Department of Biology, Boston College, Chestnut Hill, Massachusetts, United States of America.
PLoS One. 2012;7(5):e35202. doi: 10.1371/journal.pone.0035202. Epub 2012 May 2.
Many conserved noncoding sequences function as transcriptional enhancers that regulate gene expression. Here, we report that protein-coding DNA also frequently contains enhancers functioning at the transcriptional level. We tested the enhancer activity of 31 protein-coding exons, which we chose based on strong sequence conservation between zebrafish and human, and occurrence in developmental genes, using a Tol2 transposable GFP reporter assay in zebrafish. For each exon we measured GFP expression in hundreds of embryos in 10 anatomies via a novel system that implements the voice-recognition capabilities of a cellular phone. We find that 24/31 (77%) exons drive GFP expression compared to a minimal promoter control, and 14/24 are anatomy-specific (expression in four anatomies or less). GFP expression driven by these coding enhancers frequently overlaps the anatomies where the host gene is expressed (60%), suggesting self-regulation. Highly conserved coding sequences and highly conserved noncoding sequences do not significantly differ in enhancer activity (coding: 24/31 vs. noncoding: 105/147) or tissue-specificity (coding: 14/24 vs. noncoding: 50/105). Furthermore, coding and noncoding enhancers display similar levels of the enhancer-related histone modification H3K4me1 (coding: 9/24 vs noncoding: 34/81). Meanwhile, coding enhancers are over three times as likely to contain an H3K4me1 mark as other exons of the host gene. Our work suggests that developmental transcriptional enhancers do not discriminate between coding and noncoding DNA and reveals widespread dual functions in protein-coding DNA.
许多保守的非编码序列作为转录增强子发挥作用，调节基因表达。在这里，我们报告称，蛋白质编码 DNA 也经常包含在转录水平起作用的增强子。我们基于斑马鱼和人类之间的强序列保守性以及在发育基因中的存在，使用 Tol2 可转座 GFP 报告基因测定法在斑马鱼中测试了 31 个蛋白质编码外显子的增强子活性。对于每个外显子，我们通过一种新颖的系统测量了数百个胚胎在 10 个解剖结构中的 GFP 表达，该系统实现了手机的语音识别功能。我们发现，与最小启动子对照相比，有 24/31（77％）个外显子驱动 GFP 表达，而 14/24 个外显子是特定于解剖结构的（在四个解剖结构或更少的解剖结构中表达）。这些编码增强子驱动的 GFP 表达通常与宿主基因表达的解剖结构重叠（60％），表明自我调节。高度保守的编码序列和高度保守的非编码序列在增强子活性（编码：24/31 与非编码：105/147）或组织特异性（编码：14/24 与非编码：50/105）方面没有显着差异。此外，编码和非编码增强子显示出相似水平的增强子相关组蛋白修饰 H3K4me1（编码：9/24 与非编码：34/81）。同时，编码增强子比宿主基因的其他外显子更有可能包含 H3K4me1 标记三倍以上。我们的工作表明，发育转录增强子不会区分编码和非编码 DNA，并揭示了蛋白质编码 DNA 的广泛双重功能。
