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No Two Faces Are Alike

Gene disruptions can cause severe dysmorphologies like cleft palate, but what causes the subtle shifts in facial morphology that make each face unique? Studying mice, Attanasio et al. (1241006) identified over 4000 candidate genetic enhancers around genes driving craniofacial development. To avoid the challenge of recognizing individual mouse faces, optical projection tomography was used to link changes in facial morphology with alterations in the function of specific enhancers.

Structured Abstract

Introduction

The shape of the face is one of the most distinctive features among humans, and differences in facial morphology have substantial implications in areas such as social interaction, psychology, forensics, and clinical genetics. Craniofacial shape is highly heritable, including the normal spectrum of morphological variation as well as susceptibility to major craniofacial birth defects. In this study, we explored the role of transcriptional enhancers in the development of the craniofacial complex. Our study is based on the rationale that such enhancers, which can be hundreds of kilobases away from their target genes, regulate the spatial patterns, levels, and timing of gene expression in normal development. 

Methods

To identify distant-acting enhancers active during craniofacial development, we used chromatin immunoprecipitation on embryonic mouse face tissue followed by sequencing to identify noncoding genome regions bound by the enhancer-associated p300 protein. We used LacZ reporter assays in transgenic mice and optical projection tomography (OPT) to determine three-dimensional expression patterns of a subset of these candidate enhancers. Last, we deleted three of the craniofacial enhancers from the mouse genome to assess their effect on gene expression and craniofacial morphology during development.

Results

We identified more than 4000 candidate enhancer sequences predicted to be active in the developing craniofacial complex. The majority of these sequences are at least partially conserved between humans and mice, and many are located in chromosomal regions associated with normal facial morphology or craniofacial birth defects. Characterization of more than 200 candidate enhancer sequences in transgenic mice revealed a remarkable spatial complexity of in vivo expression patterns. Targeted deletions of three craniofacial enhancers near genes with known roles in craniofacial development resulted in changes of expression of those genes as well as quantitatively subtle but definable alterations of craniofacial shape. 

Discussion

Our analysis identifies enhancers that fine tune expression of genes during craniofacial development in mice. These results support that variation in the sequence or copy number of craniofacial enhancers may contribute to the spectrum of facial variation we find in human populations. Because many craniofacial enhancers are located in genome regions associated with craniofacial birth defects, such as clefts of the lip and palate, our results also offer a starting point for exploring the contribution of noncoding sequences to these disorders.

Abstract

The shape of the human face and skull is largely genetically determined. However, the genomic basis of craniofacial morphology is incompletely understood and hypothesized to involve protein-coding genes, as well as gene regulatory sequences. We used a combination of epigenomic profiling, in vivo characterization of candidate enhancer sequences in transgenic mice, and targeted deletion experiments to examine the role of distant-acting enhancers in craniofacial development. We identified complex regulatory landscapes consisting of enhancers that drive spatially complex developmental expression patterns. Analysis of mouse lines in which individual craniofacial enhancers had been deleted revealed significant alterations of craniofacial shape, demonstrating the functional importance of enhancers in defining face and skull morphology. These results demonstrate that enhancers are involved in craniofacial development and suggest that enhancer sequence variation contributes to the diversity of human facial morphology.

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Supplementary Material

Summary

Materials and Methods
Supplementary Text
Figs. S1 to S6
Tables S1 to S6
References (6291)
Movies S1 to S20

Resources

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References and Notes

1
Christensen K., Juel K., Herskind A. M., Murray J. C., Long term follow up study of survival associated with cleft lip and palate at birth. BMJ 328, 1405 (2004).
2
Wehby G. L., Cassell C. H., The impact of orofacial clefts on quality of life and healthcare use and costs. Oral Dis. 16, 3–10 (2010).
3
Kayser M., Schneider P. M., DNA-based prediction of human externally visible characteristics in forensics: Motivations, scientific challenges, and ethical considerations. Forensic Sci. Int. Genet. 3, 154–161 (2009).
4
Kohn L. A. P., The role of genetics in craniofacial morphology and growth. Annu. Rev. Anthropol. 20, 261–278 (1991).
5
Manfredi C., Martina R., Grossi G. B., Giuliani M., Heritability of 39 orthodontic cephalometric parameters on MZ, DZ twins and MN-paired singletons. Am. J. Orthod. Dentofacial Orthop. 111, 44–51 (1997).
6
Johannsdottir B., Thorarinsson F., Thordarson A., Magnusson T. E., Heritability of craniofacial characteristics between parents and offspring estimated from lateral cephalograms. Am. J. Orthod. Dentofacial Orthop. 127, 200–207, quiz 260–261 (2005).
7
Satokata I., Maas R., Msx1 deficient mice exhibit cleft palate and abnormalities of craniofacial and tooth development. Nat. Genet. 6, 348–356 (1994).
8
van den Boogaard M. J., Dorland M., Beemer F. A., van Amstel H. K., MSX1 mutation is associated with orofacial clefting and tooth agenesis in humans. Nat. Genet. 24, 342–343 (2000).
9
Kondo S., Schutte B. C., Richardson R. J., Bjork B. C., Knight A. S., Watanabe Y., Howard E., de Lima R. L., Daack-Hirsch S., Sander A., McDonald-McGinn D. M., Zackai E. H., Lammer E. J., Aylsworth A. S., Ardinger H. H., Lidral A. C., Pober B. R., Moreno L., Arcos-Burgos M., Valencia C., Houdayer C., Bahuau M., Moretti-Ferreira D., Richieri-Costa A., Dixon M. J., Murray J. C., Mutations in IRF6 cause Van der Woude and popliteal pterygium syndromes. Nat. Genet. 32, 285–289 (2002).
10
Suzuki S., Marazita M. L., Cooper M. E., Miwa N., Hing A., Jugessur A., Natsume N., Shimozato K., Ohbayashi N., Suzuki Y., Niimi T., Minami K., Yamamoto M., Altannamar T. J., Erkhembaatar T., Furukawa H., Daack-Hirsch S., L’heureux J., Brandon C. A., Weinberg S. M., Neiswanger K., Deleyiannis F. W., de Salamanca J. E., Vieira A. R., Lidral A. C., Martin J. F., Murray J. C., Mutations in BMP4 are associated with subepithelial, microform, and overt cleft lip. Am. J. Hum. Genet. 84, 406–411 (2009).
11
Dixon M. J., Treacher Collins syndrome. Hum. Mol. Genet. 5, 1391–1396 (1996).
12
Ng S. B., Bigham A. W., Buckingham K. J., Hannibal M. C., McMillin M. J., Gildersleeve H. I., Beck A. E., Tabor H. K., Cooper G. M., Mefford H. C., Lee C., Turner E. H., Smith J. D., Rieder M. J., Yoshiura K., Matsumoto N., Ohta T., Niikawa N., Nickerson D. A., Bamshad M. J., Shendure J., Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome. Nat. Genet. 42, 790–793 (2010).
13
Ng S. B., Buckingham K. J., Lee C., Bigham A. W., Tabor H. K., Dent K. M., Huff C. D., Shannon P. T., Jabs E. W., Nickerson D. A., Shendure J., Bamshad M. J., Exome sequencing identifies the cause of a Mendelian disorder. Nat. Genet. 42, 30–35 (2010).
14
Dixon M. J., Marazita M. L., Beaty T. H., Murray J. C., Cleft lip and palate: Understanding genetic and environmental influences. Nat. Rev. Genet. 12, 167–178 (2011).
15
Boehringer S., van der Lijn F., Liu F., Günther M., Sinigerova S., Nowak S., Ludwig K. U., Herberz R., Klein S., Hofman A., Uitterlinden A. G., Niessen W. J., Breteler M. M., van der Lugt A., Würtz R. P., Nöthen M. M., Horsthemke B., Wieczorek D., Mangold E., Kayser M., Genetic determination of human facial morphology: Links between cleft-lips and normal variation. Eur. J. Hum. Genet. 19, 1192–1197 (2011).
16
Liu F., van der Lijn F., Schurmann C., Zhu G., Chakravarty M. M., Hysi P. G., Wollstein A., Lao O., de Bruijne M., Ikram M. A., van der Lugt A., Rivadeneira F., Uitterlinden A. G., Hofman A., Niessen W. J., Homuth G., de Zubicaray G., McMahon K. L., Thompson P. M., Daboul A., Puls R., Hegenscheid K., Bevan L., Pausova Z., Medland S. E., Montgomery G. W., Wright M. J., Wicking C., Boehringer S., Spector T. D., Paus T., Martin N. G., Biffar R., Kayser M., A genome-wide association study identifies five loci influencing facial morphology in Europeans. PLOS Genet. 8, e1002932 (2012).
17
Paternoster L., Zhurov A. I., Toma A. M., Kemp J. P., St Pourcain B., Timpson N. J., McMahon G., McArdle W., Ring S. M., Smith G. D., Richmond S., Evans D. M., Genome-wide association study of three-dimensional facial morphology identifies a variant in PAX3 associated with nasion position. Am. J. Hum. Genet. 90, 478–485 (2012).
18
Stern D. L., Evolutionary developmental biology and the problem of variation. Evolution 54, 1079–1091 (2000).
19
Shen Y., Yue F., McCleary D. F., Ye Z., Edsall L., Kuan S., Wagner U., Dixon J., Lee L., Lobanenkov V. V., Ren B., A map of the cis-regulatory sequences in the mouse genome. Nature 488, 116–120 (2012).
20
Zhu J., Adli M., Zou J. Y., Verstappen G., Coyne M., Zhang X., Durham T., Miri M., Deshpande V., De Jager P. L., Bennett D. A., Houmard J. A., Muoio D. M., Onder T. T., Camahort R., Cowan C. A., Meissner A., Epstein C. B., Shoresh N., Bernstein B. E., Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell 152, 642–654 (2013).
21
Visel A., Blow M. J., Li Z., Zhang T., Akiyama J. A., Holt A., Plajzer-Frick I., Shoukry M., Wright C., Chen F., Afzal V., Ren B., Rubin E. M., Pennacchio L. A., ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature 457, 854–858 (2009).
22
Young N. M., Chong H. J., Hu D., Hallgrímsson B., Marcucio R. S., Quantitative analyses link modulation of sonic hedgehog signaling to continuous variation in facial growth and shape. Development 137, 3405–3409 (2010).
23
Simões-Costa M., Bronner M. E., Insights into neural crest development and evolution from genomic analysis. Genome Res. 23, 1069–1080 (2013).
24
Bagheri-Fam S., Barrionuevo F., Dohrmann U., Günther T., Schüle R., Kemler R., Mallo M., Kanzler B., Scherer G., Long-range upstream and downstream enhancers control distinct subsets of the complex spatiotemporal Sox9 expression pattern. Dev. Biol. 291, 382–397 (2006).
25
Betancur P., Bronner-Fraser M., Sauka-Spengler T., Genomic code for Sox10 activation reveals a key regulatory enhancer for cranial neural crest. Proc. Natl. Acad. Sci. U.S.A. 107, 3570–3575 (2010).
26
Yanagisawa H., Clouthier D. E., Richardson J. A., Charité J., Olson E. N., Targeted deletion of a branchial arch-specific enhancer reveals a role of dHAND in craniofacial development. Development 130, 1069–1078 (2003).
27
Rada-Iglesias A., Bajpai R., Prescott S., Brugmann S. A., Swigut T., Wysocka J., Epigenomic annotation of enhancers predicts transcriptional regulators of human neural crest. Cell Stem Cell 11, 633–648 (2012).
28
M. H. Kaufman, The Atlas of Mouse Development (Academic Press, London, 1992).
29
Feng W., Leach S. M., Tipney H., Phang T., Geraci M., Spritz R. A., Hunter L. E., Williams T., Spatial and temporal analysis of gene expression during growth and fusion of the mouse facial prominences. PLOS ONE 4, e8066 (2009).
30
Materials and methods are available as supplementary materials on Science Online.
31
Blow M. J., McCulley D. J., Li Z., Zhang T., Akiyama J. A., Holt A., Plajzer-Frick I., Shoukry M., Wright C., Chen F., Afzal V., Bristow J., Ren B., Black B. L., Rubin E. M., Visel A., Pennacchio L. A., ChIP-Seq identification of weakly conserved heart enhancers. Nat. Genet. 42, 806–810 (2010).
32
Visel A., Taher L., Girgis H., May D., Golonzhka O., Hoch R. V., McKinsey G. L., Pattabiraman K., Silberberg S. N., Blow M. J., Hansen D. V., Nord A. S., Akiyama J. A., Holt A., Hosseini R., Phouanenavong S., Plajzer-Frick I., Shoukry M., Afzal V., Kaplan T., Kriegstein A. R., Rubin E. M., Ovcharenko I., Pennacchio L. A., Rubenstein J. L., A high-resolution enhancer atlas of the developing telencephalon. Cell 152, 895–908 (2013).
33
McLean C. Y., Bristor D., Hiller M., Clarke S. L., Schaar B. T., Lowe C. B., Wenger A. M., Bejerano G., GREAT improves functional interpretation of cis-regulatory regions. Nat. Biotechnol. 28, 495–501 (2010).
34
Pennacchio L. A., Ahituv N., Moses A. M., Prabhakar S., Nobrega M. A., Shoukry M., Minovitsky S., Dubchak I., Holt A., Lewis K. D., Plajzer-Frick I., Akiyama J., De Val S., Afzal V., Black B. L., Couronne O., Eisen M. B., Visel A., Rubin E. M., In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499–502 (2006).
35
Sharpe J., Ahlgren U., Perry P., Hill B., Ross A., Hecksher-Sørensen J., Baldock R., Davidson D., Optical projection tomography as a tool for 3D microscopy and gene expression studies. Science 296, 541–545 (2002).
36
Heintzman N. D., Hon G. C., Hawkins R. D., Kheradpour P., Stark A., Harp L. F., Ye Z., Lee L. K., Stuart R. K., Ching C. W., Ching K. A., Antosiewicz-Bourget J. E., Liu H., Zhang X., Green R. D., Lobanenkov V. V., Stewart R., Thomson J. A., Crawford G. E., Kellis M., Ren B., Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459, 108–112 (2009).
37
Holland L. Z., Albalat R., Azumi K., Benito-Gutiérrez E., Blow M. J., Bronner-Fraser M., Brunet F., Butts T., Candiani S., Dishaw L. J., Ferrier D. E., Garcia-Fernàndez J., Gibson-Brown J. J., Gissi C., Godzik A., Hallböök F., Hirose D., Hosomichi K., Ikuta T., Inoko H., Kasahara M., Kasamatsu J., Kawashima T., Kimura A., Kobayashi M., Kozmik Z., Kubokawa K., Laudet V., Litman G. W., McHardy A. C., Meulemans D., Nonaka M., Olinski R. P., Pancer Z., Pennacchio L. A., Pestarino M., Rast J. P., Rigoutsos I., Robinson-Rechavi M., Roch G., Saiga H., Sasakura Y., Satake M., Satou Y., Schubert M., Sherwood N., Shiina T., Takatori N., Tello J., Vopalensky P., Wada S., Xu A., Ye Y., Yoshida K., Yoshizaki F., Yu J. K., Zhang Q., Zmasek C. M., de Jong P. J., Osoegawa K., Putnam N. H., Rokhsar D. S., Satoh N., Holland P. W., The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res. 18, 1100–1111 (2008).
38
May D., Blow M. J., Kaplan T., McCulley D. J., Jensen B. C., Akiyama J. A., Holt A., Plajzer-Frick I., Shoukry M., Wright C., Afzal V., Simpson P. C., Rubin E. M., Black B. L., Bristow J., Pennacchio L. A., Visel A., Large-scale discovery of enhancers from human heart tissue. Nat. Genet. 44, 89–93 (2012).
39
Visel A., Prabhakar S., Akiyama J. A., Shoukry M., Lewis K. D., Holt A., Plajzer-Frick I., Afzal V., Rubin E. M., Pennacchio L. A., Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat. Genet. 40, 158–160 (2008).
40
Hochheiser H., Aronow B. J., Artinger K., Beaty T. H., Brinkley J. F., Chai Y., Clouthier D., Cunningham M. L., Dixon M., Donahue L. R., Fraser S. E., Hallgrimsson B., Iwata J., Klein O., Marazita M. L., Murray J. C., Murray S., de Villena F. P., Postlethwait J., Potter S., Shapiro L., Spritz R., Visel A., Weinberg S. M., Trainor P. A., The FaceBase Consortium: a comprehensive program to facilitate craniofacial research. Dev. Biol. 355, 175–182 (2011).
41
Alappat S., Zhang Z. Y., Chen Y. P., Msx homeobox gene family and craniofacial development. Cell Res. 13, 429–442 (2003).
42
Visel A., Rubin E. M., Pennacchio L. A., Genomic views of distant-acting enhancers. Nature 461, 199–205 (2009).
43
Birnbaum S., Ludwig K. U., Reutter H., Herms S., Steffens M., Rubini M., Baluardo C., Ferrian M., Almeida de Assis N., Alblas M. A., Barth S., Freudenberg J., Lauster C., Schmidt G., Scheer M., Braumann B., Bergé S. J., Reich R. H., Schiefke F., Hemprich A., Pötzsch S., Steegers-Theunissen R. P., Pötzsch B., Moebus S., Horsthemke B., Kramer F. J., Wienker T. F., Mossey P. A., Propping P., Cichon S., Hoffmann P., Knapp M., Nöthen M. M., Mangold E., Key susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24. Nat. Genet. 41, 473–477 (2009).
44
Mangold E., Reutter H., Birnbaum S., Walier M., Mattheisen M., Henschke H., Lauster C., Schmidt G., Schiefke F., Reich R. H., Scheer M., Hemprich A., Martini M., Braumann B., Krimmel M., Opitz C., Lenz J. H., Kramer F. J., Wienker T. F., Nöthen M. M., Diaz Lacava A., Genome-wide linkage scan of nonsyndromic orofacial clefting in 91 families of central European origin. Am. J. Med. Genet. A. 149A, 2680–2694 (2009).
45
Nikopensius T., Ambrozaityte L., Ludwig K. U., Birnbaum S., Jagomägi T., Saag M., Matuleviciene A., Linkeviciene L., Herms S., Knapp M., Hoffmann P., Nöthen M. M., Kucinskas V., Metspalu A., Mangold E., Replication of novel susceptibility locus for nonsyndromic cleft lip with or without cleft palate on chromosome 8q24 in Estonian and Lithuanian patients. Am. J. Med. Genet. A. 149A, 2551–2553 (2009).
46
Beaty T. H., Murray J. C., Marazita M. L., Munger R. G., Ruczinski I., Hetmanski J. B., Liang K. Y., Wu T., Murray T., Fallin M. D., Redett R. A., Raymond G., Schwender H., Jin S. C., Cooper M. E., Dunnwald M., Mansilla M. A., Leslie E., Bullard S., Lidral A. C., Moreno L. M., Menezes R., Vieira A. R., Petrin A., Wilcox A. J., Lie R. T., Jabs E. W., Wu-Chou Y. H., Chen P. K., Wang H., Ye X., Huang S., Yeow V., Chong S. S., Jee S. H., Shi B., Christensen K., Melbye M., Doheny K. F., Pugh E. W., Ling H., Castilla E. E., Czeizel A. E., Ma L., Field L. L., Brody L., Pangilinan F., Mills J. L., Molloy A. M., Kirke P. N., Scott J. M., Arcos-Burgos M., Scott A. F., A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat. Genet. 42, 525–529 (2010).
47
Yuan Q., Blanton S. H., Hecht J. T., Association of ABCA4 and MAFB with non-syndromic cleft lip with or without cleft palate. Am. J. Med. Genet. A. 155A, 1469–1471 (2011).
48
Leslie E. J., Mansilla M. A., Biggs L. C., Schuette K., Bullard S., Cooper M., Dunnwald M., Lidral A. C., Marazita M. L., Beaty T. H., Murray J. C., Expression and mutation analyses implicate ARHGAP29 as the etiologic gene for the cleft lip with or without cleft palate locus identified by genome-wide association on chromosome 1p22. Birth Defects Res. A Clin. Mol. Teratol. 94, 934–942 (2012).
49
Rahimov F., Marazita M. L., Visel A., Cooper M. E., Hitchler M. J., Rubini M., Domann F. E., Govil M., Christensen K., Bille C., Melbye M., Jugessur A., Lie R. T., Wilcox A. J., Fitzpatrick D. R., Green E. D., Mossey P. A., Little J., Steegers-Theunissen R. P., Pennacchio L. A., Schutte B. C., Murray J. C., Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat. Genet. 40, 1341–1347 (2008).
50
Oram K. F., Carver E. A., Gridley T., Slug expression during organogenesis in mice. Anat. Rec. A Discov. Mol. Cell. Evol. Biol. 271, 189–191 (2003).
51
Mitsiadis T. A., Angeli I., James C., Lendahl U., Sharpe P. T., Role of Islet1 in the patterning of murine dentition. Development 130, 4451–4460 (2003).
52
Lieberman D. E., Hallgrímsson B., Liu W., Parsons T. E., Jamniczky H. A., Spatial packing, cranial base angulation, and craniofacial shape variation in the mammalian skull: Testing a new model using mice. J. Anat. 212, 720–735 (2008).
53
Hallgrímsson B., Lieberman D. E., Liu W., Ford-Hutchinson A. F., Jirik F. R., Epigenetic interactions and the structure of phenotypic variation in the cranium. Evol. Dev. 9, 76–91 (2007).
54
Murray S. A., Oram K. F., Gridley T., Multiple functions of Snail family genes during palate development in mice. Development 134, 1789–1797 (2007).
55
Mangold E., Ludwig K. U., Nöthen M. M., Breakthroughs in the genetics of orofacial clefting. Trends Mol. Med. 17, 725–733 (2011).
56
MacKenzie A., Purdie L., Davidson D., Collinson M., Hill R. E., Two enhancer domains control early aspects of the complex expression pattern of Msx1. Mech. Dev. 62, 29–40 (1997).
57
Yokoyama S., Ito Y., Ueno-Kudoh H., Shimizu H., Uchibe K., Albini S., Mitsuoka K., Miyaki S., Kiso M., Nagai A., Hikata T., Osada T., Fukuda N., Yamashita S., Harada D., Mezzano V., Kasai M., Puri P. L., Hayashizaki Y., Okado H., Hashimoto M., Asahara H., A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev. Cell 17, 836–848 (2009).
58
Balczerski B., Zakaria S., Tucker A. S., Borycki A. G., Koyama E., Pacifici M., Francis-West P., Distinct spatiotemporal roles of hedgehog signalling during chick and mouse cranial base and axial skeleton development. Dev. Biol. 371, 203–214 (2012).
59
Vaahtokari A., Aberg T., Jernvall J., Keränen S., Thesleff I., The enamel knot as a signaling center in the developing mouse tooth. Mech. Dev. 54, 39–43 (1996).
60
Koyama E., Yamaai T., Iseki S., Ohuchi H., Nohno T., Yoshioka H., Hayashi Y., Leatherman J. L., Golden E. B., Noji S., Pacifici M., Polarizing activity, Sonic hedgehog, and tooth development in embryonic and postnatal mouse. Dev. Dyn. 206, 59–72 (1996).
61
Tucker A. S., Al Khamis A., Ferguson C. A., Bach I., Rosenfeld M. G., Sharpe P. T., Conserved regulation of mesenchymal gene expression by Fgf-8 in face and limb development. Development 126, 221–228 (1999).
62
Li H., Durbin R., Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
63
Zhang Y., Liu T., Meyer C. A., Eeckhoute J., Johnson D. S., Bernstein B. E., Nusbaum C., Myers R. M., Brown M., Li W., Liu X. S., Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9, R137 (2008).
64
J. Feng, T. Liu, Y. Zhang, Curr. Protoc. Bioinformatics, chap. 2, unit 2.14 (2011).
65
Siepel A., Bejerano G., Pedersen J. S., Hinrichs A. S., Hou M., Rosenbloom K., Clawson H., Spieth J., Hillier L. W., Richards S., Weinstock G. M., Wilson R. K., Gibbs R. A., Kent W. J., Miller W., Haussler D., Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 15, 1034–1050 (2005).
66
Kothary R., Clapoff S., Brown A., Campbell R., Peterson A., Rossant J., A transgene containing lacZ inserted into the dystonia locus is expressed in neural tube. Nature 335, 435–437 (1988).
67
Ahituv N., Zhu Y., Visel A., Holt A., Afzal V., Pennacchio L. A., Rubin E. M., Deletion of ultraconserved elements yields viable mice. PLoS Biol. 5, e234 (2007).
68
Livak K. J., Schmittgen T. D., Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25, 402–408 (2001).
69
Martínez-Abadías N., Mitteroecker P., Parsons T. E., Esparza M., Sjøvold T., Rolian C., Richtsmeier J. T., Hallgrímsson B., The developmental basis of quantitative craniofacial variation in humans and mice. Evol. Biol. 39, 554–567 (2012).
70
Hallgrímsson B., Jamniczky H., Young N. M., Rolian C., Parsons T. E., Boughner J. C., Marcucio R. S., Deciphering the palimpsest: Studying the relationship between morphological integration and phenotypic covariation. Evol. Biol. 36, 355–376 (2009).
71
Klingenberg C. P., MorphoJ: An integrated software package for geometric morphometrics. Mol. Ecol. Resour. 11, 353–357 (2011).
72
Aybar M. J., Nieto M. A., Mayor R., Snail precedes slug in the genetic cascade required for the specification and migration of the Xenopus neural crest. Development 130, 483–494 (2003).
73
Nieto M. A., The early steps of neural crest development. Mech. Dev. 105, 27–35 (2001).
74
Jiang R., Lan Y., Norton C. R., Sundberg J. P., Gridley T., The Slug gene is not essential for mesoderm or neural crest development in mice. Dev. Biol. 198, 277–285 (1998).
75
Cobaleda C., Pérez-Caro M., Vicente-Dueñas C., Sánchez-García I., Function of the zinc-finger transcription factor SNAI2 in cancer and development. Annu. Rev. Genet. 41, 41–61 (2007).
76
Sánchez-Martín M., Rodríguez-García A., Pérez-Losada J., Sagrera A., Read A. P., Sánchez-García I., SLUG (SNAI2) deletions in patients with Waardenburg disease. Hum. Mol. Genet. 11, 3231–3236 (2002).
77
Hill R. E., Jones P. F., Rees A. R., Sime C. M., Justice M. J., Copeland N. G., Jenkins N. A., Graham E., Davidson D. R., A new family of mouse homeo box-containing genes: molecular structure, chromosomal location, and developmental expression of Hox-7.1. Genes Dev. 3, 26–37 (1989).
78
Robert B., Sassoon D., Jacq B., Gehring W., Buckingham M., Hox-7, a mouse homeobox gene with a novel pattern of expression during embryogenesis. EMBO J. 8, 91–100 (1989).
79
Catron K. M., Zhang H., Marshall S. C., Inostroza J. A., Wilson J. M., Abate C., Transcriptional repression by Msx-1 does not require homeodomain DNA-binding sites. Mol. Cell. Biol. 15, 861–871 (1995).
80
Blin-Wakkach C., Lezot F., Ghoul-Mazgar S., Hotton D., Monteiro S., Teillaud C., Pibouin L., Orestes-Cardoso S., Papagerakis P., Macdougall M., Robert B., Berdal A., Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc. Natl. Acad. Sci. U.S.A. 98, 7336–7341 (2001).
81
Mackenzie A., Leeming G. L., Jowett A. K., Ferguson M. W., Sharpe P. T., The homeobox gene Hox 7.1 has specific regional and temporal expression patterns during early murine craniofacial embryogenesis, especially tooth development in vivo and in vitro. Development 111, 269–285 (1991).
82
Houzelstein D., Cohen A., Buckingham M. E., Robert B., Insertional mutation of the mouse Msx1 homeobox gene by an nlacZ reporter gene. Mech. Dev. 65, 123–133 (1997).
83
Vastardis H., Karimbux N., Guthua S. W., Seidman J. G., Seidman C. E., A human MSX1 homeodomain missense mutation causes selective tooth agenesis. Nat. Genet. 13, 417–421 (1996).
84
Jumlongras D., Bei M., Stimson J. M., Wang W. F., DePalma S. R., Seidman C. E., Felbor U., Maas R., Seidman J. G., Olsen B. R., A nonsense mutation in MSX1 causes Witkop syndrome. Am. J. Hum. Genet. 69, 67–74 (2001).
85
Jezewski P. A., Vieira A. R., Nishimura C., Ludwig B., Johnson M., O’Brien S. E., Daack-Hirsch S., Schultz R. E., Weber A., Nepomucena B., Romitti P. A., Christensen K., Orioli I. M., Castilla E. E., Machida J., Natsume N., Murray J. C., Complete sequencing shows a role for MSX1 in non-syndromic cleft lip and palate. J. Med. Genet. 40, 399–407 (2003).
86
Tsuchida T., Ensini M., Morton S. B., Baldassare M., Edlund T., Jessell T. M., Pfaff S. L., Topographic organization of embryonic motor neurons defined by expression of LIM homeobox genes. Cell 79, 957–970 (1994).
87
Laugwitz K. L., Moretti A., Lam J., Gruber P., Chen Y., Woodard S., Lin L. Z., Cai C. L., Lu M. M., Reth M., Platoshyn O., Yuan J. X., Evans S., Chien K. R., Postnatal isl1+ cardioblasts enter fully differentiated cardiomyocyte lineages. Nature 433, 647–653 (2005).
88
Ahlgren U., Pfaff S. L., Jessell T. M., Edlund T., Edlund H., Independent requirement for ISL1 in formation of pancreatic mesenchyme and islet cells. Nature 385, 257–260 (1997).
89
Sheng H. Z., Moriyama K., Yamashita T., Li H., Potter S. S., Mahon K. A., Westphal H., Multistep control of pituitary organogenesis. Science 278, 1809–1812 (1997).
90
Pfaff S. L., Mendelsohn M., Stewart C. L., Edlund T., Jessell T. M., Requirement for LIM homeobox gene Isl1 in motor neuron generation reveals a motor neuron-dependent step in interneuron differentiation. Cell 84, 309–320 (1996).
91
Hindorff L. A., Sethupathy P., Junkins H. A., Ramos E. M., Mehta J. P., Collins F. S., Manolio T. A., Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc. Natl. Acad. Sci. U.S.A. 106, 9362–9367 (2009).

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Published In

Science
Volume 342 | Issue 6157
25 October 2013

Submission history

Received: 24 May 2013
Accepted: 20 August 2013
Published in print: 25 October 2013

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Acknowledgments

The authors thank J. Harkes and M. Satyanarayanan for development of the OPT viewer; S. Shen and H. Hochheiser for integration of the OPT viewer and data sets into FaceBase; and J. Murray, M. Marazita, J. Manak, B. Schutte, and all FaceBase members for help in the selection of relevant craniofacial intervals and comments on results. A.V. and L.A.P. were supported by NIDCR FaceBase grant U01DE020060 and by National Human Genome Research Institute grants R01HG003988 and U54HG006997. C.A. was supported by a Swiss National Science Foundation advanced researcher fellowship. A.S.N. was supported by a F32 NIH/National Institute of General Medical Sciences National Research Service Award fellowship GM105202. B.H. was supported by NIH 1R01DE021708, NIH 1R01DE01963, NIH 1U01DE020054, and Natural Sciences and Engineering Research Council of Canada #238992-11 grants. D.R.F. and H.M. were supported by a UK Medical Research Council core program grant. B.R. was supported by the Ludwig Institute for Cancer Research and NIH grants U54HG006997 and R01HG003991. B.H. was supported by NIH 1R01DE01963. Research was conducted at the E. O. Lawrence Berkeley National Laboratory and performed under Department of Energy contract DE-AC02-05CH11231, University of California. ChIP-Seq data are available through GEO (accession no. GSE49413) and FaceBase.org. In vivo reporter data are available through the Vista Enhancer Browser (http://enhancer.lbl.gov) and FaceBase.org. OPT data, including raw images and interactive 3D viewing option, is available through http://facebase.org. All enhancer reporter vectors, as well as archived surplus LacZ-stained embryos for selected enhancers, are available from the authors. Craniofacial enhancer knockout lines are available through the Mutant Mouse Regional Resource Centers (Δhs1431, MMRRC 03895; Δhs746, MMRRC 03888; and Δhs586, MMRRCC 03894).

Authors

Affiliations

Catia Attanasio
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Alex S. Nord
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Yiwen Zhu
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Matthew J. Blow
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
Zirong Li*
Ludwig Institute for Cancer Research, and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Denise K. Liberton
Department of Cell Biology and Anatomy, McCaig Bone and Joint Institute, University of Calgary, Calgary T2N 4N1, Canada.
Harris Morrison
MRC Human Genetics Unit, MRC Institute for Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
Ingrid Plajzer-Frick
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Amy Holt
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Roya Hosseini
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Sengthavy Phouanenavong
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jennifer A. Akiyama
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Malak Shoukry
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Veena Afzal
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Edward M. Rubin
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
David R. FitzPatrick
MRC Human Genetics Unit, MRC Institute for Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK.
Royal Hospital for Sick Children, Edinburgh EH9 1LF, UK.
Bing Ren
Ludwig Institute for Cancer Research, and Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, CA 92093, USA.
Benedikt Hallgrímsson
Department of Cell Biology and Anatomy, McCaig Bone and Joint Institute, University of Calgary, Calgary T2N 4N1, Canada.
Alberta Children's Hospital Research Institute, University of Calgary, Calgary T2N 4N1, Canada.
Len A. Pennacchio
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.

Notes

†Corresponding author. E-mail: [email protected]
*
Present address: EMD Millipore, 28820 Single Oak Drive, Temecula, CA 92590, USA.

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