Genetic variability of the activity of bidirectional promoters: a pilot study in bovine muscle.
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.
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.|GMA, INRA, Université de Limoges, 87060 Limoges, France.
Cédric
C
Meersseman
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Rabia
R
Letaief
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Véronique
V
Léjard
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Emmanuelle
E
Rebours
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Gabriel
G
Guillocheau
GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet Tolosan, France.
Diane
D
Esquerré
SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France.
Anis
A
Djari
Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.|AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia.
Amanda
A
Chamberlain
Dairy Futures Cooperative Research Centre, AgriBio, Bundoora, Victoria, Australia.|AgriBio, Department of Economic Development, Jobs, Transport & Resources, Victoria, Australia.
Christy
C
Vander Jagt
SIGENAE, UR 875, INRA, 31362 Castanet-Tolosan, France.
Christophe
C
Klopp
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Mekki
M
Boussaha
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Gilles
G
Renand
GMA, INRA, Université de Limoges, 87060 Limoges, France.
Abderrahman
A
Maftah
GMA, INRA, Université de Limoges, 87060 Limoges, France.
Daniel
D
Petit
GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
Dominique
D
Rocha
D000818:Animals; D064131:Back Muscles / Q000378:metabolism*; D002417:Cattle; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D008297:Male; D010865:Pilot Projects; D020641:Polymorphism, Single Nucleotide; D011401:Promoter Regions, Genetic; D011506:Proteins / Q000235:genetics*
D011506:Proteins
bidirectional promoter; cattle genome; genetic variability; muscle