Meersseman Cédric, Letaief Rabia, Léjard Véronique, Rebours Emmanuelle, Guillocheau Gabriel, Esquerré Diane, Djari Anis, Chamberlain Amanda, Vander Jagt Christy, Klopp Christophe, Boussaha Mekki, Renand Gilles, Maftah Abderrahman, Petit Daniel, Rocha Dominique
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
GMA, INRA, Université de Limoges, 87060 Limoges, France.
DNA Res. 2017 Jun 1;24(3):221-233. doi: 10.1093/dnares/dsx004.
Bidirectional promoters are regulatory regions co-regulating the expression of two neighbouring genes organized in a head-to-head orientation. In recent years, these regulatory regions have been studied in many organisms; however, no investigation to date has been done to analyse the genetic variation of the activity of this type of promoter regions. In our study, we conducted an investigation to first identify bidirectional promoters sharing genes expressed in bovine Longissimus thoracis and then to find genetic variants affecting the activity of some of these bidirectional promoters. Combining bovine gene information and expression data obtained using RNA-Seq, we identified 120 putative bidirectional promoters active in bovine muscle. We experimentally validated in vitro 16 of these bidirectional promoters. Finally, using gene expression and whole-genome genotyping data, we explored the variability of the activity in muscle of the identified bidirectional promoters and discovered genetic variants affecting their activity. We found that the expression level of 77 genes is correlated with the activity of 12 bidirectional promoters. We also identified 57 single nucleotide polymorphisms associated with the activity of 5 bidirectional promoters. To our knowledge, our study is the first analysis in any species of the genetic variability of the activity of bidirectional promoters.
双向启动子是调控区域，共同调控以头对头方向排列的两个相邻基因的表达。近年来，这些调控区域已在许多生物体中得到研究；然而，迄今为止尚未进行任何调查来分析这类启动子区域活性的遗传变异。在我们的研究中，我们首先进行了一项调查，以鉴定在牛的胸最长肌中表达的共享基因的双向启动子，然后寻找影响其中一些双向启动子活性的遗传变异。结合牛基因信息和使用RNA测序获得的表达数据，我们鉴定出120个在牛肌肉中活跃的假定双向启动子。我们在体外实验验证了其中16个双向启动子。最后，利用基因表达和全基因组基因分型数据，我们探索了已鉴定的双向启动子在肌肉中的活性变异性，并发现了影响其活性的遗传变异。我们发现77个基因的表达水平与12个双向启动子的活性相关。我们还鉴定出与5个双向启动子的活性相关的57个单核苷酸多态性。据我们所知，我们的研究是对任何物种中双向启动子活性的遗传变异性的首次分析。
