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Literature DB >> 17640913

Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis.

Joanne L Attema¹, Peter Papathanasiou, E Camilla Forsberg, Jian Xu, Stephen T Smale, Irving L Weissman.

Abstract

Hematopoietic stem cells (HSC) produce all blood cell lineages by virtue of their capacity to self-renew and differentiate into progenitors with decreasing cellular potential. Recent studies suggest that epigenetic mechanisms play an important role in controlling stem cell potency and cell fate decisions. To investigate this hypothesis in HSC, we have modified the conventional chromatin immunoprecipitation assay allowing for the analysis of 50,000 prospectively purified stem and progenitor cells. Together with bisulfite sequencing analysis, we found that methylated H3K4 and AcH3 and unmethylated CpG dinucleotides colocalize across defined regulatory regions of lineage-affiliated genes in HSC. These active epigenetic histone modifications either accumulated or were replaced by increased DNA methylation and H3K27 trimethylation in committed progenitors consistent with gene expression. We also observed bivalent histone modifications at a lymphoid-affiliated gene in HSC and downstream transit-amplifying progenitors. Together, these data support a model in which epigenetic modifications serve as an important mechanism to control HSC multipotency.

Entities: Chemical

Mesh：

Substances：
Histones
Sulfites

Year: 2007 PMID： 17640913 PMCID： PMC1924790 DOI： 10.1073/pnas.0704468104

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

50 in total

1. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain.

Authors: E C Forsberg; K M Downs; H M Christensen; H Im; P A Nuzzi; E H Bresnick
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2. Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment.

Authors: Toshihiro Miyamoto; Hiromi Iwasaki; Boris Reizis; Min Ye; Thomas Graf; Irving L Weissman; Koichi Akashi
Journal: Dev Cell Date: 2002-07 Impact factor: 12.270

3. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells.

Authors: Jian Xu; Scott D Pope; Ali R Jazirehi; Joanne L Attema; Peter Papathanasiou; Jason A Watts; Kenneth S Zaret; Irving L Weissman; Stephen T Smale
Journal: Proc Natl Acad Sci U S A Date: 2007-07-18 Impact factor: 11.205

Review 4. Stem cells, cancer, and cancer stem cells.

Authors: T Reya; S J Morrison; M F Clarke; I L Weissman
Journal: Nature Date: 2001-11-01 Impact factor: 49.962

5. Flk-2 is a marker in hematopoietic stem cell differentiation: a simple method to isolate long-term stem cells.

Authors: J L Christensen; I L Weissman
Journal: Proc Natl Acad Sci U S A Date: 2001-11-27 Impact factor: 11.205

6. Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines.

Authors: M Kondo; D C Scherer; T Miyamoto; A G King; K Akashi; K Sugamura; I L Weissman
Journal: Nature Date: 2000-09-21 Impact factor: 49.962

7. Transcription factor complex formation and chromatin fine structure alterations at the murine c-fms (CSF-1 receptor) locus during maturation of myeloid precursor cells.

Authors: Hiromi Tagoh; Roy Himes; Deborah Clarke; Pieter J M Leenen; Arthur D Riggs; David Hume; Constanze Bonifer
Journal: Genes Dev Date: 2002-07-01 Impact factor: 11.361

8. Active genes are tri-methylated at K4 of histone H3.

Authors: Helena Santos-Rosa; Robert Schneider; Andrew J Bannister; Julia Sherriff; Bradley E Bernstein; N C Tolga Emre; Stuart L Schreiber; Jane Mellor; Tony Kouzarides
Journal: Nature Date: 2002-09-11 Impact factor: 49.962

9. Chromatin signatures of pluripotent cell lines.

Authors: Véronique Azuara; Pascale Perry; Stephan Sauer; Mikhail Spivakov; Helle F Jørgensen; Rosalind M John; Mina Gouti; Miguel Casanova; Gary Warnes; Matthias Merkenschlager; Amanda G Fisher
Journal: Nat Cell Biol Date: 2006-03-29 Impact factor: 28.824

10. The upstream enhancer is necessary and sufficient for the expression of the pre-T cell receptor alpha gene in immature T lymphocytes.

Authors: B Reizis; P Leder
Journal: J Exp Med Date: 2001-10-01 Impact factor: 14.307

66 in total

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2. Labeling human embryonic stem cell-derived cardiomyocytes with indocyanine green for noninvasive tracking with optical imaging: an FDA-compatible alternative to firefly luciferase.

Authors: Sophie E Boddington; Tobias D Henning; Priyanka Jha; Christopher R Schlieve; Lydia Mandrussow; David DeNardo; Harold S Bernstein; Carissa Ritner; Daniel Golovko; Ying Lu; Shoujun Zhao; Heike E Daldrup-Link
Journal: Cell Transplant Date: 2010 Impact factor: 4.064

3. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.

Authors: Mazhar Adli; Bradley E Bernstein
Journal: Nat Protoc Date: 2011-09-29 Impact factor: 13.491

Epigenetic characterization of hematopoietic stem cell differentiation using miniChIP and bisulfite sequencing analysis.

1. Developmentally dynamic histone acetylation pattern of a tissue-specific chromatin domain.

2. Myeloid or lymphoid promiscuity as a critical step in hematopoietic lineage commitment.

3. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells.

Review 4. Stem cells, cancer, and cancer stem cells.

5. Flk-2 is a marker in hematopoietic stem cell differentiation: a simple method to isolate long-term stem cells.

6. Cell-fate conversion of lymphoid-committed progenitors by instructive actions of cytokines.

7. Transcription factor complex formation and chromatin fine structure alterations at the murine c-fms (CSF-1 receptor) locus during maturation of myeloid precursor cells.

8. Active genes are tri-methylated at K4 of histone H3.

9. Chromatin signatures of pluripotent cell lines.

10. The upstream enhancer is necessary and sufficient for the expression of the pre-T cell receptor alpha gene in immature T lymphocytes.

1. Going small is the new big.

2. Labeling human embryonic stem cell-derived cardiomyocytes with indocyanine green for noninvasive tracking with optical imaging: an FDA-compatible alternative to firefly luciferase.

3. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.

4. Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells.

5. Genome-scale ChIP-chip analysis using 10,000 human cells.

6. Id3 is a direct transcriptional target of Pax7 in quiescent satellite cells.

7. Expansion of human hematopoietic stem cells for transplantation: trends and perspectives.

Review 8. GATA1 insufficiencies in primary myelofibrosis and other hematopoietic disorders: consequences for therapy.

Review 9. Role of chromatin states in transcriptional memory.

10. Coactivator-associated arginine methyltransferase 1 regulates fetal hematopoiesis and thymocyte development.