title: TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms.
abstract: Terminal uridylyl transferases (TUTs) function as integral regulators of microRNA (miRNA) biogenesis. Using biochemistry, single-molecule, and deep sequencing techniques, we here investigate the mechanism by which human TUT7 (also known as ZCCHC6) recognizes and uridylates precursor miRNAs (pre-miRNAs) in the absence of Lin28. We find that the overhang of a pre-miRNA is the key structural element that is recognized by TUT7 and its paralogues, TUT4 (ZCCHC11) and TUT2 (GLD2/PAPD4). For group II pre-miRNAs, which have a 1-nt 3' overhang, TUT7 restores the canonical end structure (2-nt 3' overhang) through mono-uridylation, thereby promoting miRNA biogenesis. For pre-miRNAs where the 3' end is further recessed into the stem (as in 3' trimmed pre-miRNAs), TUT7 generates an oligo-U tail that leads to degradation. In contrast to Lin28-stimulated oligo-uridylation, which is processive, a distributive mode is employed by TUT7 for both mono- and oligo-uridylation in the absence of Lin28. The overhang length dictates the frequency (but not duration) of the TUT7-RNA interaction, thus explaining how TUT7 differentiates pre-miRNA species with different overhangs. Our study reveals dual roles and mechanisms of uridylation in repair and removal of defective pre-miRNAs.
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea.
authors.forename: Boseon
authors.initials: B
authors.lastname: Kim
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea.
authors.forename: Minju
authors.initials: M
authors.lastname: Ha
authors.affiliation: Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
authors.forename: Luuk
authors.initials: L
authors.lastname: Loeff
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea.
authors.forename: Hyeshik
authors.initials: H
authors.lastname: Chang
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Dhirendra K
authors.initials: DK
authors.lastname: Simanshu
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Sisi
authors.initials: S
authors.lastname: Li
authors.affiliation: Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Fareh
authors.affiliation: Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
authors.forename: Dinshaw J
authors.initials: DJ
authors.lastname: Patel
authors.affiliation: Kavli Institute of NanoScience, Department of BioNanoScience, Delft University of Technology, Delft, The Netherlands c.joo@tudelft.nl narrykim@snu.ac.kr.
authors.forename: Chirlmin
authors.initials: C
authors.lastname: Joo
authors.affiliation: Center for RNA Research, Institute for Basic Science, Seoul, Korea School of Biological Sciences, Seoul National University, Seoul, Korea c.joo@tudelft.nl narrykim@snu.ac.kr.
authors.forename: V Narry
authors.initials: VN
authors.lastname: Kim
mesh_terms: D000227:Adenine Nucleotides / Q000378:metabolism; D001483:Base Sequence; D057809:HEK293 Cells; D006367:HeLa Cells; D006801:Humans; D035683:MicroRNAs / Q000378:metabolism*; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000378:metabolism; D012316:RNA Nucleotidyltransferases / Q000502:physiology*; D012322:RNA Precursors / Q000378:metabolism*; D012323:RNA Processing, Post-Transcriptional / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D014500:Uracil Nucleotides / Q000378:metabolism; D014542:Uridine Monophosphate / Q000378:metabolism*
chemical_list: D000227:Adenine Nucleotides; D035683:MicroRNAs; D009843:Oligoribonucleotides; D012322:RNA Precursors; D014500:Uracil Nucleotides; C027916:oligo(U); C023505:2',5'-oligoadenylate; D014542:Uridine Monophosphate; D012316:RNA Nucleotidyltransferases; C576505:TUT7 protein, human
keywords: TUT4 (ZCCHC11); TUT7 (ZCCHC6); precursor microRNA; single‐molecule fluorescence; uridylation