title: LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.
abstract: LIN28 is a conserved RNA-binding protein implicated in pluripotency, reprogramming, and oncogenesis. It was previously shown to act primarily by blocking let-7 microRNA (miRNA) biogenesis, but here we elucidate distinct roles of LIN28 regulation via its direct messenger RNA (mRNA) targets. Through crosslinking and immunoprecipitation coupled with high-throughput sequencing (CLIP-seq) in human embryonic stem cells and somatic cells expressing exogenous LIN28, we have defined discrete LIN28-binding sites in a quarter of human transcripts. These sites revealed that LIN28 binds to GGAGA sequences enriched within loop structures in mRNAs, reminiscent of its interaction with let-7 miRNA precursors. Among LIN28 mRNA targets, we found evidence for LIN28 autoregulation and also direct but differing effects on the protein abundance of splicing regulators in somatic and pluripotent stem cells. Splicing-sensitive microarrays demonstrated that exogenous LIN28 expression causes widespread downstream alternative splicing changes. These findings identify important regulatory functions of LIN28 via direct mRNA interactions.
authors.affiliation: Department of Cellular and Molecular Medicine, Stem Cell Program and Institute for Genomic Medicine, University of California, San Diego, CA, USA.
authors.forename: Melissa L
authors.initials: ML
authors.lastname: Wilbert
authors.forename: Stephanie C
authors.initials: SC
authors.lastname: Huelga
authors.forename: Katannya
authors.initials: K
authors.lastname: Kapeli
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Stark
authors.forename: Tiffany Y
authors.initials: TY
authors.lastname: Liang
authors.forename: Stella X
authors.initials: SX
authors.lastname: Chen
authors.forename: Bernice Y
authors.initials: BY
authors.lastname: Yan
authors.forename: Jason L
authors.initials: JL
authors.lastname: Nathanson
authors.forename: Kasey R
authors.initials: KR
authors.lastname: Hutt
authors.forename: Michael T
authors.initials: MT
authors.lastname: Lovci
authors.forename: Hilal
authors.initials: H
authors.lastname: Kazan
authors.forename: Anthony Q
authors.initials: AQ
authors.lastname: Vu
authors.forename: Katlin B
authors.initials: KB
authors.lastname: Massirer
authors.forename: Quaid
authors.initials: Q
authors.lastname: Morris
authors.forename: Shawn
authors.initials: S
authors.lastname: Hoon
authors.forename: Gene W
authors.initials: GW
authors.lastname: Yeo
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001665:Binding Sites / Q000235:genetics; D053595:Embryonic Stem Cells; D018507:Gene Expression Regulation, Developmental; D057809:HEK293 Cells; D006801:Humans; D059372:Nucleotide Motifs; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D016601:RNA-Binding Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: C000715187:Lin28A protein, human; D012333:RNA, Messenger; D016601:RNA-Binding Proteins