Skip to main content
Protein & Cell logoLink to Protein & Cell
. 2012 Jun 6;3(7):483–486. doi: 10.1007/s13238-012-2806-y

Higher-order genomic organization in pluripotent stem cells

Ping Wang 1, Weiqi Zhang 1, Jiping Yang 1, Jing Qu 1,, Guang-Hui Liu 1,
PMCID: PMC4875389  PMID: 22673779

Abstract

Recent applications of new tools for genome-wide mapping of long-range and spatial interactions have shed light onto the fundamental mechanisms of three dimensional chromatin organizations in pluripotent stem cells and their derivatives.

Footnotes

These authors contributed equally to the work.

Contributor Information

Jing Qu, Email: jqu@salk.edu.

Guang-Hui Liu, Email: ghliu@ibp.ac.cn.

References

  1. Cremer T., Cremer M. Chromosome territories. Cold Spring Harb Perspect Biol. 2010;2:a003889. doi: 10.1101/cshperspect.a003889. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Dixon, J.R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J.S., and Ren, B. (2012). Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 2012 Apr 11. doi: 10.1038/nature11082. [Epub ahead of print] [DOI] [PMC free article] [PubMed]
  3. Dostie J., Richmond T.A., Arnaout R.A., Selzer R.R., Lee W.L., Honan T.A., Rubio E.D., Krumm A., Lamb J., Nusbaum C., et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 2006;16:1299–1309. doi: 10.1101/gr.5571506. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Guelen L., Pagie L., Brasset E., Meuleman W., Faza M.B., Talhout W., Eussen B.H., de Klein A., Wessels L., de Laat W., et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature. 2008;453:948–951. doi: 10.1038/nature06947. [DOI] [PubMed] [Google Scholar]
  5. Lanctôt C., Cheutin T., Cremer M., Cavalli G., Cremer T. Dynamic genome architecture in the nuclear space: regulation of gene expression in three dimensions. Nat Rev Genet. 2007;8:104–115. doi: 10.1038/nrg2041. [DOI] [PubMed] [Google Scholar]
  6. Li M., Suzuki K., Qu J., Saini P., Dubova I., Yi F., Lee J., Sancho-Martinez I., Liu G.H., Izpisua Belmonte J.C. Efficient correction of hemoglobinopathy-causing mutations by homologous recombination in integration-free patient iPSCs. Cell Res. 2011;21:1740–1744. doi: 10.1038/cr.2011.186. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Lieberman-Aiden E., van Berkum N.L., Williams L., Imakaev M., Ragoczy T., Telling A., Amit I., Lajoie B.R., Sabo P.J., Dorschner M.O., et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009;326:289–293. doi: 10.1126/science.1181369. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Liu G.H., Barkho B.Z., Ruiz S., Diep D., Qu J., Yang S.L., Panopoulos A.D., Suzuki K., Kurian L., Walsh C., et al. Recapitulation of premature ageing with iPSCs from Hutchinson-Gilford progeria syndrome. Nature. 2011;472:221–225. doi: 10.1038/nature09879. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Liu G.H., Sancho-Martinez I., Izpisua Belmonte J.C. Cut and paste: restoring cellular function by gene correction. Cell Res. 2012;22:283–284. doi: 10.1038/cr.2011.192. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Liu G.H., Suzuki K., Qu J., Sancho-Martinez I., Yi F., Li M., Kumar S., Nivet E., Kim J., Soligalla R.D., et al. Targeted gene correction of laminopathy-associated LMNA mutations in patient-specific iPSCs. Cell Stem Cell. 2011;8:688–694. doi: 10.1016/j.stem.2011.04.019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Meaburn K.J., Misteli T. Cell biology: chromosome territories. Nature. 2007;445:379–781. doi: 10.1038/445379a. [DOI] [PubMed] [Google Scholar]
  12. Melcer S., Meshorer E. The silence of the LADs: dynamic genome-lamina interactions during ESC differentiation. Cell Stem Cell. 2010;6:495–497. doi: 10.1016/j.stem.2010.05.006. [DOI] [PubMed] [Google Scholar]
  13. Noordermeer D., Leleu M., Splinter E., Rougemont J., De Laat W., Duboule D. The dynamic architecture of Hox gene clusters. Science. 2011;334:222–225. doi: 10.1126/science.1207194. [DOI] [PubMed] [Google Scholar]
  14. Nora, E.P., Lajoie, B.R., Schulz, E.G., Giorgetti, L., Okamoto, I., Servant, N., Piolot, T., van Berkum, N.L., Meisig, J., Sedat, J., et al. (2012). Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature 2012 Apr 11. doi: 10.1038/nature11049. [Epub ahead of print] [DOI] [PMC free article] [PubMed]
  15. Peric-Hupkes D., Meuleman W., Pagie L., Bruggeman S.W., Solovei I., Brugman W., Gräf S., Flicek P., Kerkhoven R.M., van Lohuizen M., et al. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell. 2010;38:603–613. doi: 10.1016/j.molcel.2010.03.016. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Phillips J.E., Corces V.G. CTCF: master weaver of the genome. Cell. 2009;137:1194–1211. doi: 10.1016/j.cell.2009.06.001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. van Steensel B., Dekker J. Genomics tools for unraveling chromosome architecture. Nat Biotechnol. 2010;28:1089–1095. doi: 10.1038/nbt.1680. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Yaffe E., Tanay A. Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture. Nat Genet. 2011;43:1059–1065. doi: 10.1038/ng.947. [DOI] [PubMed] [Google Scholar]
  19. Zhang W., Ding Z., Liu G.H. Evolution of iPSC disease models. Protein Cell. 2012;3:1–4. doi: 10.1007/s13238-012-2005-x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from Protein & Cell are provided here courtesy of Oxford University Press

RESOURCES