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Francois Spitz

InstitutionUniversity of Chicago
DepartmentHuman Genetics
AddressChicago IL 60637
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    Collapse Overview 
    Collapse overview
    Our group is interested in understanding how the architecture of the genome contributes to the specificity and robustness of the gene expression programs that govern embryonic development and cell differentiation.
    Vertebrate genomes contain hundreds of thousands of regulatory sequences that can influence the expression of genes sometimes located hundreds of kilobases away. Our main goal is to understand how the folding of the genome in specific domains and dynamic structures contributes to transform such a dispersed information into highly specific regulatory ensembles. We study as well how perturbations of these processes, notably due to chromosomal rearrangements, could lead to developmental or oncogenic pathologies, but may have also participated to animal evolution.

    Collapse Biography 
    Collapse education and training
    Université Pierre et Marie Curie - Paris 6, Paris - FranceDEA09/1993Cellular and Molecular Genetics
    Université Pierre et Marie Curie - Paris 6, Paris - FrancePhD12/1997Cellular and Molecular Genetics
    University of Geneva, Geneva - Switzerland08/2006Developmental Genetics
    Collapse awards and honors
    2016elected member, European Molecular Biology Organisation

    Collapse Bibliographic 
    Collapse selected publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Yu A, Yesilkanal AE, Thakur A, Wang F, Yang Y, Phillips W, Wu X, Muir A, He X, Spitz F, Yang L. HYENA detects oncogenes activated by distal enhancers in cancer. bioRxiv. 2023 Nov 28. PMID: 38076958; PMCID: PMC10705271.
    2. Comai GE, Exelby K, Pryce B, Kaiser J, Briscoe J, Schweitzer R, Tajbakhsh S, Tesarová M, Dupé V, Rhinn M, Vallecillo-García P, da Silva F, Feret B, Dollé P, Carlsson L, Spitz F, Stricker S, Zikmund T, Schedl A, Ghyselinck NB. Local retinoic acid signaling directs emergence of the extraocular muscle functional unit. PLoS Biol. 2020 11; 18(11):e3000902. PMID: 33201874; PMCID: PMC7707851.
      Citations: 11     Fields:    Translation:AnimalsCells
    3. Spitz F. Chromosomes come together to help mice distinguish odours. Nature. 2019 01; 565(7740):439-440. PMID: 30666054.
      Citations: 1     Fields:    Translation:AnimalsCells
    4. Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, Murison A, Langenfeld K, Petretich M, Scognamiglio R, Zeisberger P, Benk AS, Amit I, Zandstra PW, Lupien M, Dick JE, Trumpp A, Spitz F. Author Correction: A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature. 2018 06; 558(7711):E4. PMID: 29769714.
      Citations: 3     Fields:    
    5. Saudemont B, Chomsky E, Renno J, Loe-Mie Y, Lifshitz A, Mukamel Z, Schmutz S, Novault S, Tanay A, Marlow H, Sebé-Pedrós A, Plessier F, Mailhé MP, Steinmetz PRH, Spitz F. Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq. Cell. 2018 05 31; 173(6):1520-1534.e20. PMID: 29856957.
      Citations: 117     Fields:    Translation:AnimalsCells
    6. Bahr C, von Paleske L, Uslu VV, Remeseiro S, Takayama N, Ng SW, Murison A, Langenfeld K, Petretich M, Scognamiglio R, Zeisberger P, Benk AS, Amit I, Zandstra PW, Lupien M, Dick JE, Trumpp A, Spitz F. A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature. 2018 01 25; 553(7689):515-520. PMID: 29342133.
      Citations: 165     Fields:    Translation:HumansAnimalsCells
    7. Schwarzer W, Abdennur N, Goloborodko A, Pekowska A, Fudenberg G, Loe-Mie Y, Fonseca NA, Huber W, Haering CH, Mirny L, Spitz F. Two independent modes of chromatin organization revealed by cohesin removal. Nature. 2017 11 02; 551(7678):51-56. PMID: 29094699; PMCID: PMC5687303.
      Citations: 465     Fields:    Translation:AnimalsCells
    8. Symmons O, Pan L, Remeseiro S, Aktas T, Klein F, Huber W, Spitz F. The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances. Dev Cell. 2016 12 05; 39(5):529-543. PMID: 27867070; PMCID: PMC5142843.
      Citations: 103     Fields:    Translation:AnimalsCells
    9. Franke M, Ibrahim DM, Andrey G, Schwarzer W, Kraft K, Kempfer R, Jerkovic I, Spielmann M, Timmermann B, Wittler L, Kurth I, Zuffardi O, Houge G, Lambie L, Brancati F, Pombo A, Vingron M, Spitz F, Mundlos S, Heinrich V, Schöpflin R, Chan WL, Cambiaso P. Formation of new chromatin domains determines pathogenicity of genomic duplications. Nature. 2016 Oct 13; 538(7624):265-269. PMID: 27706140.
      Citations: 283     Fields:    Translation:AnimalsCells
    10. Yao Y, Minor PJ, Zhao YT, Jeong Y, Pani AM, King AN, Symmons O, Gan L, Cardoso WV, Lowe CJ, Epstein DJ, Spitz F. Erratum: Cis-regulatory architecture of a brain signaling center predates the origin of chordates. Nat Genet. 2016 07 27; 48(8):970. PMID: 27463400.
      Citations: 1     Fields:    
    11. Spitz F. Gene regulation at a distance: From remote enhancers to 3D regulatory ensembles. Semin Cell Dev Biol. 2016 09; 57:57-67. PMID: 27364700.
      Citations: 45     Fields:    Translation:HumansAnimalsCells
    12. Yao Y, Minor PJ, Zhao YT, Jeong Y, Pani AM, King AN, Symmons O, Gan L, Cardoso WV, Lowe CJ, Epstein DJ, Spitz F. Cis-regulatory architecture of a brain signaling center predates the origin of chordates. Nat Genet. 2016 05; 48(5):575-80. PMID: 27064252; PMCID: PMC4848136.
      Citations: 31     Fields:    Translation:AnimalsCells
    13. Remeseiro S, Hörnblad A, Spitz F. Gene regulation during development in the light of topologically associating domains. Wiley Interdiscip Rev Dev Biol. 2016 Mar-Apr; 5(2):169-85. PMID: 26558551.
      Citations: 15     Fields:    Translation:AnimalsCells
    14. Liu X, Tamada K, Kishimoto R, Okubo H, Ise S, Ohta H, Ruf S, Nakatani J, Kohno N, Takumi T, Spitz F. Transcriptome profiling of white adipose tissue in a mouse model for 15q duplication syndrome. Genom Data. 2015 Sep; 5:394-6. PMID: 26484295; PMCID: PMC4583688.
      Citations: 5     
    15. Kishimoto R, Tamada K, Liu X, Okubo H, Ise S, Ohta H, Ruf S, Nakatani J, Kohno N, Takumi T, Spitz F. Model mice for 15q11-13 duplication syndrome exhibit late-onset obesity and altered lipid metabolism. Hum Mol Genet. 2015 Aug 15; 24(16):4559-72. PMID: 26002101.
      Citations: 6     Fields:    Translation:HumansAnimalsCells
    16. Amin S, Donaldson IJ, Zannino DA, Hensman J, Rattray M, Losa M, Ladam F, Spitz F, Sagerström C, Bobola N. Hoxa2 selectively enhances Meis binding to change a branchial arch ground state. Dev Cell. 2015 Feb 09; 32(3):265-77. PMID: 25640223; PMCID: PMC4333904.
      Citations: 45     Fields:    Translation:AnimalsCells
    17. Tsujimura T, Klein FA, Langenfeld K, Glaser J, Huber W, Spitz F. A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet. 2015 Jan; 11(1):e1004897. PMID: 25569170; PMCID: PMC4288730.
      Citations: 26     Fields:    Translation:AnimalsCells
    18. Schwarzer W, Spitz F. The architecture of gene expression: integrating dispersed cis-regulatory modules into coherent regulatory domains. Curr Opin Genet Dev. 2014 Aug; 27:74-82. PMID: 24907448.
      Citations: 24     Fields:    Translation:HumansAnimalsCells
    19. Uslu VV, Petretich M, Ruf S, Langenfeld K, Fonseca NA, Marioni JC, Spitz F. Long-range enhancers regulating Myc expression are required for normal facial morphogenesis. Nat Genet. 2014 Jul; 46(7):753-8. PMID: 24859337.
      Citations: 70     Fields:    Translation:HumansAnimalsCells
    20. Symmons O, Uslu VV, Tsujimura T, Ruf S, Nassari S, Schwarzer W, Ettwiller L, Spitz F. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014 Mar; 24(3):390-400. PMID: 24398455; PMCID: PMC3941104.
      Citations: 208     Fields:    Translation:AnimalsCells
    21. Kirchmaier S, Bornhorst D, Spitz F, Wittbrodt J, Höckendorf B, Möller EK. Efficient site-specific transgenesis and enhancer activity tests in medaka using PhiC31 integrase. Development. 2013 Oct; 140(20):4287-95. PMID: 24048591; PMCID: PMC3809364.
      Citations: 13     Fields:    Translation:AnimalsCells
    22. Andrey G, Montavon T, Gonzalez F, Noordermeer D, Leleu M, Trono D, Duboule D, Mascrez B, Spitz F. A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science. 2013 Jun 07; 340(6137):1234167. PMID: 23744951.
      Citations: 199     Fields:    Translation:AnimalsCells
    23. Symmons O, Spitz F. From remote enhancers to gene regulation: charting the genome's regulatory landscapes. Philos Trans R Soc Lond B Biol Sci. 2013; 368(1620):20120358. PMID: 23650632; PMCID: PMC3682723.
      Citations: 16     Fields:    Translation:HumansAnimalsCells
    24. Chen CK, Symmons O, Uslu VV, Tsujimura T, Ruf S, Smedley D, Spitz F. TRACER: a resource to study the regulatory architecture of the mouse genome. BMC Genomics. 2013 Apr 02; 14:215. PMID: 23547943; PMCID: PMC3618316.
      Citations: 11     Fields:    Translation:Animals
    25. Marinic M, Aktas T, Ruf S, Spitz F. An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell. 2013 Mar 11; 24(5):530-42. PMID: 23453598.
      Citations: 75     Fields:    Translation:HumansAnimalsCells
    26. Weischenfeldt J, Symmons O, Korbel JO, Spitz F. Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet. 2013 Feb; 14(2):125-38. PMID: 23329113.
      Citations: 274     Fields:    Translation:HumansAnimals
    27. Furlong EE, Spitz F. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012 Sep; 13(9):613-26. PMID: 22868264.
      Citations: 982     Fields:    Translation:HumansAnimalsCells
    28. Soshnikova N, Joye E, Thevenet L, Splinter E, de Laat W, Duboule D, Montavon T, Mascrez B, Spitz F. A regulatory archipelago controls Hox genes transcription in digits. Cell. 2011 Nov 23; 147(5):1132-45. PMID: 22118467.
      Citations: 233     Fields:    Translation:HumansAnimalsCells
    29. Ruf S, Symmons O, Uslu VV, Dolle D, Ettwiller L, Hot C, Spitz F. Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet. 2011 Mar 20; 43(4):379-86. PMID: 21423180.
      Citations: 78     Fields:    Translation:HumansAnimalsCells
    30. Friedli M, Barde I, Verp S, Quazzola A, Zakany J, Lin-Marq N, Robyr D, Attanasio C, Duboule D, Trono D, Antonarakis SE, Arcangeli M, Spitz F. A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One. 2010 Dec 29; 5(12):e15741. PMID: 21206754; PMCID: PMC3012086.
      Citations: 17     Fields:    Translation:HumansAnimalsCells
    31. Jakobsson J, Mesnard D, Rougemont J, Aktas T, Maillard PV, Layard-Liesching H, Verp S, Marquis J, Constam DB, Trono D, Rowe HM, Reynard S, Spitz F. KAP1 controls endogenous retroviruses in embryonic stem cells. Nature. 2010 Jan 14; 463(7278):237-40. PMID: 20075919.
      Citations: 430     Fields:    Translation:AnimalsCells
    32. Spitz F. Control of vertebrate Hox clusters by remote and global cis-acting regulatory sequences. Adv Exp Med Biol. 2010; 689:63-78. PMID: 20795322.
      Citations: 3     Fields:    Translation:HumansAnimalsCells
    33. Tschopp P, Tarchini B, Zakany J, Duboule D, Spitz F. Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genet. 2009 Mar; 5(3):e1000398. PMID: 19266017; PMCID: PMC2642670.
      Citations: 35     Fields:    Translation:AnimalsCells
    34. Ettwiller L, Budd A, Wittbrodt J, Spitz F. Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. Genome Biol. 2008; 9(12):R172. PMID: 19087242; PMCID: PMC2646276.
      Citations: 2     Fields:    Translation:HumansAnimalsCells
    35. Dorr AP, Stevenson B, Quazzola A, Wiznerowicz M, Jongeneel V, Duboule D, Trono D, Sauvain MO, Naef F, Schütz F, Spitz F. Genotypic features of lentivirus transgenic mice. J Virol. 2008 Jul; 82(14):7111-9. PMID: 18463153; PMCID: PMC2446968.
      Citations: 18     Fields:    Translation:AnimalsCells
    36. Friedli M, Nikolaev S, Lyle R, Duboule D, Antonarakis SE, Arcangeli M, Spitz F. Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3. Mamm Genome. 2008 Apr; 19(4):272-8. PMID: 18392654.
      Citations: 11     Fields:    Translation:HumansAnimalsCells
    37. Spitz F, Duboule D. Global control regions and regulatory landscapes in vertebrate development and evolution. Adv Genet. 2008; 61:175-205. PMID: 18282506.
      Citations: 26     Fields:    Translation:HumansAnimalsCells
    38. Gonzalez F, Duboule D, Spitz F. Transgenic analysis of Hoxd gene regulation during digit development. Dev Biol. 2007 Jun 15; 306(2):847-59. PMID: 17448461.
      Citations: 38     Fields:    Translation:AnimalsCells
    39. Furlong EE, Spitz F. Genomics and development: Taking developmental biology to new heights. Dev Cell. 2006 Oct; 11(4):451-7. PMID: 17051688.
      Citations: 2     Fields:    Translation:Animals
    40. Herkenne C, Hinard C, Duboule D, Spitz F. [A STRING lifts the veil on the mechanisms controlling Hox genes expression]. Med Sci (Paris). 2006 Jan; 22(1):14-6. PMID: 16386210.
      Citations:    Fields:    Translation:Animals
    41. Herkenne C, Morris MA, Duboule D, Spitz F. Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet. 2005 Aug; 37(8):889-93. PMID: 15995706.
      Citations: 59     Fields:    Translation:Animals
    42. Duboule D, Spitz F. Developmental biology: reproduction in clusters. Nature. 2005 Apr 07; 434(7034):715-6. PMID: 15815616.
      Citations: 3     Fields:    Translation:AnimalsCells
    43. Laclef C, Lopez S, Demignon J, Guidotti JE, Kawakami K, Xu PX, Kelly R, Petrof BJ, Daegelen D, Concordet JP, Maire P, Grifone R, Spitz F. Six1 and Eya1 expression can reprogram adult muscle from the slow-twitch phenotype into the fast-twitch phenotype. Mol Cell Biol. 2004 Jul; 24(14):6253-67. PMID: 15226428; PMCID: PMC434262.
      Citations: 83     Fields:    Translation:AnimalsCells
    44. Haramis AP, Panman L, Galli A, Vintersten K, Klasen C, Mansfield W, Kuc S, Duboule D, Dono R, Zeller R, Zuniga A, Michos O, Spitz F. Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev. 2004 Jul 01; 18(13):1553-64. PMID: 15198975; PMCID: PMC443518.
      Citations: 56     Fields:    Translation:AnimalsCells
    45. Gonzalez F, Duboule D, Spitz F. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell. 2003 May 02; 113(3):405-17. PMID: 12732147.
      Citations: 186     Fields:    Translation:HumansAnimalsCells
    46. Sabourin JC, Salminen M, Chen F, Cywiner C, Kahn A, Maire P, Daegelen D, Sabourin JC, Salminen M, Chen F, Cywiner C, Kahn A, Maire P, Daegelen D. Fiber-type specific and position-dependent expression of a transgene in limb muscles. Differentiation. 2002 Oct; 70(8):457-67. PMID: 12366383.
      Citations: 3     Fields:    Translation:AnimalsCells
    47. Montavon T, Monso-Hinard C, Morris M, Ventruto ML, Antonarakis S, Ventruto V, Duboule D, Spitz F. A t(2;8) balanced translocation with breakpoints near the human HOXD complex causes mesomelic dysplasia and vertebral defects. Genomics. 2002 Apr; 79(4):493-8. PMID: 11944980.
      Citations: 12     Fields:    Translation:HumansCells
    48. Spitz F, Gonzalez F, Peichel C, Vogt TF, Duboule D, Zákány J. Large scale transgenic and cluster deletion analysis of the HoxD complex separate an ancestral regulatory module from evolutionary innovations. Genes Dev. 2001 Sep 01; 15(17):2209-14. PMID: 11544178; PMCID: PMC312772.
      Citations: 51     Fields:    Translation:HumansAnimals
    49. Tada H, Maron DJ, Choi EA, Barsoum J, Lei H, Xie Q, Liu W, Ellis L, Moscioni AD, Tazelaar J, Fawell S, Qin X, Propert KJ, Davis A, Fraker DL, Wilson JM, Spitz FR. Systemic IFN-beta gene therapy results in long-term survival in mice with established colorectal liver metastases. J Clin Invest. 2001 Jul; 108(1):83-95. PMID: 11435460; PMCID: PMC209332.
      Citations: 10     Fields:    Translation:HumansAnimalsCells
    50. Bauer TW, Hahn SM, Spitz FR, Kachur A, Glatstein E, Fraker DL. Preliminary report of photodynamic therapy for intraperitoneal sarcomatosis. Ann Surg Oncol. 2001 Apr; 8(3):254-9. PMID: 11314943.
      Citations: 6     Fields:    Translation:HumansCTClinical Trials
    51. Hendren SK, Hahn SM, Spitz FR, Bauer TW, Rubin SC, Zhu T, Glatstein E, Fraker DL, Hendren SK, Hahn SM, Spitz FR, Bauer TW, Rubin SC, Zhu T, Glatstein E, Fraker DL. Phase II trial of debulking surgery and photodynamic therapy for disseminated intraperitoneal tumors. Ann Surg Oncol. 2001 Jan-Feb; 8(1):65-71. PMID: 11206227.
      Citations: 33     Fields:    Translation:HumansCTClinical Trials
    52. Fan X, Brass LF, Poncz M, Spitz F, Maire P, Manning DR. The alpha subunits of Gz and Gi interact with the eyes absent transcription cofactor Eya2, preventing its interaction with the six class of homeodomain-containing proteins. J Biol Chem. 2000 Oct 13; 275(41):32129-34. PMID: 10906137.
      Citations: 19     Fields:    Translation:HumansAnimalsCells
    53. Bedrosian I, Faries MB, Guerry D, Elenitsas R, Schuchter L, Mick R, Spitz FR, Bucky LP, Alavi A, Elder DE, Fraker DL, Czerniecki BJ. Incidence of sentinel node metastasis in patients with thin primary melanoma (< or = 1 mm) with vertical growth phase. Ann Surg Oncol. 2000 May; 7(4):262-7. PMID: 10819365.
      Citations: 31     Fields:    Translation:Humans
    54. Bedrosian I, Scheff AM, Mick R, Callans LS, Bucky LP, Spitz FR, Helsabeck C, Elder DE, Alavi A, Fraker DF, Czerniecki BJ. 99mTc-human serum albumin: an effective radiotracer for identifying sentinel lymph nodes in melanoma. J Nucl Med. 1999 Jul; 40(7):1143-8. PMID: 10405134.
      Citations: 6     Fields:    Translation:Humans
    55. Demignon J, Kahn A, Daegelen D, Maire P, Spitz F. Developmental regulation of the aldolase A muscle-specific promoter during in vivo muscle maturation is controlled by a nuclear receptor binding element. J Mol Biol. 1999 Jun 18; 289(4):893-903. PMID: 10369770.
      Citations: 1     Fields:    Translation:AnimalsCells
    56. Czerniecki BJ, Scheff AM, Callans LS, Spitz FR, Bedrosian I, Conant EF, Orel SG, Berlin J, Helsabeck C, Fraker DL, Reynolds C. Immunohistochemistry with pancytokeratins improves the sensitivity of sentinel lymph node biopsy in patients with breast carcinoma. Cancer. 1999 Mar 01; 85(5):1098-103. PMID: 10091794.
      Citations: 17     Fields:    Translation:Humans
    57. Demignon J, Porteu A, Kahn A, Concordet JP, Daegelen D, Maire P, Spitz F. Expression of myogenin during embryogenesis is controlled by Six/sine oculis homeoproteins through a conserved MEF3 binding site. Proc Natl Acad Sci U S A. 1998 Nov 24; 95(24):14220-5. PMID: 9826681; PMCID: PMC24354.
      Citations: 85     Fields:    Translation:AnimalsCells
    58. Bauer TW, Spitz FR. Adjuvant and neoadjuvant chemoradiation therapy for primary colorectal cancer. Surg Oncol. 1998 Nov-Dec; 7(3-4):175-81. PMID: 10677168.
      Citations: 5     Fields:    Translation:Humans
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