Potential small guide RNAs for tRNase ZL from human plasma, peripheral blood mononuclear cells, and cultured cell lines.
Several pieces of evidence suggest that small RNA degradation products together with tRNase ZL appear to form another layer of the whole gene regulatory network. The degraded RNA such as a 5'-half-tRNA and an rRNA fragment function as small guide RNA (sgRNA) to guide the enzyme to target RNA. We were curious whether there exist RNAs in plasma that can function as sgRNAs for tRNase ZL, whether these RNAs are working as signaling molecules between cells to fulfill physiological roles, and whether there are any differences in plasma sgRNA species and levels between normal and pathological conditions. Here, we analyzed small plasma RNAs from three healthy persons and three multiple myeloma patients for potential sgRNAs by deep sequencing. We also examined small RNAs from peripheral blood mononuclear cells (PBMC) of three healthy persons and three myeloma patients and from various cultured human cell lines for sgRNAs. We found that read-number distribution patterns of plasma and PBMC RNAs differ between persons in the range of 5-40 nt and that there are many RNA species that exist significantly more or less abundantly in the plasma or PBMC of the myeloma patients than those of the healthy persons. Furthermore, we found that there are many potential sgRNAs in the 5-40-nt RNAs and that, among them, a 31-nt RNA fragment derived from 94-nt Y4-RNA, which can function as a 5'-half-tRNA-type sgRNA, is overwhelmingly abundant in the plasma of 2/3 of the examinees. These observations suggest that the gene regulatory network via tRNase ZL and sgRNA may be extended intercellularly.
Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan.
Sho
S
Ninomiya
Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan; Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan.
Mitsuoki
M
Kawano
Department of Information Engineering, Niigata University, Niigata, Japan.
Takashi
T
Abe
Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan.
Tatsuya
T
Ishikawa
Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan.
Masayuki
M
Takahashi
Department of Biochemistry and Molecular Biology, Hokkaido University Graduate School of Dental Medicine, Sapporo, Japan.
Masato
M
Tamura
Laboratory of Biochemistry, Niigata University Graduate School of Health Sciences, Niigata, Japan.
Yoshiaki
Y
Takahashi
Department of Applied Life Sciences, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan; Research Institute for Healthy Living, Niigata University of Pharmacy and Applied Life Sciences, Niigata, Japan.
Masayuki
M
Nashimoto
D001483:Base Sequence; D002478:Cells, Cultured; D004722:Endoribonucleases / Q000097:blood; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D019169:Jurkat Cells; D007963:Leukocytes, Mononuclear / Q000166:cytology / Q000378:metabolism*; D009101:Multiple Myeloma / Q000097:blood / Q000473:pathology; D009690:Nucleic Acid Conformation; D012313:RNA / Q000032:analysis / Q000097:blood / Q000302:isolation & purification; D017423:Sequence Analysis, RNA; D000094704:RNA, Guide, CRISPR-Cas Systems
D004722:Endoribonucleases; D012313:RNA; D000094704:RNA, Guide, CRISPR-Cas Systems; C531011:tRNase Z, human