The accessible chromatin landscape of the human genome
10.1038/nature11232
Crossref journal-article
Springer Science and Business Media LLC
Nature (297)
Bibliography

Thurman, R. E., Rynes, E., Humbert, R., Vierstra, J., Maurano, M. T., Haugen, E., Sheffield, N. C., Stergachis, A. B., Wang, H., Vernot, B., Garg, K., John, S., Sandstrom, R., Bates, D., Boatman, L., Canfield, T. K., Diegel, M., Dunn, D., Ebersol, A. K., … Stamatoyannopoulos, J. A. (2012). The accessible chromatin landscape of the human genome. Nature, 489(7414), 75–82.

Authors 62
  1. Robert E. Thurman (first)
  2. Eric Rynes (additional)
  3. Richard Humbert (additional)
  4. Jeff Vierstra (additional)
  5. Matthew T. Maurano (additional)
  6. Eric Haugen (additional)
  7. Nathan C. Sheffield (additional)
  8. Andrew B. Stergachis (additional)
  9. Hao Wang (additional)
  10. Benjamin Vernot (additional)
  11. Kavita Garg (additional)
  12. Sam John (additional)
  13. Richard Sandstrom (additional)
  14. Daniel Bates (additional)
  15. Lisa Boatman (additional)
  16. Theresa K. Canfield (additional)
  17. Morgan Diegel (additional)
  18. Douglas Dunn (additional)
  19. Abigail K. Ebersol (additional)
  20. Tristan Frum (additional)
  21. Erika Giste (additional)
  22. Audra K. Johnson (additional)
  23. Ericka M. Johnson (additional)
  24. Tanya Kutyavin (additional)
  25. Bryan Lajoie (additional)
  26. Bum-Kyu Lee (additional)
  27. Kristen Lee (additional)
  28. Darin London (additional)
  29. Dimitra Lotakis (additional)
  30. Shane Neph (additional)
  31. Fidencio Neri (additional)
  32. Eric D. Nguyen (additional)
  33. Hongzhu Qu (additional)
  34. Alex P. Reynolds (additional)
  35. Vaughn Roach (additional)
  36. Alexias Safi (additional)
  37. Minerva E. Sanchez (additional)
  38. Amartya Sanyal (additional)
  39. Anthony Shafer (additional)
  40. Jeremy M. Simon (additional)
  41. Lingyun Song (additional)
  42. Shinny Vong (additional)
  43. Molly Weaver (additional)
  44. Yongqi Yan (additional)
  45. Zhancheng Zhang (additional)
  46. Zhuzhu Zhang (additional)
  47. Boris Lenhard (additional)
  48. Muneesh Tewari (additional)
  49. Michael O. Dorschner (additional)
  50. R. Scott Hansen (additional)
  51. Patrick A. Navas (additional)
  52. George Stamatoyannopoulos (additional)
  53. Vishwanath R. Iyer (additional)
  54. Jason D. Lieb (additional)
  55. Shamil R. Sunyaev (additional)
  56. Joshua M. Akey (additional)
  57. Peter J. Sabo (additional)
  58. Rajinder Kaul (additional)
  59. Terrence S. Furey (additional)
  60. Job Dekker (additional)
  61. Gregory E. Crawford (additional)
  62. John A. Stamatoyannopoulos (additional)
References 36 Referenced 2,448
  1. Felsenfeld, G., Boyes, J., Chung, J., Clark, D. & Studitsky, V. Chromatin structure and gene expression. Proc. Natl Acad. Sci. USA 93, 9384–9388 (1996) (10.1073/pnas.93.18.9384) / Proc. Natl Acad. Sci. USA by G Felsenfeld (1996)
  2. Gross, D. S. & Garrard, W. T. Nuclease hypersensitive sites in chromatin. Annu. Rev. Biochem. 57, 159–197 (1988) (10.1146/annurev.bi.57.070188.001111) / Annu. Rev. Biochem. by DS Gross (1988)
  3. Gaszner, M. & Felsenfeld, G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev. Genet. 7, 703–713 (2006) (10.1038/nrg1925) / Nature Rev. Genet. by M Gaszner (2006)
  4. Li, Q., Harju, S. & Peterson, K. R. Locus control regions: coming of age at a decade plus. Trends Genet. 15, 403–408 (1999) (10.1016/S0168-9525(99)01780-1) / Trends Genet. by Q Li (1999)
  5. Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007) (10.1038/ng1966) / Nature Genet. by ND Heintzman (2007)
  6. Hesselberth, J. R. et al. Global mapping of protein-DNA interactions in vivo by digital genomic footprinting. Nature Methods 6, 283–289 (2009) (10.1038/nmeth.1313) / Nature Methods by JR Hesselberth (2009)
  7. Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008) (10.1016/j.cell.2007.12.014) / Cell by AP Boyle (2008)
  8. John, S. et al. Chromatin accessibility pre-determines glucocorticoid receptor binding patterns. Nature Genet. 43, 264–268 (2011) (10.1038/ng.759) / Nature Genet. by S John (2011)
  9. Song, L. et al. Open chromatin defined by DNase I and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res. 21, 1757–1767 (2010) (10.1101/gr.121541.111) / Genome Res. by L Song (2010)
  10. Harrow, J. et al. GENCODE: The reference human genome annotation for the ENCODE project. Genome Res. (in the press)
  11. Griffiths-Jones, S., Saini, H. K., van Dongen, S. & Enright, A. J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 36, D154–D158 (2008) (10.1093/nar/gkm952) / Nucleic Acids Res. by S Griffiths-Jones (2008)
  12. Farazi, T. A., Spitzer, J. I., Morozov, P. & Tuschl, T. miRNAs in human cancer. J. Pathol. 223, 102–115 (2011) (10.1002/path.2806) / J. Pathol. by TA Farazi (2011)
  13. Djebali, S. et al. Landscape of transcription in human cells. Nature http://dx.doi.org/10.1038/nature11233 (this issue) (10.1038/nature11233)
  14. ENCODE Project Consortium An integrated encyclopedia of DNA elements in the human genome. Nature http://dx.doi.org/10.1038/nature11247 (this issue) (10.1038/nature11247)
  15. Biggin, M. D. Animal transcription networks as highly connected, quantitative continua. Dev. Cell 21, 611–626 (2011) (10.1016/j.devcel.2011.09.008) / Dev. Cell by MD Biggin (2011)
  16. Reddy, P. M., Stamatoyannopoulos, G., Papayannopoulou, T. & Shen, C. K. Genomic footprinting and sequencing of human β-globin locus. Tissue specificity and cell line artifact. J. Biol. Chem. 269, 8287–8295 (1994) (10.1016/S0021-9258(17)37191-0) / J. Biol. Chem. by PM Reddy (1994)
  17. Forsberg, E. C., Downs, K. M. & Bresnick, E. H. Direct interaction of NF-E2 with hypersensitive site 2 of the β-globin locus control region in living cells. Blood 96, 334–339 (2000) (10.1182/blood.V96.1.334) / Blood by EC Forsberg (2000)
  18. Talbot, D. & Grosveld, F. The 5′HS2 of the globin locus control region enhances transcription through the interaction of a multimeric complex binding at two functionally distinct NF-E2 binding sites. EMBO J. 10, 1391–1398 (1991) (10.1002/j.1460-2075.1991.tb07659.x) / EMBO J. by D Talbot (1991)
  19. Weisbrod, S. & Weintraub, H. Isolation of a subclass of nuclear proteins responsible for conferring a DNase I-sensitive structure on globin chromatin. Proc. Natl Acad. Sci. USA 76, 630–634 (1979) (10.1073/pnas.76.2.630) / Proc. Natl Acad. Sci. USA by S Weisbrod (1979)
  20. Schultz, D. C., Ayyanathan, K., Negorev, D., Maul, G. G. & Rauscher, F. J. SETDB1: a novel KAP-1-associated histone H3, lysine 9-specific methyltransferase that contributes to HP1-mediated silencing of euchromatic genes by KRAB zinc-finger proteins. Genes Dev. 16, 919–932 (2002) (10.1101/gad.973302) / Genes Dev. by DC Schultz (2002)
  21. Frietze, S., O’Geen, H., Blahnik, K. R., Jin, V. X. & Farnham, P. J. ZNF274 recruits the histone methyltransferase SETDB1 to the 3′ ends of ZNF genes. PLoS ONE 5, e15082 (2010) (10.1371/journal.pone.0015082) / PLoS ONE by S Frietze (2010)
  22. Stergachis, A. B., Maclean, B., Lee, K., Stamatoyannopoulos, J. A. & MacCoss, M. J. Rapid empirical discovery of optimal peptides for targeted proteomics. Nature Methods 8, 1041–1043 (2011) (10.1038/nmeth.1770) / Nature Methods by AB Stergachis (2011)
  23. Henikoff, S., Henikoff, J. G., Sakai, A., Loeb, G. B. & Ahmad, K. Genome-wide profiling of salt fractions maps physical properties of chromatin. Genome Res. 19, 460–469 (2009) (10.1101/gr.087619.108) / Genome Res. by S Henikoff (2009)
  24. Li, G. et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell 148, 84–98 (2012) (10.1016/j.cell.2011.12.014) / Cell by G Li (2012)
  25. Siegfried, Z. et al. DNA methylation represses transcription in vivo. Nature Genet. 22, 203–206 (1999) (10.1038/9727) / Nature Genet. by Z Siegfried (1999)
  26. O’Geen, H. et al. Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs. PLoS Genet. 3, e89 (2007) (10.1371/journal.pgen.0030089) / PLoS Genet. by H O’Geen (2007)
  27. Stadler, M. B. et al. DNA-binding factors shape the mouse methylome at distal regulatory regions. Nature 480, 490–495 (2011) (10.1038/nature10716) / Nature by MB Stadler (2011)
  28. Rasheed, Z. A., Saleem, A., Ravee, Y., Pandolfi, P. P. & Rubin, E. H. The topoisomerase I-binding RING protein, topors, is associated with promyelocytic leukemia nuclear bodies. Exp. Cell Res. 277, 152–160 (2002) (10.1006/excr.2002.5550) / Exp. Cell Res. by ZA Rasheed (2002)
  29. Dahle, Ø., Bakke, O. & Gabrielsen, O. S. c-Myb associates with PML in nuclear bodies in hematopoietic cells. Exp. Cell Res. 297, 118–126 (2004) (10.1016/j.yexcr.2004.03.014) / Exp. Cell Res. by Ø Dahle (2004)
  30. 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) (10.1101/gr.5571506) / Genome Res. by J Dostie (2006)
  31. Sanyal, A., Lajoie, B., Jain, G. & Dekker, J. The long-range interaction landscape of gene promoters. Nature http://dx.doi.org/10.1038/nature11279 (this issue) (10.1038/nature11279)
  32. Kim, J., Chu, J., Shen, X., Wang, J. & Orkin, S. H. An extended transcriptional network for pluripotency of embryonic stem cells. Cell 132, 1049–1061 (2008) (10.1016/j.cell.2008.02.039) / Cell by J Kim (2008)
  33. Tuan, D., Kong, S. & Hu, K. Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc. Natl Acad. Sci. USA 89, 11219–11223 (1992) (10.1073/pnas.89.23.11219) / Proc. Natl Acad. Sci. USA by D Tuan (1992)
  34. Neph, S. et al. An expansive human regulatory lexicon encoded in transcription factor footprints. Nature http://dx.doi.org/10.1038/nature11212 (this issue) (10.1038/nature11212)
  35. Vernot, B. et al. Personal and population genomics of human regulatory variation. Genome Res. (in the press)
  36. Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011) (10.1093/bioinformatics/btr064) / Bioinformatics by CE Grant (2011)
Dates
Type When
Created 13 years ago (Sept. 4, 2012, 10:12 a.m.)
Deposited 2 years, 3 months ago (May 18, 2023, 2:02 p.m.)
Indexed 1 day, 14 hours ago (Sept. 4, 2025, 10:15 a.m.)
Issued 13 years ago (Sept. 1, 2012)
Published 13 years ago (Sept. 1, 2012)
Published Online 13 years ago (Sept. 5, 2012)
Published Print 13 years ago (Sept. 1, 2012)
Funders 0

None

@article{Thurman_2012, title={The accessible chromatin landscape of the human genome}, volume={489}, ISSN={1476-4687}, url={http://dx.doi.org/10.1038/nature11232}, DOI={10.1038/nature11232}, number={7414}, journal={Nature}, publisher={Springer Science and Business Media LLC}, author={Thurman, Robert E. and Rynes, Eric and Humbert, Richard and Vierstra, Jeff and Maurano, Matthew T. and Haugen, Eric and Sheffield, Nathan C. and Stergachis, Andrew B. and Wang, Hao and Vernot, Benjamin and Garg, Kavita and John, Sam and Sandstrom, Richard and Bates, Daniel and Boatman, Lisa and Canfield, Theresa K. and Diegel, Morgan and Dunn, Douglas and Ebersol, Abigail K. and Frum, Tristan and Giste, Erika and Johnson, Audra K. and Johnson, Ericka M. and Kutyavin, Tanya and Lajoie, Bryan and Lee, Bum-Kyu and Lee, Kristen and London, Darin and Lotakis, Dimitra and Neph, Shane and Neri, Fidencio and Nguyen, Eric D. and Qu, Hongzhu and Reynolds, Alex P. and Roach, Vaughn and Safi, Alexias and Sanchez, Minerva E. and Sanyal, Amartya and Shafer, Anthony and Simon, Jeremy M. and Song, Lingyun and Vong, Shinny and Weaver, Molly and Yan, Yongqi and Zhang, Zhancheng and Zhang, Zhuzhu and Lenhard, Boris and Tewari, Muneesh and Dorschner, Michael O. and Hansen, R. Scott and Navas, Patrick A. and Stamatoyannopoulos, George and Iyer, Vishwanath R. and Lieb, Jason D. and Sunyaev, Shamil R. and Akey, Joshua M. and Sabo, Peter J. and Kaul, Rajinder and Furey, Terrence S. and Dekker, Job and Crawford, Gregory E. and Stamatoyannopoulos, John A.}, year={2012}, month=sep, pages={75–82} }