PT  - JOURNAL ARTICLE
AU  - Ning Zhang
AU  - Shundi Shi
AU  - Xuanting Wang
AU  - Wenhao Ni
AU  - Xiaohong Yuan
AU  - Jiachen Duan
AU  - Tony Z. Jia
AU  - Barney Yoo
AU  - Ashley Ziegler
AU  - James J. Russo
AU  - Wenjia Li
AU  - Shenglong Zhang
TI  - 2D-HELS-AA MS Seq: Direct sequencing of tRNA reveals its different isoforms and multiple dynamic base modifications
AID  - 10.1101/767129
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 767129
4099  - http://biorxiv.org/content/early/2019/09/12/767129.short
4100  - http://biorxiv.org/content/early/2019/09/12/767129.full
AB  - We report a direct method for sequencing tRNAPhe without cDNA by combining 2-dimensional hydrophobic RNA end-labeling with an anchor-based algorithm in mass spectrometry-based sequencing (2D-HELS-AA MS Seq). The entire tRNAPhe was sequenced and the identity, location and abundance of all 11 base modifications were determined. Changes in ratios of wybutosine and its depurinated form under different conditions were quantified, pointing to the ability of our technology to determine dynamic changes of nucleotide modifications. Two truncated isoforms at 3’CCA tail of the tRNAPhe (75 nt CC, 80% and 74 nt C, 3%) were identified in addition to the 76 nt tRNAPhe with a full-length 3’CCA tail (17%). We also discovered a new isoform with A-G transitions at both the 44 and 45 positions in the tRNAPhe variable loop.One Sentence Summary Direct 2D-HELS-AA MS Seq of tRNA reveals different isoforms and base modifications