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Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.

Foret MR, Sandstrom RS, Rhodes CT, Wang Y, Berger MS, Lin CH - Front Genet (2014)

Bottom Line: Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability.Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human.Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Texas at San Antonio San Antonio, TX, USA.

ABSTRACT
Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability. In this study, we show that trimethylation at H3K9 (H3K9me3) is enriched in an adult neural stem cell niche- the subventricular zone (SVZ) on the walls of the lateral ventricle in both rodent and non-human primate baboon brain. Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human. To understand the function of H3K9me3 in this adult neurogenic niche, we performed genome-wide analyses using ChIP-Seq (chromatin immunoprecipitation and deep-sequencing) and RNA-Seq for in vivo SVZ cells purified from baboon brain. Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed. As neurogenesis progresses in the adult SVZ, cell fate restriction is essential to direct proper lineage commitment. Our findings highlight that H3K9me3 repression in undifferentiated SVZ cells is engaged in the maintenance of cell type integrity, implicating a role for H3K9me3 as an epigenetic mechanism to control cell fate transition within this adult germinal niche.

No MeSH data available.


Quantification of co-localization percentages between H3K9me3 and subpopulations of SVZ cells by flow cytometry. After SVZ dissection, dissociated cells were analyzed by flow cytometry with antibodies against H3K9me3 and cell-type markers including GFAP (quiescent and active NSC marker), Vimentin (relatively active NSCs), PSA-NCAM (migrating neuroblast), and DCX (early and migrating neuroblast marker). Bar graph represents undifferentiated SVZ cells for each population positive for GFAP, Vimentin, PSA-NCAM, and DCX (light green). Blue annotates H3K9me3-positive percentage within each SVZ subpopulation.
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Figure 3: Quantification of co-localization percentages between H3K9me3 and subpopulations of SVZ cells by flow cytometry. After SVZ dissection, dissociated cells were analyzed by flow cytometry with antibodies against H3K9me3 and cell-type markers including GFAP (quiescent and active NSC marker), Vimentin (relatively active NSCs), PSA-NCAM (migrating neuroblast), and DCX (early and migrating neuroblast marker). Bar graph represents undifferentiated SVZ cells for each population positive for GFAP, Vimentin, PSA-NCAM, and DCX (light green). Blue annotates H3K9me3-positive percentage within each SVZ subpopulation.

Mentions: To further quantify the percentages of co-localization between H3K9me3 and SVZ subpopulations, we carried out flow cytometry analysis for dissociated SVZ cells after micro-dissection of SVZ from baboon brain. Flow cytometry analysis reveals approximately 45 and 20% of GFAP- and Doublecortin (DCX)-positive populations contain H3K9me3, respectively (Figure 3). Consistent with immunostaining results, the great majority of Vimentin- and PSA-NCAM-positive cells (~95%) are colocalized with H3K9me3 (Figure 3). This quantification confirms that H3K9me3 is enriched in undifferentiated SVZ cells, while the abundance of H3K9me3 varies across different cell populations within the SVZ.


Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.

Foret MR, Sandstrom RS, Rhodes CT, Wang Y, Berger MS, Lin CH - Front Genet (2014)

Quantification of co-localization percentages between H3K9me3 and subpopulations of SVZ cells by flow cytometry. After SVZ dissection, dissociated cells were analyzed by flow cytometry with antibodies against H3K9me3 and cell-type markers including GFAP (quiescent and active NSC marker), Vimentin (relatively active NSCs), PSA-NCAM (migrating neuroblast), and DCX (early and migrating neuroblast marker). Bar graph represents undifferentiated SVZ cells for each population positive for GFAP, Vimentin, PSA-NCAM, and DCX (light green). Blue annotates H3K9me3-positive percentage within each SVZ subpopulation.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4115620&req=5

Figure 3: Quantification of co-localization percentages between H3K9me3 and subpopulations of SVZ cells by flow cytometry. After SVZ dissection, dissociated cells were analyzed by flow cytometry with antibodies against H3K9me3 and cell-type markers including GFAP (quiescent and active NSC marker), Vimentin (relatively active NSCs), PSA-NCAM (migrating neuroblast), and DCX (early and migrating neuroblast marker). Bar graph represents undifferentiated SVZ cells for each population positive for GFAP, Vimentin, PSA-NCAM, and DCX (light green). Blue annotates H3K9me3-positive percentage within each SVZ subpopulation.
Mentions: To further quantify the percentages of co-localization between H3K9me3 and SVZ subpopulations, we carried out flow cytometry analysis for dissociated SVZ cells after micro-dissection of SVZ from baboon brain. Flow cytometry analysis reveals approximately 45 and 20% of GFAP- and Doublecortin (DCX)-positive populations contain H3K9me3, respectively (Figure 3). Consistent with immunostaining results, the great majority of Vimentin- and PSA-NCAM-positive cells (~95%) are colocalized with H3K9me3 (Figure 3). This quantification confirms that H3K9me3 is enriched in undifferentiated SVZ cells, while the abundance of H3K9me3 varies across different cell populations within the SVZ.

Bottom Line: Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability.Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human.Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, University of Texas at San Antonio San Antonio, TX, USA.

ABSTRACT
Histone 3 Lysine 9 (H3K9) methylation is known to be associated with pericentric heterochromatin and important in genomic stability. In this study, we show that trimethylation at H3K9 (H3K9me3) is enriched in an adult neural stem cell niche- the subventricular zone (SVZ) on the walls of the lateral ventricle in both rodent and non-human primate baboon brain. Previous studies have shown that there is significant correlation between baboon and human regarding genomic similarity and brain structure, suggesting that findings in baboon are relevant to human. To understand the function of H3K9me3 in this adult neurogenic niche, we performed genome-wide analyses using ChIP-Seq (chromatin immunoprecipitation and deep-sequencing) and RNA-Seq for in vivo SVZ cells purified from baboon brain. Through integrated analyses of ChIP-Seq and RNA-Seq, we found that H3K9me3-enriched genes associated with cellular maintenance, post-transcriptional and translational modifications, signaling pathways, and DNA replication are expressed, while genes involved in axon/neuron, hepatic stellate cell, or immune-response activation are not expressed. As neurogenesis progresses in the adult SVZ, cell fate restriction is essential to direct proper lineage commitment. Our findings highlight that H3K9me3 repression in undifferentiated SVZ cells is engaged in the maintenance of cell type integrity, implicating a role for H3K9me3 as an epigenetic mechanism to control cell fate transition within this adult germinal niche.

No MeSH data available.