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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.
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Genome Biology

ISSN: 1474-760X

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