Limits...
Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis.

Karantzali E, Schulz H, Hummel O, Hubner N, Hatzopoulos A, Kretsovali A - Genome Biol. (2008)

Bottom Line: At the individual gene level, we found that transcriptional reprogramming triggered by histone deacetylase inhibition correlates with rapid changes in activating K4 trimethylation and repressive K27 trimethylation of histone H3.Our data suggest that inhibition of histone deacetylases accelerates the early events of differentiation by regulating the expression of pluripotency- and differentiation-associated genes in an opposite manner.This analysis provides information about genes that are important for embryonic stem cell function and the epigenetic mechanisms that regulate their expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular Biology and Biotehnology, FORTH, Heraklion 71110 Greece.

ABSTRACT

Background: Epigenetic mechanisms regulate gene expression patterns affecting cell function and differentiation. In this report, we examine the role of histone acetylation in gene expression regulation in mouse embryonic stem cells employing transcriptomic and epigenetic analysis.

Results: Embryonic stem cells treated with the histone deacetylase inhibitor Trichostatin A (TSA), undergo morphological and gene expression changes indicative of differentiation. Gene profiling utilizing Affymetrix microarrays revealed the suppression of important pluripotency factors, including Nanog, a master regulator of stem cell identity, and the activation of differentiation-related genes. Transcriptional and epigenetic changes induced after 6-12 hours of TSA treatment mimic those that appear during embryoid body differentiation. We show here that the early steps of stem cell differentiation are marked by the enhancement of bulk activatory histone modifications. At the individual gene level, we found that transcriptional reprogramming triggered by histone deacetylase inhibition correlates with rapid changes in activating K4 trimethylation and repressive K27 trimethylation of histone H3. The establishment of H3K27 trimethylation is required for stable gene suppression whereas in its absence, genes can be reactivated upon TSA removal.

Conclusion: Our data suggest that inhibition of histone deacetylases accelerates the early events of differentiation by regulating the expression of pluripotency- and differentiation-associated genes in an opposite manner. This analysis provides information about genes that are important for embryonic stem cell function and the epigenetic mechanisms that regulate their expression.

Show MeSH

Related in: MedlinePlus

Ezh2 and H3K27 trimethylation levels on the promoters of Nanog, Sall1 and Nr0b1. (a) ChIP assays using an anti-Ezh2 antibody on the promoters of Nanog, Sall1 and Nr0b1 during TSA treatment (6 and 12 h) and EB formation (4 and 8 days). (b) ChIP assays using an anti-3mK27 antibody were performed for the promoters of TSA down-regulated genes Nanog, Sall1 and Nr0b1 after 6 and 12 h of TSA treatment and further cultivation without TSA for an additional 6 and 12 h.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2643936&req=5

Figure 7: Ezh2 and H3K27 trimethylation levels on the promoters of Nanog, Sall1 and Nr0b1. (a) ChIP assays using an anti-Ezh2 antibody on the promoters of Nanog, Sall1 and Nr0b1 during TSA treatment (6 and 12 h) and EB formation (4 and 8 days). (b) ChIP assays using an anti-3mK27 antibody were performed for the promoters of TSA down-regulated genes Nanog, Sall1 and Nr0b1 after 6 and 12 h of TSA treatment and further cultivation without TSA for an additional 6 and 12 h.

Mentions: Trimethylation of K27 is catalyzed by Enhancer of Zeste 2 (Ezh2), a methyl-transferase component of the PRC2 complex. Employing ChIP assays, we confirmed the recruitment of Ezh2 on Nanog, Sall1 and Nr0b1 promoters (Figure 7a), in agreement with the appearance of K27 trimethylation during suppression either by TSA or in EBs (Figure 6a,b). Gene activation or repression of all six genes in both TSA-treated ES cells and EBs correlates with a respective increase or decrease in promoter-bound RNA polymerase II (Figure 6a,b). These results indicate that the observed chromatin modifications correlate well with the expected recruitment of transcriptional regulators and enzymes to the corresponding gene promoters.


Histone deacetylase inhibition accelerates the early events of stem cell differentiation: transcriptomic and epigenetic analysis.

Karantzali E, Schulz H, Hummel O, Hubner N, Hatzopoulos A, Kretsovali A - Genome Biol. (2008)

Ezh2 and H3K27 trimethylation levels on the promoters of Nanog, Sall1 and Nr0b1. (a) ChIP assays using an anti-Ezh2 antibody on the promoters of Nanog, Sall1 and Nr0b1 during TSA treatment (6 and 12 h) and EB formation (4 and 8 days). (b) ChIP assays using an anti-3mK27 antibody were performed for the promoters of TSA down-regulated genes Nanog, Sall1 and Nr0b1 after 6 and 12 h of TSA treatment and further cultivation without TSA for an additional 6 and 12 h.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2643936&req=5

Figure 7: Ezh2 and H3K27 trimethylation levels on the promoters of Nanog, Sall1 and Nr0b1. (a) ChIP assays using an anti-Ezh2 antibody on the promoters of Nanog, Sall1 and Nr0b1 during TSA treatment (6 and 12 h) and EB formation (4 and 8 days). (b) ChIP assays using an anti-3mK27 antibody were performed for the promoters of TSA down-regulated genes Nanog, Sall1 and Nr0b1 after 6 and 12 h of TSA treatment and further cultivation without TSA for an additional 6 and 12 h.
Mentions: Trimethylation of K27 is catalyzed by Enhancer of Zeste 2 (Ezh2), a methyl-transferase component of the PRC2 complex. Employing ChIP assays, we confirmed the recruitment of Ezh2 on Nanog, Sall1 and Nr0b1 promoters (Figure 7a), in agreement with the appearance of K27 trimethylation during suppression either by TSA or in EBs (Figure 6a,b). Gene activation or repression of all six genes in both TSA-treated ES cells and EBs correlates with a respective increase or decrease in promoter-bound RNA polymerase II (Figure 6a,b). These results indicate that the observed chromatin modifications correlate well with the expected recruitment of transcriptional regulators and enzymes to the corresponding gene promoters.

Bottom Line: At the individual gene level, we found that transcriptional reprogramming triggered by histone deacetylase inhibition correlates with rapid changes in activating K4 trimethylation and repressive K27 trimethylation of histone H3.Our data suggest that inhibition of histone deacetylases accelerates the early events of differentiation by regulating the expression of pluripotency- and differentiation-associated genes in an opposite manner.This analysis provides information about genes that are important for embryonic stem cell function and the epigenetic mechanisms that regulate their expression.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institute of Molecular Biology and Biotehnology, FORTH, Heraklion 71110 Greece.

ABSTRACT

Background: Epigenetic mechanisms regulate gene expression patterns affecting cell function and differentiation. In this report, we examine the role of histone acetylation in gene expression regulation in mouse embryonic stem cells employing transcriptomic and epigenetic analysis.

Results: Embryonic stem cells treated with the histone deacetylase inhibitor Trichostatin A (TSA), undergo morphological and gene expression changes indicative of differentiation. Gene profiling utilizing Affymetrix microarrays revealed the suppression of important pluripotency factors, including Nanog, a master regulator of stem cell identity, and the activation of differentiation-related genes. Transcriptional and epigenetic changes induced after 6-12 hours of TSA treatment mimic those that appear during embryoid body differentiation. We show here that the early steps of stem cell differentiation are marked by the enhancement of bulk activatory histone modifications. At the individual gene level, we found that transcriptional reprogramming triggered by histone deacetylase inhibition correlates with rapid changes in activating K4 trimethylation and repressive K27 trimethylation of histone H3. The establishment of H3K27 trimethylation is required for stable gene suppression whereas in its absence, genes can be reactivated upon TSA removal.

Conclusion: Our data suggest that inhibition of histone deacetylases accelerates the early events of differentiation by regulating the expression of pluripotency- and differentiation-associated genes in an opposite manner. This analysis provides information about genes that are important for embryonic stem cell function and the epigenetic mechanisms that regulate their expression.

Show MeSH
Related in: MedlinePlus