The 5’ regulatory region of the β actin gene in Clarias species is complex and variable in relation to ecological needs

Abstract The β actin gene is involved in various cellular housekeeping processes including transcription, mRNA processing, cell signaling and chromosome remodeling. For regulating the expression of this gene under different environmental conditions, the promoter region of the β actin gene is structurally dynamic with multiple regulatory features in the upstream region. Most previous information about the 5’ regulatory region of the β actin gene has been limited to in vitro laboratory experiments. Considering the need for functional versatility of expression of this gene in the Catfish Clarias batrachus in different environments, here we have analyzed the 5’ regulatory region of β actin and identified numerous elements that are variable. We have made comparisons of individuals from three populations found in three different diverse ecological systems, as well as in three sister species, to elucidate its structural diversity. Our results show that the 5’ regulatory region has considerable diversity and changes in architecture with respect Cis -acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5’ regulatory region of a housekeeping gene like β actin, modify its architecture as per the environmental conditions. These modifications specifically includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5’ regulatory region is conserved which was yet not highlighted. Author summary Promoter is a regulatory region where the basal transcription machinery assembles to initiate the process of transcription. It plays crucial role in controlling the gene expression. The 5’ regulatory region includes TATA box, CAAT box, GC box and Cis -acting regulatory elements. Most previous information about the 5’ regulatory region of the β actin gene has been limited to in vitro laboratory experiments. Our study results show that the 5’ regulatory region has considerable diversity and changes in architecture with respect Cis -acting regulatory elements. These changes may be linked to positive selection in combating pollution or disease like conditions encountered by the organism. These observations leads to the conclusion that 5’ regulatory region of a housekeeping gene like β actin, modify its architecture as per the environmental requirements. These modifications precisely includes diversity of TF binding sites indicating the assortment of environmental variables and only one third region of 5’ regulatory region is conserved. These findings clearly define a novel role of promotor of β actin gene which was yet not highlighted. These findings can broaden our understanding in linking TF in 5’ regulatory regions to a specific environmental variable/disease conditions. This may become a simple strategy in understanding complex gene-environment interactions.