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Sequencing-based quantitative mapping of the cellular small RNA landscape

ABSTRACT: Current next-generation RNA sequencing methods do not provide accurate quantification of small RNAs within a sample due to sequence-dependent biases in capture, ligation, and amplification during library preparation. We present a method – AQRNA-seq – that minimizes biases and provides a direct, linear correlation between sequencing read count and copy number for small RNAs in a sample. The library preparation and data processing steps were optimized and validated using a 963-member microRNA reference library, oligonucleotide standards of varying lengths, and northern blots. Application of AQRNA-seq to a panel of human cancer cells revealed >800 detectable miRNAs that varied as a function of cancer progression, while application to bacterial tRNA pools, a traditionally hard-to-sequence class of RNAs, revealed 80-fold variation in tRNA isoacceptor levels, stress-induced site-specific tRNA fragmentation, quantitative modification maps, and evidence for stress-induced tRNA-driven codon-biased translation. AQRNA-seq thus provides a means to quantitatively map the small RNA landscape in cells.

ORGANISM(S): Homo sapiens

PROVIDER: GSE159434 | GEO | 2021/05/31

REPOSITORIES: GEO

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