Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle

Abstract

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.

Survey of allele specific expression in bovine muscle

“…On average, 89% (86–91%) of the reads were uniquely mapped (Table S3 ). In a previous study 26 , 17 of our 19 RNA samples were sequenced and mapping was performed using BWA (version 0.5.9-r16) 21 . 63–76% of the mapped reads were aligned.…”

“…RNA extraction and sequencing was performed as previously described 24 – 26 . Briefly, after transfer to ice-cold RNeasy RLT lysis buffer (Qiagen), LT tissue samples were homogenized using a Precellys tissue homogeniser (Bertin Technologie).…”

Safe-Harbor-Targeted CRISPR/Cas9 System and Cmhyd1 Overexpression Enhances Disease Resistance in Cordyceps militaris

“…Based on the well-annotated genomes of strain CM01, a total of 9639 intergenic regions were identified, which were classified into convergent, divergent, or tandem according to the orientation of the two neighboring genes (Figure B). The intergenic regions with the convergent orientation were concerned as they are unlikely to contain promoters, which are important for transcription regulation . There were 2835 intergenic regions with convergent orientation (Figure B).…”

“…The intergenic regions with the convergent orientation were concerned as they are unlikely to contain promoters, which are important for transcription regulation. 34 There were 2835 intergenic regions with convergent orientation (Figure 1B). Further, the intergenic regions with convergent orientation larger than 6 kb were excluded, as they may contain unpredicted genes or be enriched with repetitive elements, which may affect the expression of the inserted DNA construct.…”