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Gene expression changes in 48hr APF retinas and optic lobes in Blimp-1 loss of function and gain of function flies

ABSTRACT: Blimp-1 encodes a zinc-finger transcription factor, which is involved in the terminal differentiation of the Drosophila eye. We found that Blimp-1 mutants display plano-covex corneal lenses and rhabdomere extension defects. To identify genes that it regulates in the retina, we performed an RNA-seq experiemtn to compare retinas expressing Blimp-1 RNAi or UAS-Blimp-1 in all cell types in the eye with lGMR-GAL4 to control lGMR-GAL4/+. We examined RNA from dissected retinas and attached optic lobes from 48 hr APF pupae. Among the genes that were affected, we found that the transcription factor Slow border cells (Slbo) was significantly up-regulated in Blimp-1 knockdown samples, and Slbo overexpression could recapitulate Blimp-1 loss of function phenotypes. Many other affected genes may collectively contribute to the corneal lens and photoreceptor phenotypes caused by loss of Blimp-1..

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE183734 | GEO | 2022/03/07

REPOSITORIES: GEO

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Project description:Purpose: To compare transcriptomic changes in 3rd instar larval eye discs following sev-GAL4 driven down- or up- regulation of hsrω lncRNAs. Method: Eye disc total RNA profiles of wandering late third instar larvae of sev-GAL4>UAS-GFP, sev-GAL4>UAS-hsrωRNAi, sev-GAL4>EP3037 were generated by sequencing, in duplicate, using Illumina Hiseq2500 platform using 50bp pair-end reads, 6 samples per lane and each sample run across 2 lanes. This resulted in a sequencing depth of ~20 million reads. The resulting sequencing FastQ files were mapped to the Drosophila genome (dm6) using Tophat with Bowtie. The aligned SAM/BAM file for each was processed for guided transcript assembly using Cufflink 2.1.1 and gene counts were determined. Mapped reads were assembled using Cufflinks. Transcripts from all samples were subjected to Cuffmerge to get final transcriptome assembly across samples. In order to ascertain differential expression of gene transcripts between different samples, Cuffdiff 2.1.1 was used (Trapnell et al., 2012). Result: Using an optimized data analysis workflow, we mapped about 20 million sequence reads per sample to the Drosophila genome (dm6) and identified 15,905 transcripts with TopHat workflow in each genotypes studied. The sev-GAL4 driven expression of RNAi for hsromega gene transcripts in eye discs resulted in differential expression of many genes, with 409 genes being down-regulated and 100 up-regulated, when compared with those in sev-GAL4>UAS-GFP eye discs. Compared to control eye discs in case of up regulation of hsrω RNA, 66 gene were up-regulated while 635 were down-regulated. Some of these (11 genes) were validated using qRT-PCR. Conclusion: Analysis of RNA-seq data revealed that a large proportion of transcripts were indeed similarly affected by down- or up-regulation of hsrω RNA in normal as well as activated Ras expression background. A comparison of transcriptomes of sev-GAL4>hsrωRNAi and sev-GAL4>EP3037 eye discs revealed that in each case the number of genes down regulated was more than those up-regulated. Interestingly, while 319 genes were commonly down regulated and 15 were commonly up-regulated in the two genotypes, only 2 genes showed opposing trends between sev-GAL4>UAS-hsrωRNAi and sev-GAL4>EP3037 eye discs.

Dataset Information

Gene expression changes in 48hr APF retinas and optic lobes in Blimp-1 loss of function and gain of function flies

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