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Direct Sequencing of tRNA by 2D-HELS-AA MS Seq Reveals Its Different Isoforms and Dynamic Base Modifications.
Zhang, Ning; Shi, Shundi; Wang, Xuanting; Ni, Wenhao; Yuan, Xiaohong; Duan, Jiachen; Jia, Tony Z; Yoo, Barney; Ziegler, Ashley; Russo, James J; Li, Wenjia; Zhang, Shenglong.
Afiliación
  • Zhang N; Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States.
  • Shi S; Department of Chemical Engineering, Columbia University, New York, New York 10027, United States.
  • Wang X; Department of Chemical Engineering, Columbia University, New York, New York 10027, United States.
  • Ni W; Department of Chemical Engineering, Columbia University, New York, New York 10027, United States.
  • Yuan X; Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States.
  • Duan J; Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States.
  • Jia TZ; Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States.
  • Yoo B; Earth-Life Science Institute, Tokyo Institute of Technology, Meguro-ku, Tokyo 152-8550, Japan.
  • Ziegler A; Blue Marble Space Institute of Science, Seattle, Washington 98154, United States.
  • Russo JJ; Department of Chemistry, Hunter College, City University of New York, New York, New York 10065, United States.
  • Li W; Department of Biological and Chemical Sciences, New York Institute of Technology, New York, New York 10023, United States.
  • Zhang S; Department of Chemical Engineering, Columbia University, New York, New York 10027, United States.
ACS Chem Biol ; 15(6): 1464-1472, 2020 06 19.
Article en En | MEDLINE | ID: mdl-32364699
Post-transcriptional modifications are intrinsic to RNA structure and function. However, methods to sequence RNA typically require a cDNA intermediate and are either not able to sequence these modifications or are tailored to sequence one specific nucleotide modification only. Interestingly, some of these modifications occur with <100% frequency at their particular sites, and site-specific quantification of their stoichiometries is another challenge. Here, we report a direct method for sequencing tRNAPhe without cDNA by integrating a two-dimensional hydrophobic RNA end-labeling strategy 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 stoichiometry of all eleven different RNA modifications was determined, five of which were not 100% modified, including a 2'-O-methylated G (Gm) in the wobble anticodon position as well as an N2, N2-dimethylguanosine (m22G), a 7-methylguanosine (m7G), a 1-methyladenosine (m1A), and a wybutosine (Y), suggesting numerous post-transcriptional regulations in tRNA. Two truncated isoforms at the 3'-CCA tail of the tRNAPhe (75 nt with a 3'-CC tail (80% abundance) and 74 nt with a 3'-C tail (3% abundance)) were identified in addition to the full-length 3'-CCA-tailed tRNAPhe (76 nt, 17% abundance). We discovered a new isoform with A-G transitions/editing at the 44 and 45 positions in the tRNAPhe variable loop, and discuss possible mechanisms related to the emergence and functions of the isoforms with these base transitions or editing. Our method revealed new isoforms, base modifications, and RNA editing as well as their stoichiometries in the tRNA that cannot be determined by current cDNA-based methods, opening new opportunities in the field of epitranscriptomics.
Asunto(s)

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Espectrometría de Masas / ARN de Transferencia / Emparejamiento Base Tipo de estudio: Prognostic_studies Idioma: En Revista: ACS Chem Biol Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos

Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Espectrometría de Masas / ARN de Transferencia / Emparejamiento Base Tipo de estudio: Prognostic_studies Idioma: En Revista: ACS Chem Biol Año: 2020 Tipo del documento: Article País de afiliación: Estados Unidos Pais de publicación: Estados Unidos