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

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.

The short stature homeobox gene (SHOX) is located in the short-arm PAR1 region of human sex chromosomes and is a member of the homeobox gene transcription factor family [14]. It plays a crucial role in bone development and growth. Mutations in the SHOX gene affect bone growth in a dosedependent manner. Studies have found that in patients with a karyotype of 47, XXY with Kline syndrome and a karyotype of 47,XXX patients with triple X syndrome, the increase in SHOX dose is associated with a high body phenotype [15]. In addition, studies have found triploids in the PAR1 region containing the SHOX gene in tall women [16]. The reduction in SHOX dose is associated with short stature. A single dose de ciency of the SHOX gene affects approximately 2-3% of patients with Idiopathic Short Stature (ISS) and 70% of patients with Léri-Weill dyschondrosteosis (LWD). The homozygous deletion of the SHOX gene results in Langer mesomelic dysplasia (LMD) characterized by more severe short stature and skeletal malformations [17] . In addition to short stature, patients with SHOX gene deletions will show many skeletal malformations ranging from mild to severe, such as forearm shortening and exion, Madelung malformation, short fourth metacarpal, elbow valgus and small mandible. However, some studies have found that the deletion of the SHOX gene regulatory region in the PRA1 region is identical to the phenotype caused by the deletion of the SHOX gene coding region [18].
Like most growth and development genes, the SHOX gene requires the regulation of spatio-temporal expression with the help of cis-regulatory elements such as enhancers [19]. Nitin Sabherwal et al [8] analyzed four LWD families and found that the SHOX gene coding region was intact, while the SHK downstream 200Kb sequence fragment was deleted. It is speculated that the missing region of the patient contains some special components to regulate the expression of SHOX gene. This fragment was analyzed by comparative genomics to obtain 8 highly conserved non-coding sequences (CNEs). Studies have shown that three conserved non-coding sequences CNE4, CNE5, and CNE9 have enhanced activity in chicken embryonic limb development. Subsequently, the conserved non-coding sequences CNE-5, CNE-3, and CNE-2 upstream of SHOX were also con rmed to have enhanced activity, and sequence fragments containing CNEs upstream of the SHOX gene were con rmed to be deleted in short stature patients [20][21][22][23]. The clinical phenotypes of CNEs deletion and SHOX coding region mutations in the SHOX gene are di cult to distinguish, so CNEs may act as cis-regulators to enhance the expression of SHOX gene.
It was found that CNEs with enhancer activity upstream and downstream of SHOX gene include CNE-2, CNE-3, CNE-5, CNE4, CNE5 and CNE9, of which CNE9 is the strongest enhancement sequence [8].
However, the existing research is basically located within 850 kb of the SHOX gene. In our previous study of 354 patients with ISS, we found that there is a deletion in the 1300 kb region downstream of the SHOX gene, but the clinical phenotype is relatively light, and it is estimated that the SHOX gene is 800 kb downstream. There are also CNEs that are present and cis-regulatory activity is present during limb development. At present, human genome CNEs are obtained by comparative genomics and bioinformatics methods, so this study will obtain and screen all CNEs (up to 1300 kb downstream) of SHOX genes by comparing genomics and bioinformatics.
At present, little is known about the regulation mechanism of SHOX gene by CNEs upstream and downstream of SHOX gene. Blaschke et al [24] found that the SHOX gene has two promoters, the second promoter is located in exon 2, and the two promoters produce different mRNAs encoding the same protein, with the same coding ability and different translational potency. . Clandia Durand et al [25] found that HOXA9 up-regulates the expression of SHOX gene in U2OS cells by binding to SHOX promoter 2.
According to the "core promoter" concept [24], different promoters compete for transcription factors and tissue-speci c enhancer elements, and we speculate that these CNEs may exert potentiation by binding to different promoters of SHOX. Since SHOX has no orthologs in rodents, we chose to construct two pairs of SHOX genes with CNEs (-2, -, - 5,9,10,11) in vitro. In the luciferase reporter gene system, the relationship between each CNE and the SHOX gene promoter was investigated.

Materials And Methods
Genomics analysis of CNEs for SHOX gene PRA1 The ECR Browser and CONDOR databases were combined to determine the location of all CNEs of the SHOX gene PRA1, and the genomic sequence was searched using the UCSC genome browser (www.ucsc.edu/genome).
Construction of green uorescent protein particles containing different CNE As was shown in Table 2, each CNEs primer was designed, and each CNE was ampli ed by PCR to construct a pEGFP-N1 plasmid containing different CNE.

Transfection of HEK293 cells with plasmids containing different CNE
As was shown in Figure 2, the plasmid containing each CNEs was ampli ed and extracted, and transfected into HEK293T cell culture. HEK293T cells were cultured in DMEM medium containing 10% fetal bovine serum (Gibco), added with double antibody, and cultured in a 37°C, 5% CO 2 incubator. The cells were passaged in 24-well plates 20 h to 24 h before transfection, and the cell density was about 0.7×10 5 cells/mL. Plasmid transfection was carried out according to the lipofectamine 2000 liposome transfection instructions. After 48 h of transfection, cells were harvested.
Identi cation of different CNE enhancing activities by real-time uorescent quantitative nucleic acid ampli cation detection system (Q-PCR) After the transfected cells were extracted with RNA, they were reverse transcribed into cDNA, and the enhanced activity of all CNEs was identi ed by Q-PCR. SHOX gene primer: upstream 5'-GCATAAAGGCGTCATCTTGG-3', downstream 5'-GTTGGAAAGGCATCCGTAAG-3'.

Localization of SHOX Promoter 2 Sequence
The SHOX promoter 2 is located 432 bp upstream of the initiation codon AUG in the second exon of SHOX [24], and the position of the SHOX promoter 2 sequence on the X chromosome is determined by the UCSC genome browser (www.ucsc.edu/genome) as chrX511202 -511634.

Construction of dual luciferase vectors
As was shown in Figure 3, using psiCHECK-2 vector (Promega), CNE-2, CNE-3, and CNE-5 were located upstream of the SHOX promoter, and the two promoters of CNES and SHOX were spliced together by Overlap. The fragment was cloned into the upstream of the Luc gene using BglII and NheI. CNE9, CNE10 and CNE11 are located downstream of the SHOX promoter. The SHOX promoter was cloned upstream of the hRLuc gene with BglII and NheI, and the CNES gene was inserted into the XhoI and NotI sites. That is, the T7 promoter was replaced with the SHOX promoter.
Each CNEs fragment was synthesized, and the design of each CNEs primer was as shown in Table 2. Each CNEs fragment and the control fragment were digested by PCR, and the enzyme was cut to complete the gel recovery. The competent cells were transformed, and the cells were picked up after transformation. The bacteria were shaken at 37°C for 250 hours at rpm for 14 hours, and the positive bacteria were sequenced by PCR.

Dual luciferase assay
The transfected cells were plated into 96-well plates and operated according to the instructions of the Dual-Luciferase Assay Kit (Promega).

Statistical analysis method
The count data in the study were described by frequency and percentage, and the measurement data were described by means of mean (standard deviation). The comparison between the two groups of samples was analyzed by chi-square analysis or t-test, and the comparison between the three groups and above was analyzed by differential analysis. Statistical analysis of data was performed using SPSS 23.0 software. Bilateral P<0.05 was considered statistically signi cant.

Results
Screening out CNEs of SHOX gene PRA1 We screened 18 conserved non-coding sequences using the comparative genomic approach. The positions of each CNE on the X chromosome are shown in Table 3 and Figure 4 (NCBI build 36.1). Q-PCR identi ed the expression of SHOX gene after transfection of cells containing different CNE plasmids, as shown in Table 5.

Homogeneity test of variance
The homogeneity test of SHOX gene expression was tested. The homogeneity test of variance showed that the SHOX gene expression was uneven between groups (P=0.000, <0.05), and the sample size was small. Therefore, one-way ANOVA and nonparametric tests cannot be performed on SHOX gene expression. The use of t-test analysis method will increase the type I error. Therefore, the SHOX gene expression is changed to the SAS programming calculation using the Bootstrap method, and the sample rate is compared multiple times. The results are shown in Table 6 and Table 7.
From the above data, using the Bootstrap method for multi-sample pairwise comparison (Table 6), we can see that the untransfected group (no intervention on the cells, ie, not transferred into the plasmid) and the control group (adding an empty plasmid without CNEs) For comparison, P=0.96 (>0.05), that is, H1 was rejected, and H0 was accepted, and there was no statistical difference between the untransfected group and the control group. That is to say, the plasmid itself has no effect on the expression level of SHOX gene, that is, the in uence of the plasmid on the cells is excluded, thereby affecting the change of the expression level of the SHOX gene.The P values of CNE-4, CNE2, CNE3, CNE4, CNE5, CNE6, CNE7, CNE8, CNE12, CNE13, CNE14, and CNE15 compared with the untransfected group were 0.706, 0.942, 1, 1, and 0.416, respectively. 0.109, 0.416, 0.838, 1, 0.108, 0.866, and 0.932 are all greater than 0.05. That is to say, there was no statistical difference between CNE-4, CNE2, CNE3, CNE4, CNE5, CNE6, CNE7, CNE8, CNE12, CNE13, CNE14, CNE15 and untransfected groups. That is, after the above CNEs interfere with the cells, there is no effect on the expression level of the SHOX gene.The P values of CNE-5, CNE-3, CNE-2, CNE9, CNE10, and CNE11 compared with the untransfected group were <.0001, <.0001, <.0001, 0.015, 0.01, and 0.007, respectively, less than 0.05. . That is to say, there are statistical differences between the above six groups of CNE-5, CNE-3, CNE-2, CNE9, CNE10 and CNE11 and the untransfected group. Therefore, the above 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.

Relationship between CNEs and SHOX promoter
Control group and experimental group, two duplicate wells, three biological replicates. Using SPSS22.
software, the mean and standard deviation of Rluc/Fluc in each CNE group are shown in Table 8. Compared with the control group, when SHOX Promoter1 was used, the values of Rluc/Fluc in CNE-2 and CNE-3 groups decreased, while the values of Rluc/Fluc in other groups increased in different magnitudes.
When using SHOX Promoter2, the result is just the opposite. One-way analysis of variance was performed and the results of Tamhane's ST2 test are shown in Table 9. Thus, 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.

Discussion
Human height is determined by genetic factors and environmental factors, and is dominated by genetic factors. Short stature is one of the most common endocrine diseases in children. The abnormal incidence of SHOX gene in a large number of genes related to height is about 12.5% of all short stature patients, which is the focus of research on short stature and skeletal deformity.
SHOX gene defects or abnormalities in their CNEs can result in short stature of different phenotypes. The conserved non-coding sequences of the PAR1 region that have an enhancer effect on the SHOX gene have been reported in the international literature: CNE-2, CNE-3, CNE-5, CNE4, CNE5, CNE9. By expanding the screening region to 1300 kb downstream of the SHOX gene, we screened two new CNEs downstream of the SHOX gene, and veri ed that they also have enhanced activity.
Among all the conserved non-coding elements that have been reported, CNE9 is the most important regulatory element of the SHOX gene. Studies have con rmed that SHOX promoter 1 interacts with CNE9 through chromatin conformation capture technology, and CNE9 may enhance the expression of SHOX protein through chromatin loop formation [8]. The SHOX gene has two promoters, and the transcript 5'UTR obtained by the promoter 2 is short and the translation e ciency is high. The transcript obtained by promoter 1 signi cantly inhibited translational e ciency due to the long 5' UTR upstream of the major open reading frame [24]. Therefore, we speculate that each CNE may bind to a different promoter of SHOX, thereby exerting an enhancing effect. SHOX promoter 2 is a promoter within the gene. Currently, there is little research in the world. Claudia Durand [25] found that SHOX gene is a target gene of HOXA9, which can up-regulate the expression of SHOX gene in U2OS cells. The HOXA9 binding site was located in SHOX promoter 2 by immunoprecipitation and electrophoretic migration experiments, suggesting that HOXA9 may regulate SHOX gene expression through SHOX promoter 2.
In this study, plasmids containing SHOX different promoters and CNE were transfected into HEK293T cells. The relationship between CNEs and SHOX promoters was studied by dual luciferase assay. The results showed that 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. Therefore, we hypothesized that CNE-2 and CNE-3 mainly regulate the expression of SHOX gene through SHOX promoter 2, and CNE-5, CNE9, CNE10 and CNE11 regulate SHOX gene expression mainly through SHOX promoter 1. The expression of SHOX gene is enhanced by the action of different promoters, which may be the mechanism by which non-coding sequences (CNEs) regulate the expression of SHOX genes.
The team of Guoliang Li [24] identi ed the interaction between thousands of promoters and enhancers, including approximately 1000 ultra-long-range components (greater than 500 Kb). The study observed that ≥40% of enhancers did not interact with their nearest promoter, but instead skipped their target promoter. The promoter 1 of SHOX is located between the upstream CNE-2, CNE-3 and SHOX promoter 2. We have introduced 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.

Declarations
Ethics approval and consent to participate This article does not contain any studies with human participants or animals performed by any of the authors.

Consent for publication:
Not applicable.
Availability of data and material: Not applicable.

Funding
This study was funded by the National Natural Science Foundation (81170723).

Competing interests:
There are no potential con icts of interest to disclose.

Figure 3
The schematic diagram of PsiCHECK-2 vector. Conserved non-coding sequence