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For: Haines JE, Eisen MB. Patterns of chromatin accessibility along the anterior-posterior axis in the early Drosophila embryo. PLoS Genet 2018;14:e1007367. [PMID: 29727464 PMCID: PMC5955596 DOI: 10.1371/journal.pgen.1007367] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 05/16/2018] [Accepted: 04/17/2018] [Indexed: 12/20/2022]  Open
Number Cited by Other Article(s)
1
Cardamone F, Piva A, Löser E, Eichenberger B, Romero-Mulero MC, Zenk F, Shields EJ, Cabezas-Wallscheid N, Bonasio R, Tiana G, Zhan Y, Iovino N. Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis. Nat Commun 2025;16:3007. [PMID: 40148291 PMCID: PMC11950382 DOI: 10.1038/s41467-025-57719-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 03/03/2025] [Indexed: 03/29/2025]  Open
2
Amiri EE, Tenger-Trolander A, Li M, Thomas Julian A, Kasan K, Sanders SA, Blythe S, Schmidt-Ott U. Conservation of symmetry breaking at the level of chromatin accessibility between fly species with unrelated anterior determinants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632851. [PMID: 39868093 PMCID: PMC11760685 DOI: 10.1101/2025.01.13.632851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
3
Albright AR, Yan C, Angeles-Albores D, Makushok T, Allen-Henderson J, Marshall WF. Genome-wide analysis of anterior-posterior mRNA regionalization in Stentor coeruleus reveals a role for the microtubule cytoskeleton. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.09.523364. [PMID: 36711710 PMCID: PMC9882060 DOI: 10.1101/2023.01.09.523364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
4
Ciabrelli F, Atinbayeva N, Pane A, Iovino N. Epigenetic inheritance and gene expression regulation in early Drosophila embryos. EMBO Rep 2024;25:4131-4152. [PMID: 39285248 PMCID: PMC11467379 DOI: 10.1038/s44319-024-00245-z] [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: 02/22/2024] [Revised: 05/13/2024] [Accepted: 08/21/2024] [Indexed: 10/12/2024]  Open
5
Benner L, Muron S, Gomez JG, Oliver B. OVO positively regulates essential maternal pathways by binding near the transcriptional start sites in the Drosophila female germline. eLife 2024;13:RP94631. [PMID: 39291827 PMCID: PMC11410370 DOI: 10.7554/elife.94631] [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] [Indexed: 09/19/2024]  Open
6
Hu Y, Feng B, Wang F. Analysis of maternal effect genes from maternal mRNA in eggs of Sogatella furcifera. Heliyon 2024;10:e34014. [PMID: 39055844 PMCID: PMC11269863 DOI: 10.1016/j.heliyon.2024.e34014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 06/07/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024]  Open
7
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Dev Cell 2023;58:1898-1916.e9. [PMID: 37557175 PMCID: PMC10592203 DOI: 10.1016/j.devcel.2023.07.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 05/09/2023] [Accepted: 07/13/2023] [Indexed: 08/11/2023]
8
Harrison MM, Marsh AJ, Rushlow CA. Setting the stage for development: the maternal-to-zygotic transition in Drosophila. Genetics 2023;225:iyad142. [PMID: 37616526 PMCID: PMC10550319 DOI: 10.1093/genetics/iyad142] [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: 05/18/2023] [Accepted: 07/18/2023] [Indexed: 08/26/2023]  Open
9
Huynh K, Smith BR, Macdonald SJ, Long AD. Genetic variation in chromatin state across multiple tissues in Drosophila melanogaster. PLoS Genet 2023;19:e1010439. [PMID: 37146087 PMCID: PMC10191298 DOI: 10.1371/journal.pgen.1010439] [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: 09/23/2022] [Revised: 05/17/2023] [Accepted: 04/20/2023] [Indexed: 05/07/2023]  Open
10
Dhall JK, Kasturacharya N, Pandit A, Cp L. Optimized protocol for assay for transposase-accessible chromatin by sequencing (ATAC-seq) from Drosophila melanogaster brain tissue. STAR Protoc 2023;4:102153. [PMID: 37074906 PMCID: PMC10148076 DOI: 10.1016/j.xpro.2023.102153] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/11/2023] [Accepted: 02/13/2023] [Indexed: 04/20/2023]  Open
11
Li M, Kasan K, Saha Z, Yoon Y, Schmidt-Ott U. Twenty-seven ZAD-ZNF genes of Drosophila melanogaster are orthologous to the embryo polarity determining mosquito gene cucoid. PLoS One 2023;18:e0274716. [PMID: 36595500 PMCID: PMC9810180 DOI: 10.1371/journal.pone.0274716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/16/2022] [Indexed: 01/04/2023]  Open
12
Iwasaki-Yokozawa S, Nanjo R, Akiyama-Oda Y, Oda H. Lineage-specific, fast-evolving GATA-like gene regulates zygotic gene activation to promote endoderm specification and pattern formation in the Theridiidae spider. BMC Biol 2022;20:223. [PMID: 36203191 PMCID: PMC9535882 DOI: 10.1186/s12915-022-01421-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 09/27/2022] [Indexed: 11/23/2022]  Open
13
Calderon D, Blecher-Gonen R, Huang X, Secchia S, Kentro J, Daza RM, Martin B, Dulja A, Schaub C, Trapnell C, Larschan E, O’Connor-Giles KM, Furlong EEM, Shendure J. The continuum of Drosophila embryonic development at single-cell resolution. Science 2022;377:eabn5800. [PMID: 35926038 PMCID: PMC9371440 DOI: 10.1126/science.abn5800] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
14
Keränen SVE, Villahoz-Baleta A, Bruno AE, Halfon MS. REDfly: An Integrated Knowledgebase for Insect Regulatory Genomics. INSECTS 2022;13:618. [PMID: 35886794 PMCID: PMC9323752 DOI: 10.3390/insects13070618] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/29/2022]
15
Single-nucleus RNA-sequencing in pre-cellularization Drosophila melanogaster embryos. PLoS One 2022;17:e0270471. [PMID: 35749552 PMCID: PMC9232161 DOI: 10.1371/journal.pone.0270471] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 06/10/2022] [Indexed: 12/13/2022]  Open
16
Gong C, Ruan Y, Zhang Y, Wang Q, Wu Y, Zhan X, He Y, Liu X, Liu X, Pu J, Wang X. Resistance of Sogatella furcifera to triflumezopyrim mediated with the overexpression of CYPSF01 which was regulated by nuclear receptor USP. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022;238:113575. [PMID: 35500402 DOI: 10.1016/j.ecoenv.2022.113575] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
17
Grandi FC, Modi H, Kampman L, Corces MR. Chromatin accessibility profiling by ATAC-seq. Nat Protoc 2022;17:1518-1552. [PMID: 35478247 PMCID: PMC9189070 DOI: 10.1038/s41596-022-00692-9] [Citation(s) in RCA: 211] [Impact Index Per Article: 70.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022]
18
Merrill CB, Pabon MA, Montgomery AB, Rodan AR, Rothenfluh A. Optimized assay for transposase-accessible chromatin by sequencing (ATAC-seq) library preparation from adult Drosophila melanogaster neurons. Sci Rep 2022;12:6043. [PMID: 35411004 PMCID: PMC9001676 DOI: 10.1038/s41598-022-09869-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 03/14/2022] [Indexed: 01/07/2023]  Open
19
Schmidt-Ott U, Yoon Y. Evolution and loss of ß-catenin and TCF-dependent axis specification in insects. CURRENT OPINION IN INSECT SCIENCE 2022;50:100877. [PMID: 35104659 PMCID: PMC9133022 DOI: 10.1016/j.cois.2022.100877] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
20
Lucas T, Hafer TL, Zhang HG, Molotkova N, Kohwi M. Discrete cis-acting element regulates developmentally timed gene-lamina relocation and neural progenitor competence in vivo. Dev Cell 2021;56:2649-2663.e6. [PMID: 34529940 PMCID: PMC8629127 DOI: 10.1016/j.devcel.2021.08.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/24/2021] [Accepted: 08/20/2021] [Indexed: 01/21/2023]
21
Asma H, Halfon MS. Annotating the Insect Regulatory Genome. INSECTS 2021;12:591. [PMID: 34209769 PMCID: PMC8305585 DOI: 10.3390/insects12070591] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 11/17/2022]
22
Liu J, Hansen D, Eck E, Kim YJ, Turner M, Alamos S, Garcia HG. Real-time single-cell characterization of the eukaryotic transcription cycle reveals correlations between RNA initiation, elongation, and cleavage. PLoS Comput Biol 2021;17:e1008999. [PMID: 34003867 PMCID: PMC8162642 DOI: 10.1371/journal.pcbi.1008999] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 05/28/2021] [Accepted: 04/23/2021] [Indexed: 12/23/2022]  Open
23
Fan T, Huang Y. Accessible chromatin reveals regulatory mechanisms underlying cell fate decisions during early embryogenesis. Sci Rep 2021;11:7896. [PMID: 33846424 PMCID: PMC8042068 DOI: 10.1038/s41598-021-86919-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 03/22/2021] [Indexed: 02/01/2023]  Open
24
Arguello JR, Abuin L, Armida J, Mika K, Chai PC, Benton R. Targeted molecular profiling of rare olfactory sensory neurons identifies fate, wiring, and functional determinants. eLife 2021;10:63036. [PMID: 33666172 PMCID: PMC7993999 DOI: 10.7554/elife.63036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 03/04/2021] [Indexed: 02/06/2023]  Open
25
Reddington JP, Garfield DA, Sigalova OM, Karabacak Calviello A, Marco-Ferreres R, Girardot C, Viales RR, Degner JF, Ohler U, Furlong EEM. Lineage-Resolved Enhancer and Promoter Usage during a Time Course of Embryogenesis. Dev Cell 2020;55:648-664.e9. [PMID: 33171098 DOI: 10.1016/j.devcel.2020.10.009] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Revised: 08/04/2020] [Accepted: 10/09/2020] [Indexed: 02/01/2023]
26
Cartwright EL, Lott SE. Evolved Differences in cis and trans Regulation Between the Maternal and Zygotic mRNA Complements in the Drosophila Embryo. Genetics 2020;216:805-821. [PMID: 32928902 PMCID: PMC7648588 DOI: 10.1534/genetics.120.303626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 08/26/2020] [Indexed: 11/18/2022]  Open
27
Serizay J, Dong Y, Jänes J, Chesney M, Cerrato C, Ahringer J. Distinctive regulatory architectures of germline-active and somatic genes in C. elegans. Genome Res 2020;30:1752-1765. [PMID: 33093068 PMCID: PMC7706728 DOI: 10.1101/gr.265934.120] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 10/08/2020] [Indexed: 01/08/2023]
28
Soluri IV, Zumerling LM, Payan Parra OA, Clark EG, Blythe SA. Zygotic pioneer factor activity of Odd-paired/Zic is necessary for late function of the Drosophila segmentation network. eLife 2020;9:e53916. [PMID: 32347792 PMCID: PMC7190358 DOI: 10.7554/elife.53916] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 03/29/2020] [Indexed: 12/20/2022]  Open
29
Bozek M, Gompel N. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity. Bioessays 2020;42:e1900188. [PMID: 32142172 DOI: 10.1002/bies.201900188] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/21/2022]
30
Pálfy M, Schulze G, Valen E, Vastenhouw NL. Chromatin accessibility established by Pou5f3, Sox19b and Nanog primes genes for activity during zebrafish genome activation. PLoS Genet 2020;16:e1008546. [PMID: 31940339 PMCID: PMC6986763 DOI: 10.1371/journal.pgen.1008546] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/28/2020] [Accepted: 12/02/2019] [Indexed: 12/12/2022]  Open
31
Garcia HG, Berrocal A, Kim YJ, Martini G, Zhao J. Lighting up the central dogma for predictive developmental biology. Curr Top Dev Biol 2019;137:1-35. [PMID: 32143740 DOI: 10.1016/bs.ctdb.2019.10.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
32
Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U, Gompel N. ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Res 2019;29:771-783. [PMID: 30962180 PMCID: PMC6499308 DOI: 10.1101/gr.242362.118] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
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