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. 2012 Oct 26;48(2):195-206.
doi: 10.1016/j.molcel.2012.08.004. Epub 2012 Sep 6.

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

Melissa L Wilbert  1 , 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
Affiliations

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

Melissa L Wilbert et al. Mol Cell. .

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.

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Figures

Figure 1
Figure 1. CLIP-seq identifies LIN28 binding sites in thousands of human genes
(A) CLIPseq experimental approach performed using H9 human ES (hES) and LIN28-V5 293 cells. (i) UV cross-linking; (ii) immunoprecipitation of LIN28 protein-RNA complexes; (iii) micrococcal nuclease treatment, SDS PAGE gel size selection, and protease digestion; (iv) cDNA library preparation and high-throughput sequencing; and (v) cluster identification (in purple) based on the density of reads (in green) mapped to genes (in dark blue). (B) Venn diagrams illustrating the number of LIN28 target genes and clusters in common between hES and LIN28-V5 293 cells. For comparison, randomly located clusters in the same genes and genic regions as LIN28-V5 293 clusters and clusters from RBFOX2 in hES cells were used. The percentage of LIN28 hES gene targets or clusters in common with each comparison dataset are indicated within boxes. (C) LIN28 binding sites identified within the 3′UTR of the hnRNP F gene in both hES and LIN28-V5 293 cells. Clusters are depicted by purple rectangles representing the highest density of CLIP-seq reads (graphed as continuous densities in green). Individual RBFOX2 hES CLIP-seq reads are shown in red for comparison. The scale to the left indicates the height of aligned reads. (D) LIN28 binding enrichment in coding exons and 3′UTR sequences in both hES and LIN28-V5 293 cells, as compared to the observed percentage of nucleotides in the annotated transcriptome.
Figure 2
Figure 2. CLIP-seq defines LIN28 binding sites within miRNA precursors
(A, B) Individual LIN28 CLIP-seq reads (in green) aligned to (A) precursor miRNA let-7a-1 and (B) precursor miRNA let-7f-1, with the mature miRNA boundaries depicted below. The sequence GGAGA in the hairpin loop is depicted as a black rectangle. The scale to the left indicates the number of aligned reads. (C) Western blot analysis of LIN28 protein levels in control Flp-In-293 and LIN28-V5 293 cells. GAPDH serves as a loading control. (D) Northern blot analysis of the human let-7a miRNA in control Flp-In-293 and LIN28-V5 293 cells. The U6 snRNA serves as a loading control. (E) Scatter plot comparing the log2 RPM (reads per million mapped) for expressed mature miRNAs in control Flp-In-293 and LIN28-V5 293 cells (gray), showing significantly upregulated (red) and downregulated (green) miRNAs. (F) LIN28 CLIP-seq reads (in green) aligned to precursor mir-302d, centered on the motif GGAG (black rectangle).
Figure 3
Figure 3. LIN28 binds GGAGA(U) motifs in mRNA sequences within hairpin loop structures
(A) Scatter plot comparing pentamer Z-scores in hES and LIN28-V5 293 cells. Pentamers overrepresented (p < 10−4) in both cell-types are highlighted by colored circles, and defined on the right. (B) Consensus motifs within LIN28 clusters identified by the HOMER algorithm (Heinz et al., 2010) in hES and LIN28-V5 293 cells with corresponding p-values shown below the motif. (C and D) The positional frequency of consensus motifs GGAGA and GGAGAU relative to the center of (C) all LIN28 hES clusters and (D) clusters only in 3′UTRs. Dashed lines correspond to the positional frequency of these motifs within randomly distributed control clusters from the same type of genic region. (E and F) Cumulative distribution plots display the probability that each nucleotide of a GGAG sequence found within LIN28 hES clusters (blue) or control clusters (red) resides in a predicted hairpin loop (left panel) or base-paired region (right panels) of mRNA; (E) considering clusters only in exons, or (F) clusters only in 3′UTRs (p-values calculated by two-sample Kolgomorov-Smirnov test).
Figure 4
Figure 4. LIN28 binds to its own 3′UTR to positively autoregulate
(A) LIN28 H9 hES CLIP-seq reads (graphed as continuous densities in green) and clusters (in purple) falling within the LIN28 3′UTR. Instances of GGAGA motifs within clusters are shown (black boxes). The scale to the left indicates the height of aligned reads. A portion of the LIN28 3′UTR (orange) containing a let-7 binding site (red) was cloned downstream of a luciferase open-reading frame (ORF) reporter (see (D)). (B) Western blot (WB) analysis using an antibody recognizing endogenous LIN28 in lysates after immunoprecipitation (IP) of LIN28 and bound RNA transcripts in HUES6 hES cells. IgG was used as an IP control. RNA isolated from the IP was also used for RT-PCR experiments to confirm IP of the endogenous LIN28 3′UTR (primers shown as arrows in (A)), and a negative control, HMNT, that is not bound by LIN28. (C) Quantitative RT-PCR analysis showing increased mRNA levels of endogenous LIN28 in LIN28-V5 293 relative to control Flp-In-293 cells, and normalized to GAPDH levels (*p < 0.05, Student’s t-test, error bars ± s.d.). (D) Relative luciferase activity of reporters containing a portion of the wild-type (WT) LIN28 3’UTR (as depicted in A), or deletion (ΔLet-7) of or mutations (Mut) within a sequence complementary to the let-7f miRNA, when co-transfected in Flp-In-293 cells with a LIN28-GFP expression vector (purple) or with an unrelated control vector (grey) (*p < 0.001, Student’s t-test, error bars ±s.d.). A control luciferase reporter lacking the partial LIN28 3′UTR (Empty) was unaffected by LIN28-GFP.
Figure 5
Figure 5. LIN28 binds and regulates splicing factors
(A) Enriched Gene Ontology (GO) terms for hES LIN28 target genes were identified using the DAVID algorithm (Huang et al., 2009). Statistical comparisons to all genes with transcripts expressed in H9 hES cells were made (*p < 10−10, **p < 10−15, ***p < 10−40). (B) Western blot analysis of splicing factors in control Flp-In-293 and LIN28-V5 293 cells. Cyclin B1 is shown as a positive control (Xu et al., 2009). All membranes were probed for LIN28 and GAPDH (used as a loading control). (C) Western blot analysis of splicing factors in LIN28-V5 293 cells transfected with a let-7f miRNA mimic or control mimic. The let-7 target IMP2 was used as a positive control. (D) Relative luciferase activity of reporters containing cloned portions of the hnRNP F or FUS/TLS LIN28-bound RNA regions co-transfected into Flp-In-293 cells with a LIN28-GFP expression vector (purple) or with a control vector (grey) (*p < 0.001, Student’s t-test, error bars ±s.d.). A control luciferase reporter lacking a LIN28-bound region (Empty) was unchanged by LIN28-GFP. (E) LIN28 CLIP-seq reads (in green) and clusters (in purple) mapped to an intronic region within the 3′UTR of the human TDP-43 gene (in blue). The scale to the left indicates the height of aligned reads. Portions of the homologous mouse TDP-43 3’UTR that contain (long) or lack (short) the intronic region that harbors the majority of LIN28 binding sites are shown aligned (in orange). These regions were inserted downstream of a luciferase reporter as previously described (Polymenidou et al., 2011). Instances of GGAGA and GAAG motifs in the respective organisms are shown (black rectangles). (F) Relative luciferase activity of reporters containing the TDP-43 3’UTR with LIN28 binding sites (long), and the TDP-43 3’UTR without LIN28 binding sites (short) co-transfected into Flp-In-293 cells with a LIN28-GFP expression vector (purple) or a control vector (grey) (*p < 0.001, Student’s t-test, error bars ±s.d.). A control luciferase reporter lacking any LIN28-bound region (Empty) was unchanged by LIN28-GFP.
Figure 6
Figure 6. LIN28 expression in somatic cells results in thousands of alternative splicing events, in part through regulation of TDP-43 levels
(A) The pie charts display the number of each type of alternative splicing event changed upon overexpression of LIN28-V5 (left) or TDP-43 (right) in Flp-In-293 cells, as detected by splicing-sensitive microarray analyses. The small pie chart (center) represents the distribution of alternative splicing event types detected on the microarray. (B) RT-PCR validations of alternative cassette events detected by microarray analysis. All plots show significant differences between control Flp-In-293 and LIN28-V5 293 cells (p < 0.05, Students t-test). Bars represent an average and error bars represent the standard deviation across biological triplicates. (C) The percent of included versus skipped alternative cassette exons upon overexpression of LIN28-V5 (left) or TDP-43 (right) in Flp-In-293 cells. For the alternative cassette exons that changed in both conditions (n = 113), the percent of exons affected in the same (where the exon is included or skipped in both conditions) or opposite direction are shown below.
Figure 7
Figure 7. LIN28 and LIN28B affect splicing factors differently in human ES cells
(A) The percent of included versus skipped alternative cassette exons upon depletion of LIN28 in hES cells is shown. Of the alternative cassette events changed in both the LIN28 hES and LIN28-V5 293 experiments (n = 73), the percent of exons affected in the same (where the exon is included or skipped in both conditions) or opposite direction are shown below. The direction of cassette exon splicing changes due to LIN28 depletion in hES cells is flipped to correspond to LIN28 overexpression. (B) Western blot analysis of LIN28B levels upon shRNA-mediated depletion of LIN28 in hES cells. GAPDH serves as a loading control. (C) Western blot analysis of LIN28, LIN28B, and splicing factors upon siRNA-mediated depletion of LIN28, LIN28B, or both in hES cells.
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