Alternative polyadenylation (APA) modulates mRNA processing in the 3'-untranslated regions (3' UTR), affecting mRNA stability and translation efficiency. Research into genetically regulated APA has the potential to provide insights into cancer risk. In this study, we conducted large APA-wide association studies to investigate associations between APA levels and cancer risk. Genetic models were built to predict APA levels in multiple tissues using genotype and RNA sequencing data from 1,337 samples from the Genotype-Tissue Expression project. Associations of genetically predicted APA levels with cancer risk were assessed by applying the prediction models to data from large genome-wide association studies of six common cancers among European ancestry populations: breast, ovarian, prostate, colorectal, lung, and pancreatic cancers. A total of 58 risk genes (corresponding to 76 APA sites) were associated with at least one type of cancer, including 25 genes previously not linked to cancer susceptibility. Of the identified risk APAs, 97.4% and 26.3% were supported by 3'-UTR APA quantitative trait loci and colocalization analyses, respectively. Luciferase reporter assays for four selected putative regulatory 3'-UTR variants demonstrated that the risk alleles of 3'-UTR variants, rs324015 (STAT6), rs2280503 (DIP2B), rs1128450 (FBXO38), and rs145220637 (LDHA), significantly increased the posttranscriptional activities of their target genes compared with reference alleles. Furthermore, knockdown of the target genes confirmed their ability to promote proliferation and migration. Overall, this study provides insights into the role of APA in the genetic susceptibility to common cancers. Significance: Systematic evaluation of associations of alternative polyadenylation with cancer risk reveals 58 putative susceptibility genes, highlighting the contribution of genetically regulated alternative polyadenylation of 3'UTRs to genetic susceptibility to cancer.

• MeSH
• 3' nepřekládaná oblast * genetika   MeSH
• celogenomová asociační studie * MeSH
• genetická predispozice k nemoci * MeSH
• jednonukleotidový polymorfismus MeSH
• lidé MeSH
• lokus kvantitativního znaku MeSH
• messenger RNA genetika   metabolismus   MeSH
• nádorové buněčné linie MeSH
• nádory * genetika   MeSH
• polyadenylace * MeSH
• regulace genové exprese u nádorů MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3' nepřekládaná oblast * MeSH
• messenger RNA MeSH

Mammalian oocyte development depends on the temporally controlled translation of maternal transcripts, particularly in the coordination of meiotic and early embryonic development when transcription has ceased. The translation of mRNA is regulated by various RNA-binding proteins. We show that the absence of cytoplasmic polyadenylation element-binding protein 3 (CPEB3) negatively affects female reproductive fitness. CPEB3-depleted oocytes undergo meiosis normally but experience early embryonic arrest due to a disrupted transcriptome, leading to aberrant protein expression and the subsequent failure of embryonic transcription initiation. We found that CPEB3 stabilizes a subset of mRNAs with a significantly longer 3'UTR that is enriched in its distal region with cytoplasmic polyadenylation elements. Overall, our results suggest that CPEB3 is an important maternal factor that regulates the stability and translation of a subclass of mRNAs that are essential for the initiation of embryonic transcription and thus for embryonic development.

• Klíčová slova
• embryo, mRNA, oocyte, translation,
• MeSH
• 3' nepřekládaná oblast genetika   MeSH
• embryonální vývoj genetika   MeSH
• meióza genetika   MeSH
• messenger RNA genetika   metabolismus   MeSH
• myši MeSH
• oocyty * metabolismus   MeSH
• polyadenylace MeSH
• proteiny vázající RNA * metabolismus   genetika   MeSH
• stabilita RNA genetika   MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 3' nepřekládaná oblast MeSH
• Cpeb3 protein, mouse MeSH Prohlížeč
• messenger RNA MeSH
• proteiny vázající RNA * MeSH

Osteoblasts orchestrate bone formation through the secretion of type I collagen and other constituents of the matrix on which hydroxyapatite crystals mineralize. Here, we show that TENT5A, whose mutations were found in congenital bone disease osteogenesis imperfecta patients, is a cytoplasmic poly(A) polymerase playing a crucial role in regulating bone mineralization. Direct RNA sequencing revealed that TENT5A is induced during osteoblast differentiation and polyadenylates mRNAs encoding Col1α1, Col1α2, and other secreted proteins involved in osteogenesis, increasing their expression. We postulate that TENT5A, possibly together with its paralog TENT5C, is responsible for the wave of cytoplasmic polyadenylation of mRNAs encoding secreted proteins occurring during bone mineralization. Importantly, the Tent5a knockout (KO) mouse line displays bone fragility and skeletal hypomineralization phenotype resulting from quantitative and qualitative collagen defects. Thus, we report a biologically relevant posttranscriptional regulator of collagen production and, more generally, bone formation.

• Klíčová slova
• FAM46A, Nanopore, TENT5A, collagen, direct RNA sequencing, osteoblasts, osteogenesis, osteogenesis imperfecta, poly(A) tail, polyadenylation,
• MeSH
• buněčná diferenciace MeSH
• fyziologická kalcifikace genetika   MeSH
• kolagen typu I, řetězec alfa 1 genetika   metabolismus   MeSH
• kolagen typu I genetika   metabolismus   MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• modely nemocí na zvířatech MeSH
• myši knockoutované MeSH
• myši MeSH
• neurotrofní faktory genetika   metabolismus   MeSH
• nukleotidyltransferasy genetika   metabolismus   MeSH
• oční proteiny genetika   metabolismus   MeSH
• osteoblasty metabolismus   patologie   MeSH
• osteogenesis imperfecta genetika   metabolismus   patologie   MeSH
• osteogeneze genetika   MeSH
• osteonektin genetika   metabolismus   MeSH
• poly(A)-polymerasa genetika   metabolismus   MeSH
• polyadenylace MeSH
• protein - isoformy nedostatek   genetika   MeSH
• sekvenční analýza RNA MeSH
• serpiny genetika   metabolismus   MeSH
• signální transdukce MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Col1a1 protein, mouse MeSH Prohlížeč
• Col1a2 protein, mouse MeSH Prohlížeč
• kolagen typu I, řetězec alfa 1 MeSH
• kolagen typu I MeSH
• messenger RNA MeSH
• neurotrofní faktory MeSH
• nukleotidyltransferasy MeSH
• oční proteiny MeSH
• osteonektin MeSH
• pigment epithelium-derived factor MeSH Prohlížeč
• poly(A)-polymerasa MeSH
• protein - isoformy MeSH
• serpiny MeSH
• SPARC protein, mouse MeSH Prohlížeč
• TENT5A protein, human MeSH Prohlížeč
• Tent5A protein, mouse MeSH Prohlížeč
• Tent5c protein, mouse MeSH Prohlížeč

The RNA exosome processes a wide variety of RNA and mediates RNA maturation, quality control and decay. In marked contrast to its high processivity in vivo, the purified exosome exhibits only weak activity on RNA substrates in vitro. Its activity is regulated by several auxiliary proteins, and protein complexes. In budding yeast, the activity of exosome is enhanced by the polyadenylation complex referred to as TRAMP. TRAMP oligoadenylates precursors and aberrant forms of RNAs to promote their trimming or complete degradation by exosomes. This chapter provides protocols for the purification of TRAMP and exosome complexes from yeast and the in vitro evaluation of exosome activation by the TRAMP complex. The protocols can be used for different purposes, such as the assessment of the role of individual subunits, protein domains or particular mutations in TRAMP-exosome RNA processing in vitro.

• Klíčová slova
• Air1, Air2, Degradation assay, Mtr4, Noncanonical poly(A) polymerase, Noncoding RNAs, Polyadenylation assay, RNA exosome, RNA quality control, Rrp6, TAP purification, TRAMP4, Trf4,
• MeSH
• buněčné jádro metabolismus   MeSH
• exozom metabolismus   MeSH
• exozómy metabolismus   MeSH
• polyadenylace fyziologie   MeSH
• RNA metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny metabolismus   MeSH
• Saccharomyces cerevisiae metabolismus   MeSH
• serinové endopeptidasy metabolismus   MeSH
• stabilita RNA fyziologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• exozom MeSH
• RNA MeSH
• Saccharomyces cerevisiae - proteiny MeSH
• serinové endopeptidasy MeSH
• tunicate retinoic acid-inducible modular protease MeSH Prohlížeč

Tens of thousands of rapidly evolving long non-coding RNA (lncRNA) genes have been identified, but functions were assigned to relatively few of them. The lncRNA contribution to the mouse oocyte physiology remains unknown. We report the evolutionary history and functional analysis of Sirena1, the most expressed lncRNA and the 10th most abundant poly(A) transcript in mouse oocytes. Sirena1 appeared in the common ancestor of mouse and rat and became engaged in two different post-transcriptional regulations. First, antisense oriented Elob pseudogene insertion into Sirena1 exon 1 is a source of small RNAs targeting Elob mRNA via RNA interference. Second, Sirena1 evolved functional cytoplasmic polyadenylation elements, an unexpected feature borrowed from translation control of specific maternal mRNAs. Sirena1 knock-out does not affect fertility, but causes minor dysregulation of the maternal transcriptome. This includes increased levels of Elob and mitochondrial mRNAs. Mitochondria in Sirena1-/- oocytes disperse from the perinuclear compartment, but do not change in number or ultrastructure. Taken together, Sirena1 contributes to RNA interference and mitochondrial aggregation in mouse oocytes. Sirena1 exemplifies how lncRNAs stochastically engage or even repurpose molecular mechanisms during evolution. Simultaneously, Sirena1 expression levels and unique functional features contrast with the lack of functional importance assessed under laboratory conditions.

• MeSH
• genový knockout MeSH
• krysa rodu Rattus MeSH
• messenger RNA genetika   MeSH
• mitochondrie genetika   ultrastruktura   MeSH
• myši MeSH
• oocyty růst a vývoj   metabolismus   ultrastruktura   MeSH
• polyadenylace genetika   MeSH
• RNA dlouhá nekódující genetika   MeSH
• RNA mitochondriální genetika   MeSH
• transkriptom genetika   MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• messenger RNA MeSH
• mitochondrial messenger RNA MeSH Prohlížeč
• RNA dlouhá nekódující MeSH
• RNA mitochondriální MeSH

Cellular mechanisms that safeguard genome integrity are often subverted in cancer. To identify cancer-related genome caretakers, we employed a convergent multi-screening strategy coupled to quantitative image-based cytometry and ranked candidate genes according to multivariate readouts reflecting viability, proliferative capacity, replisome integrity, and DNA damage signaling. This unveiled regulators of replication stress resilience, including components of the pre-mRNA cleavage and polyadenylation complex. We show that deregulation of pre-mRNA cleavage impairs replication fork speed and leads to excessive origin activity, rendering cells highly dependent on ATR function. While excessive formation of RNA:DNA hybrids under these conditions was tightly associated with replication-stress-induced DNA damage, inhibition of transcription rescued fork speed, origin activation, and alleviated replication catastrophe. Uncoupling of pre-mRNA cleavage from co-transcriptional processing and export also protected cells from replication-stress-associated DNA damage, suggesting that pre-mRNA cleavage provides a mechanism to efficiently release nascent transcripts and thereby prevent gene gating-associated genomic instability.

• Klíčová slova
• ATR, R-loops, RNA:DNA hybrids, checkpoint activation, cleavage, gene gating, origin firing, polyadenylation, pre-mRNA processing, replication catastrophe, replication stress,
• MeSH
• aktivní transport - buněčné jádro MeSH
• DNA nádorová genetika   metabolismus   MeSH
• DNA vazebné proteiny MeSH
• HeLa buňky MeSH
• heteroduplexy nukleové kyseliny genetika   metabolismus   MeSH
• jaderné proteiny genetika   metabolismus   MeSH
• lidé MeSH
• messenger RNA biosyntéza   genetika   MeSH
• nádory genetika   metabolismus   MeSH
• nestabilita genomu * MeSH
• polyadenylace MeSH
• poškození DNA * MeSH
• prekurzory RNA biosyntéza   genetika   MeSH
• proteiny buněčného cyklu genetika   metabolismus   MeSH
• proteiny vázající RNA MeSH
• regulace genové exprese u nádorů MeSH
• replikace DNA * MeSH
• RNA nádorová biosyntéza   genetika   MeSH
• štěpení RNA * MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA nádorová MeSH
• DNA vazebné proteiny MeSH
• heteroduplexy nukleové kyseliny MeSH
• jaderné proteiny MeSH
• messenger RNA MeSH
• prekurzory RNA MeSH
• proteiny buněčného cyklu MeSH
• proteiny vázající RNA MeSH
• RNA nádorová MeSH
• THOC1 protein, human MeSH Prohlížeč
• WDR33 protein, human MeSH Prohlížeč

Extrachromosomal hereditary elements such as organelles, viruses, and plasmids are important for the cell fitness and survival. Their transcription is dependent on host cellular RNA polymerase (RNAP) or intrinsic RNAP encoded by these elements. The yeast Kluyveromyces lactis contains linear cytoplasmic DNA virus-like elements (VLEs, also known as linear plasmids) that bear genes encoding putative non-canonical two-subunit RNAP. Here, we describe the architecture and identify the evolutionary origin of this transcription machinery. We show that the two RNAP subunits interact in vivo, and this complex interacts with another two VLE-encoded proteins, namely the mRNA capping enzyme and a putative helicase. RNAP, mRNA capping enzyme and the helicase also interact with VLE-specific DNA in vivo. Further, we identify a promoter sequence element that causes 5' mRNA polyadenylation of VLE-specific transcripts via RNAP slippage at the transcription initiation site, and structural elements that precede the termination sites. As a result, we present a first model of the yeast virus-like element transcription initiation and intrinsic termination. Finally, we demonstrate that VLE RNAP and its promoters display high similarity to poxviral RNAP and promoters of early poxviral genes, respectively, thereby pointing to their evolutionary origin.

• MeSH
• cytoplazma MeSH
• DNA řízené RNA-polymerasy metabolismus   MeSH
• fungální proteiny genetika   MeSH
• genetická transkripce * MeSH
• Kluyveromyces genetika   MeSH
• konformace nukleové kyseliny MeSH
• molekulární evoluce * MeSH
• polyadenylace MeSH
• promotorové oblasti (genetika) * MeSH
• regulace genové exprese u hub MeSH
• responzivní elementy * MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie MeSH
• stabilita RNA MeSH
• viry genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA řízené RNA-polymerasy MeSH
• fungální proteiny MeSH

Although the involvement of the extracellular signal-regulated kinases 1 and 2 (ERK1/2) pathway in the regulation of cytostatic factor (CSF) activity; as well as in microtubules organization during meiotic maturation of oocytes; has already been described in detail; rather less attention has been paid to the role of ERK1/2 in the regulation of mRNA translation. However; important data on the role of ERK1/2 in translation during oocyte meiosis have been documented. This review focuses on recent findings regarding the regulation of translation and the role of ERK1/2 in this process in the meiotic cycle of mammalian oocytes. The specific role of ERK1/2 in the regulation of mammalian target of rapamycin (mTOR); eukaryotic translation initiation factor 4E (eIF4E) and cytoplasmic polyadenylation element binding protein 1 (CPEB1) activity is addressed along with additional focus on the other key players involved in protein translation.

• Klíčová slova
• CPEB1, ERK1/2, MAP kinase, eIF4E, mTOR, oocyte, translation,
• MeSH
• cytoplazma genetika   metabolismus   MeSH
• eukaryotický iniciační faktor 4E metabolismus   MeSH
• faktory štěpení a polyadenylace mRNA metabolismus   MeSH
• fosfatidylinositol-3-kinasy metabolismus   MeSH
• lidé MeSH
• meióza * MeSH
• messenger RNA genetika   metabolismus   MeSH
• mitogenem aktivovaná proteinkinasa 1 metabolismus   MeSH
• mitogenem aktivovaná proteinkinasa 3 metabolismus   MeSH
• mitogenem aktivované proteinkinasy metabolismus   MeSH
• oocyty metabolismus   MeSH
• polyadenylace MeSH
• proteosyntéza * MeSH
• signální transdukce MeSH
• TOR serin-threoninkinasy metabolismus   MeSH
• vazba proteinů MeSH
• vývojová regulace genové exprese MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• eukaryotický iniciační faktor 4E MeSH
• faktory štěpení a polyadenylace mRNA MeSH
• messenger RNA MeSH
• mitogenem aktivovaná proteinkinasa 1 MeSH
• mitogenem aktivovaná proteinkinasa 3 MeSH
• mitogenem aktivované proteinkinasy MeSH
• TOR serin-threoninkinasy MeSH

Alternative polyadenylation is an important and pervasive mechanism that generates heterogeneous 3'-termini of mRNA and is considered an important regulator of gene expression. We performed bioinformatics analyses of ESTs and the 3'-UTRs of the main transcript splice variants of the translational initiation factor eIF4E1 and its family members, eIF4E2 and eIF4E3. This systematic analysis led to the prediction of new polyadenylation signals. All identified polyadenylation sites were subsequently verified by 3'RACE of transcripts isolated from human lymphoblastic cell lines. This led to the observation that multiple simultaneous polyadenylation site utilization occurs in single cell population. Importantly, we described the use of new polyadenylation site in the eIF4E1 mRNA, which lacked any known polyadenylation signal. The proportion of eIF4E1 transcripts derived from the first two polyadenylation sites in eIF4E1 mRNA achieved 15% in a wide range of cell lines. This result demonstrates the ubiquitous presence of ARE-lacking transcripts, which escape HuR/Auf1-mediated control, the main mechanism of eIF4E1 gene expression regulation. We found many EST clones documenting the significant production of transcript variants 2-4 of eIF4E2 gene that encode proteins with C-termini that were distinct from the mainly studied prototypical isoform A. Similarly, eIF4E3 mRNAs are produced as two main variants with the same very long 3'-UTR with potential for heavy post-transcriptional regulation. We identified sparsely documented transcript variant 1 of eIF4E3 gene in human placenta. eIF4E3 truncated transcript variants were found mainly in brain. We propose to elucidate the minor splice variants of eIF4E2 and eIF4E3 in great detail because they might produce proteins with modified features that fulfill different cellular roles from their major counterparts.

• Klíčová slova
• 3′RACE, 4EHP, Alternative polyadenylation, Polyadenylation signal, Translation, eIF4E, eIF4E2, eIF4E3,
• MeSH
• 3' nepřekládaná oblast MeSH
• buněčné linie MeSH
• eukaryotický iniciační faktor 4E genetika   metabolismus   MeSH
• exprimované sekvenční adresy MeSH
• lidé MeSH
• messenger RNA genetika   metabolismus   MeSH
• mozek metabolismus   MeSH
• placenta metabolismus   MeSH
• polyadenylace genetika   MeSH
• proteiny vázající čepičku mRNA genetika   MeSH
• regulace genové exprese MeSH
• sestřih RNA genetika   MeSH
• těhotenství MeSH
• Check Tag
• lidé MeSH
• těhotenství MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3' nepřekládaná oblast MeSH
• EIF4E2 protein, human MeSH Prohlížeč
• eIF4E3 protein, human MeSH Prohlížeč
• eukaryotický iniciační faktor 4E MeSH
• messenger RNA MeSH
• proteiny vázající čepičku mRNA MeSH

One recently discussed general mechanism affecting gene expression is 3'-untranslated region (3'UTR) length. Events such as shortening, translocation or loss of 3'UTRs are observed within oncogenes and are proposed to associate with increased expression. Thus, increased efforts are being made to understand constitutive and differential transcript 3'end formation. Investigation of AGR2 mRNA revealed a direct impact of its 3'UTR length on AGR2 expression. In silico analyses identified several regulatory sequences within the distal part of AGR2 mRNA that may regulate 3'UTR length and associated protein levels. Short 3'UTRs were observed in a panel of AGR2-positive cancer cell lines and in human breast cancer specimens, in which more extensive 3'UTR shortening correlated with increased AGR2 protein levels. AGR2 is an important member of PI3K/AKT signalling pathway, which along with the proposed involvement of mTOR in the regulation of alternative polyadenylation, prompted us to study the role of mTOR in relation to AGR2 mRNA 3'UTR shortening. A direct impact of mTOR signalling on AGR2 3'UTR shortening associated with increased protein synthesis was found, which led to the identification of a novel molecular mechanism involved in upregulation of AGR2 levels in mTOR-activated cells via modulating the 3'UTR length of AGR2 mRNA.

• Klíčová slova
• 3’ untranslated region, 3’UTR shortening, Anterior gradient 2, mTOR,
• MeSH
• 3' nepřekládaná oblast genetika   MeSH
• buňky A549 MeSH
• HCT116 buňky MeSH
• HEK293 buňky MeSH
• klonování DNA MeSH
• lidé MeSH
• messenger RNA genetika   MeSH
• MFC-7 buňky MeSH
• mTORC1 MeSH
• mukoproteiny MeSH
• multiproteinové komplexy genetika   MeSH
• nádorové buněčné linie MeSH
• nádory prsu genetika   MeSH
• onkogenní proteiny MeSH
• polyadenylace genetika   MeSH
• proteiny genetika   metabolismus   MeSH
• proteosyntéza genetika   MeSH
• regulace genové exprese genetika   MeSH
• regulační sekvence ribonukleových kyselin genetika   MeSH
• signální transdukce genetika   MeSH
• TOR serin-threoninkinasy genetika   metabolismus   MeSH
• upregulace genetika   MeSH
• Check Tag
• lidé MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• 3' nepřekládaná oblast MeSH
• AGR2 protein, human MeSH Prohlížeč
• messenger RNA MeSH
• MTOR protein, human MeSH Prohlížeč
• mTORC1 MeSH
• mukoproteiny MeSH
• multiproteinové komplexy MeSH
• onkogenní proteiny MeSH
• proteiny MeSH
• regulační sekvence ribonukleových kyselin MeSH
• TOR serin-threoninkinasy MeSH