A gene expression atlas of early craniofacial development
Open accessAbstract
We present a gene expression atlas of early mouse craniofacial development. Laser capture microdissection (LCM) was used to isolate cells from the principal critical microregions, whose development, differentiation and signaling interactions are responsible for the construction of the mammalian face. At E8.5, as migrating neural crest cells begin to exit the neural fold/epidermal ectoderm boundary, we examined the cranial mesenchyme, composed of mixed neural crest and paraxial mesoderm cells, as well as cells from adjacent neuroepithelium. At E9.5 cells from the cranial mesenchyme, overlying olfactory placode/epidermal ectoderm, and underlying neuroepithelium, as well as the emerging mandibular and maxillary arches were sampled. At E10.5, as the facial prominences form, cells from the medial and lateral prominences, the olfactory pit, multiple discrete regions of underlying neuroepithelium, the mandibular and maxillary arches, including both their mesenchymal and ectodermal components, as well as Rathke's pouch, were similarly sampled and profiled using both microarray and RNA-seq technologies. Further, we performed single cell studies to better define the gene expression states of the early E8.5 pioneer neural crest cells and paraxial mesoderm. Taken together, and analyzable by a variety of biological network approaches, these data provide a complementing and cross validating resource capable of fueling discovery of novel compartment specific markers and signatures whose combinatorial interactions of transcription factors and growth factors/receptors are responsible for providing the master genetic blueprint for craniofacial development.
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UQCC1 is expressed in the branchial arches and head surface ectoderm during early embryonic development in mice.
“UQCC1 is expressed in the branchial arches and head surface ectoderm during early embryonic development in mice [45].”
From Combined genome-wide association study of 136 quantitative ear morphology traits in multiple populations reveal 8 novel loci (2023) · cites this paper as [45]
The E9.5 expression-data section describes profiling the mandibular and maxillary arches and overlying epidermal ectoderm, but does not report UQCC1 expression in those tissues. Searches for “UQCC1” and its claimed expression in branchial arches and head surface ectoderm found no passage establishing the gene-specific claim in our copy. (LLM, conf=0.72)
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Cites
RNA-Seq: a revolutionary tool for transcriptomics
Wang, Z., Gerstein, M., & Snyder, M. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2484 · Cited by 13,174 · see citing works
Genome-wide atlas of gene expression in the adult mouse brain
Lein, E. S., Hawrylycz, M. J., Ao, N., Ayres, M., Bensinger, A., Bernard, A., Boe, A. F., Boguski, M. S., Brockway, K. S., Byrnes, E. J., et al. (2007) · Nature · doi:10.1038/nature05453 · Cited by 5,572 · see citing works
Cytoscape 2.8: new features for data integration and network visualization
Smoot, M. E., Ono, K., Ruscheinski, J., Wang, P., & Ideker, T. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq675 · Cited by 4,770 · see citing works
ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
Chen, J., Bardes, E. E., Aronow, B. J., & Jegga, A. G. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp427 · Cited by 2,952 · see citing works
Self-citationWidespread transcription at neuronal activity-regulated enhancers
Kim, T.-K., Hemberg, M., Gray, J. M., Costa, A. M., Bear, D. M., Wu, J., Harmin, D. A., Laptewicz, M., Barbara-Haley, K., Kuersten, S., et al. (2010) · Nature · doi:10.1038/nature09033 · Cited by 2,450 · see citing works
Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters
Core, L. J., Waterfall, J. J., & Lis, J. T. (2008) · Science · doi:10.1126/science.1162228 · Cited by 1,986 · see citing works
Stochastic mRNA Synthesis in Mammalian Cells
Raj, A., Peskin, C. S., Tranchina, D., Vargas, D. Y., & Tyagi, S. (2006) · PLoS Biology · doi:10.1371/journal.pbio.0040309 · Cited by 1,737 · see citing works
Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
Li, W., Notani, D., Ma, Q., Tanasa, B., Nunez, E., Chen, A. Y., Merkurjev, D., Zhang, J., Ohgi, K., Song, X., et al. (2013) · Nature · doi:10.1038/nature12210 · Cited by 1,049 · see citing works
Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA
Wang, D., García-Bassets, I., Benner, C. W., Li, W., Su, X. B., Zhou, Y., Qiu, J., Liu, W., Kaikkonen, M. U., Ohgi, K. A., et al. (2011) · Nature · doi:10.1038/nature10006 · Cited by 820 · see citing works
Transcriptional Pulsing of a Developmental Gene
Chubb, J. R., Trcek, T., Shenoy, S. M., & Singer, R. H. (2006) · Current Biology · doi:10.1016/j.cub.2006.03.092 · Cited by 714 · see citing works
Losick, R. M., & Desplan, C. (2008) · Science · doi:10.1126/science.1147888 · Cited by 627 · see citing works
Recent advances in craniofacial morphogenesis
Chai, Y., & Maxson, R. E. (2006) · Developmental Dynamics · doi:10.1002/dvdy.20833 · Cited by 610 · see citing works
Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription
Lam, M. T. Y., Cho, H., Lesch, H. P., Gosselin, D., Heinz, S., Tanaka-Oishi, Y., Benner, C., Kaikkonen, M. U., Kim, A. S., Kosaka, M., et al. (2013) · Nature · doi:10.1038/nature12209 · Cited by 548 · see citing works
eRNAs Are Required for p53-Dependent Enhancer Activity and Gene Transcription
Melo, C. A., Drost, J., Wijchers, P. J., van de Werken, H., de Wit, E., Vrielink, J. A. F. O., Elkon, R., Melo, S. A., Léveillé, N., Kalluri, R., et al. (2013) · Molecular Cell · doi:10.1016/j.molcel.2012.11.021 · Cited by 544 · see citing works
Palatogenesis: morphogenetic and molecular mechanisms of secondary palate development
Bush, J. O., & Jiang, R. (2011) · Development · doi:10.1242/dev.067082 · Cited by 508 · see citing works
Hah, N., Danko, C. G., Core, L. J., Waterfall, J. J., Siepel, A. C., Lis, J. T., & Kraus, W. L. (2011) · Cell · doi:10.1016/j.cell.2011.03.042 · Cited by 488 · see citing works
Kaimal, V., Bardes, E. E., Tabar, S., Jegga, A. G., & Aronow, B. J. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq418 · Cited by 369 · see citing works
Self-citationThe GUDMAP database – an online resource for genitourinary research
Harding, S. D., Armit, C. J., Armstrong, J. F., et al. (2011) · Development · doi:10.1242/dev.063594 · Cited by 252 · see citing works
McMahon, A. P., Aronow, B. J., Davidson, D. R., Davies, J. A., Gaido, K. W., Grimmond, S. M., Lessard, J. L., Little, M. H., Potter, S. S., Wilder, E. L., et al. (2008) · Journal of the American Society of Nephrology · doi:10.1681/asn.2007101078 · Cited by 247 · see citing works
Self-citationAtlas of Gene Expression in the Developing Kidney at Microanatomic Resolution
Brunskill, E. W., Aronow, B. J., Georgas, K. M., Rumballe, B. A., Valerius, M. T., Aronow, J. E., Kaimal, V., Jegga, A. G., Grimmond, S. M., McMahon, A. P., et al. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.09.007 · Cited by 213 · see citing works
Self-citationLarge Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data
Guo, Y. P., Sheng, Q., Li, J., Ye, F., Samuels, D. C., & Shyr, Y. (2013) · PLoS ONE · doi:10.1371/journal.pone.0071462 · Cited by 189 · see citing works
Cranial neural crest migration: New rules for an old road
Kulesa, P. M., Bailey, C. M., Kasemeier‐Kulesa, J. C., & McLennan, R. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.04.010 · Cited by 158 · see citing works
Isolated cleft palate in mice with a targeted mutation of the LIM homeobox gene Lhx8
Zhao, Y., Guo, Y.-J., Tomac, A. C., Taylor, N. R., Grinberg, A., Lee, E. J., Huang, S.-P., & Westphal, H. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.26.15002 · Cited by 154 · see citing works
Jeong, J., Li, X., McEvilly, R. J., Rosenfeld, M. G., Lufkin, T., & Rubenstein, J. L. R. (2008) · Development · doi:10.1242/dev.019778 · Cited by 151 · see citing works
New directions in craniofacial morphogenesis
Szabo‐Rogers, H. L., Smithers, L. E., Yakob, W., & Liu, K. J. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.11.021 · Cited by 147 · see citing works
Guo, C., Sun, Y., Zhou, B., et al. (2011) · Journal of Clinical Investigation · doi:10.1172/jci44630 · Cited by 146 · see citing works
Defining the molecular character of the developing and adult kidney podocyte
Brunskill, E. W., Georgas, K., Rumballe, B., Little, M. H., & Potter, S. S. (2011) · PLoS ONE · doi:10.1371/journal.pone.0024640 · Cited by 128 · see citing works
Self-citationGenes that Confer the Identity of the Renin Cell
Brunskill, E. W., Sequeira-Lόpez, M. L. S., Pentz, E. S., et al. (2011) · Journal of the American Society of Nephrology · doi:10.1681/asn.2011040401 · Cited by 119 · see citing works
Self-citationGenetic interplay between the transcription factors Sp8 and Emx2 in the patterning of the forebrain
Zembrzycki, A., Griesel, G., Stoykova, A., & Mansouri, A. (2007) · Neural Development · doi:10.1186/1749-8104-2-8 · Cited by 108 · see citing works
Raghavachari, N., Barb, J. J., Yang, Y., Liu, P., Woodhouse, K., Levy, D. A., O’Donnell, C. J., Munson, P. J., & Kato, G. J. (2012) · BMC Medical Genomics · doi:10.1186/1755-8794-5-28 · Cited by 90 · see citing works
Chow, K. L., Hall, D. H., & Emmons, S. W. (1995) · Development · doi:10.1242/dev.121.11.3615 · Cited by 90 · see citing works
barx1 represses joints and promotes cartilage in the craniofacial skeleton
Nichols, J. T., Pan, L., Moens, C. B., & Kimmel, C. B. (2013) · Development · doi:10.1242/dev.090639 · Cited by 77 · see citing works
The FaceBase Consortium: A comprehensive program to facilitate craniofacial research
Hochheiser, H., Aronow, B. J., Artinger, K., Beaty, T. H., Brinkley, J. F., Chai, Y., Clouthier, D. E., Cunningham, M. L., Dixon, M. J., Donahue, L. R., et al. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.02.033 · Cited by 71 · see citing works
Self-citationHomozygous Nonsense Mutations in TWIST2 Cause Setleis Syndrome
Tükel, T., Šošić, D., Al-Gazali, L. I., Erazo, M., Casasnovas, J. J., Franco, H. L., Richardson, J. A., Olson, E. N., Cadilla, C. L., & Desnick, R. J. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.07.009 · Cited by 69 · see citing works
The LIM homeodomain transcription factors Lhx6 and Lhx7 are key regulators of mammalian dentition
Denaxa, M., Sharpe, P. T., & Pachnis, V. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2009.07.001 · Cited by 68 · see citing works
Hand transcription factors cooperatively regulate development of the distal midline mesenchyme
Barbosa, A. C. C., Funato, N., Chapman, S. L., McKee, M. D., Richardson, J. A., Olson, E. N., & Yanagisawa, H. (2007) · Developmental Biology · doi:10.1016/j.ydbio.2007.07.036 · Cited by 66 · see citing works
Kinoshita, M., Nakamura, T., Ihara, M., et al. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)02520-0 · Cited by 64 · see citing works
Microarrays and RNA-Seq identify molecular mechanisms driving the end of nephron production
Brunskill, E. W., Lai, H. L., Jamison, D. C., et al. (2011) · BMC Developmental Biology · doi:10.1186/1471-213x-11-15 · Cited by 46 · see citing works
Self-citationSP8 regulates signaling centers during craniofacial development
Kasberg, A. D., Brunskill, E. W., & Potter, S. S. (2013) · Developmental Biology · doi:10.1016/j.ydbio.2013.07.007 · Cited by 41 · see citing works
Self-citationOdd-skipped related-1 controls neural crest chondrogenesis during tongue development
Liu, H., Lan, Y., Xu, J., Chang, C., Brugmann, S. A., & Jiang, R. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1306495110 · Cited by 41 · see citing works
Gene Expression Programs of Mouse Endothelial Cells in Kidney Development and Disease
Brunskill, E. W., & Potter, S. S. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012034 · Cited by 37 · see citing works
Self-citationChopra, M., Amor, D. J., Sutton, L., et al. (2010) · Reproductive BioMedicine Online · doi:10.1016/j.rbmo.2010.02.025 · Cited by 25 · see citing works
Potter, S. S., & Brunskill, E. W. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-851-1_19 · Cited by 4 · see citing works
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Wilderman, A., VanOudenhove, J., Kron, J., Noonan, J. P., & Cotney, J. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.129 · Cited by 139 · see citing works
Cadherins in early neural development
Punovuori, K., Malaguti, M., & Lowell, S. (2021) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-021-03815-9 · Cited by 39 · see citing works
Li, Y., Xiong, Z., Zhang, M., Hysi, P. G., Qian, Y., Adhikari, K., Weng, J., Wu, S., Du, S., Gonzalez-Jose, R., et al. (2023) · PLOS Genetics · doi:10.1371/journal.pgen.1010786 · Cited by 9 · see citing works
“UQCC1 is expressed in the branchial arches and head surface ectoderm during early embryonic development in mice [45].”
Background
- Authors
- Brunskill, E. W., Potter, A. S., Distasio, A., Dexheimer, P., Plassard, A., Aronow, B. J., & Potter, S. S.
- Affiliations
- Cincinnati Children's Hospital Medical Center (US)
- Corresponding author
- Potter, S. Steven
- Venue
- Developmental Biology
- Publisher
- Elsevier BV
- Published
- 2014-07
- Volume
- 391
- Issue
- 2
- Pages
- 133-146
- ISSN
- 0012-1606 (ISSN-L)
- PMC
- PMC4095820
- OpenAlex
- W2074241921
- Cited by
- 81
- References
- 43
- Citations by year
- 2026: 3 · 2025: 7 · 2024: 5 · 2023: 9 · 2022: 7 · 2021: 6 · 2020: 7 · 2019: 8 · 2018: 10 · 2017: 7 · 2016: 7 · 2015: 5
- FWCI
- 2.60
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Developmental Biology (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH (UO1 DE020049)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Craniofacial Disorders and Treatments
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Cleft Lip and Palate Research
- Keywords
- craniofacial development, gene expression atlas, mouse embryo, neural crest cells, paraxial mesoderm, cranial mesenchyme, facial prominences, olfactory placode, olfactory pit, Rathke's pouch, neuroepithelium, single-cell gene expression, transcription factors
- MeSH terms
- Animals, Base Sequence, Cell Differentiation, Cell Movement, Embryo, Mammalian, Face, Facial Bones, Maxillofacial Development, Mesoderm, Neural Crest, Skull, Signal Transduction, Gene Expression, Sequence Analysis, RNA, Gene Expression Regulation, Developmental, Gene Expression Profiling, Mice, Laser Capture Microdissection
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