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Putative alternative polyadenylation (APA) events in the early interaction of Salmonella enterica Typhimurium and human host cells.

Afonso-Grunz F - Genom Data (2015)

Bottom Line: Abstract available from the publisher.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular BioSciences, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.

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Alternative polyadenylation (APA) is a common regulatory mechanism of gene expression that generates messenger RNAs (mRNAs) with distinct untranslated regions (UTRs) as well as coding sequences from one and the same gene... The resulting transcript isoforms may not only exhibit an altered coding potential, but also harbor a distinct set of cis-regulatory elements for microRNAs (miRNAs) and other non-coding RNAs (ncRNAs) as well as RNA-binding proteins (RBPs) that affects processing, localization, stability, and translation of the mRNA... Poly(A)-position profiling by sequencing (3P-Seq ) represents another technique for global detection of PA site usage besides MACE (reviewed in ), and a recent publication features a 3P-Seq dataset of cultured HeLa cells that were grown under similar conditions as in the present study... We previously compared the high-confidence PA sites in the 3P-Seq dataset of mouse liver cells from Nam and colleagues with those obtained by MACE, and concluded that 3P-Seq and MACE provide similar results... The generated list of clusters (Supplementary Table S1) was screened for gene-specific PA sites present both in uninfected and early interacting cells... Further filtering resulted in 142 significantly differentially used PA sites (Bonferroni-adjusted p-value < 0.05) within 130 different genes... Another gene that gives rise to mRNAs with distinct 3′ UTRs encodes Peroxiredoxin 1 (PRDX1)... The predicted motifs mostly comprise binding sites of heterogeneous nuclear ribonucleoproteins (hnRNPs), followed by members of the serine/arginine (SR)-rich family of pre-mRNA splicing factors (SRSFs) along with other proteins that influence alternative splicing, transport and translation efficiency of PRDX1 (Supplementary Table S2)... The five highest ranking motifs are listed in Table 2 together with their associated RBPs... While this represents a common mechanism in prokaryotes, cytosolic polyadenylation was only relatively recently shown to contribute to RNA degradation in humans... The presence of degradation intermediates would indicate reduced levels of the labile iron pool caused by the increased iron consumption that arises from additional uptake of iron into intracellular bacteria... The highest ranking RBP motif in the region between the two major PA sites of PRDX1 recruits MATR3, an inner nuclear matrix protein that stabilizes mRNAs upon binding and that additionally binds to small ncRNAs involved in splicing... Besides their role in alternative splicing, several of the identified RBPs are involved in transport and translation of mRNAs... The comparison of the identified polyadenylation landscape in early interacting cells with the published dataset of non-interacting cells determined by 3P-Seq indicates several significantly differentially used PA sites, and some of these suggest that APA might contribute to the complex regulatory network that governs the immune response of epithelial cells... APA of PRDX1 results in transcription of mRNA isoforms with distinct sets of miRNA binding sites, while PA site usage in VAPA is likely to influence alternative splicing.

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Mapping and annotation statistics of poly(A) tail positive reads from the poly(A)+ library of early interacting HeLa-S3 cells prepared with MACE. (a) The fraction of uniquely, ambiguously and unmapped mapped reads is shown along with the number of excluded reads during quality trimming. (b) The numbers of uniquely mapped reads that aligned to intergenic regions, the mitochondrion or in antisense direction of a protein-coding gene are shown together with the number of reads that mapped to the UTRs, introns and exons of mRNAs.
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f0005: Mapping and annotation statistics of poly(A) tail positive reads from the poly(A)+ library of early interacting HeLa-S3 cells prepared with MACE. (a) The fraction of uniquely, ambiguously and unmapped mapped reads is shown along with the number of excluded reads during quality trimming. (b) The numbers of uniquely mapped reads that aligned to intergenic regions, the mitochondrion or in antisense direction of a protein-coding gene are shown together with the number of reads that mapped to the UTRs, introns and exons of mRNAs.

Mentions: A little more than one million poly(A) tail positive reads remained after filtering and approximately half of these mapped to a unique locus within the human genome (Fig. 1a). As expected, a majority of the unambiguously mapped reads aligned to the 3′ UTR (Fig. 1b). Interestingly, even more poly(A) tail positive reads were located in intergenic regions, while approximately 10% mapped to introns or the 5′ UTR, respectively. The generated list of clusters (Supplementary Table S1) was screened for gene-specific PA sites present both in uninfected and early interacting cells. Further filtering resulted in 142 significantly differentially used PA sites (Bonferroni-adjusted p-value < 0.05) within 130 different genes. These genes were screened for gained or lost miRNA and protein binding sites as well as known interactions between the encoded proteins using APADB [12] and STRING [22].


Putative alternative polyadenylation (APA) events in the early interaction of Salmonella enterica Typhimurium and human host cells.

Afonso-Grunz F - Genom Data (2015)

Mapping and annotation statistics of poly(A) tail positive reads from the poly(A)+ library of early interacting HeLa-S3 cells prepared with MACE. (a) The fraction of uniquely, ambiguously and unmapped mapped reads is shown along with the number of excluded reads during quality trimming. (b) The numbers of uniquely mapped reads that aligned to intergenic regions, the mitochondrion or in antisense direction of a protein-coding gene are shown together with the number of reads that mapped to the UTRs, introns and exons of mRNAs.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4664775&req=5

f0005: Mapping and annotation statistics of poly(A) tail positive reads from the poly(A)+ library of early interacting HeLa-S3 cells prepared with MACE. (a) The fraction of uniquely, ambiguously and unmapped mapped reads is shown along with the number of excluded reads during quality trimming. (b) The numbers of uniquely mapped reads that aligned to intergenic regions, the mitochondrion or in antisense direction of a protein-coding gene are shown together with the number of reads that mapped to the UTRs, introns and exons of mRNAs.
Mentions: A little more than one million poly(A) tail positive reads remained after filtering and approximately half of these mapped to a unique locus within the human genome (Fig. 1a). As expected, a majority of the unambiguously mapped reads aligned to the 3′ UTR (Fig. 1b). Interestingly, even more poly(A) tail positive reads were located in intergenic regions, while approximately 10% mapped to introns or the 5′ UTR, respectively. The generated list of clusters (Supplementary Table S1) was screened for gene-specific PA sites present both in uninfected and early interacting cells. Further filtering resulted in 142 significantly differentially used PA sites (Bonferroni-adjusted p-value < 0.05) within 130 different genes. These genes were screened for gained or lost miRNA and protein binding sites as well as known interactions between the encoded proteins using APADB [12] and STRING [22].

Bottom Line: Abstract available from the publisher.

View Article: PubMed Central - PubMed

Affiliation: Institute for Molecular BioSciences, Goethe University Frankfurt am Main, Frankfurt am Main, Germany.

AUTOMATICALLY GENERATED EXCERPT
Please rate it.

Alternative polyadenylation (APA) is a common regulatory mechanism of gene expression that generates messenger RNAs (mRNAs) with distinct untranslated regions (UTRs) as well as coding sequences from one and the same gene... The resulting transcript isoforms may not only exhibit an altered coding potential, but also harbor a distinct set of cis-regulatory elements for microRNAs (miRNAs) and other non-coding RNAs (ncRNAs) as well as RNA-binding proteins (RBPs) that affects processing, localization, stability, and translation of the mRNA... Poly(A)-position profiling by sequencing (3P-Seq ) represents another technique for global detection of PA site usage besides MACE (reviewed in ), and a recent publication features a 3P-Seq dataset of cultured HeLa cells that were grown under similar conditions as in the present study... We previously compared the high-confidence PA sites in the 3P-Seq dataset of mouse liver cells from Nam and colleagues with those obtained by MACE, and concluded that 3P-Seq and MACE provide similar results... The generated list of clusters (Supplementary Table S1) was screened for gene-specific PA sites present both in uninfected and early interacting cells... Further filtering resulted in 142 significantly differentially used PA sites (Bonferroni-adjusted p-value < 0.05) within 130 different genes... Another gene that gives rise to mRNAs with distinct 3′ UTRs encodes Peroxiredoxin 1 (PRDX1)... The predicted motifs mostly comprise binding sites of heterogeneous nuclear ribonucleoproteins (hnRNPs), followed by members of the serine/arginine (SR)-rich family of pre-mRNA splicing factors (SRSFs) along with other proteins that influence alternative splicing, transport and translation efficiency of PRDX1 (Supplementary Table S2)... The five highest ranking motifs are listed in Table 2 together with their associated RBPs... While this represents a common mechanism in prokaryotes, cytosolic polyadenylation was only relatively recently shown to contribute to RNA degradation in humans... The presence of degradation intermediates would indicate reduced levels of the labile iron pool caused by the increased iron consumption that arises from additional uptake of iron into intracellular bacteria... The highest ranking RBP motif in the region between the two major PA sites of PRDX1 recruits MATR3, an inner nuclear matrix protein that stabilizes mRNAs upon binding and that additionally binds to small ncRNAs involved in splicing... Besides their role in alternative splicing, several of the identified RBPs are involved in transport and translation of mRNAs... The comparison of the identified polyadenylation landscape in early interacting cells with the published dataset of non-interacting cells determined by 3P-Seq indicates several significantly differentially used PA sites, and some of these suggest that APA might contribute to the complex regulatory network that governs the immune response of epithelial cells... APA of PRDX1 results in transcription of mRNA isoforms with distinct sets of miRNA binding sites, while PA site usage in VAPA is likely to influence alternative splicing.

No MeSH data available.