Motif composition, conservation and condition-specificity of single and alternative transcription start sites in the Drosophila genome

A map of transcription start sites across the Drosophila genome, providing insights into initiation patterns and spatiotemporal conditions

Electrophysiological Evidence of Atypical Spatial Attention in Those with a High Level of Self-reported Autistic Traits

Selective attention is atypical in individuals with autism spectrum conditions. Evidence suggests this is also the case for those with high levels of autistic traits. Here we investigated the neural basis of spatial attention in those with high and low levels of self-reported autistic traits via analysis of ERP deflections associated with covert attention, target selection and distractor suppression (the N2pc, NT and PD). Larger N2pc and smaller PD amplitude was observed in those with high levels of autistic traits. These data provide neural evidence for differences in spatial attention, specifically, reduced distractor suppression in those with high levels of autistic traits, and may provide insight into the experience of perceptual overload often reported by individuals on the autism spectrum

Transcription Initiation Patterns Indicate Divergent Strategies for Gene Regulation at the Chromatin Level

The application of deep sequencing to map 5′ capped transcripts has confirmed the existence of at least two distinct promoter classes in metazoans: “focused” promoters with transcription start sites (TSSs) that occur in a narrowly defined genomic span and “dispersed” promoters with TSSs that are spread over a larger window. Previous studies have explored the presence of genomic features, such as CpG islands and sequence motifs, in these promoter classes, but virtually no studies have directly investigated the relationship with chromatin features. Here, we show that promoter classes are significantly differentiated by nucleosome organization and chromatin structure. Dispersed promoters display higher associations with well-positioned nucleosomes downstream of the TSS and a more clearly defined nucleosome free region upstream, while focused promoters have a less organized nucleosome structure, yet higher presence of RNA polymerase II. These differences extend to histone variants (H2A.Z) and marks (H3K4 methylation), as well as insulator binding (such as CTCF), independent of the expression levels of affected genes. Notably, differences are conserved across mammals and flies, and they provide for a clearer separation of promoter architectures than the presence and absence of CpG islands or the occurrence of stalled RNA polymerase. Computational models support the stronger contribution of chromatin features to the definition of dispersed promoters compared to focused start sites. Our results show that promoter classes defined from 5′ capped transcripts not only reflect differences in the initiation process at the core promoter but also are indicative of divergent transcriptional programs established within gene-proximal nucleosome organization

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

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

TCE-containing genomic regions direct testis-specific transcription.

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

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

A paired-end sequencing strategy to map the complex landscape of transcription initiation

Recent high-throughput sequencing protocols have uncovered the complexity of mammalian transcription by RNA polymerase II, helping to define several initiation patterns in which transcription start sites (TSSs) cluster within both narrow and broad genomic windows. Here, we describe a paired-end sequencing strategy, which enables more robust mapping and characterization of capped transcripts. This strategy was applied to explore the transcription initiation landscape in the Drosophila melanogaster embryo. Extending the previous findings in mammals, we found that fly promoters exhibit distinct initiation patterns, which are linked to specific promoter sequence motifs. Furthermore, we identified a large number of 5′ capped transcripts originating from coding exons; analyses support that they are unlikely the result of alternative TSSs, but rather the product of post-transcriptional modifications. Taken together, paired-end TSS analysis is demonstrated to be a powerful method to uncover the transcriptional complexity of eukaryotic genomes