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H3.3-H4 tetramer splitting events feature cell-type specific enhancers.

Huang C, Zhang Z, Xu M, Li Y, Li Z, Ma Y, Cai T, Zhu B - PLoS Genet. (2013)

Bottom Line: H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself.Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner.We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

View Article: PubMed Central - PubMed

Affiliation: College of Biological Sciences, China Agricultural University, Beijing, China.

ABSTRACT
Previously, we reported that little canonical (H3.1-H4)(2) tetramers split to form "hybrid" tetramers consisted of old and new H3.1-H(4) dimers, but approximately 10% of (H3.3-H4)2 tetramers split during each cell cycle. In this report, we mapped the H3.3 nucleosome occupancy, the H3.3 nucleosome turnover rate and H3.3 nucleosome splitting events at the genome-wide level. Interestingly, H3.3 nucleosome turnover rate at the transcription starting sites (TSS) of genes with different expression levels display a bimodal distribution rather than a linear correlation towards the transcriptional activity, suggesting genes are either active with high H3.3 nucleosome turnover or inactive with low H3.3 nucleosome turnover. H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself. Although both H3.3 nucleosome turnover and splitting events are enriched at active genes, these events only display a moderate positive correlation, suggesting H3.3 nucleosome splitting events are not the mere consequence of H3.3 nucleosome turnover. Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner. We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

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Genome-wide analysis of H3.3 nucleosome turnover.(A) Experimental scheme to determine the turnover index. (B) Two-dimensional histogram of T24 and T48 for all H3.3 nucleosomes. (C) Distribution profiles of the H3.3 nucleosome turnover index around the TSS (left panel) and TES (right panel). (D) Bimodal distribution of turnover at +1 nucleosome versus expression level. Genes were sorted by RPKM from high to low with a sliding widow of 600 genes and then plotted against their turnover index at the +1 nucleosome. (E) Genomic distribution of high turnover and low turnover H3.3 nucleosomes.
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pgen-1003558-g002: Genome-wide analysis of H3.3 nucleosome turnover.(A) Experimental scheme to determine the turnover index. (B) Two-dimensional histogram of T24 and T48 for all H3.3 nucleosomes. (C) Distribution profiles of the H3.3 nucleosome turnover index around the TSS (left panel) and TES (right panel). (D) Bimodal distribution of turnover at +1 nucleosome versus expression level. Genes were sorted by RPKM from high to low with a sliding widow of 600 genes and then plotted against their turnover index at the +1 nucleosome. (E) Genomic distribution of high turnover and low turnover H3.3 nucleosomes.

Mentions: The above experiments provided some hints about the turnover of H3.3 nucleosomes. However, these experiments were not specifically designed for determining the turnover rate of H3.3 nucleosomes. We attempted to develop a mathematic model using the above data set, but too many approximations had to be incorporated into the equations, which may affect the accuracy of the model. In order to directly measure the turnover rate of H3.3 nucleosomes, we performed a second set of experiments, in which we induced the expression of HA-H3.3 histones for 48 h and then switched it off (Figure 2A). Cells were harvested at 0 h, 24 h and 48 h after the termination of induction. Mononucleosomes were prepared from these cells and then subjected to ChIP-Seq with antibodies against HA (Figure S2D).


H3.3-H4 tetramer splitting events feature cell-type specific enhancers.

Huang C, Zhang Z, Xu M, Li Y, Li Z, Ma Y, Cai T, Zhu B - PLoS Genet. (2013)

Genome-wide analysis of H3.3 nucleosome turnover.(A) Experimental scheme to determine the turnover index. (B) Two-dimensional histogram of T24 and T48 for all H3.3 nucleosomes. (C) Distribution profiles of the H3.3 nucleosome turnover index around the TSS (left panel) and TES (right panel). (D) Bimodal distribution of turnover at +1 nucleosome versus expression level. Genes were sorted by RPKM from high to low with a sliding widow of 600 genes and then plotted against their turnover index at the +1 nucleosome. (E) Genomic distribution of high turnover and low turnover H3.3 nucleosomes.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3675017&req=5

pgen-1003558-g002: Genome-wide analysis of H3.3 nucleosome turnover.(A) Experimental scheme to determine the turnover index. (B) Two-dimensional histogram of T24 and T48 for all H3.3 nucleosomes. (C) Distribution profiles of the H3.3 nucleosome turnover index around the TSS (left panel) and TES (right panel). (D) Bimodal distribution of turnover at +1 nucleosome versus expression level. Genes were sorted by RPKM from high to low with a sliding widow of 600 genes and then plotted against their turnover index at the +1 nucleosome. (E) Genomic distribution of high turnover and low turnover H3.3 nucleosomes.
Mentions: The above experiments provided some hints about the turnover of H3.3 nucleosomes. However, these experiments were not specifically designed for determining the turnover rate of H3.3 nucleosomes. We attempted to develop a mathematic model using the above data set, but too many approximations had to be incorporated into the equations, which may affect the accuracy of the model. In order to directly measure the turnover rate of H3.3 nucleosomes, we performed a second set of experiments, in which we induced the expression of HA-H3.3 histones for 48 h and then switched it off (Figure 2A). Cells were harvested at 0 h, 24 h and 48 h after the termination of induction. Mononucleosomes were prepared from these cells and then subjected to ChIP-Seq with antibodies against HA (Figure S2D).

Bottom Line: H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself.Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner.We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

View Article: PubMed Central - PubMed

Affiliation: College of Biological Sciences, China Agricultural University, Beijing, China.

ABSTRACT
Previously, we reported that little canonical (H3.1-H4)(2) tetramers split to form "hybrid" tetramers consisted of old and new H3.1-H(4) dimers, but approximately 10% of (H3.3-H4)2 tetramers split during each cell cycle. In this report, we mapped the H3.3 nucleosome occupancy, the H3.3 nucleosome turnover rate and H3.3 nucleosome splitting events at the genome-wide level. Interestingly, H3.3 nucleosome turnover rate at the transcription starting sites (TSS) of genes with different expression levels display a bimodal distribution rather than a linear correlation towards the transcriptional activity, suggesting genes are either active with high H3.3 nucleosome turnover or inactive with low H3.3 nucleosome turnover. H3.3 nucleosome splitting events are enriched at active genes, which are in fact better markers for active transcription than H3.3 nucleosome occupancy itself. Although both H3.3 nucleosome turnover and splitting events are enriched at active genes, these events only display a moderate positive correlation, suggesting H3.3 nucleosome splitting events are not the mere consequence of H3.3 nucleosome turnover. Surprisingly, H3.3 nucleosomes with high splitting index are remarkably enriched at enhancers in a cell-type specific manner. We propose that the H3.3 nucleosomes at enhancers may be split by an active mechanism to regulate cell-type specific transcription.

Show MeSH