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Analysis of hybrid RNA/DNA profiles in blood from autistic patients reveals differences in mRNA and ncRNA regions

ABSTRACT: Autism spectrum disorder (ASD) is a set of genetically heterogenous neurodevelopmental disorders characterized by core symptoms including impaired social interaction, communication deficits, and restricted or stereotyped behaviors. While a significant number of cases are not explained by Mendelian inheritance, there is growing evidence in implication of non-coding RNAs (ncRNAs) in development and inheritance of ASD. Transcriptional studies face challenges from patient-specific variations in gene expression and technical differences in preserving RNA integrity. We propose that isolating RNA from DNA/RNA hybrids provides a robust method to capture transcriptional information. We performed a whole transcriptome analysis on blood samples from ASD patients and healthy controls to investigate transcripts associated with DNA/RNA hybrids. We identified 278,300 novel transcripts across 68,487 DNA/RNA hybrid loci, with significant enrichment in exonic and intronic regions. The novel long non-coding RNAs (lncRNAs) we found showed higher expression levels compared to known transcripts. Differential expression analysis revealed 301 significantly upregulated and 401 downregulated transcripts in ASD samples. Through qRT-PCR validation, we confirmed the significant upregulation of RN7SK and SMARCC2 associated with DNA/RNA hybrids in ASD patients. Pathway and enrichment analyses highlighted mitochondrial dysfunction and energy metabolism. Our results suggest that ncRNAs can form DNA/RNA hybrids that influence gene expression, providing preliminary insights into the mechanisms of transcriptional dysregulation in ASD.

ORGANISM(S): Homo sapiens

PROVIDER: GSE282063 | GEO | 2025/09/13

REPOSITORIES: GEO

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Project description:The general role of RNA in the cell beyond protein biosynthesis is only beginning to emerge with little knowledge about the structural or organizational functions of RNA. In turn, functional non-coding RNAs (ncRNAs) are often identified by their regulation or impact on cellular phenotypes. However, the huge number and diversity of ncRNAs highly complicate the task of their molecular characterization and rationalization into cellular processes. For the vast majority of ncRNAs as well as for non-coding functions of known mRNAs, the mechanisms underlying their modes of action as well as their impact on protein complexes are unknown. Thus, the greatest challenge in the field of RNA biology today is the elucidation of molecular mechanisms and functional interaction partners of RNA molecules. Since RNAs do not act alone, but often interact with specific protein partners, proteomic approaches have been developed to study RNA-binding proteins (RBPs) and aim at revealing the molecular mechanisms underlying RNA function. Large-scale studies aiming at globally identifying RNA-binding proteins principally focused on poly(A)-RNA transcripts. A notable limitation of such approaches is that many ncRNAs are not polyadenylated, so that their interaction partners were not detected in these screens. Most importantly however, the overlap between the numerous studies aiming to identify RBPs is limited and their specificity remains unclear. Moreover, the previous studies were based on the identification of RBPs omitting their participation in protein-protein complexes and more interestingly in RNA-dependent protein-protein complexes. Here, we introduce the concept of "RNA dependence" to overcome these challenges. We define a protein as RNA-dependent if its interactome (hence likely its function) depends on RNA without necessarily directly binding to RNA. Based on this new concept, we developed a proteome-wide screening approach to gain mechanistic insight into the function of RNAs - both coding and non-coding - in RNA-protein complexes and their impact on the function of such complexes.

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Analysis of hybrid RNA/DNA profiles in blood from autistic patients reveals differences in mRNA and ncRNA regions

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