Unknown,Transcriptomics,Genomics,Proteomics

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Zelda determines chromatin accessibility during the Drosophila maternal-to-zygotic transition

ABSTRACT: We used FAIRE-seq to perform genome-wide profiling of open chromatin in 2-3 hour Drosophila embryos lacking maternal ZLD (zldM-) and in paired control embryos (yw). We demonstrate that ZLD is required to establish or maintain specific regions of open chromatin. Using single embryo RNA-seq data (from stage 5 yw and zldM- embryos) we show that loci that lose accessibility in zldM- embryos require ZLD for robust expression of associated genes. By comparing our FAIRE peaks to publicly available ChIP data (Xu et al. 2014) we demonstrate that ZLD is required for binding of the transcription factor Bicoid. To our surprise, not all ZLD-bound loci are less accessible in the mutant, suggesting that these regions rely on additional factors for open chromatin. These constitutively accessible ZLD-bound sites are enriched for the GAGA factor (GAF) binding motif, and we therefore propose that GAF may provide this additional function. We conclude that ZLD functions like a pioneer factor to define the cis-regulatory regions that drive gene expression during the MZT. Open chromatin profiling of 2-3 hour Drosophila embryos: embryos lacking maternal ZLD (zldM-, 3 replicates) and paired control embryos (yw, 2 replicates); Genomic DNA Inputs. Sequencing performed on Illumina HiSeq 2000.

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Melissa Harrison

PROVIDER: E-GEOD-65837 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:In all animals, the initial events of embryogenesis are controlled by maternal gene products that are deposited into the developing oocyte. At some point after fertilization, control of embryogenesis is transferred to the zygotic genome in a process called the maternal to zygotic transition (MZT). During this time maternal RNAs are degraded and zygotic RNAs are transcribed1. A long standing question has been, what factors regulate these events? The recent findings that microRNAs and Smaugs mediate maternal transcript degradation brought new life to this old problem2,3, however, the transcription factors that activate zygotic gene expression remained elusive. A clue came from the finding that many early zygotic genes in Drosophila share a cis-regulatory heptamer motif, CAGGTAG and related sequences, collectively referred to as TAG-team sites4,5. We asked whether there was a dedicated transcription factor that interacts with these sites to activate early genes. Here we report the discovery of a zinc-finger protein, Zelda (Zld) that binds specifically to TAG-team sites, and is capable of activating transcription in transient transfection assays. Mutant embryos lacking zld are defective in the cellularization process, and fail to activate the transcription of many early zygotic genes involved in cellularization, sex determination, and dorsoventral patterning. Global expression profiling confirmed that Zld plays a key role in the activation of the early zygotic genome, and suggests that Zld may also play a role in maternal RNA degradation during the MZT since many RNAs are up-regulated in the absence of Zld. Experiment Overall Design: Total RNA samples were extracted from three replicate collections of 1-2 hr yw and M- zld embryos by TRIzol (invitrogen). A portion of the collected embryos was fixed and stained with DAPI; 90% were in nuclear cycles 8 to13. cDNA was prepared using the GeneChipÂ® HT One-Cycle cDNA Synthesis Kit (Manufactured by Invitrogen for Affymetrix) and labeled with the BioArrayâ¢ HighYieldâ¢ RNA Transcript Labeling Kit (Enzo). Labeled probes were hybridized to Drosophila Genome 2 Affymetrix arrays and processed by a GeneChip Fluidics Station 400. Data were acquired and normalized by the GeneChipÂ® Scanner 3000 and processed by the Affymetrix GeneChip Operating Software (GCOS). t-test analysis was performed on the data from three biological replicates.

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Zelda determines chromatin accessibility during the Drosophila maternal-to-zygotic transition

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