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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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PA site usage of FTL in uninfected and early interacting host cells. The figure shows the region encoding FTL on human chromosome 19 together with the number and mapping position of poly(A) tail positive reads from uninfected (3P-Seq) and early interacting (MACE) HeLa cells. FTL comprises four exons, and three PA sites that are located within the UTRs. PA site usage in non-interacting cells is restricted to the 3′ UTR, while more than 40% of the mRNAs appear to be terminated within the 5′ UTR in early interacting cells. The complete 3P-Seq dataset from Nam and colleagues is additionally shown, and confirms the presence of the 5′ UTR isoform that is absent in the downsampled 3P-Seq dataset. The figure is based on an image from the Integrative Genomics Viewer [30].
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f0010: PA site usage of FTL in uninfected and early interacting host cells. The figure shows the region encoding FTL on human chromosome 19 together with the number and mapping position of poly(A) tail positive reads from uninfected (3P-Seq) and early interacting (MACE) HeLa cells. FTL comprises four exons, and three PA sites that are located within the UTRs. PA site usage in non-interacting cells is restricted to the 3′ UTR, while more than 40% of the mRNAs appear to be terminated within the 5′ UTR in early interacting cells. The complete 3P-Seq dataset from Nam and colleagues is additionally shown, and confirms the presence of the 5′ UTR isoform that is absent in the downsampled 3P-Seq dataset. The figure is based on an image from the Integrative Genomics Viewer [30].

Mentions: Ferritin, light polypeptide (FTL) is involved in iron homeostasis, and the differential usage of PA sites from FTL in uninfected and early interacting host cells could contribute to the early response following bacterial infection. FTL exhibits three potential PA sites within HeLa cells (Fig. 2). Two of these give rise to transcript isoforms that solely differ in 3′ UTR length with ~ 40 nucleotides difference on average. The third putative PA site is located within the 5'UTR of FTL, thus pointing to a transcript isoform that comprises little more than 70 nucleotides. Since the slightly longer 3′ UTR isoform is only present in non-interacting cells in a vanishing low ratio (less than 1%), PA site usage primarily differs in between the shorter 3′ UTR and the very short 5′ UTR isoform. The shorter 3′ UTR isoform is preceded by a canonical poly(A) signal, and almost exclusively used in non-interacting cells. Early interacting cells, however, exhibit a prominent shift from this transcript variant to the 5′ UTR isoform. Compared to the canonical isoform, the 5′ UTR isoform appears to be almost equally abundant within these cells. Although being absent in the downsampled 3P-Seq data, the presence of this PA site is additionally confirmed by the complete 3P-Seq dataset (Fig. 2).


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

Afonso-Grunz F - Genom Data (2015)

PA site usage of FTL in uninfected and early interacting host cells. The figure shows the region encoding FTL on human chromosome 19 together with the number and mapping position of poly(A) tail positive reads from uninfected (3P-Seq) and early interacting (MACE) HeLa cells. FTL comprises four exons, and three PA sites that are located within the UTRs. PA site usage in non-interacting cells is restricted to the 3′ UTR, while more than 40% of the mRNAs appear to be terminated within the 5′ UTR in early interacting cells. The complete 3P-Seq dataset from Nam and colleagues is additionally shown, and confirms the presence of the 5′ UTR isoform that is absent in the downsampled 3P-Seq dataset. The figure is based on an image from the Integrative Genomics Viewer [30].
© Copyright Policy - CC BY
Related In: Results  -  Collection

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

f0010: PA site usage of FTL in uninfected and early interacting host cells. The figure shows the region encoding FTL on human chromosome 19 together with the number and mapping position of poly(A) tail positive reads from uninfected (3P-Seq) and early interacting (MACE) HeLa cells. FTL comprises four exons, and three PA sites that are located within the UTRs. PA site usage in non-interacting cells is restricted to the 3′ UTR, while more than 40% of the mRNAs appear to be terminated within the 5′ UTR in early interacting cells. The complete 3P-Seq dataset from Nam and colleagues is additionally shown, and confirms the presence of the 5′ UTR isoform that is absent in the downsampled 3P-Seq dataset. The figure is based on an image from the Integrative Genomics Viewer [30].
Mentions: Ferritin, light polypeptide (FTL) is involved in iron homeostasis, and the differential usage of PA sites from FTL in uninfected and early interacting host cells could contribute to the early response following bacterial infection. FTL exhibits three potential PA sites within HeLa cells (Fig. 2). Two of these give rise to transcript isoforms that solely differ in 3′ UTR length with ~ 40 nucleotides difference on average. The third putative PA site is located within the 5'UTR of FTL, thus pointing to a transcript isoform that comprises little more than 70 nucleotides. Since the slightly longer 3′ UTR isoform is only present in non-interacting cells in a vanishing low ratio (less than 1%), PA site usage primarily differs in between the shorter 3′ UTR and the very short 5′ UTR isoform. The shorter 3′ UTR isoform is preceded by a canonical poly(A) signal, and almost exclusively used in non-interacting cells. Early interacting cells, however, exhibit a prominent shift from this transcript variant to the 5′ UTR isoform. Compared to the canonical isoform, the 5′ UTR isoform appears to be almost equally abundant within these cells. Although being absent in the downsampled 3P-Seq data, the presence of this PA site is additionally confirmed by the complete 3P-Seq dataset (Fig. 2).

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.