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Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes.

He X, Chatterjee R, Tillo D, Smith A, FitzGerald P, Vinson C - Epigenetics Chromatin (2014)

Bottom Line: In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region.Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome.Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.

ABSTRACT

Background: The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with transcriptional repression, is the most highly studied chemical modification of DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated regions (HMRs) often occur in CG islands (CGIs), however, they also occur outside of CGIs and function as cell-type specific enhancers. During the process of differentiation, reorganization of chromatin and nucleosome arrangement at regulatory regions is thought to occur in order for the establishment of cell-type specific transcriptional programs. However, the specifics regarding the organization of nucleosomes at HMRs and the potential mechanisms regulating nucleosome occupancy in these regions are unknown. Here, we have investigated nucleosome organization around hypomethylated regions (HMRs) identified in two mouse primary cells.

Results: Microccocal nuclease (MNase) digested mononucleosomes from primary cultures of new-born female mouse dermal fibroblasts and keratinocytes were mapped and compared to the HMRs obtained from single base-pair resolution methylomes. In both cell types, we find that nucleosomes are enriched at HMR boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region. Nucleosomes are enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types suggesting that nucleosome organization surrounding HMR boundaries is independent of methylation status. In addition, we find potential transcription factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries.

Conclusions: Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome. Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.

No MeSH data available.


Related in: MedlinePlus

Nucleosome organization at extended HMRs in fibroblasts. (a) Heatmap of CG methylation in fibroblasts (Fb) and keratinocytes (Ker) for the common HMRs in which one boundary is identical, but the other boundary is extended in fibroblasts. The boundaries of these HMRs are grouped into three types: identical in two cells (boundary 1), not identical with short end (boundary 2), and with long end (boundary 3). These HMRs are aligned by boundary 2. (b) Heatmap of nucleosome positioning in fibroblasts and keratinocytes for the overlapping HMRs extended in fibroblasts aligned by boundary 2. (c) Average nucleosome density in fibroblasts (blue), keratinocytes (red), and intrinsic nucleosome occupancy scores (INOS, black) for each boundary type of the extended HMRs.
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Fig3: Nucleosome organization at extended HMRs in fibroblasts. (a) Heatmap of CG methylation in fibroblasts (Fb) and keratinocytes (Ker) for the common HMRs in which one boundary is identical, but the other boundary is extended in fibroblasts. The boundaries of these HMRs are grouped into three types: identical in two cells (boundary 1), not identical with short end (boundary 2), and with long end (boundary 3). These HMRs are aligned by boundary 2. (b) Heatmap of nucleosome positioning in fibroblasts and keratinocytes for the overlapping HMRs extended in fibroblasts aligned by boundary 2. (c) Average nucleosome density in fibroblasts (blue), keratinocytes (red), and intrinsic nucleosome occupancy scores (INOS, black) for each boundary type of the extended HMRs.

Mentions: A common feature of HMRs shared between keratinocytes and fibroblasts is that the boundaries are not always identical. There exist 15,747 HMRs in which the one boundary is identical; however the other boundary is extended in one cell type [32]. The extended unmethylated region is on average 280 bps in length with a median of 170 bps (Figure 3a and b and Additional file 2: Figure S7a and b). The nucleosome localization at the common boundary of these extended HMRs is similar to the boundaries of those observed for HMRs with identical boundaries (Figure 3c and Additional file 2: Figures S7c, S8a and b). However for the extended HMRs, nucleosomes are displaced from their optimal positions at the identical boundary and phased nucleosomes extend into the methylated region, reflecting the influence of CGI-containing HMRs in the averaged profiles (2,453/7,497 or 32.7% of such HMRs overlap a CGI). The tissue-specific boundary of the shorter HMR (boundary 2) also has a positioned nucleosome and some modest phasing (Figure 3c and Additional file 2: Figure S7c). The extended boundary of the longer HMR (boundary 3) is reminiscent of boundaries in TS-HMRs with nucleosomes at the boundary, with little to no phasing of nucleosomes (Figure 3c and Additional file 2: Figure S7c). Nucleosomes centered on the boundary of both short and extended HMRs (boundaries 2 and 3) are in a region of high INOS, suggesting a prominent role for DNA sequence in specifying the boundaries of extended HMRs.Figure 3


Nucleosomes are enriched at the boundaries of hypomethylated regions (HMRs) in mouse dermal fibroblasts and keratinocytes.

He X, Chatterjee R, Tillo D, Smith A, FitzGerald P, Vinson C - Epigenetics Chromatin (2014)

Nucleosome organization at extended HMRs in fibroblasts. (a) Heatmap of CG methylation in fibroblasts (Fb) and keratinocytes (Ker) for the common HMRs in which one boundary is identical, but the other boundary is extended in fibroblasts. The boundaries of these HMRs are grouped into three types: identical in two cells (boundary 1), not identical with short end (boundary 2), and with long end (boundary 3). These HMRs are aligned by boundary 2. (b) Heatmap of nucleosome positioning in fibroblasts and keratinocytes for the overlapping HMRs extended in fibroblasts aligned by boundary 2. (c) Average nucleosome density in fibroblasts (blue), keratinocytes (red), and intrinsic nucleosome occupancy scores (INOS, black) for each boundary type of the extended HMRs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4265496&req=5

Fig3: Nucleosome organization at extended HMRs in fibroblasts. (a) Heatmap of CG methylation in fibroblasts (Fb) and keratinocytes (Ker) for the common HMRs in which one boundary is identical, but the other boundary is extended in fibroblasts. The boundaries of these HMRs are grouped into three types: identical in two cells (boundary 1), not identical with short end (boundary 2), and with long end (boundary 3). These HMRs are aligned by boundary 2. (b) Heatmap of nucleosome positioning in fibroblasts and keratinocytes for the overlapping HMRs extended in fibroblasts aligned by boundary 2. (c) Average nucleosome density in fibroblasts (blue), keratinocytes (red), and intrinsic nucleosome occupancy scores (INOS, black) for each boundary type of the extended HMRs.
Mentions: A common feature of HMRs shared between keratinocytes and fibroblasts is that the boundaries are not always identical. There exist 15,747 HMRs in which the one boundary is identical; however the other boundary is extended in one cell type [32]. The extended unmethylated region is on average 280 bps in length with a median of 170 bps (Figure 3a and b and Additional file 2: Figure S7a and b). The nucleosome localization at the common boundary of these extended HMRs is similar to the boundaries of those observed for HMRs with identical boundaries (Figure 3c and Additional file 2: Figures S7c, S8a and b). However for the extended HMRs, nucleosomes are displaced from their optimal positions at the identical boundary and phased nucleosomes extend into the methylated region, reflecting the influence of CGI-containing HMRs in the averaged profiles (2,453/7,497 or 32.7% of such HMRs overlap a CGI). The tissue-specific boundary of the shorter HMR (boundary 2) also has a positioned nucleosome and some modest phasing (Figure 3c and Additional file 2: Figure S7c). The extended boundary of the longer HMR (boundary 3) is reminiscent of boundaries in TS-HMRs with nucleosomes at the boundary, with little to no phasing of nucleosomes (Figure 3c and Additional file 2: Figure S7c). Nucleosomes centered on the boundary of both short and extended HMRs (boundaries 2 and 3) are in a region of high INOS, suggesting a prominent role for DNA sequence in specifying the boundaries of extended HMRs.Figure 3

Bottom Line: In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region.Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome.Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, MD 20892 USA.

ABSTRACT

Background: The interplay between epigenetic modifications and chromatin structure are integral to our understanding of genome function. Methylation of cytosine (5mC) at CG dinucleotides, traditionally associated with transcriptional repression, is the most highly studied chemical modification of DNA, occurring at over 70% of all CG dinucleotides in the genome. Hypomethylated regions (HMRs) often occur in CG islands (CGIs), however, they also occur outside of CGIs and function as cell-type specific enhancers. During the process of differentiation, reorganization of chromatin and nucleosome arrangement at regulatory regions is thought to occur in order for the establishment of cell-type specific transcriptional programs. However, the specifics regarding the organization of nucleosomes at HMRs and the potential mechanisms regulating nucleosome occupancy in these regions are unknown. Here, we have investigated nucleosome organization around hypomethylated regions (HMRs) identified in two mouse primary cells.

Results: Microccocal nuclease (MNase) digested mononucleosomes from primary cultures of new-born female mouse dermal fibroblasts and keratinocytes were mapped and compared to the HMRs obtained from single base-pair resolution methylomes. In both cell types, we find that nucleosomes are enriched at HMR boundaries. In contrast to the nucleosomes found at boundaries of HMRs in CGIs, HMRs outside of CGIs are calculated to be preferentially bound by nucleosomes, with phased nucleosomes propagating into the methylated region. Nucleosomes are enriched at the tissue-specific HMRs (TS-HMR) boundaries in both cell types suggesting that nucleosome organization surrounding HMR boundaries is independent of methylation status. In addition, we find potential transcription factor (TF) binding sites (E-box motifs) enriched in non-CGI TS-HMR boundaries.

Conclusions: Our results show that intrinsic nucleosome occupancy score (INOS) positively correlate with the nucleosome organization surrounding non-CGI TS-HMRs, suggesting that DNA sequence plays a role in the establishment of HMRs in the genome. Since nucleosomes impact all processes involving the genome, our results provide a link between epigenetic modifications, chromatin structure, and regulatory function.

No MeSH data available.


Related in: MedlinePlus