Unmasking Activation of the Zygotic Genome Using Chromosomal Deletions in the Drosophila Embryo

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R., Carey, V., Bates, D., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome Biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 13,133 · see citing works

WebLogo: A Sequence Logo Generator: Figure 1Preprint

Crooks, G. E., Hon, G. C., Chandonia, J., & Brenner, S. E. (2004) · Genome Research · doi:10.1101/gr.849004 · Cited by 12,433 · see citing works

Targeted gene expression as a means of altering cell fates and generating dominant phenotypes

Brand, A. H., & Perrimon, N. (1993) · Development · doi:10.1242/dev.118.2.401 · Cited by 9,510 · see citing works

miRBase: microRNA sequences, targets and gene nomenclature

Griffiths‐Jones, S. (2005) · Nucleic Acids Research · doi:10.1093/nar/gkj112 · Cited by 4,713 · see citing works

A conserved AU sequence from the 3′ untranslated region of GM-CSF mRNA mediates selective mRNA degradation

Shaw, G. D., & Kamen, R. (1986) · Cell · doi:10.1016/0092-8674(86)90341-7 · Cited by 3,946 · see citing works

A Bayesian framework for the analysis of microarray expression data: regularized t -test and statistical inferences of gene changes

Baldi, P., & Long, A. D. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.6.509 · Cited by 1,622 · see citing works

Zebrafish MiR-430 Promotes Deadenylation and Clearance of Maternal mRNAs

Giraldez, A. J., Mishima, Y., Rihel, J., Grocock, R. J., Van Dongen, S., Inoue, K., Enright, A. J., & Schier, A. F. (2006) · Science · doi:10.1126/science.1122689 · Cited by 1,436 · see citing works

Demethylation of the zygotic paternal genome

Mayer, W., Niveleau, A., Walter, J., Fundele, R. H., & Haaf, T. (2000) · Nature · doi:10.1038/35000656 · Cited by 1,330 · see citing works

A major developmental transition in early xenopus embryos: II. control of the onset of transcription

Newport, J., & Kirschner, M. (1982) · Cell · doi:10.1016/0092-8674(82)90273-2 · Cited by 1,055 · see citing works

The bicoid protein determines position in the Drosophila embryo in a concentration-dependent manner

Driever, W., & Nüsslein‐Volhard, C. (1988) · Cell · doi:10.1016/0092-8674(88)90183-3 · Cited by 1,019 · see citing works

Gene Expression During the Life Cycle of Drosophila melanogaster

Arbeitman, M. N., Furlong, E. E. M., Imam, F. B., Johnson, E. A., Null, B. H., Baker, B. S., Krasnow, M. A., Scott, M. P., Davis, R. W., & White, K. P. (2002) · Science · doi:10.1126/science.1072152 · Cited by 926 · see citing works

Dynamics of Global Gene Expression Changes during Mouse Preimplantation Development

Hamatani, T., Carter, M. G., Sharov, A. A., & Ko, M. S. H. (2004) · Developmental Cell · doi:10.1016/s1534-5807(03)00373-3 · Cited by 879 · see citing works

Involvement of MicroRNA in AU-Rich Element-Mediated mRNA Instability

Jing, Q., Huang, S., Guth, S., Zarubin, T., Motoyama, A. B., Chen, J., Padova, F. D., Lin, S., Gram, H., & Han, J. (2005) · Cell · doi:10.1016/j.cell.2004.12.038 · Cited by 849 · see citing works

Systematic determination of patterns of gene expression during Drosophila embryogenesis

Tomančák, P., Beaton, A., Weiszmann, R., Kwan, E., Shu, S., Lewis, S., Richards, S., Ashburner, M., Hartenstein, V., Celniker, S., et al. (2002) · Genome biology · doi:10.1186/gb-2002-3-12-research0088 · Cited by 725 · see citing works

Regulation of zygotic gene expression in Drosophila primordial germ cells

Doren, M. V., Williamson, A., & Lehmann, R. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70091-0 · Cited by 706 · see citing works

Extensive Association of Functionally and Cytotopically Related mRNAs with Puf Family RNA-Binding Proteins in Yeast

Gerber, A. P., Herschlag, D., & Brown, P. O. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020079 · Cited by 651 · see citing works

Ensembl 2007

Hubbard, T., Aken, B. L., Beal, K. M., Ballester, B., Cáccamo, M., Chen, Y., Clarke, L., Coates, G. M. P., Cunningham, F. M., Cutts, T., et al. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl996 · Cited by 636 · see citing works

Genetic control of cell division patterns in the Drosophila embryo

Edgar, B. A., & O’Farrell, P. H. (1989) · Cell · doi:10.1016/0092-8674(89)90183-9 · Cited by 577 · see citing works

Ultrastructural patterns of RNA synthesis during early embryogenesis of drosophila melanogaster

McKnight, S. L., & Miller Jr., O. L. (1976) · Cell · doi:10.1016/0092-8674(76)90014-3 · Cited by 400 · see citing works

Parameters controlling transcriptional activation during early drosophila development

Edgar, B. A. (1986) · Cell · doi:10.1016/0092-8674(86)90009-7 · Cited by 368 · see citing works

Multiplex Detection of RNA Expression in Drosophila Embryos

Kosman, D., Mizutani, C. M., Lemons, D., Cox, W. G., McGinnis, W. J., & Bier, E. (2004) · Science · doi:10.1126/science.1099247 · Cited by 357 · see citing works

Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset

Choe, S. E., Boutros, M., Michelson, A. M., Church, G. M., & Halfon, M. S. (2005) · Genome biology · doi:10.1186/gb-2005-6-2-r16 · Cited by 354 · see citing works

Cell cycle control by the nucleo-cytoplasmic ratio in early Drosophila development

Edgar, B. A., Kiehle, C. P., & Schubiger, G. (1986) · Cell · doi:10.1016/0092-8674(86)90771-3 · Cited by 340 · see citing works

SMAUG Is a Major Regulator of Maternal mRNA Destabilization in Drosophila and Its Translation Is Activated by the PAN GU Kinase

Tadros, W., Goldman, A. L., Babak, T., Menzies, F., Vardy, L., Orr-Weaver, T., Hughes, T. R., Westwood, J. T., Smibert, C. A., & Lipshitz, H. D. (2007) · Developmental Cell · doi:10.1016/j.devcel.2006.10.005 · Cited by 330 · see citing works

Transcriptome Analysis of Zebrafish Embryogenesis Using Microarrays

Mathavan, S., Lee, S. G. P., Mak, A., Miller, L. D., Murthy, K. R. K., Govindarajan, K. R., Tong, Y., Wu, Y. L., Lam, S. H., Yang, H. H., et al. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010029 · Cited by 329 · see citing works

Recruitment of Nanos to hunchback mRNA by PumilioPreprint

Sonoda, J., & Wharton, R. P. (1999) · Genes & Development · doi:10.1101/gad.13.20.2704 · Cited by 321 · see citing works

Whole-genome analysis of dorsal-ventral patterning in the Drosophila embryo.

Stathopoulos, A., Drenth, M. V., Erives, A. J., Markstein, M., & Levine, M. (2002) · Cell · doi:10.1016/s0092-8674(02)01087-5 · Cited by 310 · see citing works

Genome-wide identification of mRNAs associated with the translational regulator PUMILIO in Drosophila melanogaster

Gerber, A. P., Luschnig, S., Krasnow, M. A., Brown, P. O., & Herschlag, D. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0509260103 · Cited by 277 · see citing works

Composition and dynamics of the Caenorhabditis elegans early embryonic transcriptome

Baugh, L. R., Hill, A. A. V., Slonim, D. K., Brown, E. L., & Hunter, C. P. (2003) · Development · doi:10.1242/dev.00302 · Cited by 255 · see citing works

Spatial and temporal control of RNA stability

Bashirullah, A., Cooperstock, R. L., & Lipshitz, H. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.111145698 · Cited by 202 · see citing works

Requirements for autosomal gene activity during precellular stages of Drosophila melanogaster

Merrill, P. T., Sweeton, D., & Wieschaus, E. F. (1988) · Development · doi:10.1242/dev.104.3.495 · Cited by 185 · see citing works

The TAGteam DNA motif controls the timing of <i>Drosophila</i> pre-blastoderm transcription

Bosch, J. R. T., Benavides, J. A., & Cline, T. W. (2006) · Development · doi:10.1242/dev.02373 · Cited by 161 · see citing works

Zygotic degradation of two maternal Cdc25 mRNAs terminates Drosophila's early cell cycle program.Preprint

Edgar, B. A., & Datar, S. A. (1996) · Genes & Development · doi:10.1101/gad.10.15.1966 · Cited by 158 · see citing works

Involvement of the pumilio gene in the transport of an abdominal signal in the Drosophila embryo

Lehmann, R., & Nüsslein‐Volhard, C. (1987) · Nature · doi:10.1038/329167a0 · Cited by 149 · see citing works

Loss of gene function through rapid mitotic cycles in the Drosophila embryo

Rothe, M., Pehl, M. J., Taubert, H., & Jäckle, H. (1992) · Nature · doi:10.1038/359156a0 · Cited by 144 · see citing works

Requirements for X-linked zygotic gene activity during cellularization of early Drosophila embryos

Wieschaus, E. F., & Sweeton, D. (1988) · Development · doi:10.1242/dev.104.3.483 · Cited by 139 · see citing works

Regulated Expression of nullo Is Required for the Formation of Distinct Apical and Basal Adherens Junctions in the Drosophila Blastoderm

Hunter, C. A., & Wieschaus, E. (2000) · Journal of Cell Biology · doi:10.1083/jcb.150.2.391 · Cited by 105 · see citing works

A Determinant for Directionality of Organelle Transport in Drosophila Embryos

Gross, S. P., Guo, Y., Martinez, J. E., & Welte, M. A. (2003) · Current Biology · doi:10.1016/j.cub.2003.08.032 · Cited by 103 · see citing works

Defects in energy homeostasis in Leigh syndrome French Canadian variant through PGC-1α/LRP130 complexPreprint

Cooper, M. P., Qu, L., Rohas, L. M., Lin, J. D., Yang, W., Erdjument‐Bromage, H., Tempst, P., & Spiegelman, B. M. (2006) · Genes & Development · doi:10.1101/gad.1483906 · Cited by 100 · see citing works

bottleneck acts as a regulator of the microfilament network governing cellularization of the Drosophila embryo

Schejter, E. D., & Wieschaus, E. F. (1993) · Cell · doi:10.1016/0092-8674(93)80078-s · Cited by 97 · see citing works

Regulation of Maternal Transcript Destabilization During Egg Activation in Drosophila

Tadros, W., Houston, S., Bashirullah, A., Cooperstock, R. L., Semotok, J. L., Reed, B. H., & Lipshitz, H. D. (2003) · Genetics · doi:10.1093/genetics/164.3.989 · Cited by 85 · see citing works

Dorsal-Ventral Pattern of Delta Trafficking Is Established by a Snail-Tom-Neuralized Pathway

Renzis, S. D., Yu, J., Zinzen, R. P., & Wieschaus, E. F. (2006) · Developmental Cell · doi:10.1016/j.devcel.2006.01.011 · Cited by 84 · see citing works

REDfly: a Regulatory Element Database for Drosophila

Gallo, S. M., Li, L., Hu, Z., & Halfon, M. S. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti794 · Cited by 80 · see citing works

BSF Binds Specifically to the bicoid mRNA 3′ Untranslated Region and Contributes to Stabilization of bicoid mRNA

Mancebo, R., Zhou, X., Shillinglaw, W., Henzel, W. J., & Macdonald, P. M. (2001) · Molecular and Cellular Biology · doi:10.1128/mcb.21.10.3462-3471.2001 · Cited by 68 · see citing works

Human antisense genes have unusually short introns: evidence for selection for rapid transcription

Chen, J., Sun, M., Hurst, L. D., Carmichael, G., & Rowley, J. D. (2005) · Trends in Genetics · doi:10.1016/j.tig.2005.02.003 · Cited by 62 · see citing works

Embryonic Transcription and the Control of Developmental Pathways

Wieschaus, E. F. (1996) · Genetics · doi:10.1093/genetics/142.1.5 · Cited by 50 · see citing works

Key aspects of the primary sex determination mechanism are conserved across the genus Drosophila

Erickson, J. W., & Cline, T. W. (1998) · Development · doi:10.1242/dev.125.16.3259 · Cited by 45 · see citing works

New invMED1 element cis-activates human multidrug-related MDR1 and MVP genes, involving the LRP130 protein

Labialle, S. (2004) · Nucleic Acids Research · doi:10.1093/nar/gkh722 · Cited by 33 · see citing works

Connecting Cell Behavior to Patterning: Lessons from the Cell Cycle

Follette, P. J., & O’Farrell, P. H. (1997) · Cell · doi:10.1016/s0092-8674(00)81869-3 · Cited by 32 · see citing works

The maternal-to-zygotic transition: a play in two acts

Tadros, W., & Lipshitz, H. D. (2009) · Development · doi:10.1242/dev.033183 · Cited by 1,177 · see citing works

Global Analysis of mRNA Localization Reveals a Prominent Role in Organizing Cellular Architecture and Function

Lécuyer, E., Yoshida, H., Parthasarathy, N., Alm, C., Babak, T., Cerovina, T., Hughes, T. R., Tomancak, P., & Krause, H. M. (2007) · Cell · doi:10.1016/j.cell.2007.08.003 · Cited by 967 · see citing works

Zygotic Genome Activation During the Maternal-to-Zygotic Transition

Lee, M. T., Bonneau, A. R., & Giráldez, A. J. (2014) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100913-013027 · Cited by 643 · see citing works

Mechanisms regulating zygotic genome activation

Schulz, K. N., & Harrison, M. M. (2018) · Nature Reviews Genetics · doi:10.1038/s41576-018-0087-x · Cited by 543 · see citing works

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

Liang, H.-L., Nien, C.-Y., Liu, H.-Y., Metzstein, M. M., Kirov, N., & Rushlow, C. (2008) · Nature · doi:10.1038/nature07388 · Cited by 478 · see citing works

Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm

Li, X., MacArthur, S., Bourgon, R., Nix, D. A., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L. L., et al. (2008) · eScholarship (California Digital Library) · doi:10.1371/journal.pbio.0060027 · Cited by 479 · see citing works

Chromatin Architecture Emerges during Zygotic Genome Activation Independent of Transcription

Hug, C. B., Grimaldi, A. G., Kruse, K., & Vaquerizas, J. M. (2017) · Cell · doi:10.1016/j.cell.2017.03.024 · Cited by 466 · see citing works

The maternal-to-zygotic transition revisited

Vastenhouw, N. L., Cao, W. X., & Lipshitz, H. D. (2019) · Development · doi:10.1242/dev.161471 · Cited by 433 · see citing works

Zelda Binding in the Early Drosophila melanogaster Embryo Marks Regions Subsequently Activated at the Maternal-to-Zygotic Transition

Harrison, M. M., Li, X.-Y., Kaplan, T., Botchan, M. R., & Eisen, M. B. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002266 · Cited by 338 · see citing works

Codon Usage and 3′ UTR Length Determine Maternal mRNA Stability in Zebrafish

Mishima, Y., & Tomari, Y. (2016) · Molecular Cell · doi:10.1016/j.molcel.2016.02.027 · Cited by 295 · see citing works

Universal Features of Post-Transcriptional Gene Regulation Are Critical for Plasmodium Zygote Development

Mair, G. R., Lasonder, E., Garver, L. S., Franke-Fayard, B. M. D., Carret, C., Wiegant, J. C. A. G., Dirks, R. W., Dimopoulos, G., Janse, C. J., & Waters, A. P. (2010) · PLoS Pathogens · doi:10.1371/journal.ppat.1000767 · Cited by 278 · see citing works

Precise Developmental Gene Expression Arises from Globally Stochastic Transcriptional Activity

Little, S. C., Tikhonov, M., & Gregor, T. (2013) · Cell · doi:10.1016/j.cell.2013.07.025 · Cited by 265 · see citing works

Indirect Effects of Ploidy Suggest X Chromosome Dose, Not the X:A Ratio, Signals Sex in Drosophila

Erickson, J. W., & Quintero, J. J. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050332 · Cited by 244 · see citing works

Scallop genome reveals molecular adaptations to semi-sessile life and neurotoxins

Li, Y., Sun, X., Hu, X., Xun, X., Zhang, J., Guo, X., Jiao, W., Zhang, L., Liu, W., Wang, J., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01927-0 · Cited by 242 · see citing works

Temporal Coordination of Gene Networks by Zelda in the Early Drosophila Embryo

Nien, C.-Y., Liang, H.-L., Butcher, S. C., Sun, Y., Fu, S., Gocha, T., Kirov, N., Manak, J. R., & Rushlow, C. A. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002339 · Cited by 234 · see citing works

The Earliest Transcribed Zygotic Genes Are Short, Newly Evolved, and Different across Species

Heyn, P. C., Kircher, M., Dahl, A., Kelso, J. F., Tomančák, P., Kalinka, A. T., & Neugebauer, K. M. (2014) · Cell Reports · doi:10.1016/j.celrep.2013.12.030 · Cited by 225 · see citing works

Dynamic multifactor hubs interact transiently with sites of active transcription in Drosophila embryos

Mir, M., Stadler, M. R., Ortiz, S. A., Hannon, C. E., Harrison, M. M., Darzacq, X., & Eisen, M. B. (2018) · eLife · doi:10.7554/elife.40497 · Cited by 207 · see citing works

Canalization of Gene Expression and Domain Shifts in the Drosophila Blastoderm by Dynamical Attractors

Manu, Surkova, S. Y., Spirov, A. V., Gursky, V. V., Janssens, H., Kim, A.-R., Radulescu, O., Vanario‐Alonso, C. E., Sharp, D. H., Samsonova, M. G., et al. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000303 · Cited by 211 · see citing works

Establishment of regions of genomic activity during the Drosophila maternal to zygotic transition

Li, X., Harrison, M. M., Villalta, J. E., Kaplan, T., & Eisen, M. B. (2014) · eLife · doi:10.7554/elife.03737 · Cited by 208 · see citing works

Maternal Epigenetic Pathways Control Parental Contributions to Arabidopsis Early Embryogenesis

Autran, D., Baroux, C., Raissig, M. T., Lenormand, T., Wittig, M., Grob, S., Steimer, A., Barann, M., Klostermeier, U. C., Leblanc, O., et al. (2011) · Cell · doi:10.1016/j.cell.2011.04.014 · Cited by 209 · see citing works

Noncanonical Compensation of Zygotic X Transcription in Early Drosophila melanogaster Development Revealed through Single-Embryo RNA-Seq

Lott, S. E., Villalta, J. E., Schroth, G. P., Luo, S. J., Tonkin, L. A., & Eisen, M. B. (2011) · PLoS Biology · doi:10.1371/journal.pbio.1000590 · Cited by 204 · see citing works

From Egg to Gastrula: How the Cell Cycle Is Remodeled During the Drosophila Mid-Blastula Transition

Farrell, J. A., & O’Farrell, P. H. (2014) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133531 · Cited by 173 · see citing works

Embryo and Endosperm Inherit Distinct Chromatin and Transcriptional States from the Female Gametes in Arabidopsis

Pillot, M., Baroux, C., Arteaga-Vazquez, M. A., Autran, D., Leblanc, O., Vielle‐Calzada, J., Grossniklaus, U., & Grimanelli, D. (2010) · The Plant Cell · doi:10.1105/tpc.109.071647 · Cited by 174 · see citing works

Transcript clearance during the maternal-to-zygotic transition

Walser, C. B., & Lipshitz, H. D. (2011) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2011.03.003 · Cited by 169 · see citing works

Establishment and maintenance of heritable chromatin structure during early Drosophila embryogenesis

Blythe, S. A., & Wieschaus, E. F. (2016) · eLife · doi:10.7554/elife.20148 · Cited by 168 · see citing works

Histone titration against the genome sets the DNA-to-cytoplasm threshold for the Xenopus midblastula transition

Amodeo, A. A., Jukam, D., Straight, A. F., & Skotheim, J. M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1413990112 · Cited by 154 · see citing works

Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos

Joseph, S. R., Pálfy, M., Hilbert, L., Kumar, M., Karschau, J., Zaburdaev, V., Shevchenko, A., & Vastenhouw, N. L. (2017) · eLife · doi:10.7554/elife.23326 · Cited by 145 · see citing works

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

Sysoev, V. O., Fischer, B., Frese, C. K., Gupta, I., Krijgsveld, J., Hentze, M. W., Castelló, A., & Ephrussi, A. (2016) · Nature Communications · doi:10.1038/ncomms12128 · Cited by 146 · see citing works

A global change in RNA polymerase II pausing during the Drosophila midblastula transition

Chen, K., Johnston, J. J., Shao, W., Meier, S. R., Staber, C. J., & Zeitlinger, J. (2013) · eLife · doi:10.7554/elife.00861 · Cited by 153 · see citing works

Aubergine iCLIP Reveals piRNA-Dependent Decay of mRNAs Involved in Germ Cell Development in the Early Embryo

Barckmann, B., Pierson, S., Dufourt, J., Papin, C., Armenise, C., Port, F., Grentzinger, T., Chambeyron, S., Baronian, G., Desvignes, J., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.07.030 · Cited by 142 · see citing works

Genome-wide analysis of mRNA decay patterns during early Drosophiladevelopment

Thomsen, S., Anders, S., Janga, S. C., Huber, W. K., & Alonso, C. R. (2010) · Genome biology · doi:10.1186/gb-2010-11-9-r93 · Cited by 138 · see citing works

Accelerated Mitochondrial Evolution and “Darwin's Corollary”: Asymmetric Viability of Reciprocal F1 Hybrids in Centrarchid Fishes

Bolnick, D. I., Turelli, M., López‐Fernández, H., Wainwright, P. C., & Near, T. J. (2008) · Genetics · doi:10.1534/genetics.107.081364 · Cited by 133 · see citing works

Graded dorsal and differential gene regulation in the Drosophila embryo.

Reeves, G. T., & Stathopoulos, A. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000836 · Cited by 119 · see citing works

Signaling Dynamics Control Cell Fate in the Early Drosophila Embryo

Johnson, H. E., Shvartsman, S. Y., & Toettcher, J. E. (2019) · Developmental Cell · doi:10.1016/j.devcel.2019.01.009 · Cited by 127 · see citing works

Coupling of zygotic transcription to mitotic control at theDrosophilamid-blastula transition

Lu, X., Li, J., Elemento, O., Tavazoie, S., & Wieschaus, E. F. (2009) · Development · doi:10.1242/dev.034421 · Cited by 110 · see citing works

The Maternal to Zygotic Transition in Animals and PlantsPreprint

Baroux, C., Autran, D., Gillmor, C. S., Grimanelli, D., & Grossniklaus, U. (2008) · Cold Spring Harbor Symposia on Quantitative Biology · doi:10.1101/sqb.2008.73.053 · Cited by 116 · see citing works

New insights into the maternal to zygotic transition

Langley, A. R., Smith, J. C., Stemple, D. L., & Harvey, S. A. (2014) · Development · doi:10.1242/dev.102368 · Cited by 113 · see citing works

Systematic study of subcellular localization of Arabidopsis PPR proteins confirms a massive targeting to organelles

Colcombet, J., Lopez‐Obando, M., Heurtevin, L., Bernard, C., Martin, K., Berthomé, R., & Claire Lurin, A. (2013) · RNA Biology · doi:10.4161/rna.26128 · Cited by 113 · see citing works

The Maternal-to-Zygotic Transition During Vertebrate Development

Yartseva, V., & Giráldez, A. J. (2015) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.07.020 · Cited by 110 · see citing works

Global regulation of mRNA translation and stability in the early Drosophilaembryo by the Smaug RNA-binding protein

Chen, L.-N., Dumelie, J. G., Li, X., Cheng, M. H. K., Yang, Z., Laver, J. D., Siddiqui, N. U., Westwood, J. T., Morris, Q., Lipshitz, H. D., et al. (2014) · Genome biology · doi:10.1186/gb-2014-15-1-r4 · Cited by 112 · see citing works

Intron Delays and Transcriptional Timing during Development

Swinburne, I. A., & Silver, P. A. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.02.002 · Cited by 107 · see citing works

Control of maternal mRNA stability in germ cells and early embryos

Barckmann, B., & Simonelig, M. (2013) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2012.12.011 · Cited by 108 · see citing works

Impact of gut microbiota on the fly’s germ line

Elgart, M., Stern, S., Salton, O., Gnainsky, Y., Heifetz, Y., & Soen, Y. (2016) · Nature Communications · doi:10.1038/ncomms11280 · Cited by 104 · see citing works

Genome Size and Species Diversification

Kraaijeveld, K. (2010) · Evolutionary Biology · doi:10.1007/s11692-010-9093-4 · Cited by 103 · see citing works

Impacts of the ubiquitous factor Zelda on Bicoid-dependent DNA binding and transcription in DrosophilaPreprint

Xu, Z., Chen, H., Jia, L., Yu, D., Struffi, P., & Small, S. (2014) · Genes & Development · doi:10.1101/gad.234534.113 · Cited by 94 · see citing works

The Heidelberg Screen for Pattern Mutants of Drosophila: A Personal Account

Wieschaus, E. F., & Nüsslein‐Volhard, C. (2016) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-113015-023138 · Cited by 99 · see citing works

REDfly 2.0: an integrated database of cis-regulatory modules and transcription factor binding sites in Drosophila

Halfon, M. S., Gallo, S. M., & Bergman, C. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm876 · Cited by 99 · see citing works

Factors Affecting Oocyte and Embryo Transcriptomes

Sirard, M. (2012) · Reproduction in Domestic Animals · doi:10.1111/j.1439-0531.2012.02069.x · Cited by 99 · see citing works

Quantifying post-transcriptional regulation in the development of Drosophila melanogaster

Becker, K., Bluhm, A., Casas-Vila, N., Dinges, N., Dejung, M., Sayols, S., Kreutz, C., Roignant, J., Butter, F., & Legewie, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07455-9 · Cited by 96 · see citing works

Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

Rach, E. A., Yuan, H., Majoros, W. H., Tomančák, P., & Ohler, U. (2009) · Genome biology · doi:10.1186/gb-2009-10-7-r73 · Cited by 96 · see citing works

Genome-wide RIP-Chip analysis of translational repressor-bound mRNAs in the Plasmodium gametocyte

Guerreiro, A., Deligianni, E., Santos, J. M., Silva, P. A. G. C., Louis, C., Pain, A., Janse, C. J., Franke-Fayard, B. M. D., Carret, C., Sidén‐Kiamos, I., et al. (2014) · Genome biology · doi:10.1186/s13059-014-0493-0 · Cited by 88 · see citing works

Grainyhead and Zelda compete for binding to the promoters of the earliest-expressed Drosophila genes

Harrison, M. M., Botchan, M. R., & Cline, T. W. (2010) · Developmental Biology · doi:10.1016/j.ydbio.2010.06.026 · Cited by 88 · see citing works

Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

Laver, J. D., Li, X., Ray, D., Cook, K. B., Hahn, N. A., Nabeel‐Shah, S., Kekis, M., Luo, H., Marsolais, A. J., Fung, K. Y., et al. (2015) · Genome biology · doi:10.1186/s13059-015-0659-4 · Cited by 85 · see citing works

Genome-wide analysis of Staufen-associated mRNAs identifies secondary structures that confer target specificity

Laver, J. D., Li, X., Ancevicius, K., Westwood, J. T., Smibert, C. A., Morris, Q., & Lipshitz, H. D. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt702 · Cited by 81 · see citing works

Concentration dependent chromatin states induced by the bicoid morphogen gradient

Hannon, C. E., Blythe, S. A., & Wieschaus, E. F. (2017) · eLife · doi:10.7554/elife.28275 · Cited by 87 · see citing works

Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages

Gibilisco, L., Zhou, Q., Mahajan, S., & Bachtrog, D. (2016) · PLoS Genetics · doi:10.1371/journal.pgen.1006464 · Cited by 82 · see citing works

Regulation and Function of Maternal Gene Products During the Maternal-to-Zygotic Transition in Drosophila

Laver, J. D., Marsolais, A. J., Smibert, C. A., & Lipshitz, H. D. (2015) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.06.007 · Cited by 78 · see citing works

An essential role for transcription before the MBT in Xenopus laevis

Skirkanich, J., Luxardi, G., Yang, J., Kodjabachian, L., & Klein, P. S. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.06.010 · Cited by 78 · see citing works

Regulatory principles governing the maternal-to-zygotic transition: insights from Drosophila melanogaster

Hamm, D. C., & Harrison, M. M. (2018) · Open Biology · doi:10.1098/rsob.180183 · Cited by 70 · see citing works

Evolutionary Mirages: Selection on Binding Site Composition Creates the Illusion of Conserved Grammars in Drosophila Enhancers

Lusk, R. W., & Eisen, M. B. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000829 · Cited by 77 · see citing works

Design flexibility in cis-regulatory control of gene expression: Synthetic and comparative evidence

Liberman, L. M., & Stathopoulos, A. (2009) · Developmental Biology · doi:10.1016/j.ydbio.2008.12.020 · Cited by 76 · see citing works

DNA methylation plays a crucial role during early Nasonia development

Zwier, M. V., Verhulst, E. C., Zwahlen, R. D., Beukeboom, L. W., & van de Zande, L. (2011) · Insect Molecular Biology · doi:10.1111/j.1365-2583.2011.01121.x · Cited by 75 · see citing works

Drosophila Maternal Hsp83 mRNA Destabilization Is Directed by Multiple SMAUG Recognition Elements in the Open Reading Frame

Semotok, J. L., Luo, H., Cooperstock, R. L., Karaiskakis, A., Vari, H. K., Smibert, C. A., & Lipshitz, H. D. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.00037-08 · Cited by 74 · see citing works

Early genome activation in Drosophila is extensive with an initial tendency for aborted transcripts and retained intronsPreprint

Kwasnieski, J. C., Orr‐Weaver, T. L., & Bartel, D. P. (2019) · Genome Research · doi:10.1101/gr.242164.118 · Cited by 72 · see citing works

The maternal-to-zygotic transition: reprogramming of the cytoplasm and nucleus

Kojima, M. L., Hoppe, C., & Giráldez, A. J. (2024) · Nature Reviews Genetics · doi:10.1038/s41576-024-00792-0 · Cited by 77 · see citing works

The timing of zygotic genome activation

Pálfy, M., Joseph, S. R., & Vastenhouw, N. L. (2017) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2016.12.001 · Cited by 69 · see citing works

Histone variant H2A.Z regulates zygotic genome activation

Ibarra-Morales, D., Rauer, M., Quarato, P., Rabbani, L., Zenk, F. L., Schulte‐Sasse, M., Cardamone, F., Gomez‐Auli, A., Cecere, G., & Iovino, N. (2021) · Nature Communications · doi:10.1038/s41467-021-27125-7 · Cited by 73 · see citing works

REDfly: the transcriptional regulatory element database for Drosophila

Rivera, J., Keränen, S. V. E., Gallo, S. M., & Halfon, M. S. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky957 · Cited by 68 · see citing works

The TATA‐binding protein regulates maternal mRNA degradation and differential zygotic transcription in zebrafish

Ferg, M., Sanges, R., Gehrig, J., Kiss, J., Bauer, M., Lovas, A., Szabó, M., Yang, L., Strähle, U., Pankratz, M. J., et al. (2007) · The EMBO Journal · doi:10.1038/sj.emboj.7601821 · Cited by 65 · see citing works

Transcriptional Activation of the Zygotic Genome in Drosophila

Harrison, M. M., & Eisen, M. B. (2015) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.07.028 · Cited by 63 · see citing works

microRNAs, the cell's Nepenthe: clearing the past during the maternal-to-zygotic transition and cellular reprogramming

Giráldez, A. J. (2010) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2010.04.003 · Cited by 63 · see citing works

Coordinating Cell Cycle Remodeling with Transcriptional Activation at the Drosophila MBT

Blythe, S. A., & Wieschaus, E. F. (2015) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.06.002 · Cited by 62 · see citing works

Dynamics of nuclear receptor gene expression during Pacific oyster development

Vogeler, S., Bean, T. P., Lyons, B. P., & Galloway, T. S. (2016) · BMC Developmental Biology · doi:10.1186/s12861-016-0129-6 · Cited by 64 · see citing works

Heads and tails: Evolution of antero-posterior patterning in insects

Rosenberg, M. I., Lynch, J., & Desplan, C. (2008) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2008.09.007 · Cited by 64 · see citing works

Histone concentration regulates the cell cycle and transcription in early development

Chari, S., Wilky, H., Govindan, J., & Amodeo, A. A. (2019) · Development · doi:10.1242/dev.177402 · Cited by 58 · see citing works

Sex and the single embryo: early deveopment in the Mediterranean fruit fly, Ceratitis capitata

Gabrieli, P., Falaguerra, A., Siciliano, P., Gomulski, L. M., Scolari, F., Zacharopoulou, A., Franz, G., Malacrida, A. R., & Gasperi, G. (2010) · BMC Developmental Biology · doi:10.1186/1471-213x-10-12 · Cited by 62 · see citing works

Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition

Cao, W. X., Kabelitz, S., Gupta, M., Yeung, E., Lin, S., Rammelt, C., Ihling, C. H., Pekovic, F., Low, T. C. H., Siddiqui, N. U., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107783 · Cited by 61 · see citing works

The Bicoid Stability Factor Controls Polyadenylation and Expression of Specific Mitochondrial mRNAs in Drosophila melanogaster

Bratić, A. M., Wredenberg, A., Grönke, S., Stewart, J. B., Mourier, A., Ruzzenente, B., Kukat, C., Wibom, R., Habermann, B. H., Partridge, L., et al. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002324 · Cited by 61 · see citing works

Genome-wide analysis of the maternal-to-zygotic transition in Drosophila primordial germ cells

Siddiqui, N. U., Li, X., Luo, H., Karaiskakis, A., Hou, H., Kislinger, T., Westwood, J. T., Morris, Q., & Lipshitz, H. D. (2012) · Genome biology · doi:10.1186/gb-2012-13-2-r11 · Cited by 60 · see citing works

CTCF, BEAF-32, and CP190 are not required for the establishment of TADs in early Drosophila embryos but have locus-specific roles

Cavalheiro, G. R., Girardot, C., Viales, R. R., Feng, S., Pollex, T., Cao, T. B. N., Lacour, P., Rabinowitz, A. H., & Furlong, E. E. M. (2023) · Science Advances · doi:10.1126/sciadv.ade1085 · Cited by 56 · see citing works

Number of Nuclear Divisions in the Drosophila Blastoderm Controlled by Onset of Zygotic Transcription

Sung, H.-W., Spangenberg, S., Vogt, N., & Großhans, J. (2013) · Current Biology · doi:10.1016/j.cub.2012.12.013 · Cited by 57 · see citing works

An Essential Role for Zygotic Expression in the Pre-Cellular Drosophila Embryo

Ali-Murthy, Z., Lott, S. E., Eisen, M. B., & Kornberg, T. B. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003428 · Cited by 57 · see citing works

Engineering the genomes of wild insect populations: Challenges, and opportunities provided by synthetic Medea selfish genetic elements

Hay, B. A., Chen, C., Ward, C. M., Huang, H., Su, J. T., & Guo, M. (2010) · Journal of Insect Physiology · doi:10.1016/j.jinsphys.2010.05.022 · Cited by 57 · see citing works

Tension and Epithelial Morphogenesis in Drosophila Early Embryos

Lye, C. M., & Sanson, B. (2011) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/b978-0-12-385065-2.00005-0 · Cited by 56 · see citing works

As the fat flies: The dynamic lipid droplets of Drosophila embryos

Welte, M. A. (2015) · Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids · doi:10.1016/j.bbalip.2015.04.002 · Cited by 54 · see citing works

RNA tales – how embryos read and discard messages from mom

Despic, V., & Neugebauer, K. M. (2018) · Journal of Cell Science · doi:10.1242/jcs.201996 · Cited by 56 · see citing works

The RNA-Binding Protein Rasputin/G3BP Enhances the Stability and Translation of Its Target mRNAs

Laver, J. D., Ly, J., Winn, J. K., Karaiskakis, A., Lin, S., Nie, K., Benic, G., Jaberi-Lashkari, N., Cao, W. X., Khademi, A., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.02.066 · Cited by 56 · see citing works

STAT Is an Essential Activator of the Zygotic Genome in the Early Drosophila Embryo

Tsurumi, A., Fan, X., Li, J., Larson, K., LaFrance, R. M., & Li, W. X. (2011) · PLoS Genetics · doi:10.1371/journal.pgen.1002086 · Cited by 55 · see citing works

Requirement for highly efficient pre-mRNA splicing during Drosophila early embryonic development

Guilgur, L. G., Prudêncio, P., Sobral, D., Beňová‐Liszeková, D., Rosa, A., & Martinho, R. G. (2014) · eLife · doi:10.7554/elife.02181 · Cited by 53 · see citing works

Zygotically controlled F-actin establishes cortical compartments to stabilize furrows duringDrosophilacellularization

Sokac, A. M., & Wieschaus, E. F. (2008) · Journal of Cell Science · doi:10.1242/jcs.025171 · Cited by 52 · see citing works

Dynamic Variations of 3′UTR Length Reprogram the mRNA Regulatory Landscape

Navarro, E., Mallén, A., & Hueso, M. (2021) · Biomedicines · doi:10.3390/biomedicines9111560 · Cited by 52 · see citing works

Genome-Wide Analysis of GLD-1–Mediated mRNA Regulation Suggests a Role in mRNA Storage

Scheckel, C., Gaidatzis, D., Wright, J. E., & Ciosk, R. (2012) · PLoS Genetics · doi:10.1371/journal.pgen.1002742 · Cited by 50 · see citing works

Transcript Length Mediates Developmental Timing of Gene Expression Across Drosophila

Artieri, C. G., & Fraser, H. B. (2014) · Molecular Biology and Evolution · doi:10.1093/molbev/msu226 · Cited by 49 · see citing works

Combinatorial activation and concentration-dependent repression of the Drosophila even skipped stripe 3+7 enhancer

Struffi, P., Corado, M., Kaplan, L., Yu, D., Rushlow, C. A., & Small, S. (2011) · Development · doi:10.1242/dev.065987 · Cited by 48 · see citing works

Transcriptional and epigenetic responses to mating and aging in Drosophila melanogaster

Zhou, S., Mackay, T. F. C., & Anholt, R. R. H. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-927 · Cited by 47 · see citing works

Identification of Early Zygotic Genes in the Yellow Fever Mosquito Aedes aegypti and Discovery of a Motif Involved in Early Zygotic Genome Activation

Biedler, J. K., Hu, W., Tae, H., & Tu, Z. J. (2012) · PLoS ONE · doi:10.1371/journal.pone.0033933 · Cited by 47 · see citing works

Regulation of zygotic genome activation and DNA damage checkpoint acquisition at the mid-blastula transition

Zhang, M., Kothari, P., Mullins, M. C., & Lampson, M. A. (2014) · Cell Cycle · doi:10.4161/15384101.2014.967066 · Cited by 45 · see citing works

dFMRP and Caprin, translational regulators of synaptic plasticity, control the cell cycle at the Drosophila mid-blastula transition

Papoulas, O., Monzo, K. F., Cantin, G. T., Ruse, C. I., Yates, J. R., Ryu, Y. H., & Sisson, J. C. (2010) · Development · doi:10.1242/dev.055046 · Cited by 47 · see citing works

CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity

Ciabrelli, F., Rabbani, L., Cardamone, F., Zenk, F. L., Löser, E., Schächtle, M., Mazina, M. Y., Loubière, V., & Iovino, N. (2023) · Science Advances · doi:10.1126/sciadv.adf2687 · Cited by 43 · see citing works

Temporal dynamics, spatial range, and transcriptional interpretation of the Dorsal morphogen gradient

Rushlow, C. A., & Shvartsman, S. Y. (2012) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2012.08.005 · Cited by 45 · see citing works

Novel Technique Shows When the Fertilized Egg’s Genome Comes into Its Own

Gross, L. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050131

The zinc-finger protein Zelda is a key activator of the early zygotic genome in Drosophila

Liang, H.-L., Nien, C.-Y., Liu, H.-Y., Metzstein, M. M., Kirov, N., & Rushlow, C. (2008) · Nature · doi:10.1038/nature07388 · Cited by 478 · see citing works

Transcriptional Activation of the Zygotic Genome in Drosophila

Harrison, M. M., & Eisen, M. B. (2015) · Current topics in developmental biology/Current Topics in Developmental Biology · doi:10.1016/bs.ctdb.2015.07.028 · Cited by 63 · see citing works

The zinc-finger protein Zelda is a key activator of the early zygotic genome

Liang, H.-L., Nien, C.-Y., Liu, H.-Y., Metzstein, M. M., Kirov, N., & Rushlow, C. A. (2008)

Mechanisms of transcript regulation in the early Drosophila embryo: degradation, localization and translational regulation

Cooperstock, R. L. (2002) · TSpace (University of Toronto)