References
- Wilczynski B, Furlong EE. Dynamic CRM occupancy reflects a temporal map of developmental progression. Mol Syst Biol. 2010;6:383.
- Ahmad K, Spens AE. Separate polycomb response elements control chromatin state and activation of the vestigial gene. PLoS Genet. 2019;15:e1007877.
- Davie K, Jacobs J, Atkins M, et al. Discovery of transcription factors and regulatory regions driving in vivo tumor development by ATAC-seq and FAIRE-seq open chromatin profiling. PLoS Genet. 2015;11:e1004994.
- Uyehara CM, McKay DJ. Direct and widespread role for the nuclear receptor EcR in mediating the response to ecdysone in Drosophila. Proc Natl Acad Sci U S A. 2019;116:9893–11.
- Flegel K, Sun D, Grushko O, et al. Live cell cycle analysis of Drosophila tissues using the attune acoustic focusing cytometer and Vybrant DyeCycle violet DNA stain. J Vis Exp. 2013;e50239. DOI:10.3791/50239-v
- Corces MR, Trevino AE, Hamilton EG, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nat Methods. 2017;14:959–962.
- Meers MP, Bryson TD, Henikoff JG, et al. Improved CUT&RUN chromatin profiling tools. Elife. 2019;8. DOI:10.7554/eLife.46314
- Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120.
- Martin M. Cutadapt removes adapter sequences from high-throughput sequencing readsCutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet journal. 2011;17:1. DOI:10.14806/ej.17.1.200
- Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–359.
- Danecek P, Bonfield JK, Liddle J, et al. Twelve years of SAMtools and BCFtools. Gigascience. 2021;10. DOI:10.1093/gigascience/giab008
- Zhang Y, Liu T, Meyer CA, et al. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008;9:R137.
- Ramirez F, Ryan DP, Gruning B, et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 2016;44:W160–165.
- Amemiya HM, Kundaje A, Boyle AP. The ENCODE blacklist: identification of problematic regions of the genome. Sci Rep. 2019;9:9354.
- Karolchik D, Hinrichs AS, Furey TS, et al. The UCSC Table Browser data retrieval tool. Nucleic Acids Res. 2004;32:D493–496.
- Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–930.
- Zhu LJ, Gazin C, Lawson ND, et al. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinf. 2010;11:237.
- Kent WJ, Sugnet CW, Furey TS, et al. The human genome browser at UCSC. Genome Res. 2002;12:996–1006.
- Reed CT, Murphy C, Fristrom D. The ultrastructure of the differentiating pupal leg ofDrosophila melanogaster. Wilehm Roux Arch Dev Biol. 1975;178:285–302.
- Ma Y, McKay DJ, Buttitta L. Changes in chromatin accessibility ensure robust cell cycle exit in terminally differentiated cells. PLoS Biol. 2019;17:e3000378.
- de la Cruz AF, Edgar BA. Flow cytometric analysis of Drosophila cells. Methods Mol Biol. 2008;420:373–389.
- Fristrom JW, Doctor J, Fristrom DK, et al. The formation of the pupal cuticle by Drosophila imaginal discs in vitro. Dev Biol. 1982;91:337–350. DOI:10.1016/0012-1606(82)90040-9
- Harris RE, Stinchfield MJ, Nystrom SL, et al. Damage-responsive, maturity-silenced enhancers regulate multiple genes that direct regeneration in Drosophila. Elife. 2020;9. DOI:10.7554/eLife.58305
- Vizcaya-Molina E, Klein CC, Serras F, et al. Damage-responsive elements in Drosophila regeneration. Genome Res. 2018;28:1852–1866.
- Uyehara CM, Nystrom SL, Niederhuber MJ, et al. Hormone-dependent control of developmental timing through regulation of chromatin accessibility. Genes Dev. 2017;31:862–875.
- Loubiere V, Delest A, Thomas A, et al. Coordinate redeployment of PRC1 proteins suppresses tumor formation during Drosophila development. Nat Genet. 2016;48:1436–1442.
- Papp B, Muller J. Histone trimethylation and the maintenance of transcriptional on and off states by trxG and PcG proteins. Genes Dev. 2006;20:2041–2054.
- Niederhuber MJ, McKay DJ. Mechanisms underlying the control of dynamic regulatory element activity and chromatin accessibility during metamorphosis. Curr Opin Insect Sci. 2021;43:21–28.