## 3 Results and Discussion
### Analysis of Mutation-Associated Motifs in Z-DNA-Intersected Enhancer Elements
Thus, the localization of mutations in low-complexity regions and tandem repeats may be associated with the underlying mechanisms of their occurrence. The identified motifs, due to their localization, exhibit certain similarities. To determine which transcription factors they interact with, a search was performed for each motif using MEME Tomtom. It was found that all the presented motifs demonstrate statistically significant binding to the following TFs: KLF4, KLF9, KLF11, KLF16, SP3, SP8, and SP9. KLF and SP (Kruppel-like factor and specificity protein) transcription factors play critical roles in processes such as cell proliferation and differentiation, embryogenesis, and other physiological processes, the dysregulation of which can lead to the development of various pathologies [58]. These TFs belong to the same family, with the only distinction being the presence of a Buttonhead box domain in SPs [59]. Of particular interest are the associations of certain KLFs/SPs with the development of neurodevelopmental disorders and cognitive impairments. For instance, KLF9 plays an essential role in adult hippocampal neurogenesis. Dysregulation of KLF9 expression in dentate granule neurons is associated with delayed cell maturation, impaired neuronal differentiation, and reduced neurogenesis-dependent synaptic plasticity [60]. KLFs are also capable of regulating axonal growth. KLF4 acts as an inhibitor of axonal growth in the central nervous system. In experiments with modified neurons, it was demonstrated that KLF15, KLF9, KLF16, KLF14, KLF13, KLF5, KLF4, KLF2, and KLF1 decreased neurite length, whereas KLF7 and KLF6 increased it [61]. Overexpression of KLF4 in neural stem cells led to the development of hydrocephalus and astrocytosis in mice and suppressed the renewal of these cells [62]. It is important to note that in the studied SE region (within the spacer chr10:119394453-119394936 and the enhancer chr10:119394156-119394453), a significant number of transcription factor binding sites are predicted. As a result, unequivocally assessing the contribution of the appearance or disappearance of one or several motifs presents a non-trivial challenge, which requires further in-depth investigation. Among the mutations leading to the formation or disappearance of these motifs, a single nucleotide polymorphism, a short insertion, and three long deletions were identified. As mentioned earlier, these mutations were previously unknown; however, they overlap with regions exhibiting altered copy number variants (CNVs). The CNVs in the region of the studied super-enhancer were classified as pathogenic based on findings from a project investigating the associations between rare CNVs and developmental disorders [63]. Analysis of the impact of these mutations on the functions of nearby genes revealed that all the studied unknown mutations are located within the intronic region of the _GRK5_ gene. _RGS10_ is the nearest active gene to the investigated SE and is considered its potential target. Functional annotation of these genes using DAVID demonstrated that both genes are involved in signaling pathways such as the G protein-coupled receptor (GPCR) signaling pathway and GPCR downstream signaling [64]. To further evaluate the clinical significance of the mutations identified within SE-Z-DNA loci, their positions were compared with clinically annotated variants from public databases, including the GWAS Catalog and ClinVar. Several notable overlaps were identified (Table S3), particularly involving loci associated with neurodevelopmental and neurodegenerative disorders. For instance, mutations detected in the super-enhancer region on chromosome 10 (positions 119394275, 119394519, 119394520, 119394546, and 119394789)  
Figure 4: Gain and loss of transcription factor binding motifs due to mutations in a Z-DNA-associated super-enhancer region, with motif logos and corresponding TF E-value distributions.