RiboRid: A low cost, advanced, and ultra-efficient method to remove ribosomal RNA for bacterial transcriptomics

Area of Science:

• Molecular Biology
• Genomics
• Biotechnology

Background:

• Ribosomal RNA (rRNA) constitutes over 90% of cellular RNA, posing a significant challenge for transcriptomic studies.
• Efficient removal of rRNA is crucial for accurate analysis of messenger RNA (mRNA) and other RNA species.
• Existing rRNA depletion methods can be costly and may not effectively remove pre-rRNAs.

Purpose of the Study:

• To develop a cost-effective and robust method for bacterial ribosomal RNA (rRNA) depletion.
• To evaluate the efficiency of the RiboRid method in removing both mature and pre-rRNAs.
• To demonstrate the applicability of RiboRid across various bacterial transcriptomic techniques.

Main Methods:

• Enzymatic degradation of bacterial rRNA using a thermostable RNase H.
• Implementation of experimental controls to minimize non-specific mRNA degradation.
• Application of the RiboRid method to RNA-Seq, differential RNA-Seq, Term-Seq, and ribosome profiling.

Main Results:

• Achieved high rRNA removal efficiency, up to 99.99%.
• Successfully depleted pre-rRNAs, which often remain after standard rRNA removal.
• Demonstrated effectiveness across multiple transcriptomic applications.
• Estimated cost of approximately $10 per sample.

Conclusions:

• RiboRid is a low-cost, robust, and highly efficient bacterial rRNA depletion method.
• The method is suitable for large-scale, high-throughput bacterial transcriptomic studies.
• RiboRid facilitates accurate gene expression profiling and analysis of other RNA species.