Screening of Conserved Non-Coding Elements with Enhanced Activity of SHOX Gene in PAR1 Region and Its Regulation Mechanism on SHOX Gene

Abstract Background: Defects in conserved non-coding elements (CNEs) are associated with a large number of genetic diseases. The short-chain homeobox gene (SHOX) is regulated by different CNEs in the upstream and downstream, and these CNEs can act as enhancers as homeopathic regulatory elements. Abnormal CNEs upstream and downstream of the SHOX gene can result in short stature of different phenotypes. Methods: This study screened all the CNEs with enhancer action in the PAR1 region of SHOX gene, of which CNE10 and CNE11 have not been reported internationally. We investigated the relationship between CNEs with enhancer action and different promoters of SHOX in HEK293T cells by dual luciferase reporter system. Among them, CNE-2 and CNE-3 up-regulated the activity of SHOX promoter 2, while CNE-5, CNE9, CNE10 and CNE11 up-regulated the activity of SHOX promoter 1.Results: The six groups (CNE-5, CNE-3, CNE-2, CNE9, CNE10, CNE11) are considered to have an enhanced effect on the expression of the SHOX gene. CNE-2 and CNE-3 up-regulated the activity of SHOX promoter 2, while CNE-5, CNE9, CNE10 and CNE11 up-regulated the activity of SHOX promoter 1. Conclusion: CNE-2 and CNE-3 and may have skipped SHOX promoter 1 to interact with SHOX promoter 2 through chromatin looping. The downstream CNE9, CNE10, and CNE11 may skip the interaction of SHOX promoter 2 with SHOX promoter 1, thereby regulating the expression of SHOX.