An oestrogen-receptor-α-bound human chromatin interactome (original) (raw)

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Primary accessions

Gene Expression Omnibus

Data deposits

The data in the ChIA-PET libraries have been deposited in NCBI’s Gene Expression Omnibus and are accessible through GEO Series accession number GSE18046.

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Acknowledgements

The authors acknowledge the Genome Technology and Biology Group at the Genome Institute of Singapore for technical support; A. Shahab, C. C. Seng and F. H. Mulawadi for computing support; S. Luo and G. Schroth for Illumina sequencing support; and W. de Laat, B. Ren and X. S. Liu for advice. M.J.F., P.Y.H.H., Y.H., P.Y.T. and Y.K.L. are supported by A*STAR Scholarships. M.J.F. is supported by a L’Oreal-UNESCO For Women In Science National Fellowship. Y.R. and C.L.W. are supported by A*STAR of Singapore and NIH ENCODE grants (R01 HG004456-01, R01HG003521-01 and part of 1U54HG004557-01).

Author Contributions M.J.F. and Y.R. conceptualized the ChIA-PET strategy. M.J.F., E.C. and Y.R. designed the experiments. M.J.F., M.H.L., Y.F.P., J.L., A.H., P.H.M., E.G.Y.C., P.Y.Y.H., W.-J.W., Y.H., Y.L., P.Y.T., P.Y.C., K.D.S.A.W., B.Z., K.S.L., S.C.L., J.S.Y., R.J., K.V.D., J.S.T., Y.K.L., T.H., H.G.S., X.R. and V.C.-R. performed experiments. M.J.F., X.H., Y.B.M., Y.L.O., S.V., H.-S.O., P.N.A., V.B.V., Y.K.L., R.K.M.K., G.B., H.G.S., X.R., V.C.-R., W-K.S., C.-L.W., E.C. and Y.R. analysed experimental data. E.T.L., E.C. and C.-L.W. commented on the manuscript drafts; M.J.F. and Y.R. wrote the paper.

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Authors and Affiliations

1. Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore 138672
   Melissa J. Fullwood, Mei Hui Liu, You Fu Pan, Jun Liu, Han Xu, Yusoff Bin Mohamed, Yuriy L. Orlov, Stoyan Velkov, Andrea Ho, Poh Huay Mei, Elaine G. Y. Chew, Phillips Yao Hui Huang, Yuyuan Han, Hong Sain Ooi, Pramila N. Ariyaratne, Vinsensius B. Vega, Yanquan Luo, Peck Yean Tan, Pei Ye Choy, K. D. Senali Abayratna Wansa, Bing Zhao, Kar Sian Lim, Shi Chi Leow, Jit Sin Yow, Roy Joseph, Haixia Li, Kartiki V. Desai, Jane S. Thomsen, Yew Kok Lee, R. Krishna Murthy Karuturi, Thoreau Herve, Guillaume Bourque, Xiaoan Ruan, Valere Cacheux-Rataboul, Wing-Kin Sung, Edison T. Liu, Chia-Lin Wei, Edwin Cheung & Yijun Ruan
2. Department of Molecular Biology, Nijmegen Centre for Molecular Life Sciences, Radboud University, 6500 HB Nijmegen, The Netherlands
   Willem-Jan Welboren & Hendrik G. Stunnenberg
3. Department of Computer Science, School of Computing, National University of Singapore, Singapore 117543
   Wing-Kin Sung
4. Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597
   Edwin Cheung & Yijun Ruan
5. School of Biological Sciences, Nanyang Technological University, Singapore 637551
   Edwin Cheung

Authors

1. Melissa J. Fullwood
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2. Mei Hui Liu
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3. You Fu Pan
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4. Jun Liu
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5. Han Xu
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6. Yusoff Bin Mohamed
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7. Yuriy L. Orlov
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8. Stoyan Velkov
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9. Andrea Ho
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10. Poh Huay Mei
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11. Elaine G. Y. Chew
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12. Phillips Yao Hui Huang
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13. Willem-Jan Welboren
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14. Yuyuan Han
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15. Hong Sain Ooi
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16. Pramila N. Ariyaratne
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17. Vinsensius B. Vega
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18. Yanquan Luo
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19. Peck Yean Tan
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20. Pei Ye Choy
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21. K. D. Senali Abayratna Wansa
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22. Bing Zhao
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23. Kar Sian Lim
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24. Shi Chi Leow
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25. Jit Sin Yow
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26. Roy Joseph
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27. Haixia Li
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28. Kartiki V. Desai
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29. Jane S. Thomsen
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30. Yew Kok Lee
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31. R. Krishna Murthy Karuturi
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32. Thoreau Herve
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33. Guillaume Bourque
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34. Hendrik G. Stunnenberg
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35. Xiaoan Ruan
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36. Valere Cacheux-Rataboul
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37. Wing-Kin Sung
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38. Edison T. Liu
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39. Chia-Lin Wei
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40. Edwin Cheung
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41. Yijun Ruan
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Corresponding authors

Correspondence toEdwin Cheung or Yijun Ruan.

Supplementary information

Supplementary Information

This file contains Supplementary Results, Supplementary Methods, Supplementary Notes, Supplementary Tables 4-7 and 9 (see separate files s2-s6 for Supplementary Tables 1-3, 8 and 10), Supplementary Figures 1-21 with Legends, Supplementary References and a Supplementary Glossary. (PDF 16985 kb)

Supplementary Table 1

This file shows all ERα binding sites found by ChIA-PET and supporting datasets, and associated genes. (XLS 3861 kb)

Supplementary Table 2

This file shows all raw interchromosomal and intrachromosomal inter-ligation PET clusters (duplex interactions) found by ChIA-PET experiments. (XLS 1763 kb)

Supplementary Table 3

This file shows processed interaction regions found by ChIA-PET experiments, and associated genes. (XLS 915 kb)

Supplementary Table 8

This file shows loop, anchor and enclosed anchor genes from ChIA-PET experiments, and their transcriptional characteristics. (XLS 2688 kb)

Supplementary Table 10

This file shows sequence and technical information used in the ChIA-PET and validation experiments. (XLS 43 kb)

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Fullwood, M., Liu, M., Pan, Y. et al. An oestrogen-receptor-α-bound human chromatin interactome.Nature 462, 58–64 (2009). https://doi.org/10.1038/nature08497

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• Received: 25 July 2009
• Accepted: 11 September 2009
• Issue Date: 05 November 2009
• DOI: https://doi.org/10.1038/nature08497