Cited by 133Genomics and Chromatin DynamicsCRISPR and Genetic EngineeringChromatin Remodeling and Cancer

Functional footprinting of regulatory DNA

Open access
Vierstra, Jeff, Reik, Andreas, Chang, Kai-Hsin, Stehling-Sun, Sandra, Zhou, Yuanyue, Hinkley, Sarah J, Paschon, David E, Zhang, Lei +16 more·2015·Nature Methods

Abstract

Regulatory regions harbor multiple transcription factor (TF) recognition sites; however, the contribution of individual sites to regulatory function remains challenging to define. We describe an approach that exploits the error-prone nature of genome editing-induced double-strand break repair to map functional elements within regulatory DNA at nucleotide resolution. We demonstrate the approach on a human erythroid enhancer, revealing single TF recognition sites that gate the majority of downstream regulatory function.

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 · 10.1038/nmeth.3554

Cites

22 of 22 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?

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: 19

  1. [1]Maurano MT Science 337 1190 2012 22955828 PMC3771521
  2. [2]Carroll D Annu Rev Biochem 83 409 2014 24606144
  3. [3]Bauer DE Science 342 253 2013 24115442 PMC4018826
  4. [4]Bauer DE Orkin SH Curr Opin Pediatr 23 1 2011 21157349 PMC3092400
  5. [5]Urnov FD Rebar EJ Holmes MC Zhang HS Gregory PD Nat Rev Genet 11 636 2010 20717154
  6. [6]Miller JC Nat Biotechnol 29 143 2011 21179091
  7. [7]Giarratana MC Blood 118 5071 2011 21885599 PMC3217398
  8. [9]Neph S Nature 489 83 2012 22955618 PMC3736582
  9. [10]Ko LJ Engel JD Mol Cell Biol 13 4011 1993 8321208 PMC359950
  10. [12]Shivdasani RA Mayer EL Orkin SH Nature 373 432 1995 7830794
  11. [13]Chen RL Chou YC Lan YJ Huang TS Shen CKJ J Biol Chem 285 10189 2010 20133935 PMC2856224
  12. [14]Findlay GM Boyle EA Hause RJ Klein JC Shendure J Nature 513 120 2014 25141179 PMC4156553
  13. [15]Klemm S Nat Meth 11 549 2014 PMC4174458 24681693
  14. [16]Miller JC Nat Biotechnol 25 778 2007 17603475
  15. [17]Guschin DY Methods Mol Biol 649 247 2010 20680839
  16. [18]Doyon Y Nat Meth 7 459 2010 20436476
  17. [19]Thorpe SJ Br J Haematol 87 125 1994 7524614
  18. [20]Chang KH Stem Cell Rev 9 397 2013 22374078 PMC3398168
  19. [21]John S Curr Protoc Mol Biol Chapter 27 Unit 21.27 2013 PMC4405172 23821440

Cited by

Sorted by citations

Authors
Vierstra, J., Reik, A., Chang, K.-H., Stehling-Sun, S., Zhou, Y., Hinkley, S. J., Paschon, D. E., Zhang, L., Psatha, N., Bendana, Y. R., O'Neil, C. M., Song, A. H., Mich, A. K., Liu, P.-Q., Lee, G., Bauer, D. E., Holmes, M. C., Orkin, S. H., Papayannopoulou, T., Stamatoyannopoulos, G., Rebar, E. J., Gregory, P. D., Urnov, F. D., & Stamatoyannopoulos, J. A.
Affiliations
  • University of Washington (US)
  • Sangamo BioSciences (United States) (US)
  • Boston Children's Hospital (US)
Corresponding author
  • Urnov, Fyodor D
  • Stamatoyannopoulos, John A
Venue
Nature Methods
Published
2015-08-31
Volume
12
Issue
10
Pages
927-930
ISSN
  • 1548-7091 (ISSN-L)
  • 1548-7105
OpenAlex
W1721542075
Cited by
133
References
22
Citations by year
2026: 2 · 2025: 4 · 2024: 10 · 2023: 3 · 2022: 9 · 2021: 12 · 2020: 8 · 2019: 17 · 2018: 21 · 2017: 18 · 2016: 24 · 2015: 5
FWCI
8.94
Type
journal article
Language
en
Open access
Locations
  • Nature Methods (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
Funders
  • National Institutes of Health
  • National Heart, Lung, and Blood Institute (P01HL053750)
  • National Human Genome Research Institute (U54HG007010)
  • National Institute of Diabetes and Digestive and Kidney Diseases (R01DK101328, R01DK045365)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
Keywords
regulatory DNA, DNA double-strand break repair, error-prone repair, transcription factor binding sites
MeSH terms
Base Sequence, Binding Sites, Carrier Proteins, DNA Repair, Enhancer Elements, Genetic, Erythrocytes, Erythropoiesis, Humans, Mutation, Nuclear Proteins, Regulatory Sequences, Nucleic Acid, Repressor Proteins, Transcription Factors, Genome, Human, DNA Footprinting, Genomics, DNA Breaks, Double-Stranded

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