The DOI matches its Crossref record; 26 of the 26 references it cites were found in a registry or an index.
The chromatin insulator CTCF and the emergence of metazoan diversity
Open accessAbstract
The great majority of metazoans belong to bilaterian phyla. They diversified during a short interval in Earth’s history known as the Cambrian explosion, ∼540 million years ago. However, the genetic basis of these events is poorly understood. Here we argue that the vertebrate genome organizer CTCF (CCCTC-binding factor) played an important role for the evolution of bilaterian animals. We provide evidence that the CTCF protein and a genome-wide abundance of CTCF-specific binding motifs are unique to bilaterian phyla, but absent in other eukaryotes. We demonstrate that CTCF-binding sites within vertebrate and Drosophila Hox gene clusters have been maintained for several hundred million years, suggesting an ancient origin of the previously known interaction between Hox gene regulation and CTCF. In addition, a close correlation between the presence of CTCF and Hox gene clusters throughout the animal kingdom suggests conservation of the Hox-CTCF link across the Bilateria. On the basis of these findings, we propose the existence of a Hox-CTCF kernel as principal organizer of bilaterian body plans. Such a kernel could explain ( i ) the formation of Hox clusters in Bilateria, ( ii ) the diversity of bilaterian body plans, and ( iii ) the uniqueness and time of onset of the Cambrian explosion.
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.
Integrity signals
Registry
Cites
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.
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
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Stamatakis, A. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl446 · Cited by 15,582
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845
The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 3,971 · cited 1×
“From the resulting positive sites, we generated 100-bp windows of genomic alignments as input for the PHASTCONS program (80).”
MethodEvolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (2007) · Nature · doi:10.1038/nature06341 · Cited by 2,010
A molecular timescale for vertebrate evolution
Kumar, S., & Hedges, S. B. (1998) · Nature · doi:10.1038/31927 · Cited by 1,936
Broad phylogenomic sampling improves resolution of the animal tree of life
Dunn, C. W., Hejnol, A., Matus, D. Q., Pang, K., Browne, W. E., Smith, S. A., Seaver, E., Rouse, G. W., Obst, M., Edgecombe, G. D., et al. (2008) · Nature · doi:10.1038/nature06614 · Cited by 1,921
Sea Anemone Genome Reveals Ancestral Eumetazoan Gene Repertoire and Genomic Organization
Putnam, N. H., Srivastava, M., Hellsten, U., Dirks, B., Chapman, J., Salamov, A., Terry, A., Shapiro, H., Lindquist, E., Kapitonov, V. V., et al. (2007) · Science · doi:10.1126/science.1139158 · Cited by 1,555
Gene Regulatory Networks and the Evolution of Animal Body Plans
Davidson, E. H., & Erwin, D. H. (2006) · Science · doi:10.1126/science.1113832 · Cited by 1,207 · cited 7×
“On the basis of these observations, we propose that the Hox-CTCF link represents at least part of what Davidson and Erwin (8) called the kernel of a gene regulatory network.”
BackgroundInfluentialCohesin mediates transcriptional insulation by CCCTC-binding factor
Wendt, K. S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., et al. (2008) · Nature · doi:10.1038/nature06634 · Cited by 1,193
Research works printed but not linked: 60
- 10.1098/rstb.2009.0038 · DOI
- 10.1038/sj.embor.7400334 · DOI · Paper page
- 10.1371/journal.pgen.1000169 · DOI
- 10.1016/S0070-2153(07)80009-3 · DOI · Paper page
- 10.1016/j.cell.2009.06.001 · DOI · Paper page
- 10.1007/s00018-009-8647-z · DOI
- 10.1073/pnas.0701811104 · DOI · Paper page
- 10.1016/j.cell.2006.12.048 · DOI · Paper page
- 10.1038/ng.857 · DOI · Paper page
- VV Lobanenkov, et al., A novel sequence-specific DNA binding protein which interacts with three regularly spaced direct repeats of the CCCTC-motif in the 5′-flanking sequence of the chicken c-myc gene. Oncogene 5, 1743–1753 (1990).
- 10.1016/S0925-4773(02)00005-9 · DOI
- 10.1016/j.gene.2006.01.036 · DOI
- 10.1186/1471-2199-6-16 · DOI
- 10.1186/1471-2199-10-84 · DOI
- 10.1038/nature07191 · DOI · Paper page
- 10.1038/nature08830 · DOI · Paper page
- 10.1016/j.ydbio.2008.12.039 · DOI
- 10.1371/journal.pgen.0030112 · DOI · Paper page
- 10.1074/jbc.M706213200 · DOI
- 10.1016/j.cell.2011.11.058 · DOI · Paper page
- 10.1038/sj.emboj.7601851 · DOI · Paper page
- 10.1038/emboj.2008.214 · DOI · Paper page
- 10.1371/journal.pone.0034915 · DOI
- 10.1038/msb.2010.79 · DOI
- 10.1074/jbc.M403121200 · DOI
- 10.1128/MCB.00327-10 · DOI
- 10.1073/pnas.1019391108 · DOI · Paper page
- 10.1093/nar/gkr1260 · DOI
- 10.1073/pnas.1018279108 · DOI
- 10.1093/nar/gkn818 · doi:10.1093/nar/gkn818
- 10.1371/journal.pgen.1001260 · DOI
- 10.1126/science.1198374 · DOI · Paper page
- 10.1093/nar/gkq1248 · doi:10.1093/nar/gkq1248
- 10.1093/molbev/msg236 · DOI · Paper page
- 10.1101/gad.5.11.2048 · DOI · Paper page
- 10.1242/dev.121.4.1077 · DOI
- 10.1242/dev.121.4.957 · DOI · Paper page
- 10.1101/gad.10.18.2326 · DOI
- 10.1242/dev.122.6.1895 · DOI
- 10.1093/emboj/16.14.4393 · DOI
- 10.1242/dev.00672 · DOI
- 10.1002/jez.b.21009 · DOI
- 10.1016/j.devcel.2010.11.009 · DOI
- MA Ferraiuolo et al. The three-dimensional architecture of Hox cluster silencing. Nucleic Acids Res 38:7472–7484. (2010). · DOI
- 10.1242/dev.024539 · DOI
- 10.1242/dev.00151 · DOI
- 10.1038/nature08789 · DOI · Paper page
- 10.1126/science.1184655 · DOI · Paper page
- 10.1016/S0960-9822(98)70174-5 · doi:10.1016/s0960-9822(98)70174-5
- 10.1038/nature02709 · DOI · Paper page
- 10.1371/journal.pgen.1000814 · DOI · Paper page
- 10.1038/emboj.2009.34 · DOI
- 10.1073/pnas.0801913105 · DOI
- 10.1073/pnas.91.15.6751 · DOI
- 10.1093/bioinformatics/14.9.755 · DOI · Paper page
- 10.1186/gb-2009-10-3-r25 · DOI · Paper page
- 10.1186/gb-2008-9-9-r137 · DOI · Paper page
- TL Bailey, C Elkan, The value of prior knowledge in discovering motifs with MEME. Proc Int Conf Intell Syst Mol Biol 3, 21–29 (1995).
- GZ Hertz, GW Hartzell, GD Stormo, Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput Appl Biosci 6, 81–92 (1990).
- 10.1073/pnas.0508169103 · DOI
Cited by
Organization and function of the 3D genome
Bonev, B., & Cavalli, G. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.112 · Cited by 1,174
Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution
Long, H. K., Prescott, S. L., & Wysocka, J. (2016) · Cell · doi:10.1016/j.cell.2016.09.018 · Cited by 945
Chromatin Domains: The Unit of Chromosome Organization
Dixon, J. R., Gorkin, D. U., & Ren, B. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.05.018 · Cited by 811
Feng, S., Cokus, S. J., Schubert, V., Zhai, J., Pellegrini, M., & Jacobsen, S. E. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.07.008 · Cited by 349
The origin of Metazoa: a unicellular perspective
Sebé-Pedrós, A., Degnan, B. M., & Ruiz-Trillo, I. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.21 · Cited by 332
Metadata
- Authors
- Heger, P., Marin, B., Bartkuhn, M., Schierenberg, E., & Wiehe, T.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2012-10-08
- Volume
- 109
- Issue
- 43
- Pages
- 17507-17512
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2067686625
- Cited by
- 198
- References
- 26
- FWCI
- 2.21
- Type
- journal article
- Language
- en
- Open access
- green
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
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: The chromatin insulator CTCF and the emergence of metazoan diversity. https://app.cochat.ai/papers/10.1073/pnas.1111941109
- The paper
- Heger, P., Marin, B., Bartkuhn, M., Schierenberg, E., & Wiehe, T. (2012). The chromatin insulator CTCF and the emergence of metazoan diversity. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1111941109
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.