The TCE (TE1/2) and related sequences, TE1 and TE2.

<p>(A) Shown are DNA sequence logos of TE1, TE2, and TE1/2, which is identical to the previously defined TCE <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045009#pone.0045009-Schfer1" target="_blank">[29]</a>. The logos have been aligned relative to the triplet adenines. (B) <i>Drosophila</i> genes that are specifically expressed in testes are aligned by the TCE. Genes indicated in bold font were subject to further analysis in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045009#pone-0045009-g004" target="_blank">Figure 4</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045009#pone.0045009.s003" target="_blank">Table S3</a>. Indicated in parentheses is the TCE location relative to the TSS. TCE nucleotides are colored to match panel A.</p

The <em>Drosophila</em> Translational Control Element (TCE) Is Required for High-Level Transcription of Many Genes That Are Specifically Expressed in Testes

<div><p>To investigate the importance of core promoter elements for tissue-specific transcription of RNA polymerase II genes, we examined testis-specific transcription in <em>Drosophila melanogaster</em>. Bioinformatic analyses of core promoter sequences from 190 genes that are specifically expressed in testes identified a 10 bp A/T-rich motif that is identical to the translational control element (TCE). The TCE functions in the 5′ untranslated region of <em>Mst(3)CGP</em> mRNAs to repress translation, and it also functions in a heterologous gene to regulate transcription. We found that among genes with focused initiation patterns, the TCE is significantly enriched in core promoters of genes that are specifically expressed in testes but not in core promoters of genes that are specifically expressed in other tissues. The TCE is variably located in core promoters and is conserved in <em>melanogaster</em> subgroup species, but conservation dramatically drops in more distant species. In transgenic flies, short (300–400 bp) genomic regions containing a TCE directed testis-specific transcription of a reporter gene. Mutation of the TCE significantly reduced but did not abolish reporter gene transcription indicating that the TCE is important but not essential for transcription activation. Finally, mutation of testis-specific TFIID (tTFIID) subunits significantly reduced the transcription of a subset of endogenous TCE-containing but not TCE-lacking genes, suggesting that tTFIID activity is limited to TCE-containing genes but that tTFIID is not an obligatory regulator of TCE-containing genes. Thus, the TCE is a core promoter element in a subset of genes that are specifically expressed in testes. Furthermore, the TCE regulates transcription in the context of short genomic regions, from variable locations in the core promoter, and both dependently and independently of tTFIID. These findings set the stage for determining the mechanism by which the TCE regulates testis-specific transcription and understanding the dual role of the TCE in translational and transcriptional regulation.</p> </div

The TCE (TE1/2) is enriched in testis-specific core promoters.

<p>The TCE (TE1/2) is enriched in testis-specific core promoters.</p

TCE-containing genomic regions direct testis-specific transcription.

<p>TCE-containing genomic regions direct testis-specific transcription.</p

TCEs are variably located in testis-specific core promoters and are conserved in <i>melanogaster</i> subgroup species.

<p>(A) A smoothed plot of the location of the TCE in testis-specific core promoters, embryo-specific core promoters, and random intergenic regions, which serve as background. The calculated background is similar to the expected background of 5.6 (100/18 bins of 5-nt each). Plotted along the x-axis is the location of the TCE relative to the TSS. Plotted along the y-axis is the fraction of genes with a TCE located within a 5-nt interval. (B) Plotted is the TCE conservation across 12 <i>Drosophila</i> species, as determined by the fraction of matches in the −5/+25 region in <i>D. melanogaster</i> as seen in panel A that are also found at corresponding locations in cross-species alignments. <i>Drosophila</i> species abbreviations are as follow: <i>dmel</i> (<i>melanogaster</i>), <i>dsim</i> (<i>simulans</i>), <i>dsec</i> (<i>sechellia</i>), <i>dyak</i> (<i>yakuba</i>), <i>dere</i> (<i>erecta</i>), <i>dana</i> (<i>ananassae</i>), <i>dpse</i> (<i>pseudoobscura</i>), <i>dper</i> (<i>persimilis</i>), <i>dwil</i> (<i>willistoni</i>), <i>dmoj</i> (<i>mojavensis</i>), <i>dvir</i> (<i>virilis</i>), and <i>dgri</i> (<i>grimshawi</i>).</p