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

DNA/RNA hybrids are present in normal cellular physiology, but when misregulated in the genome, they can contribute to human pathologies such as neurodevelopmental disorders and cancer. These hybrid structures are often abundant in repetitive genomic sequences such as telomeres and centromeres, contributing to evolutionary conserved phenomena. However, excessive accumulation can lead to DNA damage and genomic instability. Studies of autism spectrum disorders (ASDs) have revealed genome -wide disruptions, including mutations and significant deregulation of gene expression. Surprisingly, the common underlying factors remain unidentified. ASDs, which are of hereditary origin and more prevalent among boys, manifest themselves during development through disorders of various origins. In this study, we used whole-genome transcriptomic analysis of DNA/RNA hybrids from blood samples of autistic patients and healthy controls. we identified differences between numerous hybrid genomic regions with varying sequence compositions. Additionally, we observed local specificity in genomic regions, where RNA could either inhibit or enhance transcription. Our analysis of short RNAs hybridized with DNA revealed a striking example of transcriptional activity, where each gene is stably transcribed. We propose that non-coding RNAs originating from exons, introns or intergenic regions bind to DNA as hybrids (DNA/RNA) and influence gene expression. The specific levels of these short RNAs may regulate their own transcription, likely affecting cell fate. DNA-associated RNA molecules were purified form 12 blood samples (6 autism patients, 6 Controls). 10-100 ng of RNA after Dnase digestion were recovered and analyzed by high throughput sequencing on Illumina.