Efficient and cost-effective bacterial mRNA sequencing from low input samples through ribosomal RNA depletion

BMC Genomics

Estella Liu¹  Kellie A. Heom²  Chatarin Wangsanuwat²  Michelle A. O’Malley²  Siddharth S. Dey³ 

[1] Department of Chemical Engineering, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;Department of Chemical Engineering, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;Center for Bioengineering, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;Department of Chemical Engineering, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;Center for Bioengineering, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;Neuroscience Research Institute, University of California Santa Barbara, 93106, Santa Barbara, CA, USA;

关键词: Bacterial mRNA sequencing;    mRNA enrichment;    rRNA depletion;    Low input total RNA;   

DOI  :  10.1186/s12864-020-07134-4

来源: Springer

【 摘 要 】

BackgroundRNA sequencing is a powerful approach to quantify the genome-wide distribution of mRNA molecules in a population to gain deeper understanding of cellular functions and phenotypes. However, unlike eukaryotic cells, mRNA sequencing of bacterial samples is more challenging due to the absence of a poly-A tail that typically enables efficient capture and enrichment of mRNA from the abundant rRNA molecules in a cell. Moreover, bacterial cells frequently contain 100-fold lower quantities of RNA compared to mammalian cells, which further complicates mRNA sequencing from non-cultivable and non-model bacterial species. To overcome these limitations, we report EMBR-seq (Enrichment of mRNA by Blocked rRNA), a method that efficiently depletes 5S, 16S and 23S rRNA using blocking primers to prevent their amplification.ResultsEMBR-seq results in 90% of the sequenced RNA molecules from an E. coli culture deriving from mRNA. We demonstrate that this increased efficiency provides a deeper view of the transcriptome without introducing technical amplification-induced biases. Moreover, compared to recent methods that employ a large array of oligonucleotides to deplete rRNA, EMBR-seq uses a single or a few oligonucleotides per rRNA, thereby making this new technology significantly more cost-effective, especially when applied to varied bacterial species. Finally, compared to existing commercial kits for bacterial rRNA depletion, we show that EMBR-seq can be used to successfully quantify the transcriptome from more than 500-fold lower starting total RNA.ConclusionsEMBR-seq provides an efficient and cost-effective approach to quantify global gene expression profiles from low input bacterial samples.

【 授权许可】

CC BY