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For: 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] [What about the content of this article? (0)] [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
Number Cited by Other Article(s)
1
Negrón-Piñeiro LJ, Di Gregorio A. Single-cell Transcriptomic Studies Unveil Potential Nodes of the Notochord Gene Regulatory Network. Integr Comp Biol 2024;64:1194-1213. [PMID: 38914463 PMCID: PMC11579531 DOI: 10.1093/icb/icae084] [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: 03/31/2024] [Revised: 06/01/2024] [Accepted: 06/16/2024] [Indexed: 06/26/2024]  Open
2
Jindal GA, Lim F, Tellez K, Song BP, Bantle AT, Farley EK. Protocol to electroporate DNA plasmids into Ciona robusta embryos at the 1-cell stage. STAR Protoc 2024;5:103107. [PMID: 38963758 PMCID: PMC11269276 DOI: 10.1016/j.xpro.2024.103107] [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: 07/28/2023] [Revised: 03/20/2024] [Accepted: 05/13/2024] [Indexed: 07/06/2024]  Open
3
Jores T, Tonnies J, Mueth NA, Romanowski A, Fields S, Cuperus JT, Queitsch C. Plant enhancers exhibit both cooperative and additive interactions among their functional elements. THE PLANT CELL 2024;36:2570-2586. [PMID: 38513612 PMCID: PMC11218779 DOI: 10.1093/plcell/koae088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/16/2024] [Accepted: 03/04/2024] [Indexed: 03/23/2024]
4
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
5
Warin J, Vedrenne N, Tam V, Zhu M, Yin D, Lin X, Guidoux-D’halluin B, Humeau A, Roseiro L, Paillat L, Chédeville C, Chariau C, Riemers F, Templin M, Guicheux J, Tryfonidou MA, Ho JW, David L, Chan D, Camus A. In vitro and in vivo models define a molecular signature reference for human embryonic notochordal cells. iScience 2024;27:109018. [PMID: 38357665 PMCID: PMC10865399 DOI: 10.1016/j.isci.2024.109018] [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: 08/11/2023] [Revised: 11/13/2023] [Accepted: 01/22/2024] [Indexed: 02/16/2024]  Open
6
Pickett CJ, Gruner HN, Davidson B. Lhx3/4 initiates a cardiopharyngeal-specific transcriptional program in response to widespread FGF signaling. PLoS Biol 2024;22:e3002169. [PMID: 38271304 PMCID: PMC10810493 DOI: 10.1371/journal.pbio.3002169] [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: 05/04/2023] [Accepted: 12/21/2023] [Indexed: 01/27/2024]  Open
7
Schifferl D, Scholze-Wittler M, Villaronga Luque A, Pustet M, Wittler L, Veenvliet JV, Koch F, Herrmann BG. Genome-wide identification of notochord enhancers comprising the regulatory landscape of the brachyury locus in mouse. Development 2023;150:dev202111. [PMID: 37882764 PMCID: PMC10651091 DOI: 10.1242/dev.202111] [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: 06/22/2023] [Accepted: 10/17/2023] [Indexed: 10/27/2023]
8
Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK. Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. Dev Cell 2023;58:2206-2216.e5. [PMID: 37848026 PMCID: PMC10720985 DOI: 10.1016/j.devcel.2023.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 06/07/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023]
9
Farley EK. Ciona, an ideal research organism to study the role of enhancers. Genesis 2023;61:e23577. [PMID: 38009359 DOI: 10.1002/dvg.23577] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/02/2023] [Accepted: 11/03/2023] [Indexed: 11/28/2023]
10
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancers control notochord expression of vertebrate Brachyury. Nat Commun 2023;14:6594. [PMID: 37852970 PMCID: PMC10584899 DOI: 10.1038/s41467-023-42151-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023]  Open
11
Kemmler CL, Smolikova J, Moran HR, Mannion BJ, Knapp D, Lim F, Czarkwiani A, Hermosilla Aguayo V, Rapp V, Fitch OE, Bötschi S, Selleri L, Farley E, Braasch I, Yun M, Visel A, Osterwalder M, Mosimann C, Kozmik Z, Burger A. Conserved enhancer logic controls the notochord expression of vertebrate Brachyury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.20.536761. [PMID: 37131681 PMCID: PMC10153258 DOI: 10.1101/2023.04.20.536761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
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