Sequencing-based quantitative mapping of the cellular small RNA landscape
Hu, J. F.; Yim, D.; Huber, S. M.; Bacusmo, J. M.; Ma, D.; DeMott, M. S.; Levine, S. S.; Crecy-Lagard, V. d.; Dedon, P. C.; Cao, B.
Show abstract
Current next-generation RNA sequencing methods cannot provide accurate quantification of the population of small RNAs within a sample due to strong sequence-dependent biases in capture, ligation, and amplification during library preparation. We report the development of an RNA sequencing method - AQRNA-seq - that minimizes biases and enables absolute quantification of all small RNA species in a sample mixture. Validation of AQRNA-seq library preparation and data mining algorithms using a 963-member microRNA reference library, RNA oligonucleotide standards of varying lengths, and northern blots demonstrated a direct, linear correlation between sequencing read count and RNA abundance. Application of AQRNA-seq to bacterial tRNA pools, a traditionally hard-to-sequence class of RNAs, revealed 80-fold variation in tRNA isoacceptor copy numbers, patterns of site-specific tRNA fragmentation caused by stress, and quantitative maps of ribonucleoside modifications, all in a single AQRNA-seq experiment. AQRNA-seq thus provides a means to quantitatively map the small RNA landscape in cells and tissues.
Matching journals
The top 3 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- rG4-seeker enables high-confidence identification of novel and non-canonical rG4 motifs from rG4-seq experiments 94%
- Identification of RNA 3' ends and termination sites in Haloferax volcanii 93%
- Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation 93%
Similar papers in this journal
- Nanopore sequencing of intact aminoacylated tRNAs 95%
- Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct and long-read sequencing 95%
- Native RNA nanopore sequencing reveals antibiotic-induced loss of rRNA modifications in the A- and P-sites 95%
Similar papers in this journal
- ADAM-tRNA-seq: An Optimized Approach for Demultiplexing and Enhanced Hierarchal Mapping in Direct tRNA Sequencing 95%
- Optimization of Anticodon Edited Transfer RNAs (ACE-tRNAs) Function in Translation for Suppression of Nonsense Mutations 95%
- ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing 95%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.