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Table 5 Summary of comparisons of the six classes of transcripts upregulated in brat mutant embryos to other datasets a

From: Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

  Class A Class B Class C Class D Class E Class F
BRAT-associated mRNAs       
(as defined in this study)
All BRAT targets +++ ++++ +++ . . .
BRAT-not-PUM targets +++ ++++ +++ - - . .
BRAT-and-PUM co-targets . + + + . .
Maternally- vs. zygotically-expressed transcripts       
Maternally-expressed transcripts       
Tadros et al., 2007 [60] . . +++ - - - - - - - - .
De Renzis et al., 2007 [58] . ++ + - - - - - - - - - - .
Thomsen et al., 2010 [59] . +++ +++ - - - - - - - - - - .
Zygotically-expressed transcripts       
De Renzis et al., 2007 [58] +++ - - - - - - - ++++ + .
Thomsen et al., 2010 [59] - - - - - - - - - - - +++++ ++++ ++
Maternally-expressed and degraded transcripts       
Maternally-expressed and degraded in early embryos       
De Renzis et al., 2007 [58] ++++ ++++ - - - - - - - . - - - -
Thomsen et al., 2010 [59] ++++ ++++ . - - - - . - - - -
Maternally-expressed and degraded in unfertilized eggs       
Tadros et al., 2007 [60] +++ ++++ - - - - - - - . - - -
Degraded exclusively via early decay machinery       
Thomsen et al., 2010 [59] + . - - - - . .
Degraded via early and late decay machineries       
Thomsen et al., 2010 [59] +++ ++++ - - - - - - . - - - -
Degraded exclusively via late decay machinery       
Thomsen et al., 2010 [59] . +++ ++++ - - . .
Cooperation with other trans -acting factors in mRNA degradation       
Smaug-dependent unstable mRNAs       
Tadros et al., 2007 [60] . - - - . - - - - .
miR-309 cluster-dependent unstable mRNAs       
Bushati et al., 2008 [65] . . . - . .
Zelda transcriptional targets       
Bound by Zelda in promoter region by ChIP-Seq       
Harrison et al., 2011 [52]       
Nuclear cycle 8 . . . ++++ . ++
Nuclear cycle 13 . . . ++++ . +
Late nuclear cycle 14 . . - ++++ + .
Downregulated in zelda mutant embryos       
Liang et al., 2008 [53] . . . ++ . +++
  1. (+) or (−) P = 0.01 to 0.05; (++) or (− −) P = 0.001 to 0.01; (+++) or (− − −) P = 10−10 to 0.001; (++++) or (− − − −) P = 10−10 to 10−30; (+++++) or (− − − − −) P <10−30; (+) symbols indicate significant overlap or enrichment, (−) symbols indicate significant non-overlap or depletion; ‘.’ = not significant (that is, P >0.05). P values are Benjamini-Hochberg corrected Fisher’s exact test (that is, FDR). For complete details of comparisons see Additional file 15.
  2. aWe note that transcripts that were downregulated in brat mutant embryos at the 1.5- to 3.0-h and 4.5- to 6.0-h time points were also modestly enriched for mRNAs produced by direct targets of Zelda [52] (Benjamini-Hochberg corrected Fisher’s exact test P = 0.016 and 0.032, respectively) and those downregulated at 1.5 to 3.0 h were strongly enriched for genes downregulated in zelda-mutant embryos [53] (Benjamini-Hochberg corrected Fisher’s exact test P = 6.6 × 10−9). We speculate that increased Zelda expression in 0 to 1.5 h brat-mutant embryos disrupts the normal cascade of zygotic genome activation resulting in downregulation of a subset of Zelda’s targets at the later time points.