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For: Trinh LA, Chong-Morrison V, Gavriouchkina D, Hochgreb-Hägele T, Senanayake U, Fraser SE, Sauka-Spengler T. Biotagging of Specific Cell Populations in Zebrafish Reveals Gene Regulatory Logic Encoded in the Nuclear Transcriptome. Cell Rep 2017;19:425-440. [PMID: 28402863 PMCID: PMC5400779 DOI: 10.1016/j.celrep.2017.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 12/21/2016] [Accepted: 03/13/2017] [Indexed: 11/22/2022]  Open
Number Cited by Other Article(s)
1
Shah AN, Leesch F, Lorenzo-Orts L, Grundmann L, Novatchkova M, Haselbach D, Calo E, Pauli A. A dual ribosomal system in the zebrafish soma and germline. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.29.610041. [PMID: 39257781 PMCID: PMC11383705 DOI: 10.1101/2024.08.29.610041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2024]
2
Gillespie W, Zhang Y, Ruiz OE, Cerda J, Ortiz-Guzman J, Turner WD, Largoza G, Sherman M, Mosser LE, Fujimoto E, Chien CB, Kwan KM, Arenkiel BR, Devine WP, Wythe JD. Multisite Assembly of Gateway Induced Clones (MAGIC): a flexible cloning toolbox with diverse applications in vertebrate model systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.13.603267. [PMID: 39026881 PMCID: PMC11257631 DOI: 10.1101/2024.07.13.603267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
3
Weinberger M, Simões FC, Gungoosingh T, Sauka-Spengler T, Riley PR. Distinct epicardial gene regulatory programs drive development and regeneration of the zebrafish heart. Dev Cell 2024;59:351-367.e6. [PMID: 38237592 DOI: 10.1016/j.devcel.2023.12.012] [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: 08/05/2022] [Revised: 08/12/2023] [Accepted: 12/20/2023] [Indexed: 02/08/2024]
4
Chong-Morrison V, Mayes S, Simões FC, Senanayake U, Carroll DS, Riley PR, Wilson SW, Sauka-Spengler T. Ac/Ds transposition for CRISPR/dCas9-SID4x epigenome modulation in zebrafish. Biol Open 2023;12:bio059995. [PMID: 37367831 PMCID: PMC10320716 DOI: 10.1242/bio.059995] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023]  Open
5
Tornini VA, Miao L, Lee HJ, Gerson T, Dube SE, Schmidt V, Kroll F, Tang Y, Du K, Kuchroo M, Vejnar CE, Bazzini AA, Krishnaswamy S, Rihel J, Giraldez AJ. linc-mipep and linc-wrb encode micropeptides that regulate chromatin accessibility in vertebrate-specific neural cells. eLife 2023;12:e82249. [PMID: 37191016 PMCID: PMC10188112 DOI: 10.7554/elife.82249] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]  Open
6
Wang P, Kitano M, Keomanee-Dizon K, Truong TV, Fraser SE, Cutrale F. A single-shot hyperspectral phasor camera for fast, multi-color fluorescence microscopy. CELL REPORTS METHODS 2023;3:100441. [PMID: 37159674 PMCID: PMC10162951 DOI: 10.1016/j.crmeth.2023.100441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 11/16/2022] [Accepted: 03/09/2023] [Indexed: 05/11/2023]
7
Chen HJ, Barske L, Talbot JC, Dinwoodie OM, Roberts RR, Farmer DT, Jimenez C, Merrill AE, Tucker AS, Crump JG. Nuclear receptor Nr5a2 promotes diverse connective tissue fates in the jaw. Dev Cell 2023;58:461-473.e7. [PMID: 36905926 PMCID: PMC10050118 DOI: 10.1016/j.devcel.2023.02.011] [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: 09/15/2022] [Revised: 01/06/2023] [Accepted: 02/17/2023] [Indexed: 03/12/2023]
8
Collective cell migration during optic cup formation features changing cell-matrix interactions linked to matrix topology. Curr Biol 2022;32:4817-4831.e9. [PMID: 36208624 DOI: 10.1016/j.cub.2022.09.034] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 07/28/2022] [Accepted: 09/16/2022] [Indexed: 11/22/2022]
9
Pelea O, Fulga TA, Sauka-Spengler T. RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications. CRISPR J 2022;5:642-659. [PMID: 36206027 PMCID: PMC9618385 DOI: 10.1089/crispr.2022.0052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 08/17/2022] [Indexed: 01/31/2023]  Open
10
Candido-Ferreira IL, Lukoseviciute M, Sauka-Spengler T. Multi-layered transcriptional control of cranial neural crest development. Semin Cell Dev Biol 2022;138:1-14. [PMID: 35941042 DOI: 10.1016/j.semcdb.2022.07.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/23/2022] [Accepted: 07/23/2022] [Indexed: 11/28/2022]
11
Stream A, Madigan CA. Zebrafish: an underutilized tool for discovery in host-microbe interactions. Trends Immunol 2022;43:426-437. [PMID: 35527182 PMCID: PMC11302990 DOI: 10.1016/j.it.2022.03.011] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 03/31/2022] [Accepted: 03/31/2022] [Indexed: 12/31/2022]
12
Cunningham RL, Kramer ET, DeGeorgia SK, Godoy PM, Zarov AP, Seneviratne S, Grigura V, Kaufman CK. Functional in vivo characterization of sox10 enhancers in neural crest and melanoma development. Commun Biol 2021;4:695. [PMID: 34099848 PMCID: PMC8184803 DOI: 10.1038/s42003-021-02211-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 05/11/2021] [Indexed: 02/05/2023]  Open
13
Artinger KB, Monsoro-Burq AH. Neural crest multipotency and specification: power and limits of single cell transcriptomic approaches. Fac Rev 2021;10:38. [PMID: 34046642 PMCID: PMC8130411 DOI: 10.12703/r/10-38] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
14
Figiel DM, Elsayed R, Nelson AC. Investigating the molecular guts of endoderm formation using zebrafish. Brief Funct Genomics 2021:elab013. [PMID: 33754635 DOI: 10.1093/bfgp/elab013] [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] [Received: 11/14/2020] [Revised: 01/27/2021] [Accepted: 02/19/2021] [Indexed: 02/07/2023]  Open
15
Chong-Morrison V, Sauka-Spengler T. The Cranial Neural Crest in a Multiomics Era. Front Physiol 2021;12:634440. [PMID: 33732166 PMCID: PMC7956944 DOI: 10.3389/fphys.2021.634440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/08/2021] [Indexed: 01/01/2023]  Open
16
Lukoseviciute M, Ling ITC, Senanayake U, Candido-Ferreira I, Taylor G, Williams RM, Sauka-Spengler T. Tissue-Specific In Vivo Biotin Chromatin Immunoprecipitation with Sequencing in Zebrafish and Chicken. STAR Protoc 2020;1:100066. [PMID: 33111104 PMCID: PMC7580215 DOI: 10.1016/j.xpro.2020.100066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]  Open
17
Weinberger M, Simões FC, Patient R, Sauka-Spengler T, Riley PR. Functional Heterogeneity within the Developing Zebrafish Epicardium. Dev Cell 2020;52:574-590.e6. [PMID: 32084358 PMCID: PMC7063573 DOI: 10.1016/j.devcel.2020.01.023] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 12/07/2019] [Accepted: 01/22/2020] [Indexed: 12/31/2022]
18
Simões FC, Cahill TJ, Kenyon A, Gavriouchkina D, Vieira JM, Sun X, Pezzolla D, Ravaud C, Masmanian E, Weinberger M, Mayes S, Lemieux ME, Barnette DN, Gunadasa-Rohling M, Williams RM, Greaves DR, Trinh LA, Fraser SE, Dallas SL, Choudhury RP, Sauka-Spengler T, Riley PR. Macrophages directly contribute collagen to scar formation during zebrafish heart regeneration and mouse heart repair. Nat Commun 2020;11:600. [PMID: 32001677 PMCID: PMC6992796 DOI: 10.1038/s41467-019-14263-2] [Citation(s) in RCA: 269] [Impact Index Per Article: 53.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 12/27/2019] [Indexed: 12/14/2022]  Open
19
Hockman D, Chong-Morrison V, Green SA, Gavriouchkina D, Candido-Ferreira I, Ling ITC, Williams RM, Amemiya CT, Smith JJ, Bronner ME, Sauka-Spengler T. A genome-wide assessment of the ancestral neural crest gene regulatory network. Nat Commun 2019;10:4689. [PMID: 31619682 PMCID: PMC6795873 DOI: 10.1038/s41467-019-12687-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 09/23/2019] [Indexed: 12/17/2022]  Open
20
Shin M, Nozaki T, Idrizi F, Isogai S, Ogasawara K, Ishida K, Yuge S, Roscoe B, Wolfe SA, Fukuhara S, Mochizuki N, Deguchi T, Lawson ND. Valves Are a Conserved Feature of the Zebrafish Lymphatic System. Dev Cell 2019;51:374-386.e5. [PMID: 31564611 DOI: 10.1016/j.devcel.2019.08.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Revised: 05/19/2019] [Accepted: 08/28/2019] [Indexed: 12/19/2022]
21
Dooley CM, Wali N, Sealy IM, White RJ, Stemple DL, Collins JE, Busch-Nentwich EM. The gene regulatory basis of genetic compensation during neural crest induction. PLoS Genet 2019;15:e1008213. [PMID: 31199790 PMCID: PMC6594659 DOI: 10.1371/journal.pgen.1008213] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 06/26/2019] [Accepted: 05/27/2019] [Indexed: 12/15/2022]  Open
22
Lukoseviciute M, Gavriouchkina D, Williams RM, Hochgreb-Hagele T, Senanayake U, Chong-Morrison V, Thongjuea S, Repapi E, Mead A, Sauka-Spengler T. From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo. Dev Cell 2019;47:608-628.e6. [PMID: 30513303 PMCID: PMC6286384 DOI: 10.1016/j.devcel.2018.11.009] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Revised: 08/15/2018] [Accepted: 10/31/2018] [Indexed: 02/06/2023]
23
Prasad MS, Charney RM, García-Castro MI. Specification and formation of the neural crest: Perspectives on lineage segregation. Genesis 2019;57:e23276. [PMID: 30576078 PMCID: PMC6570420 DOI: 10.1002/dvg.23276] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2018] [Revised: 12/17/2018] [Accepted: 12/18/2018] [Indexed: 12/21/2022]
24
Trinh LA, Chong-Morrison V, Sauka-Spengler T. Biotagging, an in vivo biotinylation approach for cell-type specific subcellular profiling in zebrafish. Methods 2018;150:24-31. [DOI: 10.1016/j.ymeth.2018.07.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 07/16/2018] [Accepted: 07/30/2018] [Indexed: 12/21/2022]  Open
25
Rogers CD, Nie S. Specifying neural crest cells: From chromatin to morphogens and factors in between. WILEY INTERDISCIPLINARY REVIEWS. DEVELOPMENTAL BIOLOGY 2018;7:e322. [PMID: 29722151 PMCID: PMC6215528 DOI: 10.1002/wdev.322] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 03/26/2018] [Accepted: 03/27/2018] [Indexed: 12/16/2022]
26
Gurevich DB, Severn CE, Twomey C, Greenhough A, Cash J, Toye AM, Mellor H, Martin P. Live imaging of wound angiogenesis reveals macrophage orchestrated vessel sprouting and regression. EMBO J 2018;37:embj.201797786. [PMID: 29866703 PMCID: PMC6028026 DOI: 10.15252/embj.201797786] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 04/25/2018] [Accepted: 04/30/2018] [Indexed: 12/21/2022]  Open
27
Schneider RA. Neural crest and the origin of species-specific pattern. Genesis 2018;56:e23219. [PMID: 30134069 PMCID: PMC6108449 DOI: 10.1002/dvg.23219] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
28
Kenyon A, Gavriouchkina D, Zorman J, Chong-Morrison V, Napolitani G, Cerundolo V, Sauka-Spengler T. Generation of a double binary transgenic zebrafish model to study myeloid gene regulation in response to oncogene activation in melanocytes. Dis Model Mech 2018;11:dmm030056. [PMID: 29666124 PMCID: PMC5963855 DOI: 10.1242/dmm.030056] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 02/01/2018] [Indexed: 12/11/2022]  Open
29
Quillien A, Abdalla M, Yu J, Ou J, Zhu LJ, Lawson ND. Robust Identification of Developmentally Active Endothelial Enhancers in Zebrafish Using FANS-Assisted ATAC-Seq. Cell Rep 2018;20:709-720. [PMID: 28723572 DOI: 10.1016/j.celrep.2017.06.070] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Revised: 06/08/2017] [Accepted: 06/22/2017] [Indexed: 02/08/2023]  Open
30
Ackerman CM, Weber PK, Xiao T, Thai B, Kuo TJ, Zhang E, Pett-Ridge J, Chang CJ. Multimodal LA-ICP-MS and nanoSIMS imaging enables copper mapping within photoreceptor megamitochondria in a zebrafish model of Menkes disease. Metallomics 2018;10:474-485. [PMID: 29507920 DOI: 10.1039/c7mt00349h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
31
White RJ, Collins JE, Sealy IM, Wali N, Dooley CM, Digby Z, Stemple DL, Murphy DN, Billis K, Hourlier T, Füllgrabe A, Davis MP, Enright AJ, Busch-Nentwich EM. A high-resolution mRNA expression time course of embryonic development in zebrafish. eLife 2017;6. [PMID: 29144233 PMCID: PMC5690287 DOI: 10.7554/elife.30860] [Citation(s) in RCA: 237] [Impact Index Per Article: 29.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/04/2017] [Indexed: 12/18/2022]  Open
32
Martik ML, Bronner ME. Regulatory Logic Underlying Diversification of the Neural Crest. Trends Genet 2017;33:715-727. [PMID: 28851604 DOI: 10.1016/j.tig.2017.07.015] [Citation(s) in RCA: 127] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 12/29/2022]
33
Kenyon A, Gavriouchkina D, Zorman J, Napolitani G, Cerundolo V, Sauka-Spengler T. Active nuclear transcriptome analysis reveals inflammasome-dependent mechanism for early neutrophil response to Mycobacterium marinum. Sci Rep 2017;7:6505. [PMID: 28747644 PMCID: PMC5529371 DOI: 10.1038/s41598-017-06099-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 06/07/2017] [Indexed: 12/17/2022]  Open
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