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For: José-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 Genet 2015;11:e1005730. [PMID: 26684323 PMCID: PMC4684326 DOI: 10.1371/journal.pgen.1005730] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/16/2015] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Negrón-Piñeiro LJ, Wu Y, Popsuj S, José-Edwards DS, Stolfi A, Di Gregorio A. Cis-regulatory interfaces reveal the molecular mechanisms underlying the notochord gene regulatory network of Ciona. Nat Commun 2024;15:3025. [PMID: 38589372 PMCID: PMC11001920 DOI: 10.1038/s41467-024-46850-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 03/12/2024] [Indexed: 04/10/2024]  Open
2
Chen S, Lei Y, Yang Y, Liu C, Kuang L, Jin L, Finnell RH, Yang X, Wang H. A mutation in TBXT causes congenital vertebral malformations in humans and mice. J Genet Genomics 2024;51:433-442. [PMID: 37751845 DOI: 10.1016/j.jgg.2023.09.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 09/14/2023] [Accepted: 09/16/2023] [Indexed: 09/28/2023]
3
Di Gregorio A. Searching for marine embryos, finding my path. Genesis 2023;61:e23576. [PMID: 37994390 PMCID: PMC10773608 DOI: 10.1002/dvg.23576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/03/2023] [Accepted: 11/04/2023] [Indexed: 11/24/2023]
4
Lin P, Yan P, Zhu J, Huang S, Wang Z, Hu O, Jin H, Li Y, Zhang L, Zhao J, Chen L, Liu B, He J, Gan Y, Liu P. Spatially multicellular variability of intervertebral disc degeneration by comparative single-cell analysis. Cell Prolif 2023;56:e13464. [PMID: 37025067 PMCID: PMC10542621 DOI: 10.1111/cpr.13464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/10/2023] [Accepted: 03/20/2023] [Indexed: 04/08/2023]  Open
5
Oh SY, Na SB, Kang YK, Do JT. In Vitro Embryogenesis and Gastrulation Using Stem Cells in Mice and Humans. Int J Mol Sci 2023;24:13655. [PMID: 37686459 PMCID: PMC10563085 DOI: 10.3390/ijms241713655] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 08/29/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023]  Open
6
Song BP, Ragsac MF, Tellez K, Jindal GA, Grudzien JL, Le SH, Farley EK. Diverse logics and grammar encode notochord enhancers. Cell Rep 2023;42:112052. [PMID: 36729834 PMCID: PMC10387507 DOI: 10.1016/j.celrep.2023.112052] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/07/2022] [Accepted: 01/17/2023] [Indexed: 02/03/2023]  Open
7
Amadei G, Handford CE, Qiu C, De Jonghe J, Greenfeld H, Tran M, Martin BK, Chen DY, Aguilera-Castrejon A, Hanna JH, Elowitz MB, Hollfelder F, Shendure J, Glover DM, Zernicka-Goetz M. Embryo model completes gastrulation to neurulation and organogenesis. Nature 2022;610:143-153. [PMID: 36007540 PMCID: PMC9534772 DOI: 10.1038/s41586-022-05246-3] [Citation(s) in RCA: 106] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 08/17/2022] [Indexed: 11/23/2022]
8
Liu G, Yang G, Zhao G, Guo C, Zeng Y, Xue Y, Zeng F. Spatial transcriptomic profiling to identify mesoderm progenitors with precision genomic screening and functional confirmation. Cell Prolif 2022;55:e13298. [PMID: 35906841 PMCID: PMC9528766 DOI: 10.1111/cpr.13298] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/30/2022]  Open
9
Wu Y, Devotta A, José-Edwards DS, Kugler JE, Negrón-Piñeiro LJ, Braslavskaya K, Addy J, Saint-Jeannet JP, Di Gregorio A. Xbp1 and Brachyury establish an evolutionarily conserved subcircuit of the notochord gene regulatory network. eLife 2022;11:e73992. [PMID: 35049502 PMCID: PMC8803312 DOI: 10.7554/elife.73992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/19/2022] [Indexed: 11/13/2022]  Open
10
Marotta P, Salatiello F, Ambrosino L, Berruto F, Chiusano ML, Locascio A. The Ascidia Ciona robusta Provides Novel Insights on the Evolution of the AP-1 Transcriptional Complex. Front Cell Dev Biol 2021;9:709696. [PMID: 34414189 PMCID: PMC8369891 DOI: 10.3389/fcell.2021.709696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/12/2021] [Indexed: 11/13/2022]  Open
11
Gan Y, He J, Zhu J, Xu Z, Wang Z, Yan J, Hu O, Bai Z, Chen L, Xie Y, Jin M, Huang S, Liu B, Liu P. Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs. Bone Res 2021;9:37. [PMID: 34400611 PMCID: PMC8368097 DOI: 10.1038/s41413-021-00163-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/30/2021] [Accepted: 06/10/2021] [Indexed: 02/07/2023]  Open
12
Gan Y, He J, Zhu J, Xu Z, Wang Z, Yan J, Hu O, Bai Z, Chen L, Xie Y, Jin M, Huang S, Liu B, Liu P. Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs. Bone Res 2021;9:37. [PMID: 34400611 PMCID: PMC8368097 DOI: 10.1038/s41413-021-00163-z+10.1038/s41413-021-00163-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 04/30/2021] [Accepted: 06/10/2021] [Indexed: 01/21/2024]  Open
13
Spatially defined single-cell transcriptional profiling characterizes diverse chondrocyte subtypes and nucleus pulposus progenitors in human intervertebral discs. Bone Res 2021;9:37. [PMID: 34400611 PMCID: PMC8368097 DOI: 10.1038/s41413-021-00163-z 10.1038/s41413-021-00163-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]  Open
14
Oonuma K, Yamamoto M, Moritsugu N, Okawa N, Mukai M, Sotani M, Tsunemi S, Sugimoto H, Nakagome E, Hasegawa Y, Shimai K, Horie T, Kusakabe TG. Evolution of Developmental Programs for the Midline Structures in Chordates: Insights From Gene Regulation in the Floor Plate and Hypochord Homologues of Ciona Embryos. Front Cell Dev Biol 2021;9:704367. [PMID: 34235159 PMCID: PMC8256262 DOI: 10.3389/fcell.2021.704367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 05/25/2021] [Indexed: 11/24/2022]  Open
15
Reeves WM, Shimai K, Winkley KM, Veeman MT. Brachyury controls Ciona notochord fate as part of a feed-forward network. Development 2021;148:dev195230. [PMID: 33419874 PMCID: PMC7875503 DOI: 10.1242/dev.195230] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/18/2020] [Indexed: 12/22/2022]
16
Coulcher JF, Roure A, Chowdhury R, Robert M, Lescat L, Bouin A, Carvajal Cadavid J, Nishida H, Darras S. Conservation of peripheral nervous system formation mechanisms in divergent ascidian embryos. eLife 2020;9:e59157. [PMID: 33191918 PMCID: PMC7710358 DOI: 10.7554/elife.59157] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 11/13/2020] [Indexed: 01/23/2023]  Open
17
Transcription Factors of the bHLH Family Delineate Vertebrate Landmarks in the Nervous System of a Simple Chordate. Genes (Basel) 2020;11:genes11111262. [PMID: 33114624 PMCID: PMC7693978 DOI: 10.3390/genes11111262] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 10/12/2020] [Indexed: 02/07/2023]  Open
18
Tessier S, Risbud MV. Understanding embryonic development for cell-based therapies of intervertebral disc degeneration: Toward an effort to treat disc degeneration subphenotypes. Dev Dyn 2020;250:302-317. [PMID: 32564440 DOI: 10.1002/dvdy.217] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/09/2020] [Accepted: 06/14/2020] [Indexed: 12/19/2022]  Open
19
Prummel KD, Nieuwenhuize S, Mosimann C. The lateral plate mesoderm. Development 2020;147:147/12/dev175059. [PMID: 32561665 PMCID: PMC7328003 DOI: 10.1242/dev.175059] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
20
Di Gregorio A. The notochord gene regulatory network in chordate evolution: Conservation and divergence from Ciona to vertebrates. Curr Top Dev Biol 2020;139:325-374. [PMID: 32450965 DOI: 10.1016/bs.ctdb.2020.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
21
Irvine SQ, McNulty KB, Siler EM, Jacobson RE. High temperature limits on developmental canalization in the ascidian Ciona intestinalis. Mech Dev 2019;157:10-21. [DOI: 10.1016/j.mod.2019.04.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 04/03/2019] [Accepted: 04/18/2019] [Indexed: 01/28/2023]
22
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. Dev Biol 2019;448:119-135. [PMID: 30661645 DOI: 10.1016/j.ydbio.2019.01.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 12/27/2018] [Accepted: 01/01/2019] [Indexed: 11/26/2022]
23
Harder M, Reeves W, Byers C, Santiago M, Veeman M. Multiple inputs into a posterior-specific regulatory network in the Ciona notochord. Dev Biol 2018;448:136-146. [PMID: 30287118 DOI: 10.1016/j.ydbio.2018.09.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 09/04/2018] [Accepted: 09/28/2018] [Indexed: 11/28/2022]
24
Maguire JE, Pandey A, Wu Y, Di Gregorio A. Investigating Evolutionarily Conserved Molecular Mechanisms Controlling Gene Expression in the Notochord. TRANSGENIC ASCIDIANS 2018. [DOI: 10.1007/978-981-10-7545-2_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
25
Reeves WM, Wu Y, Harder MJ, Veeman MT. Functional and evolutionary insights from the Ciona notochord transcriptome. Development 2017;144:3375-3387. [PMID: 28928284 DOI: 10.1242/dev.156174] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/01/2017] [Indexed: 12/13/2022]
26
Cooperation Between T-Box Factors Regulates the Continuous Segregation of Germ Layers During Vertebrate Embryogenesis. Curr Top Dev Biol 2017;122:117-159. [DOI: 10.1016/bs.ctdb.2016.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
27
Di Gregorio A. T-Box Genes and Developmental Gene Regulatory Networks in Ascidians. Curr Top Dev Biol 2016;122:55-91. [PMID: 28057272 DOI: 10.1016/bs.ctdb.2016.08.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
28
Bernadskaya Y, Christiaen L. Transcriptional Control of Developmental Cell Behaviors. Annu Rev Cell Dev Biol 2016;32:77-101. [DOI: 10.1146/annurev-cellbio-111315-125218] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
29
Segade F, Cota C, Famiglietti A, Cha A, Davidson B. Fibronectin contributes to notochord intercalation in the invertebrate chordate, Ciona intestinalis. EvoDevo 2016;7:21. [PMID: 27583126 PMCID: PMC5006582 DOI: 10.1186/s13227-016-0056-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Accepted: 08/13/2016] [Indexed: 12/24/2022]  Open
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