GO term analysis of significantly post-reduced genes. (XLSX 16Â kb

Christopher Vincent (229420)

Daphne Cooper (4608925)

Hana Hall (605802)

Jeremiah Rounds (4608928)

Kaelan Brennan (4608922)

Patrick Medina (4608910)

Pedro Miura (48365)

Rebecca Doerge (4608913)

Spencer Escobedo (4608916)

Vikki Weake (4608919)

BMC Genomics

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Additional file 3: Table S2. of Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

Abstract Background Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavior precedes retinal degeneration. Here, we sought to identify gene expression changes and the genomic features of differentially regulated genes in photoreceptors that contribute to visual senescence. Results To identify gene expression changes that could lead to visual senescence, we characterized the aging transcriptome of Drosophila sensory neurons highly enriched for photoreceptors. We profiled the nuclear transcriptome of genetically-labeled photoreceptors over a 40 day time course and identified increased expression of genes involved in stress and DNA damage response, and decreased expression of genes required for neuronal function. We further show that combinations of promoter motifs robustly identify age-regulated genes, suggesting that transcription factors are important in driving expression changes in aging photoreceptors. However, long, highly expressed and heavily spliced genes are also more likely to be downregulated with age, indicating that other mechanisms could contribute to expression changes at these genes. Lastly, we identify that circular RNAs (circRNAs) strongly increase during aging in photoreceptors. Conclusions Overall, we identified changes in gene expression in aging Drosophila photoreceptors that could account for visual senescence. Further, we show that genomic features predict these age-related changes, suggesting potential mechanisms that could be targeted to slow the rate of age-associated visual decline

Hana Hall

Patrick Medina

Daphne A. Cooper

Spencer E. Escobedo

Jeremiah Rounds

Kaelan J. Brennan

Christopher Vincent

Pedro Miura

Rebecca Doerge

Vikki M. Weake

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Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

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Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavior precedes retinal degeneration. Here, we sought to identify gene expression changes and the genomic features of differentially regulated genes in photoreceptors that contribute to visual senescence. Results: To identify gene expression changes that could lead to visual senescence, we characterized the aging transcriptome of Drosophila sensory neurons highly enriched for photoreceptors. We profiled the nuclear transcriptome of genetically-labeled photoreceptors over a 40 day time course and identified increased expression of genes involved in stress and DNA damage response, and decreased expression of genes required for neuronal function. We further show that combinations of promoter motifs robustly identify age-regulated genes, suggesting that transcription factors are important in driving expression changes in aging photoreceptors. However, long, highly expressed and heavily spliced genes are also more likely to be downregulated with age, indicating that other mechanisms could contribute to expression changes at these genes. Lastly, we identify that circular RNAs (circRNAs) strongly increase during aging in photoreceptors. Conclusions: Overall, we identified changes in gene expression in aging Drosophila photoreceptors that could account for visual senescence. Further, we show that genomic features predict these age-related changes, suggesting potential mechanisms that could be targeted to slow the rate of age-associated visual decline

Hall, Hana

Medina, Patrick

Cooper, Daphne A.

Escobedo, Spencer E.

Rounds, Jeremiah

Brennan, Kaelan J.

Vincent, Christopher

Miura, Pedro

Doerge, Rebecca

Weake, Vikki M.

University of Nevada, Reno ScholarWorks Repository

English

Transcription factors matches for top motifs identified for age-regulated genes. (XLSX 13Â kb

Additional file 7: Table S6. of Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

Enriched sequence motifs for age-regulated genes. (XLSX 48Â kb

Additional file 6: Table S5. of Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

Age-regulated genes in photoreceptor neurons. (XLSX 121Â kb

Additional file 4: Table S3. of Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

https://figshare.com/articles/Additional_file_3_Table_S2_of_Transcriptome_profiling_of_aging_Drosophila_photoreceptors_reveals_gene_expression_trends_that_correlate_with_visual_senescence/5624047

Additional file 3: Table S2. of Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence

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University of Nevada, Reno ScholarWorks Repository

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