title: 5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves.
abstract: Transfer RNAs (tRNAs) are fundamental adapter components of translational machinery. tRNAs can further serve as a source of tRNA-derived noncoding RNAs that play important roles in various biological processes beyond translation. Among all species of tRNAs, tRNAHisGUGhas been known to uniquely contain an additional guanosine residue at the -1 position (G-1) of its 5'-end. To analyze this -1 nucleotide in detail, we developed a TaqMan qRT-PCR method that can distinctively quantify human mature cytoplasmic tRNAHisGUGcontaining G-1, U-1, A-1, or C-1or lacking the -1 nucleotide (starting from G1). Application of this method to the mature tRNA fraction of BT-474 breast cancer cells revealed the presence of tRNAHisGUGcontaining U-1as well as the one containing G-1Moreover, tRNA lacking the -1 nucleotide was also detected, thus indicating the heterogeneous expression of 5'-tRNAHisGUGvariants. A sequence library of sex hormone-induced 5'-tRNA halves (5'-SHOT-RNAs), identified via cP-RNA-seq of a BT-474 small RNA fraction, also demonstrated the expression of 5'-tRNAHisGUGhalves containing G-1, U-1, or G1as 5'-terminal nucleotides. Although the detected 5'-nucleotide species were identical, the relative abundances differed widely between mature tRNA and 5'-half from the same BT-474 cells. The majority of mature tRNAs contained the -1 nucleotide, whereas the majority of 5'-halves lacked this nucleotide, which was biochemically confirmed using a primer extension assay. These results reveal the novel identities of tRNAHisGUGmolecules and provide insights into tRNAHisGUGmaturation and the regulation of tRNA half production.
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
authors.forename: Megumi
authors.initials: M
authors.lastname: Shigematsu
authors.affiliation: Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, Pennsylvania 19107, USA.
authors.forename: Yohei
authors.identifier: 0000-0001-5232-4742
authors.initials: Y
authors.lastname: Kirino
mesh_terms: D000926:Anticodon / Q000737:chemistry* / Q000378:metabolism; D020029:Base Pairing; D045744:Cell Line, Tumor; D004847:Epithelial Cells / Q000166:cytology / Q000378:metabolism*; D014644:Genetic Variation; D006801:Humans; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry* / Q000378:metabolism; D016133:Polymerase Chain Reaction / Q000379:methods; D012354:RNA, Transfer, His / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019914:Taq Polymerase / Q000235:genetics / Q000378:metabolism
chemical_list: D000926:Anticodon; D009711:Nucleotides; D012354:RNA, Transfer, His; D019914:Taq Polymerase
keywords: SHOT-RNA; tRNA; tRNA half; tRNAHisGUG; −1 nucleotide