Variation in Homeodomain DNA Binding Revealed by High-Resolution Analysis of Sequence Preferences
Open accessAbstract
Most homeodomains are unique within a genome, yet many are highly conserved across vast evolutionary distances, implying strong selection on their precise DNA-binding specificities. We determined the binding preferences of the majority (168) of mouse homeodomains to all possible 8-base sequences, revealing rich and complex patterns of sequence specificity and showing that there are at least 65 distinct homeodomain DNA-binding activities. We developed a computational system that successfully predicts binding sites for homeodomain proteins as distant from mouse as Drosophila and C. elegans, and we infer full 8-mer binding profiles for the majority of known animal homeodomains. Our results provide an unprecedented level of resolution in the analysis of this simple domain structure and suggest that variation in sequence recognition may be a factor in its functional diversity and evolutionary success.
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Motifs for DNA-binding proteins can be highly similar among closely related proteins, allowing accurate inference of motifs.
“The motifs for DNA-binding proteins can be highly similar for closely related proteins, allowing accurate inference of motifs7,8”
From A compendium of RNA-binding motifs for decoding gene regulation (2013) · cites this paper as [8]
Cites
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625 · see citing works
Transcriptional regulatory code of a eukaryotic genome
Harbison, C. T., Gordon, D. B., Lee, T. I., Rinaldi, N. J., MacIsaac, K. D., Danford, T., Hannett, N. M., Tagne, J., Reynolds, D. B., Yoo, J. Y., et al. (2004) · Nature · doi:10.1038/nature02800 · Cited by 2,116 · see citing works
TRANSFAC(R): transcriptional regulation, from patterns to profiles
Matys, V. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg108 · Cited by 1,985 · see citing works
JASPAR: an open-access database for eukaryotic transcription factor binding profiles
Sandelin, A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh012 · Cited by 1,763 · see citing works
Carroll, J. S., Liu, X. S., Brodsky, A. S., Li, W., Meyer, C. A., Szary, A. J., Eeckhoute, J., Shao, W., Hestermann, E. V., Geistlinger, T. R., et al. (2005) · Cell · doi:10.1016/j.cell.2005.05.008 · Cited by 1,384 · see citing works
Kissinger, C. R., Liu, B., Martı́n-Blanco, E., Kornberg, T. B., & Pabo, C. O. (1990) · Cell · doi:10.1016/0092-8674(90)90453-l · Cited by 986 · see citing works
Bryne, J. C., Valen, E., Tang, M. E., Marstrand, T. T., Winther, O., da Piedade, I., Krogh, A., Lenhard, B., & Sandelin, A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm955 · Cited by 692 · see citing works
Berger, M. F., Philippakis, A., Qureshi, A. M., He, F. S., Estep, P. W., & Bulyk, M. L. (2006) · Nature Biotechnology · doi:10.1038/nbt1246 · Cited by 685 · see citing works
Self-citationA single amino acid can determine the DNA binding specificity of homeodomain proteins
Trelsman, J., Gönczy, P., Vashishtha, M., Harris, E., & Desplan, C. (1989) · Cell · doi:10.1016/0092-8674(89)90038-x · Cited by 522 · see citing works
A tissue-specific MAR/SAR DNA-binding protein with unusual binding site recognition
Dickinson, L. A. (1992) · Cell · doi:10.1016/0092-8674(92)90432-c · Cited by 502 · see citing works
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Li, X., MacArthur, S., Bourgon, R., Nix, D. A., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L. L., et al. (2008) · eScholarship (California Digital Library) · doi:10.1371/journal.pbio.0060027 · Cited by 479 · see citing works
Hanes, S. D., & Brent, R. (1989) · Cell · doi:10.1016/0092-8674(89)90063-9 · Cited by 464 · see citing works
Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins
Mann, R. S., & Chan, S.-K. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)10026-3 · Cited by 444 · see citing works
Extra specificity from extradenticle: the partnership between HOX and PBX/EXD homeodomain proteins
Mann, R. S., & Chan, S.-K. (1996) · Trends in Genetics · doi:10.1016/0168-9525(96)81471-5 · Cited by 393 · see citing works
Binding of Myc Proteins to Canonical and Noncanonical DNA Sequences
Blackwell, T. K., Huang, J., Ma, A. I., Kretzner, L., Alt, F. W., Eisenman, R. N., & Weintraub, H. M. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.9.5216 · Cited by 377 · see citing works
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays
Mukherjee, S., Berger, M. F., Jona, G., Wang, X. S., Muzzey, D., Snyder, M. P., Young, R. A., & Bulyk, M. L. (2004) · Nature Genetics · doi:10.1038/ng1473 · Cited by 367 · see citing works
Self-citationOverdier, D. G., Porcella, A., & Costa, R. H. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.4.2755 · Cited by 351 · see citing works
Functional Specificity of a Hox Protein Mediated by the Recognition of Minor Groove Structure
Joshi, R., Passner, J. M., Rohs, R., Jain, R., Sosinsky, A., Crickmore, M. A., Jacob, V., Aggarwal, A. K., Honig, B. H., & Mann, R. S. (2007) · Cell · doi:10.1016/j.cell.2007.09.024 · Cited by 338 · see citing works
Additivity in protein-DNA interactions: how good an approximation is it?
Benos, P. V. (2002) · Nucleic Acids Research · doi:10.1093/nar/gkf578 · Cited by 329 · see citing works
DNA binding specificity of homeodomains
Laughon, A. S. (1991) · Biochemistry · doi:10.1021/bi00112a001 · Cited by 295 · see citing works
Chen, C. Y., & Schwartz, R. J. (1995) · Journal of Biological Chemistry · doi:10.1074/jbc.270.26.15628 · Cited by 287 · see citing works
Dudley, A. M., Aach, J., Steffen, M. A., & Church, G. M. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.112683499 · Cited by 248 · see citing works
The degree of variation in DNA sequence recognition among four Drosophila homeotic proteins.
Ekker, S. C., Jackson, D. G., von Kessler, D. P., Sun, B. K., Young, K. E., & Beachy, P. A. (1994) · The EMBO Journal · doi:10.1002/j.1460-2075.1994.tb06662.x · Cited by 209 · see citing works
Core transcriptional regulatory circuitry in human hepatocytes
Odom, D. T., Dowell, R. D., Jacobsen, E. S., Nekludova, L., Rolfe, A., Danford, T., Gifford, D. K., Fraenkel, E., Bell, G. I., & Young, R. A. (2006) · Molecular Systems Biology · doi:10.1038/msb4100059 · Cited by 193 · see citing works
Galant, R., Walsh, C. M., & Carroll, S. B. (2002) · Development · doi:10.1242/dev.129.13.3115 · Cited by 184 · see citing works
Catron, K. M., Iler, N., & Abate, C. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.4.2354 · Cited by 182 · see citing works
The NK homeobox gene cluster predates the origin of Hox genes.
Larroux, C., Fahey, B., Degnan, S. M., Adamski, M., Rokhsar, D. S., & Degnan, B. M. (2007) · Current Biology · doi:10.1016/j.cub.2007.03.008 · Cited by 173 · cited 1× · see citing works
“…homeodomains than most vertebrates, including humans, and contains representatives of both ancient (NK, Hox) and young (Rhox, Obox) homeodomain families, encompassing striking examples of both purifying and diversifying selection (Jackson et al., 2006; Larroux et al., 2007; Rajkovic et al., 2002).”
BackgroundHox transcription factors and their elusive mammalian gene targets
Svingen, T., & Tonissen, K. F. (2006) · Heredity · doi:10.1038/sj.hdy.6800847 · Cited by 166 · see citing works
Handis a direct target of Tinman and GATA factors duringDrosophilacardiogenesis and hematopoiesis
Han, Z., & Olson, E. N. (2005) · Development · doi:10.1242/dev.01899 · Cited by 155 · see citing works
Differential DNA sequence recognition is a determinant of specificity in homeotic gene action.
Ekker, S. C., von Kessler, D. P., & Beachy, P. A. (1992) · The EMBO Journal · doi:10.1002/j.1460-2075.1992.tb05499.x · Cited by 141 · see citing works
Mapping functional specificity in the Dfd and Ubx homeo domains.Preprint
Lin, L., & McGinnis, W. J. (1992) · Genes & Development · doi:10.1101/gad.6.6.1071 · Cited by 135 · see citing works
MAGIC, an in vivo genetic method for the rapid construction of recombinant DNA molecules
Li, M. Z., & Elledge, S. J. (2005) · Nature Genetics · doi:10.1038/ng1505 · Cited by 134 · see citing works
Wolberger, C. (1996) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(96)80096-0 · Cited by 133 · see citing works
Fraenkel, E., Rould, M. A., Chambers, K. A., & Pabo, C. O. (1998) · Journal of Molecular Biology · doi:10.1006/jmbi.1998.2147 · Cited by 122 · see citing works
Wolfe, S. A., Grant, R. A., Elrod-Erickson, M., & Pabo, C. O. (2001) · Structure · doi:10.1016/s0969-2126(01)00632-3 · Cited by 117 · see citing works
Chan, S.-K., & Mann, R. S. (1993) · Genes & Development · doi:10.1101/gad.7.5.796 · Cited by 112 · see citing works
Overdier, D. G., Porcella, A., & Costa, R. H. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.4.2755-2766.1994 · Cited by 106 · see citing works
A molecular code dictates sequence‐specific DNA recognition by homeodomains.
Damante, G., Pellizzari, L., Esposito, G., Fogolari, F., Viglino, P., Fabbro, D., Tell, G., Formisano, S., & Lauro, R. D. (1996) · The EMBO Journal · doi:10.1002/j.1460-2075.1996.tb00879.x · Cited by 93 · see citing works
Functional specificity of the Antennapedia homeodomain.
Furukubo-Tokunaga, K., Flister, S., & Gehring, W. J. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.13.6360 · Cited by 92 · see citing works
Tucker‐Kellogg, L., Rould, M. A., Chambers, K. A., et al. (1997) · Structure · doi:10.1016/s0969-2126(97)00256-6 · Cited by 91 · see citing works
Carr, A., & Biggin, M. D. (1999) · The EMBO Journal · doi:10.1093/emboj/18.6.1598 · Cited by 84 · see citing works
The Mouse Genome Database (MGD): integrating biology with the genome
Bult, C. J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkh125 · Cited by 76 · see citing works
Obox, a Family of Homeobox Genes Preferentially Expressed in Germ Cells
Rajkovic, A., Yan, C., Wei, Y., Klysik, M., & Matzuk, M. M. (2002) · Genomics · doi:10.1006/geno.2002.6759 · Cited by 72 · see citing works
Miller, J. C., & Pabo, C. O. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2001.4975 · Cited by 68 · see citing works
Chen, X., Hughes, T. R., & Morris, Q. (2007) · Bioinformatics · doi:10.1093/bioinformatics/btm224 · Cited by 65 · see citing works
Self-citationCatron, K. M., Iler, N., & Abate, C. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.4.2354-2365.1993 · Cited by 64 · see citing works
Multiple Otx Binding Sites Required for Expression of the Strongylocentrotus purpuratus Spec2a Gene
Mao, C., Gan, L., & Klein, W. H. (1994) · Developmental Biology · doi:10.1006/dbio.1994.1249 · Cited by 62 · see citing works
Design of Compact, Universal DNA Microarrays for Protein Binding Microarray Experiments
Philippakis, A., Qureshi, A. M., Berger, M. F., & Bulyk, M. L. (2008) · Journal of Computational Biology · doi:10.1089/cmb.2007.0114 · Cited by 57 · see citing works
Self-citationLiberzon, A. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh156 · Cited by 34 · see citing works
Jackson, M., Watt, A. J., Gautier, P. E., Gilchrist, D. S., Driehaus, J., Graham, G. J., Keebler, J., Prugnolle, F., Awadalla, P., & Forrester, L. M. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-212 · Cited by 30 · see citing works
Structural basis of Hox specificity.
Wilson, D. S., & Desplan, C. (1999) · Nature Structural Biology · doi:10.1038/7524 · Cited by 28 · see citing works
The Homeodomain Resource: 2003 update
Banerjee‐Basu, S. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg118 · Cited by 19 · see citing works
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Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works
Mapping and analysis of chromatin state dynamics in nine human cell types
Ernst, J., Kheradpour, P., Mikkelsen, T. S., Shoresh, N., Ward, L. D., Epstein, C. B., Zhang, X., Wang, L., Issner, R., Coyne, M., et al. (2011) · Nature · doi:10.1038/nature09906 · Cited by 2,898 · see citing works
Annotation of functional variation in personal genomes using RegulomeDB
Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722 · see citing works
Ward, L. D., & Kellis, M. (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr917 · Cited by 2,229 · see citing works
A compendium of RNA-binding motifs for decoding gene regulation
Ray, D., Kazan, H., Cook, K. B., Weirauch, M. T., Najafabadi, H. S., Li, X., Gueroussov, S., Albu, M., Zheng, H., Yang, A., et al. (2013) · Nature · doi:10.1038/nature12311 · Cited by 1,480 · see citing works
A census of human transcription factors: function, expression and evolution
Vaquerizas, J. M., Kummerfeld, S. K., Teichmann, S. A., & Luscombe, N. M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2538 · Cited by 1,573 · see citing works
Cis-regulatory elements: Molecular mechanisms and evolutionary processes underlying divergence
Wittkopp, P. J., & Kalay, G. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3095 · Cited by 1,231 · see citing works
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Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.004 · Cited by 942 · see citing works
An atlas of combinatorial transcriptional regulation in mouse and man
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.044 · Cited by 715 · see citing works
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Zhu, H., Wang, G., & Qian, J. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.83 · Cited by 649 · see citing works
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Wei, G., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.106 · Cited by 568 · see citing works
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
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Neph, S., Stergachis, A. B., Reynolds, A., Sandstrom, R., Borenstein, E., & Stamatoyannopoulos, J. A. (2012) · Cell · doi:10.1016/j.cell.2012.04.040 · Cited by 467 · see citing works
Direct promoter repression by BCL11A controls the fetal to adult hemoglobin switch
Liu, N., Hargreaves, V. V., Zhu, Q., Kurland, J. V., Hong, J., Kim, W., Sher, F., Macias-Trevino, C., Rogers, J. M., Kurita, R., et al. (2018) · Cell · doi:10.1016/j.cell.2018.03.016 · Cited by 478 · see citing works
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DREAM5 Consortium, Weirauch, M. T., Cote, A., Norel, R., Annala, M., Zhao, Y., Riley, T. R., Saez-Rodriguez, J., Cokelaer, T., Vedenko, A., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2486 · Cited by 381 · see citing works
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Crocker, J., Abe, N., Rinaldi, L., McGregor, A. P., Frankel, N., Wang, S., Alsawadi, A., Valenti, P., Plaza, S., Payre, F., et al. (2015) · Cell · doi:10.1016/j.cell.2014.11.041 · Cited by 363 · see citing works
A High-Resolution Enhancer Atlas of the Developing Telencephalon
Visel, A., Taher, L., Girgis, H., May, D., Golonzhka, O., Hoch, R. V., McKinsey, G. L., Pattabiraman, K., Silberberg, S. N., Blow, M. J., et al. (2013) · Cell · doi:10.1016/j.cell.2012.12.041 · Cited by 257 · see citing works
Conservation of core gene expression in vertebrate tissues
Chan, E. T., Quon, G. T., Chua, G., Babak, T., Trochesset, M., Zirngibl, R. A., Aubin, J., Ratcliffe, M. J., Wilde, A., Brudno, M., et al. (2009) · Journal of Biology · doi:10.1186/jbiol130 · Cited by 190 · see citing works
Self-citationTranscriptional Networks Controlled by NKX2-1 in the Development of Forebrain GABAergic Neurons
Sandberg, M., Flandin, P., Silberberg, S., Su-Feher, L., Price, J. D., Hu, J. S., Kim, C., Visel, A., Nord, A. S., & Rubenstein, J. L. R. (2016) · Neuron · doi:10.1016/j.neuron.2016.08.020 · Cited by 129 · see citing works
Genetics and diet regulate vitamin A production via the homeobox transcription factor ISX
Lobo, G. P., Amengual, J., Baus, D., Shivdasani, R. A., Taylor, D., & von Lintig, J. (2013) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.444240 · Cited by 138 · see citing works
Mann, I. K., Chatterjee, R., Zhao, J., He, X., Weirauch, M. T., Hughes, T. R., & Vinson, C. (2013) · Genome Research · doi:10.1101/gr.146654.112 · Cited by 126 · see citing works
Self-citationSun, J., Rockowitz, S., Xie, Q., Ashery-Padan, R., Zheng, D., & Cvekl, A. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv589 · Cited by 113 · see citing works
Systematic interrogation of human promoters
Weingarten-Gabbay, S., Nir, R., Lubliner, S., Sharon, E., Kalma, Y., Weinberger, A., & Segal, E. (2019) · Genome Research · doi:10.1101/gr.236075.118 · Cited by 110 · see citing works
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Recognition models to predict DNA-binding specificities of homeodomain proteins
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- Authors
- Berger, M. F., Badis, G., Gehrke, A. R., Talukder, S., Philippakis, A. A., Peña-Castillo, L., Alleyne, T. M., Mnaimneh, S., Botvinnik, O. B., Chan, E. T., Khalid, F., Zhang, W., Newburger, D., Jaeger, S. A., Morris, Q. D., Bulyk, M. L., & Hughes, T. R.
- Affiliations
- Brigham and Women's Hospital (US)
- University of Toronto (CA)
- Corresponding author
- Bulyk, Martha L.
- Hughes, Timothy R.
- ORCID
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2008-06
- Volume
- 133
- Issue
- 7
- Pages
- 1266-1276
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC2531161
- OpenAlex
- W2080152736
- Cited by
- 606
- References
- 52
- Citations by year
- 2026: 4 · 2025: 19 · 2024: 25 · 2023: 19 · 2022: 22 · 2021: 28 · 2020: 25 · 2019: 28 · 2018: 26 · 2017: 29 · 2016: 36 · 2015: 45 · 2014: 35 · 2013: 57 · 2012: 48
- FWCI
- 21.96
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 1872 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion, other-oa)
- Funders
- National Human Genome Research Institute (R01HG003985)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- homeodomain, DNA binding specificity, sequence preference, homeodomain transcription factor, binding site prediction, sequence recognition, protein-DNA interactions, evolutionary conservation, Drosophila, Caenorhabditis elegans
- MeSH terms
- Animals, Base Sequence, DNA, Models, Molecular, Protein Binding, Transcription Factors, Conserved Sequence, Homeodomain Proteins, Evolution, Molecular, Computational Biology, Mice
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