Acetylation is not mere a consequence of transcription: histones are acetylated without ongoing transcription [ChIP-seq]
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ABSTRACT:
PROVIDER: PRJNA1084008 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR28230902.fastq.gz | Fastqsanger.gz | |||
| SRR28230903.fastq.gz | Fastqsanger.gz | |||
| SRR28230904.fastq.gz | Fastqsanger.gz | |||
| SRR28230905.fastq.gz | Fastqsanger.gz | |||
| SRR28230906.fastq.gz | Fastqsanger.gz |
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Project description:Acetylation is not mere a consequence of transcription: histones are acetylated without ongoing transcription
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Project description:Acetylation is not mere a consequence of transcription: histones are acetylated without ongoing transcription [EU-seq]
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Project description:In all eukaryotes, acetylation of histones lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of transcription is debated. One model suggests that transcription promotes the recruitment and/or activation of acetyltransferases and histone acetylation occurs as a consequence of ongoing transcription. However, the extent to which transcription shapes the global acetylation landscapes is not known. Here we show that global protein acetylation remains virtually unaltered after acute transcription inhibition. Transcription inhibition ablates the co-transcriptionally occurring ubiquitylation of H2BK120 but does not reduce histone acetylation. The combined inhibition of transcription and CBP/p300 further demonstrates that acetyltransferases remain active and continue to acetylate histones independently of transcription. Together, these results show that histone acetylation is not a mere consequence of transcription; acetyltransferase recruitment and activation is uncoupled from the act of transcription and histone and non-histone protein acetylation are sustained in the absence of ongoing transcription.
2024-05-20 | GSE260923 | GEO
Project description:In all eukaryotes, acetylation of histones lysine residues correlates with transcription activation. Whether histone acetylation is a cause or consequence of transcription is debated. One model suggests that transcription promotes the recruitment and/or activation of acetyltransferases and histone acetylation occurs as a consequence of ongoing transcription. However, the extent to which transcription shapes the global acetylation landscapes is not known. Here we show that global protein acetylation remains virtually unaltered after acute transcription inhibition. Transcription inhibition ablates the co-transcriptionally occurring ubiquitylation of H2BK120 but does not reduce histone acetylation. The combined inhibition of transcription and CBP/p300 further demonstrates that acetyltransferases remain active and continue to acetylate histones independently of transcription. Together, these results show that histone acetylation is not a mere consequence of transcription; acetyltransferase recruitment and activation is uncoupled from the act of transcription and histone and non-histone protein acetylation are sustained in the absence of ongoing transcription.
2024-05-20 | GSE260922 | GEO
Project description:The acetylation of multiple histone lysine residues in all eukaryotes is known to be associated with transcription activation. However, the causal relationship between histone acetylation and transcription remains a topic of debate. One hypothesis proposes that transcription plays a role in recruiting and activating acetyltransferases, resulting in histone acetylation as a consequence of ongoing transcription. Nevertheless, the extent to which transcription influences the overall acetylation patterns across the genome remains uncertain. This study aims to shed light on this matter by investigating the impact of acute transcription inhibition on global protein acetylation. Surprisingly, the findings demonstrate that global protein acetylation levels remain largely unaffected even after inhibiting transcription. While transcription inhibition leads to the cessation of co-transcriptional ubiquitylation of H2BK120, histone acetylation persists. This suggests that histone acetylation is not solely dependent on transcriptional activity. Moreover, the study delves deeper into the relationship between transcription and acetyltransferase activity. By jointly inhibiting transcription and CBP/p300 it was observed that acetyltransferases remained active and continued to acetylate histones independently of inhibited transcription. Collectively, these results challenge the idea that histone acetylation is merely a consequence of transcription. Instead, they indicate that acetyltransferase recruitment and activation are not directly coupled to the process of transcription. Furthermore, the acetylation of both histone and non-histone proteins persists even in the absence of ongoing transcription. This highlights the complexity of histone acetylation regulation and suggests that it may not be solely dictated by the presence or absence of transcriptional activity.
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Project description:Transcriptional dysregulation plays a major role in the pathology of Huntington's disease (HD). However, the mechanisms causing selective downregulation of genes remain unknown. Histones regulate chromatin structure and thereby control gene expression; recent studies have demonstrated a therapeutic role for histone deacetylase (HDAC) inhibitors in polyglutamine diseases. This study demonstrates that despite no change in overall acetylated histone levels, histone H3 is hypo-acetylated at promoters of downregulated genes in R6/2 mice, ST14a and STHdh cells, as demonstrated by in vivo chromatin immunoprecipitation. In addition, HDAC inhibitor treatment increases association of acetylated histones with downregulated genes and corrects mRNA abnormalities. In contrast, there is a decrease in mRNA levels in wild-type cells following treatment with a histone acetyltransferase inhibitor. Although changes in histone acetylation correlate with decreased gene expression, histone hypo-acetylation may be a late event, as no hypo-acetylation is observed in 4-week-old R6/2 mice. Nevertheless, treatment with HDAC inhibitors corrects mRNA abnormalities through modification of histone proteins and may prove to be of therapeutic value in HD. Keywords: cell type comparison and disease state analysis
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Project description:Transcriptional dysregulation plays a major role in the pathology of Huntington's disease (HD). However, the mechanisms causing selective downregulation of genes remain unknown. Histones regulate chromatin structure and thereby control gene expression; recent studies have demonstrated a therapeutic role for histone deacetylase (HDAC) inhibitors in polyglutamine diseases. This study demonstrates that despite no change in overall acetylated histone levels, histone H3 is hypo-acetylated at promoters of downregulated genes in R6/2 mice, ST14a and STHdh cells, as demonstrated by in vivo chromatin immunoprecipitation. In addition, HDAC inhibitor treatment increases association of acetylated histones with downregulated genes and corrects mRNA abnormalities. In contrast, there is a decrease in mRNA levels in wild-type cells following treatment with a histone acetyltransferase inhibitor. Although changes in histone acetylation correlate with decreased gene expression, histone hypo-acetylation may be a late event, as no hypo-acetylation is observed in 4-week-old R6/2 mice. Nevertheless, treatment with HDAC inhibitors corrects mRNA abnormalities through modification of histone proteins and may prove to be of therapeutic value in HD. Experiment Overall Design: Total RNA was isolated from STHdh7/7 and STHdh111/111 cell lines by extraction with TRI-Reagent (Sigma-Aldrich, St Louis, MO) and purified further over RNeasy columns (Qiagen, Valencia, CA). Fifteen µg of total RNA was pooled for each sample and used to generate labeled cRNA probes according to the Affymetrix GeneChip protocol. Biotinylated cRNA probes were hybridized to MOE40.3K oligonucleotide microarrays using the Affymetrix Fluidics Station 400 according to the manufacturer's standard protocol. Microarray analysis Chips were developed, scanned, and normalized using global scaling. All quality control parameters calculated by Affymetrix GCOS Software were monitored (38). The images of the chips were analyzed to find spotted or damaged array regions and to ensure data quality (39). The Presence/Absence calls from Affymetrix MAS5 were monitored and compared throughout the different samples. Experiment Overall Design: All data were normalized using the GeneChip Robust MultiChips Analysis (GCRMA) algorithm (40, 41), performed with R in BioConductor. Experiment Overall Design: The processed images of the arrays were analyzed for quality control, we found all the samples to be of equal very good quality, with an average of 40.5% ± 1.44% Present calls with a range of 38% to 42.4%, (the background, noise, spike in controls, housekeeping genes presented a variability over the 8 samples less than 7% pre-normalization). In addition, 31.55% of the probe sets were called Present or Marginal in all the 8 samples and 44.6% were called Absent in all the 8 samples, showing a good consistency of the quality between the samples and between the groups compared.
2008-06-20 | E-GEOD-11358 | biostudies-arrayexpress
Project description:Histone modifications commonly integrate environmental stimuli to cellular metabolic outputs by affecting gene expression. Many modifications, including some histone acetylation marks, do not always correlate to transcription, thus pointing towards an alternative role of histone modifications as potential metabolic reservoirs. Using an approach that integrates mass spectrometry- based epi-proteomics and metabolomics with stable isotope tracer studies, we demonstrate that elevated lipids in histone acetyltransferase (HAT)-depleted hepatocytes result from carbon atoms flowing from the deacetylation of multi-acetylated histone H4 to fatty acids. Consistent with this, the enhanced lipid synthesis in HAT-depleted hepatocytes is dependent on the activity of histone deacetylases (HDACs) and acetyl-CoA synthetase ACSS2. Furthermore, we show that during diet-induced lipid synthesis there is a reduction of multi-acetylated histone H4 in hepatocytes and in mouse liver. In addition, overexpression of histone acetyltransferases can reverse diet-induced lipogenesis by blocking lipid droplet accumulation and maintaining the levels of multi-acetylated histone H4. This study unveils an additional link between epigenetics and metabolism whereby histone acetylation reservoirs may serve as a carbon source for lipid synthesis.
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Project description:Trypanosomes diverged from the main eukaryotic lineage about 600 million years ago, and display some unusual genomic and epigenetic properties that provide valuable insight into the early processes employed by eukaryotic ancestors to regulate chromatin-mediated functions. We sequenced Trypanosoma brucei core histones by high mass accuracy middle-down mass spectrometry to map core histone post-translational modifications (PTMs) and elucidate cis histone combinatorial PTMs (cPTMs). T. brucei histones are heavily modified and display intricate cPTMs patterns, with numerous hypermodified cPTMs that could contribute to the formation of non repressive euchromatic states. The T. brucei H2A C terminal tail is hyperacetylated, containing up to 5 acetylated lysine residues. MNase-ChIP-seq revealed a striking enrichment of hyperacetylated H2A at Pol II transcription start regions, and showed that H2A histones that are hyperacetylated in different combinations localised to different genomic regions, suggesting distinct epigenetic functions. Our genomics and proteomics data provide insight into the complex epigenetic mechanisms used by this parasite to regulate a genome that lacks the transcriptional control mechanisms found in higher eukaryotes. The findings further demonstrate the complexity of epigenetic mechanisms that were probably shared with the last eukaryotic common ancestor.
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