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Molecular BiologyNature Communications
Peer-reviewed journal article

U1 snRNP regulates cancer cell migration and invasion

Jung‐Min OhiD, Christopher C. VentersiD, Chao Di, Anna Maria PintoiD, Lili WaniD, Ihab YounisiD, Zhiqiang Cai, Chie Arai, Byung Ran SoiD, Jingqi DuaniD, Gideon DreyfussiD

Abstract

Stimulated cells and cancer cells have widespread shortening of mRNA 3-utranslated regions (3UTRs) and switches to shorter mRNA isoforms due to usage of more proximal polyadenylation signals (PASs) in the last exon and in introns. U1 snRNA (U1), vertebrates most abundant non-coding (spliceosomal) small nuclear RNA, silences proximal PASs and its inhibition with antisense morpholino oligonucleotides (U1 AMO) triggers widespread mRNA shortening. Here we show that U1 AMO also modulates cancer cells phenotype, dose-dependently increasing migration and invasion in vitro by up to 500%, whereas U1 over-expression has the opposite effect. In addition to 3UTR length, numerous transcriptome changes that could contribute to this phenotype are observed, including alternative splicing, and mRNA expression levels of proto-oncogenes and tumor suppressors. These findings reveal an unexpected link between U1 regulation and oncogenic and activated cell states, and suggest U1 as a potential target for their modulation.

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Claude Sonnet 4.6 · max effort · 8 Nov 2026 · from the full text of version 1 (9 Aug 2019)

Moderate U1 snRNP inhibition raises cancer cell migration and invasion by up to 500% and shortens 3'UTRs in many genes, while U1 overexpression has the opposite effects.

Widespread 3'UTR shortening accompanies cancer and cell stimulation, and U1 snRNA silences proximal polyadenylation signals. Whether graded U1 changes alter cancer cell phenotype had not been tested; this work links U1 level to migration, invasion and cancer gene expression.

Key results

  1. ShownLow-dose U1 antisense morpholino (U1 AMO) increased HeLa migration and invasion in a dose-dependent way, peaking at an intermediate dose. A U2 AMO control did not reproduce the effect.

    Up to about 500% increase in 24 hours, peak at 62.5 pmole U1 AMO; doses of 2.5 to 250 pmole masked ~15-30% of U1 5' ends; proliferation rose only 38% at 62.5 pmole (48-72 h); U2 AMO showed no enhancement. · U1 level changes modulate hallmark phenotypes of…

  2. ShownU1 overexpression reduced HeLa migration and invasion. In A549, MCF-7 and MB-231, U1 AMO enhanced migration (and invasion in A549 and MB-231), while overexpression lowered both.

    1 µg and 1.5 µg plasmid raised U1 by 20% and 40%; migration fell 25-50% and invasion 25-65%. In other lines, AMO raised migration 58-72% (A549, MCF-7, MB-231) and invasion 53-64% (A549, MB-231); OE lowered both by ~50%. · U1 level changes modulate hallmark phenotypes of…; Tables

  3. ShownReduced U1 shortened 3'UTRs in many genes while U1 OE lengthened them. The authors' last-exon coding sequence ratio method (LECDS) detected more events than DaPars.

    LECDS: 1,919 genes shortened in both 12.5 and 62.5 pmole U1 AMO (p ≤ 0.01) vs 130 lengthened; U1 OE lengthened 3,210 and shortened 344. 79% overlap with DaPars; LECDS found 2,630 more events. · U1 level changes cause numerous and diverse…; LECDS calculations

  4. ShownU1 AMO caused alternative splicing changes and shifted expression of cancer-related genes, and U1 OE gave the opposite pattern for those genes.

    Alternative splicing changed in ~700 genes (U1 AMO). MYC, FOS and JUN rose with U1 AMO and fell with U1 OE; ATR, RB1, ATM and CDC genes fell with U1 AMO and rose with U1 OE (GFold, 1.5-fold, p < 0.01). · U1 level changes cause numerous and diverse…; Differential gene expression, alternative…

  5. SuggestedGenes with U1-dependent 3'UTR length changes included 204 oncogenes. Separately, genes shortened after CPSF5 knockdown in HeLa cells overlapped substantially with those shortened by U1 AMO.

    204 oncogenes in total had 3'UTR changes (Sanger/UCSF cancer gene lists). CPSF5 knockdown shortened 1,210 genes that were also shortened by U1 AMO (63% overlap). · U1 level changes alters expression of cancer…

Methods, data and reproducibility

Human cancer cells received graded U1 AMO doses or a U1 snRNA expression plasmid. Phenotypes were measured by proliferation, migration and invasion assays, and nascent (4-thiouridine-labeled) RNA-seq was analysed for expression, 3'UTR length and splicing.

  • HeLa nascent RNA-seq after U1 AMO (12.5 and 62.5 pmole) or U1 OE (1 and 1.5 µg), with matched controls · human (HeLa cell line, hg38) · n = two biological experiments (per figure legend)
  • Migration, invasion and proliferation assays in HeLa, A549, MCF-7 and MB-231 cells · human
  • Affymetrix miRNA microarray of HeLa cells with 62.5 pmole U1 AMO or control for 8 hours · human
  • CPSF5 knockdown RNA-seq in HeLa cells, analysed for 3'UTR shortening with LECDS · human
  • RT-qPCR validation of up- and down-regulated genes (with ERCC spike-in normalization) · human (HeLa) · n = n=3 independent cell cultures
Methods & tools
STAR, GFold, Junction Usage Model (JUM), DaPars, LECDS (last exon coding sequence ratio), TargetScan, Sanger and UCSF cancer gene databases, Cell Titer-Glo viability assay, Cytoselect migration assay, BD BioCoat Matrigel invasion chambers, 4-thiouridine metabolic RNA labeling, GeneChip miRNA 3.0 array
Reagents & environment
Reads aligned to UCSC hg38 with STAR default settings; no software versions or containers stated.
Reproducibility gaps
GEO accession is listed as to be assigned; analysis code is available only from the corresponding author upon request.
Limitations (4)
  • Because U1 modulation changed so many transcripts in so many ways, the authors state that the phenotype cannot be pinned on any single transcriptome change. · stated by the authors
  • Many expression changes may be secondary effects, especially at the 24 hour time point, or may arise from premature cleavage and polyadenylation or nonsense-mediated decay. · stated by the authors
  • Higher U1 AMO doses (250 pmole and above) were toxic and reduced overall cell numbers, which restricts the usable dose range for the phenotype assays. · noted in this summary
  • Phenotype assays rely on in vitro cell lines, with replicate numbers and statistical tests for migration and invasion not stated; no rescue or single-gene perturbation links specific 3'UTR changes to the phenotype. · noted in this summary

Who should read:Read this if you study U1 snRNP, telescripting, 3'UTR shortening or splicing in cancer and want dose-response phenotype data with transcriptome-wide readouts.

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