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Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway.

Ge Z, Quek BL, Beemon KL, Hogg JR - Elife (2016)

Bottom Line: When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs.PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression.Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing long 3'UTRs to perform dual roles in mRNA quality control and gene expression regulation. However, expansion of vertebrate 3'UTR functions has required a physical expansion of 3'UTR lengths, complicating the process of detecting nonsense mutations. We show that the polypyrimidine tract binding protein 1 (PTBP1) shields specific retroviral and cellular transcripts from NMD. When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs. PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression. Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD.

No MeSH data available.


Related in: MedlinePlus

PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.(A) Density of PTBP1 (green, left axis) and UPF1 (red, right axis) CLIP reads derived from peaks called using PIPE-CLIP software, plotted relative to TC position. A bin size of 20 nt was used to determine read density; bin sizes ranging from 5 nt to 20 nt and plots of peak occurrences showed similar patterns. (B) CDF plot of annotated 3’UTR lengths among mRNAs containing or lacking PTBP1 CLIP peaks centered in the indicated intervals relative to the TC. P-values were calculated in two-tailed K-S tests of 3’UTR lengths in the indicated mRNA classes compared to mRNAs lacking PTBP1 peaks. Only mRNAs with 3’UTRs greater than 500 nt were included to avoid bias due to selection of transcripts containing CLIP peaks. (C) CDF plot of log2 fold changes in mRNA abundance in UPF1 siRNA vs siNT RNAseq. mRNAs with 3’UTR lengths in the middle 50% of the overall distribution (484–2251 nt) were selected to avoid confounding effects of increased 3’UTR lengths among mRNAs with PTBP1 peaks. P-values were determined by two-tailed K-S tests, comparing the indicated mRNA classes to mRNAs lacking PTBP1 peaks from +1–400 nt. (D) CDF plot as in C. mRNAs were classified according to the presence of one or more predicted high-affinity PTBP1 hexamer binding sites in the indicated intervals relative to annotated TCs (see Materials and methods for details; the top 6 hexamers identified in previous PTBP1 CLIP seq, associated with >50% of observed CLIP peaks, were used for this analysis; Xue et al., 2009). Statistical significance was determined by two-tailed K-S tests comparing mRNAs with putative PTBP1 binding sites in the indicated positions to mRNAs lacking hexamer binding sites at positions from 1 to 50 nt downstream of the TC.DOI:http://dx.doi.org/10.7554/eLife.11155.020
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fig7: PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.(A) Density of PTBP1 (green, left axis) and UPF1 (red, right axis) CLIP reads derived from peaks called using PIPE-CLIP software, plotted relative to TC position. A bin size of 20 nt was used to determine read density; bin sizes ranging from 5 nt to 20 nt and plots of peak occurrences showed similar patterns. (B) CDF plot of annotated 3’UTR lengths among mRNAs containing or lacking PTBP1 CLIP peaks centered in the indicated intervals relative to the TC. P-values were calculated in two-tailed K-S tests of 3’UTR lengths in the indicated mRNA classes compared to mRNAs lacking PTBP1 peaks. Only mRNAs with 3’UTRs greater than 500 nt were included to avoid bias due to selection of transcripts containing CLIP peaks. (C) CDF plot of log2 fold changes in mRNA abundance in UPF1 siRNA vs siNT RNAseq. mRNAs with 3’UTR lengths in the middle 50% of the overall distribution (484–2251 nt) were selected to avoid confounding effects of increased 3’UTR lengths among mRNAs with PTBP1 peaks. P-values were determined by two-tailed K-S tests, comparing the indicated mRNA classes to mRNAs lacking PTBP1 peaks from +1–400 nt. (D) CDF plot as in C. mRNAs were classified according to the presence of one or more predicted high-affinity PTBP1 hexamer binding sites in the indicated intervals relative to annotated TCs (see Materials and methods for details; the top 6 hexamers identified in previous PTBP1 CLIP seq, associated with >50% of observed CLIP peaks, were used for this analysis; Xue et al., 2009). Statistical significance was determined by two-tailed K-S tests comparing mRNAs with putative PTBP1 binding sites in the indicated positions to mRNAs lacking hexamer binding sites at positions from 1 to 50 nt downstream of the TC.DOI:http://dx.doi.org/10.7554/eLife.11155.020

Mentions: In order to understand the global relationship between PTBP1 binding and NMD, we analyzed the RNA-seq data described above with respect to published PTBP1 (Xue et al., 2013) and UPF1 CLIP-seq datasets (Zund et al., 2013). As previously reported, analysis of aggregate binding of UPF1 to all mRNAs showed that UPF1 levels are low in coding sequences and increase downstream of TCs to reach a broad plateau throughout 3’UTRs (Figure 7A). In contrast, PTBP1 CLIP signal derived from exons was preferentially located within 200 nt of TCs, consistent with a role for PTBP1 in marking translation termination events.10.7554/eLife.11155.020Figure 7.PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.


Polypyrimidine tract binding protein 1 protects mRNAs from recognition by the nonsense-mediated mRNA decay pathway.

Ge Z, Quek BL, Beemon KL, Hogg JR - Elife (2016)

PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.(A) Density of PTBP1 (green, left axis) and UPF1 (red, right axis) CLIP reads derived from peaks called using PIPE-CLIP software, plotted relative to TC position. A bin size of 20 nt was used to determine read density; bin sizes ranging from 5 nt to 20 nt and plots of peak occurrences showed similar patterns. (B) CDF plot of annotated 3’UTR lengths among mRNAs containing or lacking PTBP1 CLIP peaks centered in the indicated intervals relative to the TC. P-values were calculated in two-tailed K-S tests of 3’UTR lengths in the indicated mRNA classes compared to mRNAs lacking PTBP1 peaks. Only mRNAs with 3’UTRs greater than 500 nt were included to avoid bias due to selection of transcripts containing CLIP peaks. (C) CDF plot of log2 fold changes in mRNA abundance in UPF1 siRNA vs siNT RNAseq. mRNAs with 3’UTR lengths in the middle 50% of the overall distribution (484–2251 nt) were selected to avoid confounding effects of increased 3’UTR lengths among mRNAs with PTBP1 peaks. P-values were determined by two-tailed K-S tests, comparing the indicated mRNA classes to mRNAs lacking PTBP1 peaks from +1–400 nt. (D) CDF plot as in C. mRNAs were classified according to the presence of one or more predicted high-affinity PTBP1 hexamer binding sites in the indicated intervals relative to annotated TCs (see Materials and methods for details; the top 6 hexamers identified in previous PTBP1 CLIP seq, associated with >50% of observed CLIP peaks, were used for this analysis; Xue et al., 2009). Statistical significance was determined by two-tailed K-S tests comparing mRNAs with putative PTBP1 binding sites in the indicated positions to mRNAs lacking hexamer binding sites at positions from 1 to 50 nt downstream of the TC.DOI:http://dx.doi.org/10.7554/eLife.11155.020
© Copyright Policy
Related In: Results  -  Collection

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fig7: PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.(A) Density of PTBP1 (green, left axis) and UPF1 (red, right axis) CLIP reads derived from peaks called using PIPE-CLIP software, plotted relative to TC position. A bin size of 20 nt was used to determine read density; bin sizes ranging from 5 nt to 20 nt and plots of peak occurrences showed similar patterns. (B) CDF plot of annotated 3’UTR lengths among mRNAs containing or lacking PTBP1 CLIP peaks centered in the indicated intervals relative to the TC. P-values were calculated in two-tailed K-S tests of 3’UTR lengths in the indicated mRNA classes compared to mRNAs lacking PTBP1 peaks. Only mRNAs with 3’UTRs greater than 500 nt were included to avoid bias due to selection of transcripts containing CLIP peaks. (C) CDF plot of log2 fold changes in mRNA abundance in UPF1 siRNA vs siNT RNAseq. mRNAs with 3’UTR lengths in the middle 50% of the overall distribution (484–2251 nt) were selected to avoid confounding effects of increased 3’UTR lengths among mRNAs with PTBP1 peaks. P-values were determined by two-tailed K-S tests, comparing the indicated mRNA classes to mRNAs lacking PTBP1 peaks from +1–400 nt. (D) CDF plot as in C. mRNAs were classified according to the presence of one or more predicted high-affinity PTBP1 hexamer binding sites in the indicated intervals relative to annotated TCs (see Materials and methods for details; the top 6 hexamers identified in previous PTBP1 CLIP seq, associated with >50% of observed CLIP peaks, were used for this analysis; Xue et al., 2009). Statistical significance was determined by two-tailed K-S tests comparing mRNAs with putative PTBP1 binding sites in the indicated positions to mRNAs lacking hexamer binding sites at positions from 1 to 50 nt downstream of the TC.DOI:http://dx.doi.org/10.7554/eLife.11155.020
Mentions: In order to understand the global relationship between PTBP1 binding and NMD, we analyzed the RNA-seq data described above with respect to published PTBP1 (Xue et al., 2013) and UPF1 CLIP-seq datasets (Zund et al., 2013). As previously reported, analysis of aggregate binding of UPF1 to all mRNAs showed that UPF1 levels are low in coding sequences and increase downstream of TCs to reach a broad plateau throughout 3’UTRs (Figure 7A). In contrast, PTBP1 CLIP signal derived from exons was preferentially located within 200 nt of TCs, consistent with a role for PTBP1 in marking translation termination events.10.7554/eLife.11155.020Figure 7.PTBP1 binding near stop codons is correlated with 3’UTR length and NMD evasion.

Bottom Line: When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs.PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression.Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD.

View Article: PubMed Central - PubMed

Affiliation: Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States.

ABSTRACT
The nonsense-mediated mRNA decay (NMD) pathway degrades mRNAs containing long 3'UTRs to perform dual roles in mRNA quality control and gene expression regulation. However, expansion of vertebrate 3'UTR functions has required a physical expansion of 3'UTR lengths, complicating the process of detecting nonsense mutations. We show that the polypyrimidine tract binding protein 1 (PTBP1) shields specific retroviral and cellular transcripts from NMD. When bound near a stop codon, PTBP1 blocks the NMD protein UPF1 from binding 3'UTRs. PTBP1 can thus mark specific stop codons as genuine, preserving both the ability of NMD to accurately detect aberrant mRNAs and the capacity of long 3'UTRs to regulate gene expression. Illustrating the wide scope of this mechanism, we use RNA-seq and transcriptome-wide analysis of PTBP1 binding sites to show that many human mRNAs are protected by PTBP1 and that PTBP1 enrichment near stop codons correlates with 3'UTR length and resistance to NMD.

No MeSH data available.


Related in: MedlinePlus