Ilaria Rebay

Research Summary
The long-term goal of research in the Rebay Lab is to understand how signaling networks, cytoskeletal dynamics and tissue geometry work together to direct specific developmental decisions and programs. We use the developing Drosophila eye and heart as tractable model systems in which to explore how cell fates are specified and organized into functional tissues and organs. Our experimental approach is multidisciplinary, and incorporates molecular genetics, genomics, quantitative imaging, biochemistry and mathematical modeling. Current projects are focused on transcriptional networks and cellular mechanisms that regulate and stabilize the transition from uncommitted progenitor to specified fate and on signaling mechanisms and tissue-level biomechanical properties that together drive terminal differentiation and morphogenesis.
Cell Fate Specification, Transcription Factor Networks, Signal Transduction Pathways, Retinal Development, Drosophila
  • Columbia University, New York, BA Mathematics 05/1987
  • Yale University, New Haven, PhD Biology 08/1993
  • University of California, Berkeley, Postdoc Biology 08/1997
Awards & Honors
  • 1988 - 1993 HHMI Pre-Doctoral Fellowship
  • 1993 - 1995 Life Sciences Research Foundation Postdoctoral Fellowship
  • 1995 - 2000 Burroughs Wellcome Fund Career Award
  • 1998 - 2001 Rita Allen Foundation Scholar Award
  • 2007 - 2008 J. and J. Neubauer Faculty Development Fellowship University of Chicago
  • 2015 - Quantrell Award for Excellence in Undergraduate Teaching University of Chicago
  1. Wu C, Boisclair Lachance JF, Ludwig MZ, Rebay I. A context-dependent bifurcation in the Pointed transcriptional effector network contributes specificity and robustness to retinal cell fate acquisition. PLoS Genet. 2020 11; 16(11):e1009216. View in: PubMed

  2. Hope CM, Webber JL, Tokamov SA, Rebay I. Tuned polymerization of the transcription factor Yan limits off-DNA sequestration to confer context-specific repression. Elife. 2018 11 09; 7. View in: PubMed

  3. Webber JL, Zhang J, Massey A, Sanchez-Luege N, Rebay I. Collaborative repressive action of the antagonistic ETS transcription factors Pointed and Yan fine-tunes gene expression to confer robustness in Drosophila. Development. 2018 07 02; 145(13). View in: PubMed

  4. Boisclair Lachance JF, Webber JL, Hong L, Dinner AR, Rebay I. Cooperative recruitment of Yan via a high-affinity ETS supersite organizes repression to confer specificity and robustness to cardiac cell fate specification. Genes Dev. 2018 03 01; 32(5-6):389-401. View in: PubMed

  5. Davis TL, Rebay I. Pleiotropy in Drosophila organogenesis: Mechanistic insights from Combgap and the retinal determination gene network. Fly (Austin). 2018 01 02; 12(1):62-70. View in: PubMed

  6. Davis TL, Hoi CSL, Rebay I. Mutations that impair Eyes absent tyrosine phosphatase activity in vitro reduce robustness of retinal determination gene network output in Drosophila. PLoS One. 2017; 12(11):e0187546. View in: PubMed

  7. Davis TL, Rebay I. Antagonistic regulation of the second mitotic wave by Eyes absent-Sine oculis and Combgap coordinates proliferation and specification in the Drosophila retina. Development. 2017 07 15; 144(14):2640-2651. View in: PubMed

  8. Hope CM, Rebay I, Reinitz J. DNA Occupancy of Polymerizing Transcription Factors: A Chemical Model of the ETS Family Factor Yan. Biophys J. 2017 Jan 10; 112(1):180-192. View in: PubMed

  9. Davis TL, Rebay I. Master regulators in development: Views from the Drosophila retinal determination and mammalian pluripotency gene networks. Dev Biol. 2017 Jan 15; 421(2):93-107. View in: PubMed

  10. Hoi CS, Xiong W, Rebay I. Retinal Axon Guidance Requires Integration of Eya and the Jak/Stat Pathway into Phosphotyrosine-Based Signaling Circuitries in Drosophila. Genetics. 2016 07; 203(3):1283-95. View in: PubMed

  11. Rebay I. Multiple Functions of the Eya Phosphotyrosine Phosphatase. Mol Cell Biol. 2015 Dec 14; 36(5):668-77. View in: PubMed

  12. Peláez N, Gavalda-Miralles A, Wang B, Navarro HT, Gudjonson H, Rebay I, Dinner AR, Katsaggelos AK, Amaral LA, Carthew RW. Dynamics and heterogeneity of a fate determinant during transition towards cell differentiation. Elife. 2015 Nov 19; 4. View in: PubMed

  13. Qi J, Wang B, Pelaez N, Rebay I, Carthew RW, Katsaggelos AK, Nunes Amaral LA. Drosophila Eye Nuclei Segmentation Based on Graph Cut and Convex Shape Prior. Int Conf Signal Process Proc. 2013 Sep 18; 670-674. View in: PubMed

  14. Webber JL, Rebay I. Long-range integration of repressive and patterning inputs. Cell Cycle. 2014; 13(11):1653-4. View in: PubMed

  15. Zhou Q, Zhang T, Jemc JC, Chen Y, Chen R, Rebay I, Pignoni F. Onset of atonal expression in Drosophila retinal progenitors involves redundant and synergistic contributions of Ey/Pax6 and So binding sites within two distant enhancers. Dev Biol. 2014 Feb 01; 386(1):152-64. View in: PubMed

  16. Boisclair Lachance JF, Peláez N, Cassidy JJ, Webber JL, Rebay I, Carthew RW. A comparative study of Pointed and Yan expression reveals new complexity to the transcriptional networks downstream of receptor tyrosine kinase signaling. Dev Biol. 2014 Jan 15; 385(2):263-78. View in: PubMed

  17. Webber JL, Zhang J, Mitchell-Dick A, Rebay I. 3D chromatin interactions organize Yan chromatin occupancy and repression at the even-skipped locus. Genes Dev. 2013 Nov 01; 27(21):2293-8. View in: PubMed

  18. Webber JL, Rebay I. Chromatin occupancy patterns of the ETS repressor Yan: a mechanism for buffering gene expression against noise? Fly (Austin). 2013 Apr-Jun; 7(2):92-8. View in: PubMed

  19. Xiong W, Morillo SA, Rebay I. The Abelson tyrosine kinase regulates Notch endocytosis and signaling to maintain neuronal cell fate in Drosophila photoreceptors. Development. 2013 Jan 01; 140(1):176-84. View in: PubMed

  20. Webber JL, Zhang J, Cote L, Vivekanand P, Ni X, Zhou J, Nègre N, Carthew RW, White KP, Rebay I. The relationship between long-range chromatin occupancy and polymerization of the Drosophila ETS family transcriptional repressor Yan. Genetics. 2013 Feb; 193(2):633-49. View in: PubMed

  21. Vivekanand P, Rebay I. The SAM domain of human TEL2 can abrogate transcriptional output from TEL1 (ETV-6) and ETS1/ETS2. PLoS One. 2012; 7(5):e37151. View in: PubMed

  22. Morillo SA, Braid LR, Verheyen EM, Rebay I. Nemo phosphorylates Eyes absent and enhances output from the Eya-Sine oculis transcriptional complex during Drosophila retinal determination. Dev Biol. 2012 May 01; 365(1):267-76. View in: PubMed

  23. Xiong W, Rebay I. Abelson tyrosine kinase is required for Drosophila photoreceptor morphogenesis and retinal epithelial patterning. Dev Dyn. 2011 Jul; 240(7):1745-55. View in: PubMed

  24. Rebay I, Fehon RG. Streamlined protocol for antibody staining of large numbers of samples in Drosophila. CSH Protoc. 2008 Sep 01; 2008:pdb.prot5000. View in: PubMed

  25. Rebay I, Fehon RG. Antibody staining of Drosophila tissues--helpful hints. CSH Protoc. 2008 Sep 01; 2008:pdb.ip56. View in: PubMed

  26. Rebay I, Fehon RG. Determining fusion protein antiserum quality by staining of transfected Drosophila S2 cultured cells. Cold Spring Harb Protoc. 2011 Jan 01; 2011(1):pdb.prot4999. View in: PubMed

  27. Rebay I, Fehon RG. Dot blot assay for determining fusion protein antiserum quality. Cold Spring Harb Protoc. 2011 Jan 01; 2011(1):pdb.prot4998. View in: PubMed

  28. Graham TG, Tabei SM, Dinner AR, Rebay I. Modeling bistable cell-fate choices in the Drosophila eye: qualitative and quantitative perspectives. Development. 2010 Jul; 137(14):2265-78. View in: PubMed

  29. Rebay I, Fehon RG. Preparation of insoluble GST fusion proteins. Cold Spring Harb Protoc. 2009 Nov; 2009(11):pdb.prot4997. View in: PubMed

  30. Rebay I, Fehon RG. Preparation of soluble GST fusion proteins. Cold Spring Harb Protoc. 2009 Nov; 2009(11):pdb.prot4996. View in: PubMed

  31. Zhang J, Graham TG, Vivekanand P, Cote L, Cetera M, Rebay I. Sterile alpha motif domain-mediated self-association plays an essential role in modulating the activity of the Drosophila ETS family transcriptional repressor Yan. Mol Cell Biol. 2010 Mar; 30(5):1158-70. View in: PubMed

  32. Xiong W, Dabbouseh NM, Rebay I. Interactions with the Abelson tyrosine kinase reveal compartmentalization of eyes absent function between nucleus and cytoplasm. Dev Cell. 2009 Feb; 16(2):271-9. View in: PubMed

  33. Jemc J, Rebay I. Identification of transcriptional targets of the dual-function transcription factor/phosphatase eyes absent. Dev Biol. 2007 Oct 15; 310(2):416-29. View in: PubMed

  34. Doroquez DB, Orr-Weaver TL, Rebay I. Split ends antagonizes the Notch and potentiates the EGFR signaling pathways during Drosophila eye development. Mech Dev. 2007 Sep-Oct; 124(9-10):792-806. View in: PubMed

  35. Jemc J, Rebay I. The eyes absent family of phosphotyrosine phosphatases: properties and roles in developmental regulation of transcription. Annu Rev Biochem. 2007; 76:513-38. View in: PubMed

  36. Mutsuddi M, Rebay I. Molecular genetics of spinocerebellar ataxia type 8 (SCA8). RNA Biol. 2005 Apr; 2(2):49-52. View in: PubMed

  37. Doroquez DB, Rebay I. Signal integration during development: mechanisms of EGFR and Notch pathway function and cross-talk. Crit Rev Biochem Mol Biol. 2006 Nov-Dec; 41(6):339-85. View in: PubMed

  38. Jemc J, Rebay I. Targeting Drosophila eye development. Genome Biol. 2006; 7(7):226. View in: PubMed

  39. Vivekanand P, Rebay I. Intersection of signal transduction pathways and development. Annu Rev Genet. 2006; 40:139-57. View in: PubMed

  40. Jemc J, Rebay I. Characterization of the split ends-like gene spenito reveals functional antagonism between SPOC family members during Drosophila eye development. Genetics. 2006 May; 173(1):279-86. View in: PubMed

  41. Badenhorst P, Xiao H, Cherbas L, Kwon SY, Voas M, Rebay I, Cherbas P, Wu C. The Drosophila nucleosome remodeling factor NURF is required for Ecdysteroid signaling and metamorphosis. Genes Dev. 2005 Nov 01; 19(21):2540-5. View in: PubMed

  42. Schober M, Rebay I, Perrimon N. Function of the ETS transcription factor Yan in border cell migration. Development. 2005 Aug; 132(15):3493-504. View in: PubMed

  43. Mutsuddi M, Chaffee B, Cassidy J, Silver SJ, Tootle TL, Rebay I. Using Drosophila to decipher how mutations associated with human branchio-oto-renal syndrome and optical defects compromise the protein tyrosine phosphatase and transcriptional functions of eyes absent. Genetics. 2005 Jun; 170(2):687-95. View in: PubMed

  44. Rebay I, Silver SJ, Tootle TL. New vision from Eyes absent: transcription factors as enzymes. Trends Genet. 2005 Mar; 21(3):163-71. View in: PubMed

  45. Tootle TL, Rebay I. Post-translational modifications influence transcription factor activity: a view from the ETS superfamily. Bioessays. 2005 Mar; 27(3):285-98. View in: PubMed

  46. Silver SJ, Rebay I. Signaling circuitries in development: insights from the retinal determination gene network. Development. 2005 Jan; 132(1):3-13. View in: PubMed

  47. Vivekanand P, Tootle TL, Rebay I. MAE, a dual regulator of the EGFR signaling pathway, is a target of the Ets transcription factors PNT and YAN. Mech Dev. 2004 Dec; 121(12):1469-79. View in: PubMed

  48. Silver SJ, Chen F, Doyon L, Zink AW, Rebay I. New class of Son-of-sevenless (Sos) alleles highlights the complexities of Sos function. Genesis. 2004 Aug; 39(4):263-72. View in: PubMed

  49. Qiao F, Song H, Kim CA, Sawaya MR, Hunter JB, Gingery M, Rebay I, Courey AJ, Bowie JU. Derepression by depolymerization; structural insights into the regulation of Yan by Mae. Cell. 2004 Jul 23; 118(2):163-73. View in: PubMed

  50. Mutsuddi M, Marshall CM, Benzow KA, Koob MD, Rebay I. The spinocerebellar ataxia 8 noncoding RNA causes neurodegeneration and associates with staufen in Drosophila. Curr Biol. 2004 Feb 17; 14(4):302-8. View in: PubMed

  51. Voas MG, Rebay I. The novel plant homeodomain protein rhinoceros antagonizes Ras signaling in the Drosophila eye. Genetics. 2003 Dec; 165(4):1993-2006. View in: PubMed

  52. Voas MG, Rebay I. Signal integration during development: insights from the Drosophila eye. Dev Dyn. 2004 Jan; 229(1):162-75. View in: PubMed

  53. Tootle TL, Silver SJ, Davies EL, Newman V, Latek RR, Mills IA, Selengut JD, Parlikar BE, Rebay I. The transcription factor Eyes absent is a protein tyrosine phosphatase. Nature. 2003 Nov 20; 426(6964):299-302. View in: PubMed

  54. Silver SJ, Davies EL, Doyon L, Rebay I. Functional dissection of eyes absent reveals new modes of regulation within the retinal determination gene network. Mol Cell Biol. 2003 Sep; 23(17):5989-99. View in: PubMed

  55. Lin HV, Doroquez DB, Cho S, Chen F, Rebay I, Cadigan KM. Splits ends is a tissue/promoter specific regulator of Wingless signaling. Development. 2003 Jul; 130(14):3125-35. View in: PubMed

  56. Tootle TL, Lee PS, Rebay I. CRM1-mediated nuclear export and regulated activity of the Receptor Tyrosine Kinase antagonist YAN require specific interactions with MAE. Development. 2003 Mar; 130(5):845-57. View in: PubMed

  57. Badenhorst P, Voas M, Rebay I, Wu C. Biological functions of the ISWI chromatin remodeling complex NURF. Genes Dev. 2002 Dec 15; 16(24):3186-98. View in: PubMed

  58. Rebay I. Keeping the receptor tyrosine kinase signaling pathway in check: lessons from Drosophila. Dev Biol. 2002 Nov 01; 251(1):1-17. View in: PubMed

  59. Hsiao FC, Williams A, Davies EL, Rebay I. Eyes absent mediates cross-talk between retinal determination genes and the receptor tyrosine kinase signaling pathway. Dev Cell. 2001 Jul; 1(1):51-61. View in: PubMed

  60. Chen F, Rebay I. split ends, a new component of the Drosophila EGF receptor pathway, regulates development of midline glial cells. Curr Biol. 2000 Jul 27-Aug 10; 10(15):943-6. View in: PubMed

  61. Rebay I, Chen F, Hsiao F, Kolodziej PA, Kuang BH, Laverty T, Suh C, Voas M, Williams A, Rubin GM. A genetic screen for novel components of the Ras/Mitogen-activated protein kinase signaling pathway that interact with the yan gene of Drosophila identifies split ends, a new RNA recognition motif-containing protein. Genetics. 2000 Feb; 154(2):695-712. View in: PubMed

  62. Fox GL, Rebay I, Hynes RO. Expression of DFak56, a Drosophila homolog of vertebrate focal adhesion kinase, supports a role in cell migration in vivo. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26):14978-83. View in: PubMed

  63. Rubin GM, Chang HC, Karim F, Laverty T, Michaud NR, Morrison DK, Rebay I, Tang A, Therrien M, Wassarman DA. Signal transduction downstream from Ras in Drosophila. Cold Spring Harb Symp Quant Biol. 1997; 62:347-52. View in: PubMed

  64. Fortini ME, Rebay I, Caron LA, Artavanis-Tsakonas S. An activated Notch receptor blocks cell-fate commitment in the developing Drosophila eye. Nature. 1993 Oct 07; 365(6446):555-7. View in: PubMed

  65. Rebay I, Fehon RG, Artavanis-Tsakonas S. Specific truncations of Drosophila Notch define dominant activated and dominant negative forms of the receptor. Cell. 1993 Jul 30; 74(2):319-29. View in: PubMed

  66. Rebay I, Fortini ME, Artavanis-Tsakonas S. Analysis of phenotypic abnormalities and cell fate changes caused by dominant activated and dominant negative forms of the Notch receptor in Drosophila development. C R Acad Sci III. 1993 Sep; 316(9):1097-123. View in: PubMed

  67. O'Neill EM, Rebay I, Tjian R, Rubin GM. The activities of two Ets-related transcription factors required for Drosophila eye development are modulated by the Ras/MAPK pathway. Cell. 1994 Jul 15; 78(1):137-47. View in: PubMed

  68. Rebay I, Rubin GM. Yan functions as a general inhibitor of differentiation and is negatively regulated by activation of the Ras1/MAPK pathway. Cell. 1995 Jun 16; 81(6):857-66. View in: PubMed

  69. Chang HC, Karim FD, O'Neill EM, Rebay I, Solomon NM, Therrien M, Wassarman DA, Wolff T, Rubin GM. Ras signal transduction pathway in Drosophila eye development. Cold Spring Harb Symp Quant Biol. 1994; 59:147-53. View in: PubMed

  70. Xu T, Rebay I, Fleming RJ, Scottgale TN, Artavanis-Tsakonas S. The Notch locus and the genetic circuitry involved in early Drosophila neurogenesis. Genes Dev. 1990 Mar; 4(3):464-75. View in: PubMed

  71. Artavanis-Tsakonas S, Delidakis C, Fehon R, Hartley D, Herndon V, Johansen K, Markopoulou K, Preiss A, Rebay I, Scottgale N, et al. Notch and the molecular genetics of neuroblast segregation in Drosophila. Mol Reprod Dev. 1990 Sep; 27(1):23-7. View in: PubMed

  72. Fehon RG, Kooh PJ, Rebay I, Regan CL, Xu T, Muskavitch MA, Artavanis-Tsakonas S. Molecular interactions between the protein products of the neurogenic loci Notch and Delta, two EGF-homologous genes in Drosophila. Cell. 1990 May 04; 61(3):523-34. View in: PubMed

  73. Fehon RG, Johansen K, Rebay I, Artavanis-Tsakonas S. Complex cellular and subcellular regulation of notch expression during embryonic and imaginal development of Drosophila: implications for notch function. J Cell Biol. 1991 May; 113(3):657-69. View in: PubMed

  74. Rebay I, Fleming RJ, Fehon RG, Cherbas L, Cherbas P, Artavanis-Tsakonas S. Specific EGF repeats of Notch mediate interactions with Delta and Serrate: implications for Notch as a multifunctional receptor. Cell. 1991 Nov 15; 67(4):687-99. View in: PubMed