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The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules

Abstract

We developed a general approach that combines chromosome conformation capture carbon copy (5C) with the Integrated Modeling Platform (IMP) to generate high-resolution three-dimensional models of chromatin at the megabase scale. We applied this approach to the ENm008 domain on human chromosome 16, containing the α-globin locus, which is expressed in K562 cells and silenced in lymphoblastoid cells (GM12878). The models accurately reproduce the known looping interactions between the α-globin genes and their distal regulatory elements. Further, we find using our approach that the domain folds into a single globular conformation in GM12878 cells, whereas two globules are formed in K562 cells. The central cores of these globules are enriched for transcribed genes, whereas nontranscribed chromatin is more peripheral. We propose that globule formation represents a higher-order folding state related to clustering of transcribed genes around shared transcription machineries, as previously observed by microscopy.

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Figure 1: ENCODE region ENm008 on human chromosome 16.
Figure 2: 5C analysis of the 500-kb ENCODE region ENm008.
Figure 3: Ensemble of solutions.
Figure 4: 3D models of the ENm008 ENCODE region containing the α-globin locus.
Figure 5: Analysis of chromatin globules.
Figure 6

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Acknowledgements

We thank the IMP community (http://www.integrativemodeling.org), especially D. Russell, B. Webb and A. Sali, as well as the Chimera developers (http://www.cgl.ucsf.edu/chimera/), especially T. Goddard and T. Ferrin. We also thank M. Umbarger, M. Wright, G. Church, M.S. Madhusudhan, M. Walhout and Dekker laboratory members for fruitful discussions. We acknowledge support from the Spanish Ministerio de Ciencia e Innovación (BIO2007/66670 and BFU2010/19310 to M.A.M.-R.), the US National Institutes of Health (NIH; HG003143 to J.D. and GM053234 to J.B.L.) and the Keck Foundation (J.D.). Finally, we are grateful to the ENCODE project (funded by the NIH and the US National Human Genome Research Institute) for providing annotations of the ENm008 region. In particular, we thank the ENCODE groups led by T. Gingeras (expression data, Cold Spring Harbor Laboratory), G. Crawford (DNase I data, Duke University) and B. Bernstein (CTCF data, H3K4me3 data, Broad Institute of Harvard and MIT). ENCODE data are publicly available through the ENCODE Data Coordination Center at the University of California, Santa Cruz (http://genome.ucsc.edu/ENCODE/).

Author information

Affiliations

Authors

Contributions

B.R.L. performed the bioinformatics design and analysis of the 5C experiments. A.S. performed the 5C experiments. D.B., E.C. and M.A.M.-R. carried out the IMP computational modeling. M.B., A.S. and J.B.L. performed the FISH experiments. D.B., B.R.L., A.S., J.D. and M.A.M.-R. wrote the manuscript. J.D. and M.A.M.-R. conceived the work.

Corresponding authors

Correspondence to Job Dekker or Marc A Marti-Renom.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Methods, Supplementary Table 1 and Supplementary Figures 1–6 (PDF 3508 kb)

Supplementary Video 1

Video of the spinning 3D structure for the ENm008 region in GM12878 cell lines. The region includes the α-globin locus, which contains, from telomere to centromere, the ζ, μ (also known as αD), α2, α1, and θ globin genes. Colored fragments contain annotated genes. Red (HS40), orange (other HSs) and green (CTCF-bound elements) spheres localize regulatory elements. (MOV 3657 kb)

Supplementary Video 2

Video of the spinning 3D structure for the ENm008 region in K562 cell lines. The region includes the α-globin locus, which contains, from telomere to centromere, the ζ, μ (also known as αD), α2, α1, and θ globin genes. Colored fragments contain annotated genes. Red (HS40), orange (other HSs) and green (CTCF-bound elements) spheres localize regulatory elements. (MOV 3627 kb)

Supplementary Data 1

Zip file with 5C results and model analysis. (TXT 15 kb)

Supplementary Data 2

5C frequency counts matrix for ENm008 in GM12878 cells in a tabulated text file. (TXT 4 kb)

Supplementary Data 3

5C frequency counts matrix for ENm008 in K562 cells in a tabulated text file. (TXT 4 kb)

Supplementary Data 4

Contact map for ENm008 in GM12878 cells in a tabulated text file. (TXT 21 kb)

Supplementary Data 5

Contact map for ENm008 in K562 cells in a tabulated text file. (TXT 17 kb)

Supplementary Data 6

Contact map for ENm008 in GM12878 cells as BED formatted file for direct upload into the UCSC Genome Browser. (TXT 403 kb)

Supplementary Data 7

Contact map for ENm008 in K562 cells as BED formatted file for direct upload into the UCSC Genome Browser. (TXT 246 kb)

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Baù, D., Sanyal, A., Lajoie, B. et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules. Nat Struct Mol Biol 18, 107–114 (2011). https://doi.org/10.1038/nsmb.1936

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