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Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes

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Abstract

High-throughput methods based on chromosome conformation capture have greatly advanced our understanding of the three-dimensional (3D) organization of genomes but are limited in resolution by their reliance on restriction enzymes. Here we describe a method called DNase Hi-C for comprehensively mapping global chromatin contacts. DNase Hi-C uses DNase I for chromatin fragmentation, leading to greatly improved efficiency and resolution over that of Hi-C. Coupling this method with DNA-capture technology provides a high-throughput approach for targeted mapping of fine-scale chromatin architecture. We applied targeted DNase Hi-C to characterize the 3D organization of 998 large intergenic noncoding RNA (lincRNA) promoters in two human cell lines. Our results revealed that expression of lincRNAs is tightly controlled by complex mechanisms involving both super-enhancers and the Polycomb repressive complex. Our results provide the first glimpse of the cell type–specific 3D organization of lincRNA genes.

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Figure 1: Validation of DNase Hi-C.
Figure 2: Validation of targeted DNase Hi-C.
Figure 3: The intrachromosomal contact profile within 500 kb of the HOTAIR promoter in H1 and K562 cells.
Figure 4: Identification of lincRNA promoter–associated cis elements.
Figure 5: Characterization of contacts connecting lincRNA promoters to super-enhancers.

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References

  1. Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).

    Article  CAS  Google Scholar 

  2. Dekker, J., Rippe, K., Dekker, M. & Kleckner, N. Capturing chromosome conformation. Science 295, 1306–1311 (2002).

    Article  CAS  Google Scholar 

  3. Dekker, J., Marti-Renom, M.A. & Mirny, L.A. Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data. Nat. Rev. Genet. 14, 390–403 (2013).

    Article  CAS  Google Scholar 

  4. de Wit, E. & de Laat, W. A decade of 3C technologies: insights into nuclear organization. Genes Dev. 26, 11–24 (2012).

    Article  CAS  Google Scholar 

  5. Simonis, M. et al. Nuclear organization of active and inactive chromatin domains uncovered by chromosome conformation capture-on-chip (4C). Nat. Genet. 38, 1348–1354 (2006).

    Article  CAS  Google Scholar 

  6. Zhao, Z. et al. Circular chromosome conformation capture (4C) uncovers extensive networks of epigenetically regulated intra- and interchromosomal interactions. Nat. Genet. 38, 1341–1347 (2006).

    Article  CAS  Google Scholar 

  7. Dostie, J. et al. Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements. Genome Res. 16, 1299–1309 (2006).

    Article  CAS  Google Scholar 

  8. Duan, Z. et al. A three-dimensional model of the yeast genome. Nature 465, 363–367 (2010).

    Article  CAS  Google Scholar 

  9. Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009).

    Article  CAS  Google Scholar 

  10. Nagano, T. et al. Single-cell Hi-C reveals cell-to-cell variability in chromosome structure. Nature 502, 59–64 (2013).

    Article  CAS  Google Scholar 

  11. Hughes, J.R. et al. Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment. Nat. Genet. 46, 205–212 (2014).

    Article  CAS  Google Scholar 

  12. Batista, P.J. & Chang, H.Y. Long noncoding RNAs: cellular address codes in development and disease. Cell 152, 1298–1307 (2013).

    Article  CAS  Google Scholar 

  13. Rinn, J.L. & Chang, H.Y. Genome regulation by long noncoding RNAs. Annu. Rev. Biochem. 81, 145–166 (2012).

    Article  CAS  Google Scholar 

  14. Ulitsky, I. & Bartel, D.P. lincRNAs: genomics, evolution, and mechanisms. Cell 154, 26–46 (2013).

    Article  CAS  Google Scholar 

  15. Cremer, T. & Cremer, M. Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010).

    Article  Google Scholar 

  16. Dixon, J.R. et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature 485, 376–380 (2012).

    Article  CAS  Google Scholar 

  17. Gnirke, A. et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat. Biotechnol. 27, 182–189 (2009).

    Article  CAS  Google Scholar 

  18. van de Werken, H.J. et al. Robust 4C-seq data analysis to screen for regulatory DNA interactions. Nat. Methods 9, 969–972 (2012).

    Article  CAS  Google Scholar 

  19. Jin, F. et al. A high-resolution map of the three-dimensional chromatin interactome in human cells. Nature 503, 290–294 (2013).

    Article  CAS  Google Scholar 

  20. Levasseur, D.N., Wang, J., Dorschner, M.O., Stamatoyannopoulos, J.A. & Orkin, S.H. Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells. Genes Dev. 22, 575–580 (2008).

    Article  CAS  Google Scholar 

  21. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012).

    Article  CAS  Google Scholar 

  22. Sanyal, A., Lajoie, B.R., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature 489, 109–113 (2012).

    Article  CAS  Google Scholar 

  23. Rada-Iglesias, A. et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 470, 279–283 (2011).

    Article  CAS  Google Scholar 

  24. Ay, F., Bailey, T.L. & Noble, W.S. Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts. Genome Res. 24, 999–1011 (2014).

    Article  CAS  Google Scholar 

  25. Kieffer-Kwon, K.R. et al. Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation. Cell 155, 1507–1520 (2013).

    Article  CAS  Google Scholar 

  26. Cabili, M.N. et al. Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev. 25, 1915–1927 (2011).

    Article  CAS  Google Scholar 

  27. Derrien, T. et al. The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 22, 1775–1789 (2012).

    Article  CAS  Google Scholar 

  28. Zhang, Y. et al. Chromatin connectivity maps reveal dynamic promoter-enhancer long-range associations. Nature 504, 306–310 (2013).

    Article  CAS  Google Scholar 

  29. The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012).

  30. Hoffman, M.M. et al. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res. 41, 827–841 (2013).

    Article  CAS  Google Scholar 

  31. Hnisz, D. et al. Super-enhancers in the control of cell identity and disease. Cell 155, 934–947 (2013).

    Article  CAS  Google Scholar 

  32. Whyte, W.A. et al. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell 153, 307–319 (2013).

    Article  CAS  Google Scholar 

  33. de Laat, W. & Duboule, D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 502, 499–506 (2013).

    Article  CAS  Google Scholar 

  34. Gorkin, D.U., Leung, D. & Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762–775 (2014).

    Article  CAS  Google Scholar 

  35. Wang, J. et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 22, 1798–1812 (2012).

    Article  CAS  Google Scholar 

  36. Denholtz, M. et al. Long-range chromatin contacts in embryonic stem cells reveal a role for pluripotency factors and Polycomb proteins in genome organization. Cell Stem Cell 13, 602–616 (2013).

    Article  CAS  Google Scholar 

  37. Burton, J.N. et al. Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions. Nat. Biotechnol. 31, 1119–1125 (2013).

    Article  CAS  Google Scholar 

  38. Kaplan, N. & Dekker, J. High-throughput genome scaffolding from in vivo DNA interaction frequency. Nat. Biotechnol. 31, 1143–1147 (2013).

    Article  CAS  Google Scholar 

  39. Selvaraj, S., Dixon, J.R., Bansal, V. & Ren, B. Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing. Nat. Biotechnol. 31, 1111–1118 (2013).

    Article  CAS  Google Scholar 

  40. Lee, T.I. et al. Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125, 301–313 (2006).

    Article  CAS  Google Scholar 

  41. Ware, C.B. et al. Histone deacetylase inhibition elicits an evolutionarily conserved self-renewal program in embryonic stem cells. Cell Stem Cell 4, 359–369 (2009).

    Article  CAS  Google Scholar 

  42. Ng, S.Y., Johnson, R. & Stanton, L.W. Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J. 31, 522–533 (2012).

    Article  CAS  Google Scholar 

  43. Kent, W.J. et al. The Human Genome Browser at UCSC. Genome Res. 12, 996–1006 (2002).

    Article  CAS  Google Scholar 

  44. Li, H. & Durbin, R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26, 589–595 (2010).

    Article  Google Scholar 

  45. Imakaev, M. et al. Iterative correction of Hi-C data reveals hallmarks of chromosome organization. Nat. Methods 9, 999–1003 (2012).

    Article  CAS  Google Scholar 

  46. Derrien, T. et al. Fast computation and applications of genome mappability. PLoS ONE 7, e30377 (2012).

    Article  CAS  Google Scholar 

  47. Bickel, P.J., Boley, N., Brown, J.B., Huang, H. & Zhang, N.R. Subsampling methods for genomic inference. Ann. Appl. Stat. 4, 1660–1697 (2010).

    Article  Google Scholar 

  48. Hoffman, M.M. et al. Unsupervised pattern discovery in human chromatin structure through genomic segmentation. Nat. Methods 9, 473–476 (2012).

    Article  CAS  Google Scholar 

  49. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).

    Article  Google Scholar 

  50. Trapnell, C. et al. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010).

    Article  CAS  Google Scholar 

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Acknowledgements

We thank S. Fields and M. Groudine for critical reading of the manuscript. This work was supported by US National Institutes of Health grants R01 GM098039 (C.A.B.), GM046883 (C.M.D.) and R01 U41HG007000 (W.S.N.).

Author information

Authors and Affiliations

Authors

Contributions

W.S.N., C.A.B., C.M.D., A.K. and Z.D. conceived of the project. Z.D. developed DNase Hi-C and targeted DNase Hi-C. Z.D., C.A.B, J.S., A.K., C.M.D., X.D., C.B.W. and W.S.N. designed experiments. Z.D., C.L., X.D., S.C., C.C. and J.H. performed experiments. W.M., F.A., G.G. and Z.D. analyzed experimental data under the supervision of W.S.N. W.S.N., J.S., C.A.B., C.M.D., A.K., W.M., F.A., X.D. and Z.D. wrote the paper.

Corresponding authors

Correspondence to William S Noble or Zhijun Duan.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–17, Supplementary Tables 1–4, 6, 7, 11–15 and 24 and Supplementary Notes 1–6 (PDF 38883 kb)

Supplementary Table 5

The 220kb P-E library (XLS 59 kb)

Supplementary Table 8

List of contact partners identified by targeted DNase Hi-C P-E in H1 cells (XLSX 153 kb)

Supplementary Table 9

List of contact partners identified by targeted DNase Hi-C P-E in K562 cells (XLSX 175 kb)

Supplementary Table 10

The lincRNA P library (XLSX 182 kb)

Supplementary Table 16

List of contact partners identified by targeted DNase Hi-C incRNA in H1 cells (XLSX 1027 kb)

Supplementary Table 17

List of contact partners identified by targeted DNase Hi-C lincRNA in K562 cells (XLSX 781 kb)

Supplementary Table 18

Summary of enrichment analysis of Segway cis-elements (XLSX 18 kb)

Supplementary Table 19

Summary of enrichment analysis of DNase hypersensitive sites(DHSs) (XLSX 9 kb)

Supplementary Table 20

Summary of enrichment analysis of FAIRE-seq peaks (XLSX 9 kb)

Supplementary Table 21

Summary of enrichment analysis of super-enhancers (XLSX 174 kb)

Supplementary Table 22

Summary of enrichment analysis of TFBSs (XLSX 23 kb)

Supplementary Table 23

Adaptor and primer sequences (XLSX 12 kb)

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Ma, W., Ay, F., Lee, C. et al. Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods 12, 71–78 (2015). https://doi.org/10.1038/nmeth.3205

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