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H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells.

Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L - BMC Genomics (2012)

Bottom Line: Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac.This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation.In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, BP 10142-67404 ILLKIRCH Cedex, CU de Strasbourg, France.

ABSTRACT

Background: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expression.

Results: Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse embryonic stem (mES) cells. Genome-wide H3K9ac and H3K14ac show very high correlation between each other as well as with other histone marks (such as H3K4me3) suggesting a coordinated regulation of active histone marks. Moreover, the levels of H3K9ac and H3K14ac directly correlate with the CpG content of the promoters attesting the importance of sequences underlying the specifically modified nucleosomes. Our data provide evidence that H3K9ac and H3K14ac are also present over the previously described bivalent promoters, along with H3K4me3 and H3K27me3. Furthermore, like H3K27ac, H3K9ac and H3K14ac can also differentiate active enhancers from inactive ones. Although, H3K9ac and H3K14ac, a hallmark of gene activation exhibit remarkable correlation over active and bivalent promoters as well as distal regulatory elements, a subset of inactive promoters is selectively enriched for H3K14ac.

Conclusions: Our study suggests that chromatin modifications, such as H3K9ac and H3K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3K9 and H3K14 acetylation could be driven by cis regulatory elements such as CpG content at promoters. Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac. This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation. In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.

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H3K9ac and H3K14ac associate with active as well as bivalent promoters. (A) Heatmap of the signal density using k-means clustering observed on 27095 mouse refseq promoters (-/+5 kb) for H3K9ac and H3K14ac along with H3K4me3 and H3K27me3 (hallmark of bivalent promoters) and Pol II. The clustering of density map shows three different categories of genes. Active promoters having H3K9ac, H3K14ac, H3K4me3 and Pol II, bivalent promoters showing H3K4me3 and H3K27me3 along with H3K9ac and H3K14ac, and inactive promoters lacking all above marks along with Pol II. (B) Presence of H3K9ac and H3K14ac over randomly chosen bivalent loci was validated by ChIP-qPCR. (C) Increase in the H3K9 and H3K14 acetylation over bivalent promoters (Hhip and Gabra4) following HDAC inhibition by sodium butyrate. The presence of H3K9ac and H3K14ac over these bivalent loci at the indicated time points after the sodium butyrate treatment was measured by ChIP-qPCR. ChIP signals for H3K9ac and H3K14ac were normalized to total H3. Primer sequences used in ChIP-qPCR is provided in Additional file 4: Table S1. Error bars represent the standard deviation for three technical replicates. (D and E) UCSC genome browser track of two representative examples of loci showing H3K9ac and H3K14ac over the bivalent promoters.
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Figure 5: H3K9ac and H3K14ac associate with active as well as bivalent promoters. (A) Heatmap of the signal density using k-means clustering observed on 27095 mouse refseq promoters (-/+5 kb) for H3K9ac and H3K14ac along with H3K4me3 and H3K27me3 (hallmark of bivalent promoters) and Pol II. The clustering of density map shows three different categories of genes. Active promoters having H3K9ac, H3K14ac, H3K4me3 and Pol II, bivalent promoters showing H3K4me3 and H3K27me3 along with H3K9ac and H3K14ac, and inactive promoters lacking all above marks along with Pol II. (B) Presence of H3K9ac and H3K14ac over randomly chosen bivalent loci was validated by ChIP-qPCR. (C) Increase in the H3K9 and H3K14 acetylation over bivalent promoters (Hhip and Gabra4) following HDAC inhibition by sodium butyrate. The presence of H3K9ac and H3K14ac over these bivalent loci at the indicated time points after the sodium butyrate treatment was measured by ChIP-qPCR. ChIP signals for H3K9ac and H3K14ac were normalized to total H3. Primer sequences used in ChIP-qPCR is provided in Additional file 4: Table S1. Error bars represent the standard deviation for three technical replicates. (D and E) UCSC genome browser track of two representative examples of loci showing H3K9ac and H3K14ac over the bivalent promoters.

Mentions: In order to test the presence of H3K9 and H3K14 acetylations over the bivalent promoters, all the 27095 mouse promoters from UCSC genome browser were taken [28] and subjected to k-means clustering using seqMiner [33]. H3K4me3 and H3K27me3 (dual hallmarks of bivalent promoters) were used to get the bivalent loci. Pol II was included in the clustering to differentiate active and inactive genes. The resulting heatmap is shown in Figure5A. In agreement with previous genome-wide studies, there are three distinct categories of loci. In respect to the studied acetylation (i) active loci marked by Pol II, H3K4me3, and devoid of strong H3K27me3 signals are highly enriched in H3K9ac and H3K14ac, (ii) bivalent loci, which are marked by H3K4me3, H3K27me3 and low Pol II signals contain both H3K9ac and H3K14ac signals, and (iii) inactive loci, on which either of the above signals is missing. Our analysis suggests that indeed on bivalent promoters H3K9 and H3K14 acetylations occur together with H3K4 and H3K27 trimethylations (Figure5A).


H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells.

Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L - BMC Genomics (2012)

H3K9ac and H3K14ac associate with active as well as bivalent promoters. (A) Heatmap of the signal density using k-means clustering observed on 27095 mouse refseq promoters (-/+5 kb) for H3K9ac and H3K14ac along with H3K4me3 and H3K27me3 (hallmark of bivalent promoters) and Pol II. The clustering of density map shows three different categories of genes. Active promoters having H3K9ac, H3K14ac, H3K4me3 and Pol II, bivalent promoters showing H3K4me3 and H3K27me3 along with H3K9ac and H3K14ac, and inactive promoters lacking all above marks along with Pol II. (B) Presence of H3K9ac and H3K14ac over randomly chosen bivalent loci was validated by ChIP-qPCR. (C) Increase in the H3K9 and H3K14 acetylation over bivalent promoters (Hhip and Gabra4) following HDAC inhibition by sodium butyrate. The presence of H3K9ac and H3K14ac over these bivalent loci at the indicated time points after the sodium butyrate treatment was measured by ChIP-qPCR. ChIP signals for H3K9ac and H3K14ac were normalized to total H3. Primer sequences used in ChIP-qPCR is provided in Additional file 4: Table S1. Error bars represent the standard deviation for three technical replicates. (D and E) UCSC genome browser track of two representative examples of loci showing H3K9ac and H3K14ac over the bivalent promoters.
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Related In: Results  -  Collection

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Figure 5: H3K9ac and H3K14ac associate with active as well as bivalent promoters. (A) Heatmap of the signal density using k-means clustering observed on 27095 mouse refseq promoters (-/+5 kb) for H3K9ac and H3K14ac along with H3K4me3 and H3K27me3 (hallmark of bivalent promoters) and Pol II. The clustering of density map shows three different categories of genes. Active promoters having H3K9ac, H3K14ac, H3K4me3 and Pol II, bivalent promoters showing H3K4me3 and H3K27me3 along with H3K9ac and H3K14ac, and inactive promoters lacking all above marks along with Pol II. (B) Presence of H3K9ac and H3K14ac over randomly chosen bivalent loci was validated by ChIP-qPCR. (C) Increase in the H3K9 and H3K14 acetylation over bivalent promoters (Hhip and Gabra4) following HDAC inhibition by sodium butyrate. The presence of H3K9ac and H3K14ac over these bivalent loci at the indicated time points after the sodium butyrate treatment was measured by ChIP-qPCR. ChIP signals for H3K9ac and H3K14ac were normalized to total H3. Primer sequences used in ChIP-qPCR is provided in Additional file 4: Table S1. Error bars represent the standard deviation for three technical replicates. (D and E) UCSC genome browser track of two representative examples of loci showing H3K9ac and H3K14ac over the bivalent promoters.
Mentions: In order to test the presence of H3K9 and H3K14 acetylations over the bivalent promoters, all the 27095 mouse promoters from UCSC genome browser were taken [28] and subjected to k-means clustering using seqMiner [33]. H3K4me3 and H3K27me3 (dual hallmarks of bivalent promoters) were used to get the bivalent loci. Pol II was included in the clustering to differentiate active and inactive genes. The resulting heatmap is shown in Figure5A. In agreement with previous genome-wide studies, there are three distinct categories of loci. In respect to the studied acetylation (i) active loci marked by Pol II, H3K4me3, and devoid of strong H3K27me3 signals are highly enriched in H3K9ac and H3K14ac, (ii) bivalent loci, which are marked by H3K4me3, H3K27me3 and low Pol II signals contain both H3K9ac and H3K14ac signals, and (iii) inactive loci, on which either of the above signals is missing. Our analysis suggests that indeed on bivalent promoters H3K9 and H3K14 acetylations occur together with H3K4 and H3K27 trimethylations (Figure5A).

Bottom Line: Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac.This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation.In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.

View Article: PubMed Central - HTML - PubMed

Affiliation: Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR 7104, INSERM U 964, Université de Strasbourg, BP 10142-67404 ILLKIRCH Cedex, CU de Strasbourg, France.

ABSTRACT

Background: Transcription regulation in pluripotent embryonic stem (ES) cells is a complex process that involves multitude of regulatory layers, one of which is post-translational modification of histones. Acetylation of specific lysine residues of histones plays a key role in regulating gene expression.

Results: Here we have investigated the genome-wide occurrence of two histone marks, acetylation of histone H3K9 and K14 (H3K9ac and H3K14ac), in mouse embryonic stem (mES) cells. Genome-wide H3K9ac and H3K14ac show very high correlation between each other as well as with other histone marks (such as H3K4me3) suggesting a coordinated regulation of active histone marks. Moreover, the levels of H3K9ac and H3K14ac directly correlate with the CpG content of the promoters attesting the importance of sequences underlying the specifically modified nucleosomes. Our data provide evidence that H3K9ac and H3K14ac are also present over the previously described bivalent promoters, along with H3K4me3 and H3K27me3. Furthermore, like H3K27ac, H3K9ac and H3K14ac can also differentiate active enhancers from inactive ones. Although, H3K9ac and H3K14ac, a hallmark of gene activation exhibit remarkable correlation over active and bivalent promoters as well as distal regulatory elements, a subset of inactive promoters is selectively enriched for H3K14ac.

Conclusions: Our study suggests that chromatin modifications, such as H3K9ac and H3K14ac, are part of the active promoter state, are present over bivalent promoters and active enhancers and that the extent of H3K9 and H3K14 acetylation could be driven by cis regulatory elements such as CpG content at promoters. Our study also suggests that a subset of inactive promoters is selectively and specifically enriched for H3K14ac. This observation suggests that histone acetyl transferases (HATs) prime inactive genes by H3K14ac for stimuli dependent activation. In conclusion our study demonstrates a wider role for H3K9ac and H3K14ac in gene regulation than originally thought.

Show MeSH