Stem Cell Reviews and Reports

, Volume 9, Issue 4, pp 397–407 | Cite as

Epigenetic Modifications and Chromosome Conformations of the Beta Globin Locus throughout Development

  • Kai-Hsin Chang
  • Xiangdong Fang
  • Hao Wang
  • Andy Huang
  • Hua Cao
  • Yadong Yang
  • Halvard Bonig
  • John A. Stamatoyannopoulos
  • Thalia Papayannopoulou
Article

Abstract

Human embryonic stem cells provide an alternative to using human embryos for studying developmentally regulated gene expression. The co-expression of high levels of embryonic ε and fetal γ globin by the hESC-derived erythroblasts allows the interrogation of ε globin regulation at the transcriptional and epigenetic level which could only be attained previously by studying cell lines or transgenic mice. In this study, we compared the histone modifications across the β globin locus of the undifferentiated hESCs and hESC-, FL-, and mobilized PB CD34+ cells-derived erythroblasts, which have distinct globin expression patterns corresponding to their developmental stages. We demonstrated that the histone codes employed by the β globin locus are conserved throughout development. Furthermore, in spite of the close proximity of the ε globin promoter, as compared to the β or γ globin promoter, with the LCR, a chromatin loop was also formed between the LCR and the active ε globin promoter, similar to the loop that forms between the β or γ globin promoters and the LCR, in contrary to the previously proposed tracking mechanism.

Keywords

Human embryonic stem cells Erythroid cells Fetal liver Peripheral blood Erythroblasts Hemoglobin Epigenetics Histone modifications Chromatin conformation 

Supplementary material

12015_2012_9355_MOESM1_ESM.docx (30 kb)
Supplementary Figure 1Long range interaction frequencies between Gγ promoter and the HSs of the LCR. Erythroblasts derived from hESC, FL, and PB were fixed and lysed to obtain intact nuclei. Nuclei were digested with HindIII over night and then religated. The cross-linking frequencies were determined using real time PCR with Taqman chemistry. Similar cross-linking frequencies were observed between Gγ promoter and HSs of the LCR in these 3 types of erythroblasts. PB-derived erythroblasts used for this assay had elevated levels of γ globin expression, which may explain the high levels of cross-linking frequencies observed. (DOCX 29 kb)
12015_2012_9355_MOESM2_ESM.docx (13 kb)
Supplementary Table 1Primer sequences for Chromatin Immunoprecipitation assays (DOCX 13 kb)
12015_2012_9355_MOESM3_ESM.docx (13 kb)
Supplementary Table 2Chromatin conformation capture primers and probes (DOCX 13 kb)
12015_2012_9355_MOESM4_ESM.docx (13 kb)
Supplementary Table 3RPKM normalized reads of transcripts across beta globin locus (DOCX 13 kb)

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Kai-Hsin Chang
    • 1
  • Xiangdong Fang
    • 2
    • 3
  • Hao Wang
    • 4
  • Andy Huang
    • 3
  • Hua Cao
    • 3
  • Yadong Yang
    • 2
  • Halvard Bonig
    • 5
  • John A. Stamatoyannopoulos
    • 4
  • Thalia Papayannopoulou
    • 1
  1. 1.Department of Medicine, Division of HematologyUniversity of WashingtonSeattleUSA
  2. 2.Laboratory of Disease Genomics and Individualized MedicineBeijing Institute of Genomics, Chinese Academy of SciencesBeijingChina
  3. 3.Department of Medicine, Division of Medical GeneticsUniversity of WashingtonSeattleUSA
  4. 4.Department of Genome SciencesUniversity of WashingtonSeattleUSA
  5. 5.Department of Cellular Therapeutics/Cell Processing (GMP)German Red Cross Blood ServiceFrankfurtGermany

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