CoChat
Sign Up
Cited by 700Genomics and Chromatin DynamicsChromosomal and Genetic VariationsGenomics and Phylogenetic Studies

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

Open access
Schmidt, Dominic, Wilson, Michael D., Ballester, Benoit, Schwalie, Petra C., Brown, Gordon D., Marshall, Aileen, Kutter, Claudia, Watt, Stephen +5 more·2010·Science
DOI 10.1126/science.1186176PMC PMC3008766
Open this paper in CoChat — free account

Abstract

Subtle Variation: Despite vast phenotypic differences, vertebrates have many readily recognizable specific cell types, like liver hepatocytes. The gene expression that defines specific cells depends on evolutionarily conserved orthologous transcription factors. Schmidt et al. (p. 1036 , published online 8 April) studied the conservation and divergence in the genome-wide binding of two such transcription factors, CEBPA and HNF4A, in livers from human, dog, mouse, short-tailed opossum, and chicken. Although the sequence bound by orthologous transcription factors was similar, the vast majority of binding events were unique to each species.

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 · 10.1126/science.1186176

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

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?

  • Enhancer conservation is typically modular, commonly preserving the sets of binding sites for the required transcription factors, but often not their exact sequence and orientation.

    “Instead, enhancer conservation is typically “modular”, commonly preserving the sets of binding sites for the required TFs, but often not their exact sequence and orientation [101–109].”

    From Transcriptional enhancers and their communication with gene promoters (2021) · cites this paper as [103]

    The paper’s discussion (page not provided in our copy) says that tissue-specific regulation can persist through regulatory architectures independent of sequence constraint, and describes nearby compensatory TF-binding events. This supports flexibility in binding-site sequence and location, but the study examines two liver TFs and does not establish that enhancers typically preserve the full set of required TF sites or that site orientation often changes. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

  • Hepatic TF cistromes can be faithfully inferred from mouse liver ChIP-seq data.

    “hepatic TF cistromes can be faithfully inferred from mouse liver ChIP‐seq data (Kyrmizi et al, 2006; Schmidt et al, 2010; Dubois‐Chevalier et al, 2017a; Sommars et al, 2019; Dubois et al, 2020a).”

    From An extended transcription factor regulatory network controls hepatocyte identity (2023) · cites this paper as Schmidt et al, 2010

Self-check

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

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

Cites

Flagged first, then by citations

Research works printed but not linked: 28

  1. [1]Wray GA Nat Rev Genet 2007 8 206 16 17304246
  2. [2]Lenhard B Sandelin A Mendoza L Engström P J Biol 2003 2 13 12760745 PMC193685
  3. [3]Boffelli D McAuliffe J Ovcharenko D Lewis KD Science 2003 299 1391 4 12610304
  4. [4]Borneman AR Gianoulis TA Zhang ZD Yu H Science 2007 317 815 9 17690298
  5. [5]Dermitzakis ET Clark AG Mol Biol Evol 2002 19 1114 21 12082130
  6. [6]ENCODE Project Consortium Birney E Stamatoyannopoulos JA Dutta A Nature 2007 447 799 816 17571346 PMC2212820
  7. [7]Odom DT Dowell RD Jacobsen ES Gordon W Nat Genet 2007 39 730 2 17529977 PMC3797512
  8. [8]Boj SF Servitja JM Martin D Rios M Diabetes 2009 58 1245 53 19188435 PMC2671044
  9. [9]Chan ET Quon GT Chua G Babak T J Biol 2009 8 33 19371447 PMC2689434
  10. [10]Martinez-Jimenez CP Kyrmizi I Cardot P Gonzalez FJ Talianidis I Mol Cell Biol 2009 PMC2812226 19933841
  11. [11]Hatzis P Kyrmizi I Talianidis I Mol Cell Biol 2006 26 7017 29 16980607 PMC1592892
  12. [12]Wilson MD Barbosa-Morais NL Schmidt D Conboy CM Science 2008 322 434 8 18787134 PMC3717767
  13. [13]Hubbard TJ Aken BL Ayling S Ballester B Nucleic Acids Res 2009 37 D690 7 19033362 PMC2686571
  14. [14]Mikkelsen TS Wakefield MJ Aken B Amemiya CT Nature 2007 447 167 77 17495919
  15. [15]Bejerano G Pheasant M Makunin I Stephen S Science 2004 304 1321 5 15131266
  16. [16]Portales-Casamar E Kirov S Lim J Lithwick S Genome Biol 2007 8 R207 17916232 PMC2246282
  17. [17]Visel A Blow MJ Li Z Zhang T Nature 2009 457 854 8 19212405 PMC2745234
  18. [18]Badis G Berger MF Philippakis AA Talukder S Science 2009 324 1720 3 19443739 PMC2905877
  19. [19]Cooper GM Stone EA Asimenos G NISC Comparative Sequencing Program Genome Res 2005 15 901 13 15965027 PMC1172034
  20. [20]Margulies EH Vinson JP NISC Comparative Sequencing Program Miller W Proc Natl Acad Sci U S A 2005 102 4795 800 15778292 PMC555705
  21. [21]Blanchette M Bataille AR Chen X Poitras C Genome Res 2006 16 656 68 16606704 PMC1457048
  22. [22]Taylor J Tyekucheva S King DC Hardison RC Genome Res 2006 16 1596 604 17053093 PMC1665643
  23. [23]Margulies EH Cooper GM Asimenos G Thomas DJ Genome Res 2007 17 760 74 17567995 PMC1891336
  24. [24]Miller W Rosenbloom K Hardison RC Hou M Genome Res 2007 17 1797 808 17984227 PMC2099589
  25. [25]Xie X Mikkelsen TS Gnirke A Lindblad-Toh K Proc Natl Acad Sci U S A 2007 104 7145 50 17442748 PMC1852749
  26. [26]Vaquerizas JM Kummerfeld SK Teichmann SA Luscombe NM Nat Rev Genet 2009 10 252 63 19274049
  27. [27]MacArthur S Li XY Li J Brown JB Genome Biol 2009 10 R80 19627575 PMC2728534
  28. [28]Gordân R Narlikar L Hartemink AJ Nucleic Acids Res 2010 PMC2847231 20047961

Cited by

Sorted by citations

Authors
Schmidt, D., Wilson, M. D., Ballester, B., Schwalie, P. C., Brown, G. D., Marshall, A., Kutter, C., Watt, S., Martinez-Jimenez, C. P., Mackay, S., Talianidis, I., Flicek, P., & Odom, D. T.
Affiliations
  • University of Cambridge (GB)
  • European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.
  • European Bioinformatics Institute (GB)
  • Cancer Research UK (GB)
  • Biomedical Sciences Research Center Alexander Fleming, 16672 Vari, Greece.
  • University of Glasgow (GB)
  • Alexander Fleming Biomedical Sciences Research Center (GR)
Corresponding author
  • Schmidt, Dominic
  • Wilson, Michael D.
  • Flicek, Paul
  • Odom, Duncan T.
ORCID
Venue
Science
Publisher
American Association for the Advancement of Science (AAAS)
Published
2010-05-21
Volume
328
Issue
5981
Pages
1036-1040
ISSN
  • 0036-8075 (ISSN-L)
  • 1095-9203
DOI
10.1126/science.1186176
PMC
PMC3008766
OpenAlex
W2095005830
Cited by
700
References
4
Citations by year
2026: 15 · 2025: 13 · 2024: 19 · 2023: 19 · 2022: 28 · 2021: 31 · 2020: 25 · 2019: 25 · 2018: 43 · 2017: 38 · 2016: 41 · 2015: 68 · 2014: 64 · 2013: 84 · 2012: 76
FWCI
34.92
Type
journal article
Language
en
Open access
Locations
  • Science (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • HAL (submittedVersion)
  • ENLIGHTEN (Jurnal Bimbingan dan Konseling Islam) (submittedVersion)
  • Repository of Digital Objects for Teaching Research and Culture (University of Valencia) (submittedVersion, other-oa)
Funders
  • Wellcome Trust (079643, 062023, WT079643, WT062023)
  • Cancer Research UK (15603, A15603)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
Keywords
transcription factor binding, regulatory evolution, C/EBPα, liver, vertebrate evolution, species-specific binding, gene expression regulation, comparative genomics
MeSH terms
Algorithms, Animals, Base Sequence, Binding Sites, Chickens, DNA, Dogs, Biological Evolution, Gene Expression Regulation, Humans, Liver, Opossums, Protein Binding, Regulatory Sequences, Nucleic Acid, Species Specificity, Vertebrates, Genome, Human, Genome, Sequence Analysis, DNA, Evolution, Molecular, CCAAT-Enhancer-Binding Protein-alpha, Chromatin Immunoprecipitation, Mice, Hepatocyte Nuclear Factor 4

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