Marine BioTechnology
Developmental Dynamics
Developmental Biology
Developmental Biology Special Issue

Current Opinion

Selected Publications


Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. Wu Y, Devotta A, José-Edwards DS, Kugler JE, Negrón-Piñeiro LJ, Braslavskaya K, Addy J, Saint-Jeannet JP, Di Gregorio A. Elife. 2022 Jan 20;11:e73992. 


The Degenerate Tale of Ascidian Tails. Fodor ACA, Powers MM, Andrykovich K, Liu J, Lowe EK, Brown CT, Di Gregorio A, Stolfi A, Swalla BJ. Integr Comp Biol. 2021 Sep 8;61(2):358-369.


Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate. Negrón-Piñeiro LJ, Wu Y, Di Gregorio A. Genes (Basel) 11:1262, 2020.

Di Gregorio A. The notochord gene regulatory network in chordate evolution: conservation and divergence from Ciona to vertebrates. Current Topics in Developmental Biology. 139:325-374


Irvine SQ, Ristoratore F, Di Gregorio A. Tunicates: From humble sea squirt to proud model organism. Special Issue on Tunicate Biology. Developmental Biology 448:69-70, 2019. (Cover).

Kugler JE, Wu Y, Katikala L, Passamaneck YJ, Addy J, Caballero N, Oda-Ishii I, Maguire JE, Li R, Di Gregorio A. Positioning a multifunctional basic helix-loop-helix transcription factor within the Ciona notochord gene regulatory network. Special Issue on Tunicate Biology. Developmental Biology 448:119-135, 2019.


Maguire JE, Pandey A, Wu Y, Di Gregorio A. Investigating evolutionarily conserved molecular mechanisms controlling gene expression in the notochord. Adv Exp Med Biol. 1029:81-99, 2018.


Di Gregorio A. T-Box Genes and Developmental Gene Regulatory Networks in Ascidians. In: M. Frasch (Ed.), Current Topics in Developmental Biology, vol. 122. Elsevier, Oxford, UK, 2017.


Brozovic M, Martin C, Dantec C, Dauga D, Mendez M, Simion P, Percher M, Laporte B, Scornavacca C, Di Gregorio A., et al., ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Nucleic Acids Research 44(D1):D808-818, 2016.

Di Gregorio A. The Brachyury Locus. In: Brenner’s Online Encyclopedia of Genetics, Third Edition, ed. Dr. Stanley Maloy and Kelly Hughes, 2016.


Jose'-Edwards DS, Oda-Ishii I, Kugler JE, Passamaneck YJ, Katikala L, Nibu Y, Di Gregorio A. Brachyury, Foxa2 and the cis-regulatory origins of the notochord. PLOS Genetics. 11(12):e1005730, 2015.

Matassi G, Imai JH, Di Gregorio A. Molecular phylogeny of four homeobox genes from the purple sea star Pisaster ochraceus. Development Genes and Evolution 225(6):359-65, 2015.


Thompson JM, Di Gregorio A. Insulin-like genes in ascidians: findings in Ciona and hypotheses on the evolutionary origins of the pancreas. Genesis – Special issue on Tunicate Biology. 53(1):82-104, [Epub ahead of print], 2014.


Katikala L, Aihara H, Passamaneck YJ, Gazdoiu S, Jose'-Edwards DS, Kugler JE, Oda-Ishii I, Imai JH, Nibu Y, Di Gregorio A. Functional Brachyury binding sites establish a temporal read-out of gene expression in the Ciona notochord. PLoS Biology 11(10):e1001697, 2013.

This article is the subject of a Primer article by Christiaen, L. “Cis-regulatory timers for developmental gene expression”. PLoS Biology 11(10):e1001698, 2013.
Press releases for this article: Weill Cornell News, Weill Cornell Dean's Bulletin, The Visible Embryo, Eurekalert, Red Orbit, Science Daily, Inspiring Science, Biology News Net, HclIndia,, and other science news websites.

Jose’-Edwards DS, Oda-Ishii I, Nibu Y, Di Gregorio A. Tbx2/3 is an essential mediator within the Brachyury gene network during Ciona notochord development. Development 140:2422-2433, 2013.
One of the movies associated with this paper was selected as Featured Movie for the Development web site.

Nibu Y, Jose’-Edwards DS, Di Gregorio A. From notochord formation to hereditary chordomas: the many roles of Brachyury. BioMed Research International 2013:826435, 2013.

Aihara H, Katikala L, Zeller RW, Di Gregorio A*, Nibu Y*. Optimization of a method for chromatin immunoprecipitation assays in the marine invertebrate chordate Ciona. Marine Biotechnology 15:520-525, 2013. (Cover) *equal contribution


Jose'-Edwards DS, Kerner P, Kugler JE, Deng W, Jiang D, Di Gregorio A. The identification of transcription factors expressed in the notochord of Ciona intestinalis adds new potential players to the Brachyury gene regulatory network. Developmental Dynamics 240:1793-1805, 2011. (Cover)

Kugler JE, Kerner P, Bouquet J-M, Jiang D, Di Gregorio A. Evolutionary changes in the notochord genetic toolkit: a comparative analysis of notochord genes in the ascidian Ciona and the larvacean Oikopleura. BMC Evolutionary Biology 11:21, 2011.

This article is the subject of a commentary: Ferrier, D.E. “Tunicates push the limits of animal evo-devo.” BMC Biology 9:3, 2011.


Kugler JE, Gazdoiu S, Oda-Ishii I, Passamaneck YJ, Erives AJ, Di Gregorio A. Temporal regulation of the muscle gene cascade by Macho1 and Tbx6 transcription factors in Ciona intestinalis. Journal of Cell Science 123:2453-2463, 2010.
This paper was featured in Development 137(15) as “Paper of interest in other CoB journals”.


Passamaneck YJ, Katikala L, Perrone L, Dunn MP, Oda-Ishii I, Di Gregorio, A. Direct Activation of a Notochord Cis-regulatory Module by Brachyury and FoxA in the Ascidian Ciona. Development 136:3679-3689, 2009.

Dunn MP, Di Gregorio A. The evolutionarily conserved leprecan gene: its regulation by Brachyury and its role in the developing Ciona notochord. Developmental Biology 328:561-574, 2009.


Kugler JE, Passamaneck YJ, Feldman TG, Regnier TW, Di Gregorio A. Evolutionary conservation of vertebrate notochord genes in the ascidian Ciona intestinalis. Genesis - Special Issue on Chordate Origins and Evolution 46:697-710, 2008.

Capellini TD, Dunn MP, Passamaneck YJ, Selleri L, Di Gregorio A. Conservation of notochord gene expression across chordates: insights from the Leprecan gene family. Genesis - Special Issue on Chordate Origins and Evolution 46:683-696, 2008.

Capellini TD, Zewdu R, Di Giacomo G, Asciutti S, Kugler JE, Di Gregorio A, Selleri L. Pbx1/Pbx2 govern axial skeletal development by controlling Polycomb and 3' Hox in mesoderm and Pax1/Pax9 in sclerotome. Developmental Biology 321:500-514, 2008.

Coric T, Passamaneck YJ, Zhang P, Di Gregorio A, Canessa, CM. Simple chordates exhibit a proton-independent function of acid-sensing ion channels. FASEB Journal 22:1914-1923, 2008.


Passamaneck YJ, Hadjantonakis A-K, Di Gregorio A. Dynamic and polarized muscle cell behaviors accompany tail morphogenesis in the ascidian Ciona intestinalis. PLoS ONE 2(8):e714, 2007.

Oda-Ishii I, Di Gregorio A. Lineage-independent mosaic expression and regulation of the Ciona multidom gene in the ancestral notochord. Developmental Dynamics 236:1806-1819, 2007.
Images from this article were featured in the “Art Pix” section, Dev. Dyn., September 2007


Di Gregorio A, Hadjantonakis A-K. The multidimensionality of cell behaviors underlying morphogenesis: a case study in ascidians. Bioessays 28:874-879, 2006.

Passamaneck YJ, Di Gregorio A, Papaioannou VE, Hadjantonakis A-K. Live imaging of fluorescent proteins in chordate embryos: from ascidians to mice. Microscopy Research and Techniques 69:160-167, 2006.
Highlighted in Microscopy and Analysis 20:37, 2006.


Rhee JM, Oda-Ishii I, Passamaneck YJ, Hadjantonakis A-K, Di Gregorio A. Live imaging and morphometric analysis of embryonic development in the ascidian, Ciona intestinalis. Genesis 43:136-147, 2005. (Cover)

Passamaneck YJ, Di Gregorio A. Ciona intestinalis: chordate development made simple. Developmental Dynamics 233:1-19, 2005.

Keys DN, Lee B, Di Gregorio A, Harafuji N, Detter C, Wang M, Kahsai O, Ahn S, Zhang Q, Doyle S, Satoh N, Satou Y, Saiga H, Christian A, Rokhsar D, Hawkins T, Levine M, Richardson P. A saturation screen for cis-acting regulatory DNA in the Hox genes of Ciona intestinalis. Proceedings of the National Academy of Sciences (USA) 102:679-683, 2005.


Wada S, Tokuoka M, Shouguchi E, Kobayashi K, Di Gregorio A, Spagnuolo A, Branno M, Di Lauro R, Rokhsar D, Levine M, Kohara Y, Saiga H, Satou Y, Satoh N. A genome wide survey of developmental genes in Ciona intestinalis: (II) genes for homeobox transcription factors. Development Genes and Evolution 213:222-234, 2003.

Spagnuolo A*, Ristoratore F*, Di Gregorio A*, Aniello F, Branno M, Di Lauro R. Unusual number and genomic organization of Hox genes in the tunicate Ciona intestinalis. Gene 309:71-79, 2003. *equal contribution

Previous Publications


Dehal P, Satou Y, Campbell RK, Chapman J, Degnan B, De Tomaso A, Davidson B, Di Gregorio A, et al. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science 298:2157-2167, 2002.

Di Gregorio A, Levine M. Analyzing gene regulation in ascidian embryos: new tools for new perspectives. Review. Differentiation 70:132-139, 2002. (Cover)

Di Gregorio A, Harland RM, Levine M, Casey, ES. Tail morphogenesis in the ascidian, Ciona intestinalis, requires cooperation between notochord and muscle. Developmental Biology 244:385-395, 2002. (Cover)


Di Gregorio A, Levine, M. T-box genes and the development of axial tissues in Ciona intestinalis. In: “Biology of Ascidians”, H. Sawada, H. Yokosawa, and C.C. Lambert eds., Springer-Verlag, Tokyo, 2001.

Corbo JC, Di Gregorio A, Levine M. The ascidian as a model organism in developmental and evolutionary biology. Review. Cell 106:535-538, 2001. 12. Di Gregorio A, Corbo JC, Levine M. The regulation of forkhead/HNF-3beta expression in the Ciona embryo. Developmental Biology 229:31-43, 2001.


Caracciolo A*, Di Gregorio A*, Aniello F, Di Lauro R, Branno M. Identification and developmental expression of three Distal-less homeobox containing genes in the ascidian Ciona intestinalis. Mechanisms of Development 99:173-176, 2000. *equal contribution.


Di Gregorio A, Levine M. Regulation of Ci-tropomyosin-like, a Brachyury target gene in the ascidian, Ciona intestinalis. Development 126:5599-5609, 1999.

Aniello F, Locascio A, Villani MG, Di Gregorio A, Fucci L, Branno M. Identification and developmental expression of Ci-msh-b: a novel homologue of Drosophila msh gene in Ciona intestinalis. Mechanisms of Development 88:123-126, 1999.

Takahashi H, Hotta K, Erives A, Di Gregorio A, Zeller RW, Levine M, Satoh N. Brachyury downstream notochord differentiation in the ascidian embryo. Genes & Development 13:1519-1523, 1999.


Corbo JC, Fujiwara S, Levine M, Di Gregorio A. Suppressor of Hairless activates Brachyury expression in the Ciona embryo. Developmental Biology 203:358-368, 1998.

Di Gregorio A, Levine M. Ascidian embryogenesis and the origins of the chordate body plan. – Review. Current Opinion in Genetics & Development 8:457-463, 1998. (Cover)

Di Gregorio A, Villani MG, Locascio A, Ristoratore F, Aniello F, Branno M. Developmental regulation and tissue-specific localization of calmodulin mRNA in the protochordate Ciona intestinalis. Development Growth and Differentiation 40:387-394, 1998. (Cover)

Gionti M, Ristoratore F, Di Gregorio A, Aniello F, Branno M, Di Lauro, R. Cihox5, a new Ciona intestinalis Hox-related gene, is involved in regionalization of the spinal cord. Development Genes and Evolution 207:515-523, 1998.


Corbo JC, Erives A, Di Gregorio A, Chang A, Levine, M. Dorsoventral patterning of the vertebrate neural tube is conserved in a protochordate. Development 124:2335-2344, 1997.


Di Gregorio A, Spagnuolo A, Ristoratore F, Pischetola M, Aniello F, Branno M, Cariello L, Di Lauro R. Cloning of ascidian homeobox genes provides evidence for a primordial chordate cluster. Gene 156:253-257, 1995.

Fucci L, Piscopo A, Aniello F, Di Gregorio A, Calogero R, Branno M, Geraci G. Cloning and characterization of a developmentally regulated sea urchin cDNA encoding glutamine synthetase. Gene 152:205-208, 1995.  

Published Abstracts

Di Gregorio A, Kugler JE, Oda-Ishii I, Keys DN, Imai JH, DeWan A, Ott J, Richardson PM. Gene regulation in the ancestral notochord: insights from a collection of cis-regulatory elements from the ascidian Ciona intestinalis. Developmental Biology 306:350, 2007.

Di Gregorio A, Silva Casey E, Harland RM, Levine M. Tail morphogenesis in the ascidian, Ciona intestinalis. -- 14th International Congress of Developmental Biology. Kyoto, Japan. Development Growth and Differentiation 43(supplement): S66, 2001.

Giebing T, Langer M, Serwe C, Di Gregorio A, Di Lauro R, D'Haese J. Gelsolin-like proteins from Tunicates-Analytical approach at both protein and DNA level. -- International Meeting on Cell Motility, Firenze, Italy. Journal of Muscle Research and Cell Motility 17:111, 1996.


Recent Publications