1 reads from sense and antisense strands of DNA. Red and blue lines indicate the nucleosome reads from sense and antisense strands of DNA. The inferred nucleosome positions are shown as ovals. (F) HMGN1 and nucleosome signals at the CD4 locus. (G) HMGN1 and nucleosome profiles in a 2-kb region surrounding transcription start sites of genes that are not expressed in CD4+ T cells. Red and blue lines indicate nucleosome reads from the sense and antisense strands, respectively. Gray and black dashed lines indicate HMGN1 reads from the sense and antisense strands, respectively.

Suresh Cuddapah, et al. Mol Cell Biol. 2011 February;31(4):700-709.

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