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Tracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition?

Laura De Clerck (UGent)
(2019)
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Abstract
In this dissertation, we profile the histone epigenome of hESCs during conversion from the primed to the naive state using an untargeted mass spectrometry (MS)-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with what was recently described in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency. Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS has great potential for large-scale analysis of hPTMs and their combinatorial patterns, as it allows for untargeted accurate identification and quantification of hPTMs. In this dissertation, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). More specifically, the workflow was optimized to ensure a maximal coverage of the histone code and a high specificity for isobaric and co-eluting peptides. We assessed the validity of the workflow on a technical dataset of a time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e. acetylated substrate peptides reduce in intensity. Finally, xe successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.
Keywords
Epigenetics, Histones, Post-translational modifications, Mass spectrometry, SWATH

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Please use this url to cite or link to this publication:

MLA
De Clerck, Laura. “Tracking Changes in the Histone Modification Pattern by Untargeted Mass Spectrometry : How Naïve Are Human Embryonic Stem Cells and Data-dependent Acquisition?” 2019 : n. pag. Print.
APA
De Clerck, L. (2019). Tracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition? Ghent University. Faculty of Pharmaceutical Sciences, Ghent, Belgium.
Chicago author-date
De Clerck, Laura. 2019. “Tracking Changes in the Histone Modification Pattern by Untargeted Mass Spectrometry : How Naïve Are Human Embryonic Stem Cells and Data-dependent Acquisition?” Ghent, Belgium: Ghent University. Faculty of Pharmaceutical Sciences.
Chicago author-date (all authors)
De Clerck, Laura. 2019. “Tracking Changes in the Histone Modification Pattern by Untargeted Mass Spectrometry : How Naïve Are Human Embryonic Stem Cells and Data-dependent Acquisition?” Ghent, Belgium: Ghent University. Faculty of Pharmaceutical Sciences.
Vancouver
1.
De Clerck L. Tracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition? [Ghent, Belgium]: Ghent University. Faculty of Pharmaceutical Sciences; 2019.
IEEE
[1]
L. De Clerck, “Tracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition?,” Ghent University. Faculty of Pharmaceutical Sciences, Ghent, Belgium, 2019.
@phdthesis{8628387,
  abstract     = {In this dissertation, we profile the histone epigenome of hESCs during conversion from the primed to the naive state using an untargeted mass spectrometry (MS)-based approach. In total, 23 histone post-translational modifications (hPTMs) changed significantly over time. H3K27me3 was the most prominently increasing marker hPTM in naive hESCs. This is in line with what was recently described in mouse, prompting us to compare all the shared hPTM fold changes between mouse and human, revealing a set of conserved hPTM markers for the naive state. Principally, we present the first roadmap of the changing human histone epigenome during the conversion of hESCs from the primed to the naive state. This further revealed similarities with mouse, which hint at a conserved mammalian epigenetic signature of the ground state of pluripotency.
Sequential window acquisition of all theoretical fragment ion spectra (SWATH)-MS has great potential for large-scale analysis of hPTMs and their combinatorial patterns, as it allows for untargeted accurate identification and quantification of hPTMs. In this dissertation, we present a complete SWATH workflow specifically adapted for the untargeted study of histones (hSWATH). More specifically, the workflow was optimized to ensure a maximal coverage of the histone code and a high specificity for isobaric and co-eluting peptides. We assessed the validity of the workflow on a technical dataset of a time-lapse deacetylation of a commercial histone extract using HDAC1, which contains a ground truth, i.e. acetylated substrate peptides reduce in intensity. Finally, xe successfully apply this workflow in a biological setting and subsequently investigate the differential response to HDAC inhibition in different breast cancer cell lines.},
  author       = {De Clerck, Laura},
  keywords     = {Epigenetics,Histones,Post-translational modifications,Mass spectrometry,SWATH},
  language     = {eng},
  pages        = {190},
  publisher    = {Ghent University. Faculty of Pharmaceutical Sciences},
  school       = {Ghent University},
  title        = {Tracking changes in the histone modification pattern by untargeted mass spectrometry : how naïve are human embryonic stem cells and data-dependent acquisition?},
  year         = {2019},
}