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Comprehensive architecture of the bacterial RNA Interactome

ABSTRACT: RNA-based regulation is ubiquitous in all microbes yet generating a global map of RNA–RNA interactions has been a formidable challenge. Here, TRIC-seq is introduced as an unbiased approach to map transcriptome-wide RNA–RNA interactions in several bacterial species. Applying TRIC-seq to Escherichia coli captured thousands of unique interactions, unveiling not only the targets of regulatory small RNAs (sRNAs) but also novel non-canonical regulatory interactions involving ribosomal RNAs, transfer RNAs, and messenger RNAs, including a widespread interaction between the 3’ extension of the 16S rRNA and the 5'UTRs of stress-response mRNAs. Unsupervised clustering of the interactome revealed a highly modular architecture, clustered by sRNA interactions. TRIC-seq is presented as a genetics-free approach that can be applied to any bacteria to de novo reveal regulatory RNAs along with their regulons at high specificity and resolution. TRIC-seq revealed a vast, functionally coherent cluster of mRNAs that aggregates and is excluded from ribosomes, providing compelling evidence for bacterial RNA condensates that share key properties with eukaryotic stress granules. TRIC-seq’s robust mapping provides a powerful platform to uncover RNA structures and generating foundational data for the next generation of biological models.

ORGANISM(S): Escherichia coli Myxococcus xanthus Staphylococcus aureus Stutzerimonas stutzeri

PROVIDER: GSE305265 | GEO | 2025/10/01

REPOSITORIES: GEO

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Project description:<p>Non-coding elements in our genomes that play critical roles in complex disease are frequently marked by highly unstable RNA species. Sequencing nascent RNAs attached to an actively transcribing RNA polymerase complex can identify unstable RNAs, including those templated from gene-distal enhancers (eRNAs). However, nascent RNA sequencing techniques remain challenging to apply in some cell lines and especially to intact tissues, limiting broad applications in fields such as cancer genomics and personalized medicine. Here we report the development of chromatin run-on and sequencing (ChRO-seq), a novel run-on technology that maps the location of RNA polymerase using virtually any frozen tissue sample, including samples with degraded RNA that are intractable to conventional RNA-seq. We used ChRO-seq to develop the first maps of nascent transcription in 23 human glioblastoma (GBM) brain tumors and patient derived xenografts. Remarkably, >90,000 distal enhancers discovered using the signature of eRNA biogenesis within primary GBMs closely resemble those found in the normal human brain, and diverge substantially from GBM cell models. Despite extensive overall similarity, 12% of enhancers in each GBM distinguish normal and malignant brain tissue. These enhancers drive regulatory programs similar to the developing nervous system and are enriched for transcription factor binding sites that specify a stem-like cell fate. These results demonstrate that GBMs largely retain the enhancer landscape associated with their tissue of origin, but selectively adopt regulatory programs that are responsible for driving stem-like cell properties. We also identified enhancers and their associated transcription factors that regulate genes characteristic of each known GBM subtype, and discovered a core group of transcription factors that control the expression of genes associated with clinical outcomes. This study uncovers new insights into the molecular etiology of GBM and introduces ChRO-seq which can now be used to map regulatory programs contributing to a variety of complex diseases.</p>

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Comprehensive architecture of the bacterial RNA Interactome

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