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Open Access Research article

The ribonuclease Dis3 is an essential regulator of the developmental transcriptome

Dezhi Hou, Miriam Ruiz and Erik D Andrulis*

Author Affiliations

Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Wood Building, W212, Cleveland, OH, 44106, USA

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BMC Genomics 2012, 13:359  doi:10.1186/1471-2164-13-359

Published: 1 August 2012

Additional files

Additional file 1:

Figure S1. Dis3 depletion has little or no effect on Rrp6 localization in the fly brain. (a) Wild-type w1118 and Dis3 RNAi brains were dissected and stained with anti-Dis3 (green) and anti-Rrp6 (red) antibodies. Nuclei were stained with DAPI (blue). (b) Close-up visualization of anti-Dis3 antibody and DAPI staining of brains.

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Additional file 2:

Table S1. Raw RNA-seq data.

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Additional file 3:

Table S2. Filtered RNA-seq data.

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Additional file 4:

Figure S2. A subset of mitochondria- and nucleotide-related RNAs highly up-regulated in day 0 and day 4 Dis3KD flies. (a) Comparative heatmap shows the 850 up-regulated RNAs in the Dis3KD flies. (b) GO analysis of the 850 increased transcripts reveals the enriched subset.

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Additional file 5:

Table S3. 2-fold affected RNAs.

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Additional file 6:

Table S4. 5-fold affected RNAs.

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Additional file 7:

Figure S3. Detail fold change analysis. 2 fold- and 5 fold-increased and decreased RNAs in Dis3KD samples in all 6 developmental stages. This figure complements Figure 3c.

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Additional file 8:

Figure S4. Gene ontology enrichment analyses of 5 fold-increased and -decreased RNAs for the later developmental time points. Bars depict the percentage of RNAs in selected GO term; black triangles represent fold enrichment, plotted on the right Y axis and calculated by dividing the % count in selection by % count in total. GO terms are sorted by P-value and top 10 were picked at each time point. This figure complements Figure 4.

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Additional file 9:

Table S5. Gene ontology analysis.

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Additional file 10:

Figure S5. Transcriptomic changes observed in the Dis3KD flies are not detected in the daughterless-Gal4 early embryos. Expression of hunchback (hb), Krüppel (kr), and CG12011 was assessed by qRT-PCR.

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Additional file 11:

Figure S6. Relative expression level of Rrp6 and exosome subunit RNAs in wild type and Dis3KD flies over developmental time course. (a) Rrp6, (b) Csl4, (c) Rrp4, (d) Rrp40, (e) Mtr3, (f) Ski6, (g) Rrp46, (h) Rrp45, and (i) Rrp46.

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