Anatomic Demarcation of Cells: Genes to Patterns
Abstract
An organizing principle of the diverse cell types in multicellular organisms is their anatomic location. In turn, anatomic location is patterned by the positional identities of cells along developmental axes. Recent progress in functional genomics and chromatin biology illustrates how cells use specific gene expression programs to encode location. Dynamic chromatin states of key genes, notably the Hox loci, serve as the internal representation in cells of their positional identity within the animal.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
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?
There is evidence for positional identity among VSMCs along the anterior-posterior, dorso-ventral, and right-left axes of the embryo.
“Furthermore, there is evidence for positional identity among VSMCs along the anterior-posterior, dorso-ventral, and right-left axes of the embryo 28-30 .”
From Vascular smooth muscle cells in atherosclerosis (2019) · cites this paper as [29]
Cites
Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs
Rinn, J. L., Kertesz, M., Wang, J. K., Squazzo, S. L., Xu, X. H., Brugmann, S. A., Goodnough, L. H., Helms, J. A., Farnham, P., Segal, E., et al. (2007) · Cell · doi:10.1016/j.cell.2007.05.022 · Cited by 4,246 · see citing works
Self-citationKhalil, A. M., Guttman, M., Huarte, M., Garber, M., Raj, A., Rivea Morales, D., Thomas, K., Presser, A., Bernstein, B. E., van Oudenaarden, A., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0904715106 · Cited by 2,872 · see citing works
Genomic Maps and Comparative Analysis of Histone Modifications in Human and Mouse
Bernstein, B., Kamal, M., Lindblad‐Toh, K., Bekiranov, S., Bailey, D. K., Huebert, D. J., McMahon, S., Karlsson, E. K., Kulbokas, E. J., Gingeras, T., et al. (2005) · Cell · doi:10.1016/j.cell.2005.01.001 · Cited by 1,509 · see citing works
Genome Regulation by Polycomb and Trithorax Proteins
Schuettengruber, B., Chourrout, D. M., Vervoort, M., Leblanc, B., & Cavalli, G. (2007) · Cell · doi:10.1016/j.cell.2007.02.009 · Cited by 1,433 · see citing works
Polycomb silencers control cell fate, development and cancer
Sparmann, A., & van Lohuizen, M. (2006) · Nature reviews. Cancer · doi:10.1038/nrc1991 · Cited by 1,294 · see citing works
Diversity, topographic differentiation, and positional memory in human fibroblasts
Chang, H. Y., Chi, J., Dudoit, S., Bondre, C., van de Rijn, M., Botstein, D., & Brown, P. O. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.162488599 · Cited by 1,151 · see citing works
Self-citationDeep homology and the origins of evolutionary novelty
Shubin, N., Tabin, C., & Carroll, S. (2009) · Nature · doi:10.1038/nature07891 · Cited by 842 · see citing works
Endothelial cell diversity revealed by global expression profiling
Chi, J., Chang, H. Y., Haraldsen, G., Jahnsen, F. L., Troyanskaya, O. G., Chang, D. S., Wang, Z., Rockson, S. G., van de Rijn, M., Botstein, D., et al. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1434429100 · Cited by 773 · see citing works
Self-citationLong noncoding RNAs in mouse embryonic stem cell pluripotency and differentiationPreprint
Dinger, M. E., Amaral, P., Mercer, T. R., Pang, K. C., Bruce, S. J., Gardiner, B., Askarian-Amiri, M., Ru, K., Soldà, G., Simons, C., et al. (2008) · Genome Research · doi:10.1101/gr.078378.108 · Cited by 729 · see citing works
Evidence for a role of developmental genes in the origin of obesity and body fat distribution
Gesta, S., Blüher, M., Yamamoto, Y., Norris, A. W., Berndt, J., Kralisch, S., Boucher, J., Lewis, C. R., & Kahn, C. R. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601752103 · Cited by 617 · see citing works
The rise and fall of Hox gene clusters
Duboule, D. (2007) · Development · doi:10.1242/dev.001065 · Cited by 525 · see citing works
Organizing Axes in Time and Space; 25 Years of Colinear Tinkering
Kmita, M., & Duboule, D. (2003) · Science · doi:10.1126/science.1085753 · Cited by 522 · see citing works
Anatomic Demarcation by Positional Variation in Fibroblast Gene Expression Programs
Rinn, J. L., Bondre, C., Gladstone, H. B., Brown, P. O., & Chang, H. Y. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020119 · Cited by 505 · see citing works
Self-citationPositional information revisited
Wolpert, L. (1989) · Development · doi:10.1242/dev.107.supplement.3 · Cited by 329 · see citing works
Genome-Wide Views of Chromatin Structure
Rando, O. J., & Chang, H. Y. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.071107.134639 · Cited by 323 · see citing works
Self-citationEmbryonic origin and Hox status determine progenitor cell fate during adult bone regeneration
Leucht, P., Kim, J., Amasha, R. R., James, A. W., Girod, S. C., & Helms, J. A. (2008) · Development · doi:10.1242/dev.023788 · Cited by 319 · see citing works
Deciphering skeletal patterning: clues from the limb
Mariani, F. V., & Martin, G. R. (2003) · Nature · doi:10.1038/nature01655 · Cited by 257 · see citing works
Epigenetic Temporal Control of Mouse Hox Genes in Vivo
Soshnikova, N. V., & Duboule, D. (2009) · Science · doi:10.1126/science.1171468 · Cited by 251 · see citing works
Serial deletions and duplications suggest a mechanism for the collinearity of Hoxd genes in limbs
Kmita, M., Fraudeau, N., Hérault, Y., & Duboule, D. (2002) · Nature · doi:10.1038/nature01189 · Cited by 225 · see citing works
Control of Hoxd genes' collinearity during early limb development
Tarchini, B., & Duboule, D. (2006) · Developmental Cell · doi:10.1016/j.devcel.2005.11.014 · Cited by 222 · see citing works
A dermal HOX transcriptional program regulates site-specific epidermal fatePreprint
Rinn, J. L., Wang, J. K., Allen, N., Brugmann, S. A., Mikels, A. J., Liu, H., Ridky, T. W., Stadler, H. S., Nusse, R., Helms, J. A., et al. (2008) · Genes & Development · doi:10.1101/gad.1610508 · Cited by 201 · see citing works
Self-citationPolycomb Proteins Remain Bound to Chromatin and DNA during DNA Replication In Vitro
Francis, N. J., Follmer, N. E., Simon, M. D., Aghia, G., & Butler, J. D. (2009) · Cell · doi:10.1016/j.cell.2009.02.017 · Cited by 181 · see citing works
The ins and outs of gene regulation and chromosome territory organisation
Heard, É., & Bickmore, W. A. (2007) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2007.04.016 · Cited by 132 · see citing works
Positional information and pattern formation in development
Wolpert, L. (1994) · Developmental Genetics · doi:10.1002/dvg.1020150607 · Cited by 80 · see citing works
Mesenchymal Stem Cells from Different Organs are Characterized by Distinct Topographic Hox Codes
Ackema, K. B., & Charité, J. (2008) · Stem Cells and Development · doi:10.1089/scd.2007.0220 · Cited by 70 · see citing works
Chi, J., Rodriguez, E. H., Wang, Z., Nuyten, D. S. A., Mukherjee, S., van de Rijn, M., van de Vijver, M. J., Hastie, T. J., & Brown, P. O. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030164 · Cited by 65 · see citing works
Ectopic nuclear reorganisation driven by a Hoxb1 transgene transposed into Hoxd
Morey, C., Silva, N. D., Kmita, M., Duboule, D., & Bickmore, W. A. (2008) · Journal of Cell Science · doi:10.1242/jcs.023234 · Cited by 43 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression
Wang, K., Yang, Y. W., Liu, B., Sanyal, A., Corces, M. R., Chen, Y., Lajoie, B. R., Protacio, A., Flynn, R. A., Gupta, R. A., et al. (2011) · Nature · doi:10.1038/nature09819 · Cited by 1,963 · see citing works
Self-citationVascular smooth muscle cells in atherosclerosis
Basatemur, G. L., Jørgensen, H. F., Clarke, M. C. H., Bennett, M. R., & Mallat, Z. (2019) · Nature Reviews Cardiology · doi:10.1038/s41569-019-0227-9 · Cited by 1,099 · see citing works
Biology of upper-body and lower-body adipose tissue—link to whole-body phenotypes.
Karpe, F., & Pinnick, K. E. (2015) · Nature Reviews Endocrinology · doi:10.1038/nrendo.2014.185 · Cited by 543 · see citing works
Laser-based direct-write techniques for cell printing
Schiele, N. R., Corr, D. T., Huang, Y. H., Raof, N. A., Xie, Y., & Chrisey, D. B. (2010) · Biofabrication · doi:10.1088/1758-5082/2/3/032001 · Cited by 335 · see citing works
Melanocytes and Their DiseasesPreprint
Yamaguchi, Y., & Hearing, V. J. (2014) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a017046 · Cited by 240 · see citing works
Dermal fibroblast in cutaneous development and healing
Thulabandu, V., Chen, D.-M., & Atit, R. (2017) · Wiley Interdisciplinary Reviews: Developmental Biology · doi:10.1002/wdev.307 · Cited by 194 · see citing works
Wound healing and blastema formation in regenerating digit tips of adult mice
Fernando, W. A., Leininger, E., Simkin, J., Li, N., Malcom, C. A., Sathyamoorthi, S., Han, M., & Muneoka, K. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.11.035 · Cited by 176 · see citing works
The maintenance of pluripotency following laser direct-write of mouse embryonic stem cells
Raof, N. A., Schiele, N. R., Xie, Y., Chrisey, D. B., & Corr, D. T. (2010) · Biomaterials · doi:10.1016/j.biomaterials.2010.11.015 · Cited by 92 · see citing works
Leng, N., Li, Y., McIntosh, B. E., Nguyen, B. K., Duffin, B. M., Tian, S., Thomson, J. A., Dewey, C. N., Stewart, R. M., & Kendziorski, C. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv193 · Cited by 85 · see citing works
Fibroblast Memory in Development, Homeostasis and Disease
Kirk, T., Ahmed, A., & Rognoni, E. (2021) · Cells · doi:10.3390/cells10112840 · Cited by 78 · see citing works
Lineage tracking of origin and fate of smooth muscle cells in atherosclerosis
Bentzon, J. F., & Majesky, M. W. (2017) · Cardiovascular Research · doi:10.1093/cvr/cvx251 · Cited by 72 · see citing works
Hoxc-Dependent Mesenchymal Niche Heterogeneity Drives Regional Hair Follicle Regeneration
Zhou, Y. J., Jiang, K., Xu, Z., Huang, H., Qian, N., Lü, Z., Chen, D., Di, R., Yuan, T., Du, Z., et al. (2018) · Cell stem cell · doi:10.1016/j.stem.2018.07.016 · Cited by 71 · see citing works
Age-related changes in mesenchymal stem cells identified using a multi-omics approach
Peffers, M. J., Collins, J., Fang, Y., Goljanek‐Whysall, K., Rushton, Loughlin, J. A., Proctor, C. J., & Clegg, P. (2016) · European Cells and Materials · doi:10.22203/ecm.v031a10 · Cited by 67 · see citing works
DNA methylation of genes in adipose tissue
Pinnick, K. E., & Karpe, F. (2010) · Proceedings of The Nutrition Society · doi:10.1017/s0029665110004015 · Cited by 56 · see citing works
Dermal Fibroblast Heterogeneity and Its Contribution to the Skin Repair and Regeneration
Xue, M., Zhao, R., MARCH, L. M., & Jackson, C. (2021) · Advances in Wound Care · doi:10.1089/wound.2020.1287 · Cited by 55 · see citing works
Dong, W., Zhang, P., Fu, Y., Ge, J., Cheng, J., Yuan, H., & Jiang, H. (2014) · Journal of Cellular Physiology · doi:10.1002/jcp.24792 · Cited by 46 · see citing works
Tissue Biology: In Search of a New Paradigm
Adler, M., Chavan, A. R., & Medzhitov, R. (2023) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-120420-113830 · Cited by 40 · see citing works
Emerging patterns of epigenomic variation
Milosavljevic, A. (2011) · Trends in Genetics · doi:10.1016/j.tig.2011.03.001 · Cited by 39 · see citing works
Sato, R., Nakano, T., Hosonaga, M., Sampetrean, O., Harigai, R., Sasaki, T., Koya, I., Okano, H., Kudoh, J., Saya, H., et al. (2017) · BioMed Research International · doi:10.1155/2017/8032910 · Cited by 35 · see citing works
Hughes, M. W., Wu, P., Jiang, T., Lin, S., Dong, C., Li, A., Hsieh, F.-J., Widelitz, R. B., & Chuong, C. (2011) · Integrative Biology · doi:10.1039/c0ib00108b · Cited by 31 · see citing works
Onorati, M., Binetti, M., Conti, L., Camnasio, S., Calabrese, G., Albieri, I., Febo, F. D., Toselli, M., Biella, G. R., Martynoga, B., et al. (2010) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-010-0548-7 · Cited by 28 · see citing works
Tuning of synaptic responses: an organizing principle for optimization of neural circuits
O’Donnell, C., & Nolan, M. F. (2010) · Trends in Neurosciences · doi:10.1016/j.tins.2010.10.003 · Cited by 24 · see citing works
Laser-Induced Forward Transfer on Regenerative Medicine Applications
Kryou, C., & Zergioti, I. (2022) · Biomedical Materials & Devices · doi:10.1007/s44174-022-00040-1 · Cited by 23 · see citing works
Long noncoding RNA HOTTIP cooperates with CCCTC-binding factor to coordinate HOXA gene expression
Wang, F., Tang, Z., Shao, H., Guo, J., Tan, T., Dong, Y., & Lin, L. (2018) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2018.04.173 · Cited by 23 · see citing works
The origins of skin diversity: lessons from dermal fibroblasts
Myung, P. S., Andl, T., & Atit, R. P. (2022) · Development · doi:10.1242/dev.200298 · Cited by 23 · see citing works
Lawler, K., Hammond-Kosack, K. E., Brāzma, A., & Coulson, R. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-52 · Cited by 21 · see citing works
Precise patterning of biopolymers and cells by direct write technique
Nara, S., Chameettachal, S., & Ghosh, S. (2013) · Materials Technology · doi:10.1179/1753555713y.0000000112 · Cited by 17 · see citing works
Huang, L., Ying, H., Chen, Z., Zhu, Y., Gu, Y., Hu, L., Chen, D., & Zhong, N. A. (2019) · Placenta · doi:10.1016/j.placenta.2019.03.001 · Cited by 17 · see citing works
Tropini, C., & Huang, K. C. (2012) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002602 · Cited by 12 · see citing works
Laser‐Assisted Bioprinting of Cells for Tissue Engineering
Kérourédan, O., Rémy, M., Oliveira, H., Guillemot, F., & Devillard, R. (2018) · doi:10.1002/9783527805105.ch15 · Cited by 12 · see citing works
Lau, F. H., Deo, R. C., Mowrer, G., Caplin, J., Ahfeldt, T., Kaplan, A. N., Ptaszek, L. M., Walker, J. D., Rosengard, B. R., & Cowan, C. A. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026092 · Cited by 11 · see citing works
Remembering where we are: Positional information in salamander limb regeneration
Flowers, G. P., & Crews, C. M. (2020) · Developmental Dynamics · doi:10.1002/dvdy.167 · Cited by 10 · see citing works
Bioimage informatics for understanding spatiotemporal dynamics of cellular processes
Yang, G. (2013) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1214 · Cited by 10 · see citing works
Region-specific gene expression and sex inform about disease susceptibility in the aorta
Romay, M. C., Ma, F., Mompeón, A., Silvestro, M., Hernandez, G. E., Salvador, J., Wang, A. L., Vandestienne, M., Bardin, N., Blot‐Chabaud, M., et al. (2025) · Nature Cardiovascular Research · doi:10.1038/s44161-025-00692-4 · Cited by 8 · see citing works
Soil Primes the Seed: Epigenetic Landscape Drives Tumor Behavior
Whitson, R. J., & Oro, A. E. (2017) · Cell stem cell · doi:10.1016/j.stem.2017.01.007 · Cited by 8 · see citing works
Is the future scarless? – Fibroblasts as targets for scarless wound healing: a narrative review
Parry, D., & Allison, K. P. (2022) · Scars Burns & Healing · doi:10.1177/20595131221095348 · Cited by 4 · see citing works
Zhou, Y. J., & Chen, T. (2017) · eLife · doi:10.7554/elife.30249 · Cited by 3 · see citing works
Chromatin Regulation by Long Non-coding RNAs
Factor, D. C., Tesar, P. J., & Khalil, A. M. (2013) · Springer eBooks · doi:10.1007/978-1-4614-8621-3_1 · Cited by 3 · see citing works
The novel insights into spatiotemporal cell biology and its schematic frame, triple W
Hou, Y., Hou, Y., He, S., & Xing, R. (2011) · Journal of Cellular Physiology · doi:10.1002/jcp.22952 · Cited by 3 · see citing works
Hou, Y., Xing, R., Hou, Y., Mu, M., Yang, Y., & Ge, Y.-T. (2010) · Journal of Cellular Physiology · doi:10.1002/jcp.22332 · Cited by 3 · see citing works
The RNA HOTAIR Promotes Chromatin Alteration in Cancer.
Axelsdottir, E. (2014) · Biochemistry and Molecular Biology Education · Cited by 1 · see citing works
The remarkable diversity of vascular smooth muscle in development and disease
Majesky, M. W. (2022) · Elsevier eBooks · doi:10.1016/b978-0-12-822546-2.00030-7 · Cited by 1 · see citing works
Positional transcriptomics shed light on site-specific pathologies of the aortaPreprint
Romay, M. C., Ma, F., Hernandez, G. E., Vandestienne, M., Kimball, T. H., Silvestro, M., Hadi, T., Reyes, A. D. L., Ramirez, M., Bardin, N., et al. (2021) · Research Square · doi:10.21203/rs.3.rs-951818/v1 · Cited by 1 · see citing works
Human whole-epigenome modelling for clinical applications with PleiadesPreprint
Niki, P., Nalmpantis, C., Ganbat, J.-O., Byrne, D., Kathail, P., Fang, C., Wong, A., Karailiev, A., Babikir, H. A., Jhutty, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.07.16.665231 · Cited by 1 · see citing works
Pinnick, K. E., & Karpe, F. (2014) · Frontiers in diabetes · doi:10.1159/000362472
- Authors
- Chang, H. Y.
- Affiliations
- Howard Hughes Medical Institute (US)
- Corresponding author
- Chang, Howard Y.
- ORCID
- Chang, Howard Y.
- Venue
- Science
- Published
- 2009-11-27
- Volume
- 326
- Issue
- 5957
- Pages
- 1206-1207
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2085870515
- Cited by
- 45
- References
- 27
- Citations by year
- 2025: 2 · 2023: 1 · 2022: 4 · 2021: 3 · 2020: 1 · 2019: 2 · 2018: 3 · 2017: 5 · 2016: 1 · 2015: 1 · 2014: 5 · 2013: 4 · 2012: 1
- FWCI
- 1.74
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- cell fate specification, positional identity, Hox genes, chromatin state, transcriptional programs, anatomical location, cell type diversity, chromatin biology
- MeSH terms
- Animals, Cell Differentiation, Chromatin, Genes, Homeobox, Regulatory Sequences, Nucleic Acid, Gene Expression, Homeodomain Proteins, Gene Expression Regulation, Developmental, Gene Expression Profiling
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