RNA-DNA interactomes
Led DNA-RNA analysis pipeline optimization as Senior Bioinformatician, culminating in a publication in Nature.
Challenge
The classic method for analyzing the spatial arrangement of DNA is HiC. Our goal was to develop a similar method for analyzing the spatial arrangement of DNA and RNA – thus RedC was conceived.
Results
RedC offers numerous advantages, as it allows for almost complete analysis of spatial arrangements. Using RedC, an RNA-DNA proximity ligation approach, we assessed the distribution of major RNA types along the genomes of E. coli, B. subtilis, and T. adornatum. Our findings revealed that messenger RNAs interact preferentially with their cognate genes and downstream genes in the same operon, indicative of polycistronic transcription. Ribosomal RNAs showed a preference for active protein-coding genes in both bacteria and archaea, suggesting co-transcriptional translation. Interestingly, 6S noncoding RNA, a regulator of bacterial transcription, was found depleted from active genes in E. coli and B. subtilis. RedC thus provides a rich resource for studying transcription dynamics and noncoding RNA functions in microbial organisms.