title: YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs.
abstract: Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes.
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Megumi
authors.initials: M
authors.lastname: Shigematsu
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Shozo
authors.initials: S
authors.lastname: Honda
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Phillipe
authors.initials: P
authors.lastname: Loher
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Aristeidis G
authors.initials: AG
authors.lastname: Telonis
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Isidore
authors.initials: I
authors.lastname: Rigoutsos
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA.
authors.forename: Yohei
authors.initials: Y
authors.lastname: Kirino
mesh_terms: D045744:Cell Line, Tumor; D019295:Computational Biology; D018076:DNA, Complementary; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D012343:RNA, Transfer / Q000737:chemistry*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D018076:DNA, Complementary; D012343:RNA, Transfer