2D-HELS-AA MS Seq: Direct sequencing of tRNA reveals its different isoforms and multiple dynamic base modifications
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 mod...
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          | Published in | bioRxiv | 
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| Main Authors | , , , , , , , , , , , | 
| Format | Paper | 
| Language | English | 
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        Cold Spring Harbor
          Cold Spring Harbor Laboratory Press
    
        12.09.2019
     Cold Spring Harbor Laboratory  | 
| Edition | 1.1 | 
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| ISSN | 2692-8205 2692-8205  | 
| DOI | 10.1101/767129 | 
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| Abstract | 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. | 
    
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| AbstractList | 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.
Direct 2D-HELS-AA MS Seq of tRNA reveals different isoforms and base modifications 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.  | 
    
| Author | Shi, Shundi Ni, Wenhao Yoo, Barney Li, Wenjia Duan, Jiachen Ziegler, Ashley Russo, James J Wang, Xuanting Yuan, Xiaohong Jia, Tony Z Zhang, Ning Zhang, Shenglong  | 
    
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| References_xml | – volume: 1 start-page: 183 year: 1974 end-page: 192 ident: 767129v1.19 article-title: Effects of dilute HCl on yeast tRNAPhe and E. coli tRNA1fMet publication-title: Nucleic Acids Res – volume: 51 start-page: 7110 year: 2012 end-page: 7131 ident: 767129v1.6 article-title: Structure and function of noncanonical nucleobases publication-title: Angew Chem Int Ed Engl – volume: 137 start-page: 14430 year: 2015 end-page: 14438 ident: 767129v1.14 article-title: Bidirectional direct sequencing of noncanonical RNA by two-dimensional analysis of mass chromatograms publication-title: J Am Chem Soc – volume: 461 start-page: 814 year: 2009 end-page: 818 ident: 767129v1.8 article-title: Direct RNA sequencing publication-title: Nature – volume: 66 start-page: 5216 year: 2006 end-page: 5223 ident: 767129v1.20 article-title: Acid-mediated tumor invasion: a multidisciplinary study publication-title: Cancer Res – volume: 243 start-page: 575 year: 1968 end-page: 583 ident: 767129v1.18 article-title: Studies on polynucleotides. LXXIX. Yeast phenylalanine transfer ribonucleic acid: products obtained by degradation with pancreatic ribonuclease publication-title: J Biol Chem – volume: 15 start-page: 201 year: 2018 end-page: 206 ident: 767129v1.9 article-title: Highly parallel direct RNA sequencing on an array of nanopores publication-title: Nat Methods – volume: 7 start-page: 237 year: 2010 end-page: 247 ident: 767129v1.7 article-title: Detection of RNA modifications publication-title: RNA Biol – volume: 62 start-page: 251 year: 2010 end-page: 260 ident: 767129v1.24 article-title: CCA addition to tRNA: implications for tRNA quality control publication-title: IUBMB Life – volume: 12 start-page: 835 year: 2015 end-page: 837 ident: 767129v1.4 article-title: Efficient and quantitative high-throughput tRNA sequencing publication-title: Nat Methods – volume: 82 start-page: 7055 year: 2010 end-page: 7062 ident: 767129v1.26 article-title: The concept of spectral accuracy for MS publication-title: Anal Chem – volume: 42 start-page: 7346 year: 2014 end-page: 7357 ident: 767129v1.12 article-title: A complete landscape of post-transcriptional modifications in mammalian mitochondrial tRNAs publication-title: Nucleic Acids Res – volume: 5 start-page: 546 year: 1968 end-page: 555 ident: 767129v1.21 article-title: A specific modification next to the anticodon of phenylalanine transfer ribonucleic acid publication-title: Eur J Biochem – volume: 147 start-page: 1462 year: 1965 end-page: 1465 ident: 767129v1.3 article-title: Structure of a Ribonucleic Acid publication-title: Science – volume: 51 start-page: 11289 year: 2012 end-page: 11292 ident: 767129v1.10 article-title: Characterization of modified RNA by top-down mass spectrometry publication-title: Angew Chem Int Ed Engl – volume: 57 start-page: 16785 year: 2018 end-page: 16790 ident: 767129v1.17 article-title: AlkAniline-Seq: Profiling of m(7) G and m(3) C RNA Modifications at Single Nucleotide Resolution publication-title: Angew Chem Int Ed Engl – volume: 31 start-page: 173 year: 2006 end-page: 181 ident: 767129v1.13 article-title: Mass spectrometry of RNA publication-title: Trends Biochem Sci – start-page: gkz731 year: 2019 ident: 767129v1.15 article-title: A general LC-MS-based RNA sequencing method for direct analysis of multiple-base modifications in RNA mixtures publication-title: Nucleic Acids Research – volume: 9 start-page: 741 year: 2002 end-page: 746 ident: 767129v1.22 article-title: A bifunctional tRNA for in vitro selection publication-title: Chem Biol – volume: 138 start-page: 215 year: 2009 end-page: 219 ident: 767129v1.23 article-title: Stressing Out over tRNA Cleavage publication-title: Cell – volume: 47 start-page: 2533 year: 2019 end-page: 2545 ident: 767129v1.16 article-title: Transfer RNA demethylase ALKBH3 promotes cancer progression via induction of tRNA-derived small RNAs publication-title: Nucleic Acids Res – volume: 8 start-page: 1023 year: 1980 end-page: 1032 ident: 767129v1.25 article-title: The nucleotide sequence of phenylalanine tRNA from the cytoplasm of Neurospora crassa publication-title: Nucleic Acids Res – volume: 46 start-page: 1386 year: 2018 end-page: 1394 ident: 767129v1.2 article-title: Unveiling structural and functional divergences of bacterial tRNA dihydrouridine synthases: perspectives on the evolution scenario publication-title: Nucleic Acids Res – volume: 31 start-page: 439 year: 2006 end-page: 451 ident: 767129v1.5 article-title: Early days of tRNA research: discovery, function, purification and sequence analysis publication-title: J Biosci – volume: 7 year: 2017 ident: 767129v1.1 article-title: tRNA Modifications: Impact on Structure and Thermal Adaptation publication-title: Biomolecules – volume: 21 start-page: 890 year: 2010 end-page: 898 ident: 767129v1.11 article-title: Top-down tandem mass spectrometry of tRNA via ion trap collision-induced dissociation publication-title: J Am Soc Mass Spectrom  | 
    
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| Title | 2D-HELS-AA MS Seq: Direct sequencing of tRNA reveals its different isoforms and multiple dynamic base modifications | 
    
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