LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance.

Melissa L Wilbert, Stephanie C Huelga, Katannya Kapeli, Thomas J Stark, Tiffany Y Liang, Stella X Chen, Bernice Y Yan, Jason L Nathanson, Kasey R Hutt, Michael T Lovci, Hilal Kazan, Anthony Q Vu, Katlin B Massirer, Quaid Morris, Shawn Hoon, Gene W Yeo

Molecular cell · 2012 · Vol. 48 (2) · pp. 195-206

PubMed DOI PMC Full Text

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.

Publication Types

["Journal Article", "Research Support, N.I.H., Extramural", "Research Support, Non-U.S. Gov't", "Research Support, U.S. Gov't, Non-P.H.S."]

Keywords

[]

MeSH Terms

["Alternative Splicing", "Binding Sites", "Embryonic Stem Cells", "Gene Expression Regulation, Developmental", "HEK293 Cells", "Humans", "Nucleotide Motifs", "RNA, Messenger", "RNA-Binding Proteins"]

Funding

R01 HG004659 NHGRI NIH HHS (United States)

T32 GM008666 NIGMS NIH HHS (United States)

R01 NS075449 NINDS NIH HHS (United States)

HG004659 NHGRI NIH HHS (United States)

NS075449 NINDS NIH HHS (United States)

R01 GM084317 NIGMS NIH HHS (United States)

GM084317 NIGMS NIH HHS (United States)

Linked Datasets (3)

GSE39855 GSE via ncbi_elink

GEO

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (splicing array)

Homo sapiens

GSE39873 GSE via ncbi_elink

GEO

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance

Homo sapiens

GSE39872 GSE via ncbi_elink

GEO

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance (HTS)

Homo sapiens

18 data files

File	Type	Size
LIN28KD_H9_rnaseq.fastq	RNA-Seq	627.8 MB
LIN28KD_H9_rnaseq.fastq	RNA-Seq	627.8 MB
SRR531463	RNA-Seq	51.5 MB
SRR531463	RNA-Seq	51.5 MB
SRR531464	RNA-Seq	357.0 MB
SRR531464	RNA-Seq	357.0 MB
SRR531465	RNA-Seq	287.3 MB
SRR531465	RNA-Seq	287.3 MB
SRR531466	RNA-Seq	668.8 MB
SRR531466	RNA-Seq	668.8 MB
SRR531468	RNA-Seq	501.1 MB
SRR531468	RNA-Seq	501.1 MB
SRR531469	RNA-Seq	52.7 MB
SRR531469	RNA-Seq	52.7 MB
SRR531470	RNA-Seq	206.7 MB
SRR531470	RNA-Seq	206.7 MB
SRR531471	RNA-Seq	42.9 MB
SRR531471	RNA-Seq	42.9 MB

Analysis Pipelines (3)

GSE39855 Microarray Data Processing 3 steps

Microarray geo_data_processing GSE39855

GSE39872 CLIP-seq Data Processing 3 steps

CLIP-seq geo_data_processing GSE39872

GSE39873 Microarray Data Processing 3 steps

Microarray geo_data_processing GSE39873