title: Identification of mRNAs bound and regulated by human LIN28 proteins and molecular requirements for RNA recognition.
abstract: Human LIN28A and LIN28B are RNA-binding proteins (RBPs) conserved in animals with important roles during development and stem cell reprogramming. We used Photoactivatable-Ribonucleoside-Enhanced Crosslinking and Immunoprecipitation (PAR-CLIP) in HEK293 cells and identified a largely overlapping set of ∼3000 mRNAs at ∼9500 sites located in the 3' UTR and CDS. In vitro and in vivo, LIN28 preferentially bound single-stranded RNA containing a uridine-rich element and one or more flanking guanosines and appeared to be able to disrupt base-pairing to access these elements when embedded in predicted secondary structure. In HEK293 cells, LIN28 protein binding mildly stabilized target mRNAs and increased protein abundance. The top targets were its own mRNAs and those of other RBPs and cell cycle regulators. Alteration of LIN28 protein levels also negatively regulated the abundance of some but not all let-7 miRNA family members, indicating sequence-specific binding of let-7 precursors to LIN28 proteins and competition with cytoplasmic miRNA biogenesis factors.
authors.affiliation: Howard Hughes Medical Institute and Laboratory for RNA Molecular Biology, The Rockefeller University, New York, New York 10065, USA.
authors.forename: Markus
authors.initials: M
authors.lastname: Hafner
authors.forename: Klaas E A
authors.initials: KE
authors.lastname: Max
authors.forename: Pradeep
authors.initials: P
authors.lastname: Bandaru
authors.forename: Pavel
authors.initials: P
authors.lastname: Morozov
authors.forename: Stefanie
authors.initials: S
authors.lastname: Gerstberger
authors.forename: Miguel
authors.initials: M
authors.lastname: Brown
authors.forename: Henrik
authors.initials: H
authors.lastname: Molina
authors.forename: Thomas
authors.initials: T
authors.lastname: Tuschl
mesh_terms: D020413:3' Untranslated Regions; D001665:Binding Sites; D003593:Cytoplasm / Q000378:metabolism; D005786:Gene Expression Regulation; D057809:HEK293 Cells; D006801:Humans; D047468:Immunoprecipitation; D035683:MicroRNAs / Q000378:metabolism*; D011485:Protein Binding; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism; D013234:Stem Cells / Q000378:metabolism
chemical_list: D020413:3' Untranslated Regions; C000715187:Lin28A protein, human; D035683:MicroRNAs; D012333:RNA, Messenger; D016601:RNA-Binding Proteins