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Computational and experimental methods for deciphering the epigenetic code in hematopoietic stem cell lineage commitment

Weishaupt, Holger LU (2012) In Lund University, Faculty of Medicine Doctoral Dissertation Series 2012:40.
Abstract
The emergence of post-genomic approaches that couple chromatin immunoprecipitation (ChIP) assays to high-throughput technique has greatly advanced our ability to investigate epigenetic features associated with normal cell development and disease. Nevertheless, these techniques exhibit some limitations. Firstly, standard protocols usually require millions of cells, thus limiting their application to the study of abundant cell populations. Second, high-throughput techniques generate vast amounts of data, the handling and analysis of which pose several bioinformatic challenges to biomedical researchers.

In this thesis we present a miniaturized ChIP-chip assay (miniChIP-chip) for the genome-wide analysis of chromatin modifications... (More)
The emergence of post-genomic approaches that couple chromatin immunoprecipitation (ChIP) assays to high-throughput technique has greatly advanced our ability to investigate epigenetic features associated with normal cell development and disease. Nevertheless, these techniques exhibit some limitations. Firstly, standard protocols usually require millions of cells, thus limiting their application to the study of abundant cell populations. Second, high-throughput techniques generate vast amounts of data, the handling and analysis of which pose several bioinformatic challenges to biomedical researchers.

In this thesis we present a miniaturized ChIP-chip assay (miniChIP-chip) for the genome-wide analysis of chromatin modifications from 10,000 cells as well as software (ChIPeasy) for the visualization and analysis of ChIP-chip datasets.

Employing the experimental and computational approaches described in these articles, we investigated the signatures of selected histone modifications in rare murine hematopoietic stem cells (HSCs) and progeny, the analysis of which had previously been limited due to low frequencies of purified HSCs in adult animals.

The distinct histone modification maps generated in this study indicated that promoters of mature blood cell regulators were primed for lineage-specific expression by bivalent histone methylation marks (co-modification of H3K4me3 and H3K27me3) in HSCs and progenitors prior to lineage commitment. In HSCs, bivalent signatures at promoters associated differently with combinations of other histone modifications depending on the downstream resolution of the bivalent marks, suggesting that the fate of lineage-specific genes is partly established already at the stem cell level.

During T cell maturation, gene expression programs that are important for other lineages acquired increased H3K27me3 and H3K9me3 silencing, but a large majority also retained the activating and bivalent chromatin states. This result suggested that a residual epigenetic plasticity or perhaps priming capacity might be retained in these mature cells.

In summary, this study has provided insight into some of the unique epigenetic features of hematopoietic stem cell lineage commitment and differentiation. (Less)
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author
supervisor
opponent
  • Porse, Bo T., Finsen Laboratory, Copenhagen University Hospital & Biotech Research and Innovation Centre (BRIC), Copenhagen University, Denmark
organization
publishing date
type
Thesis
publication status
published
subject
in
Lund University, Faculty of Medicine Doctoral Dissertation Series
volume
2012:40
pages
100 pages
publisher
Immunology Section, Dept of Experimental Medical Science
defense location
Segerfalksalen, BMC A10, Lund
defense date
2012-05-29 10:00
ISSN
1652-8220
ISBN
978-91-87189-02-9
language
English
LU publication?
yes
id
32d8517d-e0b4-40c0-93e5-285575bb1ef8 (old id 2535100)
date added to LUP
2012-05-08 14:28:56
date last changed
2016-09-19 08:44:49
@phdthesis{32d8517d-e0b4-40c0-93e5-285575bb1ef8,
  abstract     = {The emergence of post-genomic approaches that couple chromatin immunoprecipitation (ChIP) assays to high-throughput technique has greatly advanced our ability to investigate epigenetic features associated with normal cell development and disease. Nevertheless, these techniques exhibit some limitations. Firstly, standard protocols usually require millions of cells, thus limiting their application to the study of abundant cell populations. Second, high-throughput techniques generate vast amounts of data, the handling and analysis of which pose several bioinformatic challenges to biomedical researchers.<br/><br>
In this thesis we present a miniaturized ChIP-chip assay (miniChIP-chip) for the genome-wide analysis of chromatin modifications from 10,000 cells as well as software (ChIPeasy) for the visualization and analysis of ChIP-chip datasets.<br/><br>
Employing the experimental and computational approaches described in these articles, we investigated the signatures of selected histone modifications in rare murine hematopoietic stem cells (HSCs) and progeny, the analysis of which had previously been limited due to low frequencies of purified HSCs in adult animals.<br/><br>
The distinct histone modification maps generated in this study indicated that promoters of mature blood cell regulators were primed for lineage-specific expression by bivalent histone methylation marks (co-modification of H3K4me3 and H3K27me3) in HSCs and progenitors prior to lineage commitment. In HSCs, bivalent signatures at promoters associated differently with combinations of other histone modifications depending on the downstream resolution of the bivalent marks, suggesting that the fate of lineage-specific genes is partly established already at the stem cell level. <br/><br>
During T cell maturation, gene expression programs that are important for other lineages acquired increased H3K27me3 and H3K9me3 silencing, but a large majority also retained the activating and bivalent chromatin states. This result suggested that a residual epigenetic plasticity or perhaps priming capacity might be retained in these mature cells.<br/><br>
In summary, this study has provided insight into some of the unique epigenetic features of hematopoietic stem cell lineage commitment and differentiation.},
  author       = {Weishaupt, Holger},
  isbn         = {978-91-87189-02-9},
  issn         = {1652-8220},
  language     = {eng},
  pages        = {100},
  publisher    = {Immunology Section, Dept of Experimental Medical Science},
  school       = {Lund University},
  series       = {Lund University, Faculty of Medicine Doctoral Dissertation Series},
  title        = {Computational and experimental methods for deciphering the epigenetic code in hematopoietic stem cell lineage commitment},
  volume       = {2012:40},
  year         = {2012},
}