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U1 snRNP telescripting regulates a size–function-stratified human genome

Abstract

U1 snRNP (U1) functions in splicing introns and telescripting, which suppresses premature cleavage and polyadenylation (PCPA). Using U1 inhibition in human cells, we show that U1 telescripting is selectively required for sustaining long-distance transcription elongation in introns of large genes (median 39 kb). Evidence of widespread PCPA in the same locations in normal tissues reveals that large genes incur natural transcription attrition. Underscoring the importance of U1 telescripting as a gene-size-based mRNA-regulation mechanism, small genes were not sensitive to PCPA, and the spliced-mRNA productivity of 1,000 small genes (median 6.8 kb) increased upon U1 inhibition. Notably, these small, upregulated genes were enriched in functions related to acute stimuli and cell-survival response, whereas genes subject to PCPA were enriched in cell-cycle progression and developmental functions. This gene size–function polarization increased in metazoan evolution by enormous intron expansion. We propose that telescripting adds an overarching layer of regulation to size–function-stratified genomes, leveraged by selective intron expansion to rapidly shift gene expression priorities.

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Figure 1: U1 inhibition causes widespread PCPA from intronic PASs.
Figure 2: The effect of U1 inhibition and gene size on PCPA and full-length mRNA productivity.
Figure 3: mRNA productivity upregulation in small non-PCPAed genes.
Figure 4: PCPA is cotranscriptional and prematurely terminates pol II elongation in gene bodies.
Figure 5: PCPA is a natural phenomenon.
Figure 6: Functional and gene-size correlations of PCPAed and non-PCPAed genes that are up- or downregulated.

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Acknowledgements

We thank members of our laboratory for helpful discussions and comments on the manuscript. This work was supported by the US National Institutes of Health (R01GM112923 to G.D.). G.D. is supported by the Howard Hughes Medical Institute.

Author information

Authors and Affiliations

Authors

Contributions

J.-M.O., I.Y., A.M.P., L.W. and G.D. conceived and designed the study. J.-M.O., C.C.V., C.A., I.Y., B.R.S. and Z.Z. performed the experiments. C.D. and C.C.V. performed the bioinformatics analysis. All authors contributed to data analysis. J.-M.O., C.C.V., C.D., J.G., I.Y. and G.D. wrote the manuscript with input from all authors. G.D. is responsible for the project's planning and experimental design.

Corresponding author

Correspondence to Gideon Dreyfuss.

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Competing interests

The authors declare no competing financial interests.

Integrated supplementary information

Supplementary Figure 1 U1 inhibition causes a shift of RNA-seq reads from exons to introns.

(a) Evidence for the high purity of 4-shU-labeled RNAs used for RNA-seq. HeLa cells transfected with control or U1 AMO either not labeled or metabolically labeled with 4-shU and RNA purified as described in Methods. RT-qPCR was used to quantify two regions in PELO (exon 2-3 junction) and PRPF38B (exon 1-2 junction). After 2 cycles of 4-shU-labeled RNA selection, significant enrichment of these regions were detected in the elution, in contrast to separate, unlabeled RNA samples where they were exclusively detected in the flow through (wash) (b). Data are represented as mean ± standard deviation (n=3, independent cell cultures). The high stringency procedure achieved very strong enrichment (80-200 fold) of 4-shU RNAs over unlabeled. (c) Pie charts representing the mapping distribution of 4-shU labeled RNA-seq reads distribution in CDS, 5’ UTR, 3’ UTR and introns of control and U1 AMO treated HeLa cells, as indicated. Histogram showing the (d) total number of junction reads as a percent of the total sequencing depth, and (e) percentage of these junction reads spanning canonical (previously annotated) exon-exon splice junctions (blue) versus aberrant (non-canonical or de novo) spliced reads (red) in control and U1 AMO samples. Shown are both 4 and 8 hours 4-shU labeled RNA-seq.

Supplementary Figure 2 U1 inhibition causes multiple, moderate PCPAs.

(a) PCPA validation by 3’ RACE. Cells transfected with control or U1 AMO for 8 hours and metabolically labeled with 4-shU were used for analysis. After 2 cycles of 4-shU-labeled RNA selection, RNA was converted into cDNA and 3’RACE was performed as described previously1. Blue arrow indicates the forward primer location of 3’ RACE. (b) Genome browser views of RNA-seq of representative genes showed multiple moderate PCPAs in several introns. Venn diagrams showing the overlaps between PCPAed genes detected in 4 and 8 hours post transfection (c), and between PCPAed genes and down-regulated genes 8h post transfection sample (d). (e) Gene size highly correlates with size of introns. Scatterplots showing the Spearman correlation between total gene size and total intron size in all expressed genes (RPKM ≥ 1) in HeLa cells.

Supplementary Figure 3 PCPAed genes are more down-regulated than non-PCPAed genes.

(a) Boxplots showing the gene expression changes in non-PCPAed genes (n=5,052) and PCPAed genes (n=3,590) in the 8 h 4-shU labeled RNA-seq from cells treated with U1 AMO. For boxplots: center line, median; box limits, first and third quartiles; whiskers, 1.5x IQR; points, outliers. Statistical tests used are described in Methods. (b) Genome browser view of Non-PCPAed and small genes with no expression change. (c-e) RT-qPCR confirms gene expression in RNA-seq. HeLa cells transfected with control or U1 AMO and metabolically labeled with 4-shU were used for RT-qPCR analysis. ERCC RNA spike-in controls were added to each sample before the rRNA depletion process and used for normalization. Data are represented as mean ± standard deviation (n=3, independent cell cultures). P value was calculated with two-tailed Student’s t-test. A Poisson test measuring RNA-seq reads in exons normalized to the total mapped reads (P value < 0.01) confirmed the RT-qPCR results. (f) Intronless genes are PCPA resistant in U1 AMO. Histogram showing the 3’-poly(A) reads in gene body (internal) and 3’ end region in intronless genes (n = 143), non-PCPAed genes (n = 3,254) and PCPAed genes (n = 2,692). For all genes expressed in HeLa cells (RPKM ≥ 1), only those with 3’-poly(A) reads in either their gene body or 3’ end were selected for each group in this analysis.

Supplementary Figure 4 PCPAed genes lose more exon-exon junctions near the TES than non-PCPAed genes.

Metagene plot showing the ratio of exon-exon junction reads (U1 AMO/control, grey line) binned along the gene body, 5' to 3', in the PCPAed genes (a) and the non-PCPAed genes (b). All genes used for this analysis, from TSS to TES, were scaled to the same length (3 kb). The thick red line represents a smoothed fit line for each data point.

Supplementary Figure 5 Pol II metagenes of all expressed genes and non-PCPAed genes.

(a) U1 inhibition’s effect on upstream, antisense transcription. Genome browser view of each gene and its upstream, antisense transcript showing PCPA in both directions by U1 AMO. (b) Metagene plot of pol II ChIP-seq reads for all expressed genes (n = 9,744) and highly up-regulated, non-PCPAed genes (n = 115) in control (black) or with U1 AMO (red), relative to TSS regions (TSS -1000 bp to +500 bp) and TES (500 bp upstream of the annotated mRNA 3’ ends and 1000 bp downstream) in control and U1 AMO. Each gene’s body, between TSS + 500 bp and TES - 500 bp, was scaled to 2 kb.

Supplementary Figure 6 U1 AMO increases transcription attrition in large genes.

(a) Transcription attrition naturally occurs in large genes. Genome browser views of RNA-seq of representative genes with transcription attrition. RefSeq gene structures along with any additional isoforms from AceView are shown underneath the panels (RefSeq is the top track). (b) Internal and last exon 3’-poly(A) reads distribution versus gene size. Scatter plot of each gene’s 3’-ploy(A) reads in either the gene body (from TSS up to, but excluding, the last exon) or only the last exon in several human tissues12. Regression lines of internal poly(A) reads is dependent on gene size (left panel, R2 = 0.15, P value < 0.05) while last exon poly(A) reads is not (right panel, R2 = 5e-4, P value > 0.05). Arrow in x-axis represents the location of median gene length of all expressed genes, 22.8 kb. (c) Scatter plot of ratio of the total number of 3’-poly(A) reads found in the last exon compared to those in the gene body (from TSS up to, but excluding, the last exon) in control (left panel) and U1 AMO (right panel) RNA-seq. Arrow and vertical blue dashed line in x-axis represents the location of median gene length of all expressed genes, 22.8 kb. Fewer genes in the upper right blue colored zone represents increased transcription attrition (less full-length mRNA) in large genes by U1 AMO treatment.

Supplementary Figure 7 U2 AMO induces splicing inhibition.

Cells transfected with control, U1 or U2 AMO for 8 h and metabolically labeled with 4-shU were used for analysis. The decreases in spliced products with U2 AMOs show that splicing is dependent on the U2 snRNP.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7 and Supplementary Tables 1, 3, 6, 7. (PDF 1356 kb)

Life Sciences Reporting Summary (PDF 130 kb)

Supplementary Table 2

The list of PCPAed genes. (XLSX 2496 kb)

Supplementary Table 4

The ratio of 3′-poly(A) reads in the last exon vs. gene body. (XLSX 394 kb)

Supplementary Table 5

Gene ontology enrichment analysis of non-PCPAed, upregulated or PCPAed, down-regulated genes. (XLSX 83 kb)

Supplementary Data Set 1

Original western blot images shown in Figure 3c. a. Uncropped immuno-blot of Cyr61 and Magoh b. Un-cropped immunoblot of Myc. Arrows in a and b indicate corresponding full-length proteins. (PDF 246 kb)

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Oh, JM., Di, C., Venters, C. et al. U1 snRNP telescripting regulates a size–function-stratified human genome. Nat Struct Mol Biol 24, 993–999 (2017). https://doi.org/10.1038/nsmb.3473

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