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

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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.

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Acknowledgments

The authors express their gratitude towards Drs. Theresa Canfield, Erika Giste, Richard Sandstrom, and R. Scott Hansen for assistance with high throughput sequencing. This research was supported by the National Institute of Health grants DK077864 (K-H.C), HL46557 (T.P.) and 1RC2HG005654 (J.A.S.).

Author Disclosure Statement

The authors declare no potential conflicts of interest.

Author information

Authors and Affiliations

  1. Department of Medicine, Division of Hematology, University of Washington, NE Pacific St, Box 357710, Seattle, WA, 98195, USA

    Kai-Hsin Chang & Thalia Papayannopoulou

  2. Laboratory of Disease Genomics and Individualized Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China

    Xiangdong Fang & Yadong Yang

  3. Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, 98195, USA

    Xiangdong Fang, Andy Huang & Hua Cao

  4. Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA

    Hao Wang & John A. Stamatoyannopoulos

  5. Department of Cellular Therapeutics/Cell Processing (GMP), German Red Cross Blood Service, Frankfurt, 60528, Germany

    Halvard Bonig

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  1. Kai-Hsin Chang
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  2. Xiangdong Fang
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  3. Hao Wang
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  4. Andy Huang
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  8. John A. Stamatoyannopoulos
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  9. Thalia Papayannopoulou
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Corresponding author

Correspondence to Thalia Papayannopoulou.

Additional information

Drs. Kai-Hsin Chang and Xiangdong Fang contributed equally to this work.

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Supplementary Figure 1

Long 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)

Supplementary Table 1

Primer sequences for Chromatin Immunoprecipitation assays (DOCX 13 kb)

Supplementary Table 2

Chromatin conformation capture primers and probes (DOCX 13 kb)

Supplementary Table 3

RPKM normalized reads of transcripts across beta globin locus (DOCX 13 kb)

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Chang, KH., Fang, X., Wang, H. et al. Epigenetic Modifications and Chromosome Conformations of the Beta Globin Locus throughout Development. Stem Cell Rev and Rep 9, 397–407 (2013). https://doi.org/10.1007/s12015-012-9355-x

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