Abstract
Translation is pervasive outside of canonical coding regions, occurring in long noncoding RNAs, canonical untranslated regions and introns1,2,3,4, especially in ageing4,5,6, neurodegeneration5,7 and cancer8,9,10. Notably, the majority of tumour-specific antigens are results of noncoding translation11,12,13. Although the resulting polypeptides are often nonfunctional, translation of noncoding regions is nonetheless necessary for the birth of new coding sequences14,15. The mechanisms underlying the surveillance of translation in diverse noncoding regions and how escaped polypeptides evolve new functions remain unclear10,16,17,18,19. Functional polypeptides derived from annotated noncoding sequences often localize to membranes20,21. Here we integrate massively parallel analyses of more than 10,000 human genomic sequences and millions of random sequences with genome-wide CRISPR screens, accompanied by in-depth genetic and biochemical characterizations. Our results show that the intrinsic nucleotide bias in the noncoding genome and in the genetic code frequently results in polypeptides with a hydrophobic C-terminal tail, which is captured by the ribosome-associated BAG6 membrane protein triage complex for either proteasomal degradation or membrane targeting. By contrast, canonical proteins have evolved to deplete C-terminal hydrophobic residues. Our results reveal a fail-safe mechanism for the surveillance of unwanted translation from diverse noncoding regions and suggest a possible biochemical route for the preferential membrane localization of newly evolved proteins.
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Scripts for data analysis are available at https://github.com/xuebingwu/noncoding-translation-code.
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Acknowledgements
The authors thank D. Bartel for supporting some of the early work on this project; C. Zhang, P. Sims, B. Honig and M. AlQuraishi for discussion; and S. Diederichs for sharing the SMAD4 readthrough cells. X.W. is supported by NIH Director’s New Innovator Award (1DP2GM140977), Pershing Square Sohn Prize for Cancer Research, Pew-Stewart Scholar for Cancer Research Award, and the Impetus Longevity Grants. N.M. is supported by the National Institute of Aging (NIA) grants R01AG064244 and RF1AG070075. This research was funded in part through the NIH/NCI Cancer Center Support Grant P30CA013696 and used the Genomics and High Throughput Screening Shared Resource and CCTI Flow Cytometry Core. The CCTI Flow Cytometry Core is supported in part by the Office of the Director, National Institutes of Health under awards S10RR027050 and S10OD020056. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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Contributions
J.S.K. and Z.C. performed the majority of experiments. P.S. performed BAG6 and RNF126 overexpression and RNF126 knockdown. A.O.A. generated AMD1-deletion reporters, the SMAD4 readthrough reporter, and assisted in validating the BAG6-KO cell line. A.T., M.R.M., P.S. and Y.G. cloned and analysed representative noncoding sequences in multiple reporters. P.S. and Y.G. performed the XBP1 reporter assay. J.S.K. and M.R.M. performed SMAD4–BAG6 co-immunoprecipitation. J.E.L. and N.M. performed in-gel proteasome activity assays. Y.R. assisted in sequencing the replicate of Pep30 rescue in BAG6-KO cells. X.W. initiated and supervised the project. J.S.K. and X.W. drafted the manuscript with input from all authors.
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Extended data figures and tables
Extended Data Fig. 1 Translation surveillance of representative noncoding sequences.
a, Noncoding sequences in the HSP90B1 3’ UTR, an ACTB intron, and a GAPDH intron were cloned into the bicistronic reporter system shown in Fig. 1b. b, Density plots for the distribution of EGFP/mCherry ratios as measured by flow cytometry 24 hours after reporter transfection. The median fold loss of EGFP/mCherry ratio relative to control is shown on the top left corner of each density plot. c, Density plot of the EGFP/mCherry ratio for cells transfected with either the control or the ACTB intron reporter, alone or with simultaneous treatment of either proteasome inhibitor (lactacystin) or lysosome inhibitor (chloroquine). The numbers indicate the median fold loss of EGFP/mCherry relative to control. d—f, six noncoding sequences from the Pep30 library (KRT2 intron, APOL4 intron, LINC00222, LINC02885, ASPAY 3’ UTR, and IFT81 3’ UTR) were selected and cloned into either the original mCherry-EGFP bicistronic reporter (d, cloning failed for KRT2), fused to the C-terminus of HA-tagged PspCas13b protein (e, cloning failed for APOL4), or fused to the C-terminus of RPL3 (f, cloning failed for IFT81). d, Same as b for indicated noncoding sequences. e, Equal amount of HA-dPspCas13b-pep30 reporter plasmids were co-transfected with a HA-RfxCas13d plasmid and the protein abundance was assayed by western blotting with an HA antibody. HA-dCas13b fused to human protein eIF4E was used as a control. The abundance of HA-dCas13b-pep30 was quantified by first normalizing to HA-Cas13d then to eIF4E fusion. f, Equal amount of RPL3 reporter plasmids were transfected into HEK293T cells and western blots were performed using an RPL3 antibody, which detects both endogenous RPL3 (lower bands) and the RPL3 reporter protein (upper bands). NT: no transfection control. The level of the reporter protein was first normalized to endogenous RPL3 and then to the RPL3-3xHA sample. N = 4 biological replicates.
Extended Data Fig. 2 Characterization of the Pep30 library.
a, Sequence diversity in the Pep30 library. The pairwise hamming distance (number of nucleotides that are different) between any two sequences (of 90-nt) in the library was calculated. Subsequently for each sequence, we identify the shortest distance to any other sequence in the library. The result showed that the vast majority (98%) of Pep30 sequences are at least 40 nt (out of 90 nt) different from other sequences in the library, with a median distance of 48. This is very close the distribution when the Pep30 library sequences are shuffled (median: 50). The result indicated that our Pep30 library is nearly as diverse as one can get from entirely unrelated sequences. b—d, Effect of proteasome inhibition or lysosome inhibition on the Pep30 library. b, Pep30 cells were treated with proteasome inhibitors for 8 h and then analyzed with flow cytometry. Ctrl: Pep30 cells without treatment. c, Same as (b) for multiple lysosome inhibitors. d, longer (24 h vs. 6 h) proteasome inhibition but not lysosome inhibition resulted in more rescue.
Extended Data Fig. 3 Hydrophobicity analyses in the Pep30 library and the human genome.
a, The correlation coefficient between Pep30 reporter expression and average hydrophobicity calculated using various scales. b, Spearman correlation coefficient (light bar) between various properties of the Pep30 sequences and reporter expression. Dark bar: partial correlation conditioned on average hydrophobicity. c. Same as Fig. 2f with a different hydrophobicity scale (Ponnuswamy instead of Miyazawa). d, Average hydrophobicity for the first 100 aa (N-termini) of annotated proteins (N = 38,933). e, Average hydrophobicity of the C-termini of annotated proteins without any annotated protein domains in the last 100aa (N = 8,586). Shown are the Spearman correlation coefficient R and the P value of a two-sided Spearman’s correlation test. No adjustments were made for multiple comparisons.
Extended Data Fig. 4 Bias in the genetic code drives hydrophobicity.
a, Same as Fig. 3b (right) for all peptide lengths. b, Codons ranked by the hydrophobicity of the corresponding amino acids. c, Nucleotide composition in different types of regions in the human genome.
Extended Data Fig. 5 AMD1 3’ UTR translation mitigation.
a, Western blot confirming the loss of the EGFP-AMD1 tail fusion protein. HEK293T cells were transfected with varying amount of the AMD1 3’ UTR readthrough reporter plasmid, from 50 ng to 850 ng. (N = 2 biologically independent samples). b, The AMD1 3’ UTR translation reporter with the hydrophobic region in the AMD1 tail highlighted (A-E). c, Impact of deleting individual hydrophobic regions or larger regions on the EGFP/mCherry ratio. The number in each plot is the median decrease of the EGFP/mCherry ratio relative to controls. d, BAG6 co-immunoprecipitates with EGFP:AMD1 fusion protein but not a mutated fusion protein with the functional hydrophobic region C-to-E deleted (AMD1∆H). N = 4 biologically independent samples over 2 independent experiments for the quantification. Data are presented as mean values +/− s.d. P values calculated using two-sided Student’ t-test. No adjustments were made for multiple comparisons. ****: P < 0.0001.
Extended Data Fig. 6 Ribosome roadblock effect: comparing the AMD1 tail sequence, poly(A) and the XBP1 stalling sequence.
a—e, Reporter constructs shown on the left were transfected into HEK293T cells. The EGFP/mCherry ratio was quantified in individual cells using flow cytometry with distributions shown on the right on a log-10 scale. The number in each plot is the median fold-decrease of the EGFP/mCherry ratio. Note that AMD1 sequence causes less decrease in EGFP compared to both XBP1 and poly(A) sequences, and even this weak effect is independent of the putative pausing sequence in AMD1.
Extended Data Fig. 7 Characterization of the BAG6 KO cells and RNF126 KO cells.
a, Genotyping the BAG6 clonal knockout cell line. Sanger sequencing of 10 clones of PCR-amplified genomic DNA confirmed that the BAG6 KO cells contain a frameshift mutation in both alleles, one with a 5-nt deletion and the other with an 11-nt deletion around the expected Cas9 cut site. b, Re-expressing wild type BAG6 but not an inactive mutant missing the UBL domain for recruiting RNF126 (BAG6-UBL) partially reverses BAG6 KO phenotype as measured by the destabilization of AMD1 readthrough product. c, Same as b but comparing wild type RNF126 and an inactive mutant with a C237A mutation in the active site. d-e, Growth defect of BAG6 KO cells (d) and RNF126 KO cells (N = 3 biologically independent samples) (e) revealed by competitive growth assays. KO cells and WT cells were mixed and co-cultured for 15 days and the relative cell numbers (KO/WT) at each time point was determined by decomposition of sanger sequencing traces as described in Methods. N = 1 for day 0 of BAG6 and N = 3 biologically independent samples for all other time points. Data are presented as mean values +/− s.d.
Extended Data Fig. 8 BAG6 or TRC35 knockout does not affect proteasome activity or level.
a, Representative result from in-gel proteasome activity assay showing proteasome hydrolysis activity (left) and representative immunoblot probing for a subunits levels of the 26S 1- and 2-cap proteasome and 20S proteasome (middle). Cell lysates were run on 4% non-denaturing (native) gels and incubated with fluorogenic Suc-LLVY-amc proteasome substrate to determine relative activities or immunoblotted to determine relative levels. Samples (10.5 µg protein/well) were run separately under denaturing conditions for immunoblot probing for actin as a sample processing control (right). b, The level of 26S 1- and 2-cap proteasome detected by immunoblotting normalized to actin in the same sample (left), densitometric quantification of 26S 1- and 2-cap proteasome in-gel activity normalized by actin in the same sample (middle), and the activity/level ratio (right). Data are expressed mean ± SEM for three biological replicates, where each value represents the activity/level ratio calculated by averaging four technical replicates of activity and level values. One-way ANOVA was used for statistical analysis, with P < 0.05 considered significant. c, Similar result with in vivo proteasome activity reporter assays. The proteasome activity reporter UbG76V-EGFP was co-transfected with mCherry (1:1) into cells and the EGFP/mCherry ratio measured by flow cytometry was used as an indicator of proteasome activity in cells. The distribution the EGFP/mCherry ratio in WT, BAG6 KO, and TRC35 KO cells at 250 ng, 500 ng, and 1000 ng total plasmid were shown.
Extended Data Fig. 9 Replicating the Pep30 reporter assay in BAG6 KO cells.
The sequencing-based assay shown in Fig. 5f–h was repeated starting from cell sorting. a, Same as Fig. 5g. b, Same as Fig. 5h. c, full-length Pep30 reporter sequences with a minimum of 3000 reads (all four bins combined) were divided into three groups: those that are stable in wild-type cells (normalized expression >0.8), those that are unstable in wild type cells but are stabilized (increased expression) in BAG6 KO cells, and those that are unstable in wild type cells and are not stabilized in BAG6 KO cells. Shown are the density plot of the hydrophobicity of sequences in each group. d, same as c for the replicate shown in Fig. 5. P values were calculated using two-sided Mann-Whitney U test. No adjustments were made for multiple comparisons.
Extended Data Fig. 10 BAG6 and RNF126 mediate the degradation of SMAD4 readthrough products.
a, A dual color reporter fusing SMAD4 3’ UTR encoded peptide to the C-terminus of EGFP was tested in wild-type HEK293T cells, BAG6 KO cells, and RNF126 KO cells using flow cytometry as a readout. The number on the top left corner of each density plot is the median fold loss of EGFP/mCherry in the readthrough reporter relative to control. b, No significant change of SMAD4 mRNA level with BAG6 KO. RT: readthrough. N = 4 biologically independent samples. Data are presented as mean values +/− s.d. c, Efficient RNF126 knockdown and the lack of impact on endogenous SMAD4 mRNA (qRT-PCR). N = 4 biologically independent samples. Data are presented as mean values +/− s.d. d, Endogenous SMAD4 readthrough protein is stabilized by both BAG6 KO and RNF126 knockdown. Representative western blots on the left and quantification on the right. N = 3 biologically independent samples. Data are presented as mean values +/− s.d. One-way ANOVA was used for statistical analysis, with P < 0.05 considered significant. **: P < 0.01. No adjustments were made for multiple comparisons.
Supplementary information
Supplementary figures
This file contains the uncropped gels (Supplementary Fig. 1) and the flow cytometry gating strategy.
Supplementary Table 1
Subcellular localization of functional peptides. A list of 64 polypeptides with experimentally determined function and subcellular localization. Shown are peptide name, transcript name, localization, and publication.
Supplementary Table 2
Sequences of the Pep30 library. Tab-delimited text file listing with an ID in column 1 and the sequence in column 2. The first and last 15-nts are constant.
Supplementary Table 3
The CRISPR screen analyzed by MAGeCK. Shown is the gene summary file from MAGeCK output. Adjustments were made for multiple comparisons.
Supplementary Table 4
Oligonucleotide sequences used in this study. A list of all oligonucleotide sequences used in this study, including name, sequence, and a brief annotation.
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Kesner, J.S., Chen, Z., Shi, P. et al. Noncoding translation mitigation. Nature 617, 395–402 (2023). https://doi.org/10.1038/s41586-023-05946-4
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DOI: https://doi.org/10.1038/s41586-023-05946-4
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