CoChat
Sign Up
Cited by 170

The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

Pedersen, Jakob Skou, Valen, Eivind, Velazquez, Amhed M. Vargas, Parker, Brian J., Rasmussen, Morten, Lindgreen, Stinus, Lilje, Berit, Tobin, Desmond J., Kelly, Theresa K., Vang, Søren, Andersson, Robin, Jones, Peter A., Hoover, Cindi A., Tikhonov, Alexei, Prokhortchouk, Egor, Rubin, Edward M., Sandelin, Albin, Gilbert, M. Thomas P., Krogh, Anders, Willerslev, Eske, Orlando, Ludovic·2014·Genome Research
DOI 10.1101/gr.163592.113PMC PMC3941110
Open this paper in CoChat — free account

Abstract

Epigenetic information is available from contemporary organisms, but is difficult to track back in evolutionary time. Here, we show that genome-wide epigenetic information can be gathered directly from next-generation sequence reads of DNA isolated from ancient remains. Using the genome sequence data generated from hair shafts of a 4000-yr-old Paleo-Eskimo belonging to the Saqqaq culture, we generate the first ancient nucleosome map coupled with a genome-wide survey of cytosine methylation levels. The validity of both nucleosome map and methylation levels were confirmed by the recovery of the expected signals at promoter regions, exon/intron boundaries, and CTCF sites. The top-scoring nucleosome calls revealed distinct DNA positioning biases, attesting to nucleotide-level accuracy. The ancient methylation levels exhibited high conservation over time, clustering closely with modern hair tissues. Using ancient methylation information, we estimated the age at death of the Saqqaq individual and illustrate how epigenetic information can be used to infer ancient gene expression. Similar epigenetic signatures were found in other fossil material, such as 110,000- to 130,000-yr-old bones, supporting the contention that ancient epigenomic information can be reconstructed from a deep past. Our findings lay the foundation for extracting epigenomic information from ancient samples, allowing shifts in epialleles to be tracked through evolutionary time, as well as providing an original window into modern epigenomics.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/gr.163592.113

Cites

15 of 15 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The second category of methods for ancient DNA methylation analysis relies on indirect statistical inference based on patterns of post-mortem DNA decay that are ubiquitous in plants and animals.

    “The second category of methods for ancient DNA methylation analysis relies on indirect statistical inference based on patterns of post-mortem DNA decay that are ubiquitous in plants 246 and animals 28,29 .”

    From Ancient DNA analysis (2021) · cites this paper as [29]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 72

  1. 10.1101/gr.125187.111 · DOI
  2. 10.1371/journal.pone.0011217 · DOI
  3. 10.1038/nbt.1533 · DOI
  4. 10.1016/j.diff.2009.06.004 · DOI
  5. 10.1126/science.291.5503.447 · DOI
  6. 10.1093/nar/gks001 · DOI · Paper page
  7. 10.1038/nature10549 · DOI · Paper page
  8. 10.1038/sj.jid.5700007 · DOI
  9. 10.2217/epi.13.5 · DOI
  10. 10.1371/journal.pone.0014524 · DOI
  11. 10.1073/pnas.0704665104 · DOI · Paper page
  12. 10.1093/nar/gkp1163 · DOI · Paper page
  13. 10.1038/nature11142 · DOI
  14. 10.1073/pnas.95.15.8544 · DOI
  15. 10.1021/pr200721u · DOI
  16. 10.1371/journal.pone.0015754 · DOI
  17. 10.1371/journal.pone.0010933 · DOI
  18. 10.1038/35055536 · DOI
  19. 2012, Length and GC-biases during sequencing library amplification: A comparison of various polymerase-buffer systems with ancient and modern DNA sequencing libraries, Biotechniques, 52, 87, 10.2144/000113809 · DOI · Paper page
  20. 10.1101/gad.2037511 · DOI · Paper page
  21. 10.1101/gr.5636607 · DOI
  22. 1997, Internucleosomal DNA cleavage triggered by plasma membrane damage during necrotic cell death. Involvement of serine but not cysteine proteases, Am J Pathol, 151, 1205
  23. 10.1093/nar/gkq742 · DOI
  24. 10.1371/journal.pgen.1000138 · DOI
  25. 10.1371/journal.pgen.1003036 · DOI
  26. 10.1371/journal.pone.0024161 · DOI
  27. 10.1016/j.tree.2005.07.005 · DOI · Paper page
  28. 10.1016/j.molcel.2011.12.023 · DOI
  29. 10.1126/science.1188021 · DOI · Paper page
  30. 10.1038/ng.857 · DOI
  31. 10.1038/312282a0 · DOI
  32. 10.1101/gr.091678.109 · DOI
  33. 10.1038/nprot.2008.211 · DOI · Paper page
  34. 10.1101/gr.116228.110 · DOI
  35. 10.1371/journal.pone.0067378 · DOI
  36. 10.1101/gr.143008.112 · DOI · Paper page
  37. 2011, Targeted high throughput sequencing in clinical cancer settings: Formaldehyde fixed-paraffin embedded (FFPE) tumor tissues, input amount and tumor heterogeneity, BMC Med Genet, 4, 68
  38. 2006, Gene expression in head hair follicles plucked from men and women, Ann Clin Lab Sci Spring, 36, 115
  39. 2011, Epigenetic-aging-signature to determine age in different tissues, Aging, 3, 1018, 10.18632/aging.100395 · DOI
  40. 10.1080/07391102.2006.10507097 · DOI
  41. 10.1038/nature04432 · DOI
  42. 10.1016/j.cub.2009.11.068 · DOI · Paper page
  43. 10.1038/nmeth.1828 · DOI
  44. 10.1038/jid.2009.192 · DOI · Paper page
  45. 10.1101/gr.101907.109 · DOI
  46. 10.1074/mcp.M500278-MCP200 · DOI
  47. 10.1093/bioinformatics/btp324 · DOI · Paper page
  48. 10.1101/gr.083451.108 · DOI
  49. 10.1371/journal.pone.0030226 · DOI · Paper page
  50. 10.1038/nature10574 · DOI · Paper page
  51. 10.1038/ncomms3172 · DOI
  52. 10.1038/nature07446 · DOI
  53. 10.1073/pnas.1210506109 · DOI · Paper page
  54. 10.1007/s00418-008-0435-6 · DOI · Paper page
  55. 10.1038/34112 · DOI
  56. 10.1126/science.1113485 · DOI
  57. 10.1016/S1055-7903(03)00023-X · DOI
  58. 10.1038/nature12323 · DOI · Paper page
  59. 10.1038/nbt1279 · DOI
  60. 10.1073/pnas.86.6.1939 · DOI
  61. 10.1016/j.bpj.2012.03.056 · DOI
  62. 10.1093/nar/gkp727 · DOI
  63. 10.1016/j.cell.2008.02.022 · DOI
  64. 10.1126/science.1238286 · DOI · Paper page
  65. 10.1038/nature04979 · DOI
  66. 10.1126/science.1101074 · DOI
  67. 10.1186/1756-8935-6-26 · DOI
  68. 10.1038/nsmb.1594 · DOI
  69. 10.1038/nsmb.2506 · DOI
  70. 2011, Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer, Genome Res, 20, 440
  71. 10.1038/nature10002 · DOI
  72. 10.7554/eLife.00731 · DOI

Cited by

Sorted by citations

Metadata

Authors
Pedersen, J. S., Valen, E., Velazquez, A. M. V., Parker, B. J., Rasmussen, M., Lindgreen, S., Lilje, B., Tobin, D. J., Kelly, T. K., Vang, S., Andersson, R., Jones, P. A., Hoover, C. A., Tikhonov, A., Prokhortchouk, E., Rubin, E. M., Sandelin, A., Gilbert, M. T. P., Krogh, A., Willerslev, E., & Orlando, L.
Venue
Genome Research
Publisher
Cold Spring Harbor Laboratory
Published
2013-12-03
Volume
24
Issue
3
Pages
454-466
ISSN
1088-9051
DOI
10.1101/gr.163592.113
PMC
PMC3941110
Cited by
170
References
15
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review