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Relevant bibliographies by topics / RNA 3' Polyadenylation Signals

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Academic literature on the topic 'RNA 3' Polyadenylation Signals'

Author: Grafiati

Published: 4 June 2021

Last updated: 10 February 2022

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Journal articles on the topic "RNA 3' Polyadenylation Signals"

1

Denome, R. M., and C. N. Cole. "Patterns of polyadenylation site selection in gene constructs containing multiple polyadenylation signals." Molecular and Cellular Biology 8, no. 11 (November 1988): 4829–39. http://dx.doi.org/10.1128/mcb.8.11.4829.

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We have constructed a series of plasmids containing multiple polyadenylation signals downstream of the herpes simplex virus type 1 (HSV) thymidine kinase (tk)-coding region. The signals used were from the simian virus 40 (SV40) late gene, the HSV tk gene, and an AATAAA-containing segment of the SV40 early region. This last fragment signals polyadenylation poorly in our constructs and not at all during SV40 infection. All plasmids contained the SV40 origin of replication. Plasmids were transfected into Cos-1 cells; after 48 h, cytoplasmic RNA was isolated and the quantity and 3'-end structure of tk mRNAs was analyzed by using S1 nuclease protection assays. In all constructs, all polyadenylation signals were used. Increasing the number of poly(A) signals 3' to the tk-coding region did not affect the total amount of polyadenylated RNA produced, even with the weakest signal. Increasing the distance between two signals caused an increase in the use of the 5' signal and a decrease in the use of the 3' signal. Changing the distance between the 5' cap and first signal did not affect signal use. Analyses of cytoplasmic mRNA stability, nuclear RNA distribution, and transcription in the polyadenylation signal region indicated that the distribution of tk RNAs ending at different poly(A) sites was the result of poly(A) signal choice, not other aspects of RNA metabolism. Four possible mechanisms of polyadenylation signal recognition are discussed.

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Denome, R. M., and C. N. Cole. "Patterns of polyadenylation site selection in gene constructs containing multiple polyadenylation signals." Molecular and Cellular Biology 8, no. 11 (November 1988): 4829–39. http://dx.doi.org/10.1128/mcb.8.11.4829-4839.1988.

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We have constructed a series of plasmids containing multiple polyadenylation signals downstream of the herpes simplex virus type 1 (HSV) thymidine kinase (tk)-coding region. The signals used were from the simian virus 40 (SV40) late gene, the HSV tk gene, and an AATAAA-containing segment of the SV40 early region. This last fragment signals polyadenylation poorly in our constructs and not at all during SV40 infection. All plasmids contained the SV40 origin of replication. Plasmids were transfected into Cos-1 cells; after 48 h, cytoplasmic RNA was isolated and the quantity and 3'-end structure of tk mRNAs was analyzed by using S1 nuclease protection assays. In all constructs, all polyadenylation signals were used. Increasing the number of poly(A) signals 3' to the tk-coding region did not affect the total amount of polyadenylated RNA produced, even with the weakest signal. Increasing the distance between two signals caused an increase in the use of the 5' signal and a decrease in the use of the 3' signal. Changing the distance between the 5' cap and first signal did not affect signal use. Analyses of cytoplasmic mRNA stability, nuclear RNA distribution, and transcription in the polyadenylation signal region indicated that the distribution of tk RNAs ending at different poly(A) sites was the result of poly(A) signal choice, not other aspects of RNA metabolism. Four possible mechanisms of polyadenylation signal recognition are discussed.

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3

Stolow, D. T., and S. M. Berget. "UV cross-linking of polypeptides associated with 3'-terminal exons." Molecular and Cellular Biology 10, no. 11 (November 1990): 5937–44. http://dx.doi.org/10.1128/mcb.10.11.5937.

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Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro.

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4

Stolow, D. T., and S. M. Berget. "UV cross-linking of polypeptides associated with 3'-terminal exons." Molecular and Cellular Biology 10, no. 11 (November 1990): 5937–44. http://dx.doi.org/10.1128/mcb.10.11.5937-5944.1990.

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Association of nuclear proteins with chimeric vertebrate precursor RNAs containing both polyadenylation signals and an intron was examined by UV cross-linking. One major difference in cross-linking pattern was observed between this chimeric precursor RNA and precursors containing only polyadenylation or splicing signals. The heterogeneous nuclear ribonucleoprotein (hnRNP) polypeptide C cross-linked strongly to sequences downstream of the A addition site in polyadenylation precursor RNA containing only the polyadenylation signal from the simian virus 40 (SV40) late transcription unit. In contrast, the hnRNP C polypeptide cross-linked to chimeric RNA containing the same SV40 late poly(A) cassette very poorly, at a level less than 5% of that observed with the precursor RNA containing just the poly(A) site. Observation that cross-linking of the hnRNP C polypeptide to elements within the SV40 late poly(A) site was altered by the presence of an upstream intron suggests differences in the way nuclear factors associate with poly(A) sites in the presence and absence of an upstream intron. Cross-linking of C polypeptide to chimeric RNA increased with RNAs mutated for splicing or polyadenylation consensus sequences and under reaction conditions (high magnesium) that inhibited polyadenylation. Furthermore, cross-linking of hnRNP C polypeptide to precursors containing just the SV40 late poly(A) site was eliminated in the presence of competing poly(U); polyadenylation, however, was unaffected. Correlation of loss of activity with high levels of hnRNP C polypeptide cross-linking raises questions about the specificity of the interaction between the hnRNP C polypeptide and polyadenylation precursor RNAs in vitro.

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5

Sanfaçon, Hélène. "Regulation of mRNA formation in plants: lessons from the cauliflower mosaic virus transcription signals." Canadian Journal of Botany 70, no. 5 (May 1, 1992): 885–99. http://dx.doi.org/10.1139/b92-113.

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The cauliflower mosaic virus (CaMV) transcription signals are common tools of plant molecular biologists. In this article, the transcription signals are discussed in light of the life cycle of CaMV, a plant pararetrovirus. Production of mature 35S RNA, the terminally redundant genomic RNA, is regulated by the 35S promoter, a very strong promoter, and by the polyadenylation signal that is present twice on the RNA but recognized only at its 3′ end. Dissection of the promoter has identified several organ-specific elements acting in concert to express the 35S RNA in most plant cells. Studies on the polyadenylation signal have revealed upstream elements inducing recognition of the AATAAA sequence and have led to the proposal that the conditional recognition of this signal is dependent on its distance from the promoter. Comparison of the CaMV signals with other plant signals allows speculation on the plant transcriptional machinery and on some striking resemblances and differences to the animal and yeast systems. Finally, potential applications of this knowledge will be described such as the construction of hybrid plant promoters or polyadenylation signals using the 35S minimal elements. Key words: cauliflower mosaic virus, 35S promoter, polyadenylation signal, 35S RNA, transcription, retroviruses.

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Das, Atze T., Bep Klaver, and Ben Berkhout. "A Hairpin Structure in the R Region of the Human Immunodeficiency Virus Type 1 RNA Genome Is Instrumental in Polyadenylation Site Selection." Journal of Virology 73, no. 1 (January 1, 1999): 81–91. http://dx.doi.org/10.1128/jvi.73.1.81-91.1999.

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ABSTRACT Some retroviruses with an extended repeat (R) region encode the polyadenylation signal within the R region such that this signal is present at both the 5′ and 3′ ends of the viral transcript. This necessitates differential regulation to either repress recognition of the 5′ polyadenylation signal or enhance usage of the 3′ signal. The human immunodeficiency virus type 1 (HIV-1) genome encodes an inherently efficient polyadenylation signal within the 97-nucleotide R region. Polyadenylation at the 5′ HIV-1 polyadenylation site is inhibited by downstream splicing signals, and usage of the 3′ polyadenylation site is triggered by an upstream enhancer element. In this paper, we demonstrate that this on-off switch of the HIV-1 polyadenylation signal is controlled by a secondary RNA structure that occludes part of the AAUAAA hexamer motif, which we have termed the polyA hairpin. Opening the 5′ hairpin by mutation triggered premature polyadenylation and caused reduced synthesis of viral RNA, indicating that the RNA structure plays a pivotal role in repression of the 5′ polyadenylation site. Apparently, the same hairpin structure does not interfere with efficient usage of the 3′ polyadenylation site, which may be due to the presence of the upstream enhancer element. However, when the 3′ hairpin was further stabilized by mutation, we measured a complete loss of 3′ polyadenylation. Thus, the thermodynamic stability of the polyA hairpin is delicately balanced to allow nearly complete repression of the 5′ site yet efficient activation of the 3′ site. This is the first report of regulated polyadenylation that is mediated by RNA secondary structure. A similar hairpin motif that occludes the polyadenylation signal can be proposed for other lentiviruses and members of the spumaretroviruses, suggesting that this represents a more general gene expression strategy of complex retroviruses.

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Rothnie, Helen M., Gang Chen, Johannes Fütterer, and Thomas Hohn. "Polyadenylation in Rice Tungro Bacilliform Virus:cis-Acting Signals and Regulation." Journal of Virology 75, no. 9 (May 1, 2001): 4184–94. http://dx.doi.org/10.1128/jvi.75.9.4184-4194.2001.

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ABSTRACT The polyadenylation signal of rice tungro bacilliform virus (RTBV) was characterized by mutational and deletion analysis. Thecis-acting signals required to direct polyadenylation conformed to what is known for plant poly(A) signals in general and were very similar to those of the related cauliflower mosaic virus. Processing was directed by a canonical AAUAAA poly(A) signal, an upstream UG-rich region considerably enhanced processing efficiency, and sequences downstream of the cleavage site were not required. When present at the end of a transcription unit, thecis-acting signals for 3′-end processing were highly efficient in both monocot (rice) and dicot (Nicotiana plumbaginifolia) protoplasts. In a promoter-proximal position, as in the viral genome, the signal was also efficiently processed in rice protoplasts, giving rise to an abundant “short-stop” (SS-) RNA. The proportion of SS-RNA was considerably lower in N. plumbaginifolia protoplasts. In infected plants, SS-RNA was hardly detectable, suggesting either that SS-RNA is unstable in infected plants or that read-through of the promoter-proximal poly(A) site is very efficient. SS-RNA is readily detectable in transgenic rice plants (A. Klöti, C. Henrich, S. Bieri, X. He, G. Chen, P. K. Burkhardt, J. Wünn, P. Lucca, T. Hohn, I. Potrylus, and J. Fütterer, 1999. Plant Mol. Biol. 40:249–266), thus the absence of SS-RNA in infected plants can be attributed to poly(A) site bypass in the viral context to ensure production of the full-length pregenomic viral RNA. RTBV poly(A) site suppression thus depends both on context and the expression system; our results suggest that the circular viral minichromosome directs assembly of a transcription-processing complex with specific properties to effect read-through of the promoter-proximal poly(A) signal.

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Butler, J. S., P. P. Sadhale, and T. Platt. "RNA processing in vitro produces mature 3' ends of a variety of Saccharomyces cerevisiae mRNAs." Molecular and Cellular Biology 10, no. 6 (June 1990): 2599–605. http://dx.doi.org/10.1128/mcb.10.6.2599.

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Ammonium sulfate fractionation of a Saccharomyces cerevisiae whole-cell extract yielded a preparation which carried out correct and efficient endonucleolytic cleavage and polyadenylation of yeast precursor mRNA substrates corresponding to a variety of yeast genes. These included CYC1 (iso-1-cytochrome c), HIS4 (histidine biosynthesis), GAL7 (galactose-1-phosphate uridyltransferase), H2B2 (histone H2B2), PRT2 (a protein of unknown function), and CBP1 (cytochrome b mRNA processing). The reaction processed these pre-mRNAs with varying efficiencies, with cleavage and polyadenylation exceeding 70% in some cases. In each case, the poly(A) tail corresponded to the addition of approximately 60 adenosine residues, which agrees with the usual length of poly(A) tails formed in vivo. Addition of cordycepin triphosphate or substitution of CTP for ATP in these reactions inhibited polyadenylation but not endonucleolytic cleavage and resulted in accumulation of the cleaved RNA product. Although this system readily generated yeast mRNA 3' ends, no processing occurred on a human alpha-globin pre-mRNA containing the highly conserved AAUAAA polyadenylation signal of higher eucaryotes. This sequence and adjacent signals used in mammalian systems are thus not sufficient to direct mRNA 3' end formation in yeast. Despite the lack of a highly conserved nucleotide sequence signal, the same purified fraction processed the 3' ends of a variety of unrelated yeast pre-mRNAs, suggesting that endonuclease cleavage and polyadenylation may produce the mature 3' ends of all mRNAs in S. cerevisiae.

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Butler, J. S., P. P. Sadhale, and T. Platt. "RNA processing in vitro produces mature 3' ends of a variety of Saccharomyces cerevisiae mRNAs." Molecular and Cellular Biology 10, no. 6 (June 1990): 2599–605. http://dx.doi.org/10.1128/mcb.10.6.2599-2605.1990.

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Ammonium sulfate fractionation of a Saccharomyces cerevisiae whole-cell extract yielded a preparation which carried out correct and efficient endonucleolytic cleavage and polyadenylation of yeast precursor mRNA substrates corresponding to a variety of yeast genes. These included CYC1 (iso-1-cytochrome c), HIS4 (histidine biosynthesis), GAL7 (galactose-1-phosphate uridyltransferase), H2B2 (histone H2B2), PRT2 (a protein of unknown function), and CBP1 (cytochrome b mRNA processing). The reaction processed these pre-mRNAs with varying efficiencies, with cleavage and polyadenylation exceeding 70% in some cases. In each case, the poly(A) tail corresponded to the addition of approximately 60 adenosine residues, which agrees with the usual length of poly(A) tails formed in vivo. Addition of cordycepin triphosphate or substitution of CTP for ATP in these reactions inhibited polyadenylation but not endonucleolytic cleavage and resulted in accumulation of the cleaved RNA product. Although this system readily generated yeast mRNA 3' ends, no processing occurred on a human alpha-globin pre-mRNA containing the highly conserved AAUAAA polyadenylation signal of higher eucaryotes. This sequence and adjacent signals used in mammalian systems are thus not sufficient to direct mRNA 3' end formation in yeast. Despite the lack of a highly conserved nucleotide sequence signal, the same purified fraction processed the 3' ends of a variety of unrelated yeast pre-mRNAs, suggesting that endonuclease cleavage and polyadenylation may produce the mature 3' ends of all mRNAs in S. cerevisiae.

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Castelo-Branco, Pedro, Andre Furger, Matthew Wollerton, Christopher Smith, Alexandra Moreira, and Nick Proudfoot. "Polypyrimidine Tract Binding Protein Modulates Efficiency of Polyadenylation." Molecular and Cellular Biology 24, no. 10 (May 15, 2004): 4174–83. http://dx.doi.org/10.1128/mcb.24.10.4174-4183.2004.

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ABSTRACT Polypyrimidine tract binding protein (PTB) is a major hnRNP protein with multiple roles in mRNA metabolism, including regulation of alternative splicing and internal ribosome entry site-driven translation. We show here that a fourfold overexpression of PTB results in a 75% reduction of mRNA levels produced from transfected gene constructs with different polyadenylation signals (pA signals). This effect is due to the reduced efficiency of mRNA 3′ end cleavage, and in vitro analysis reveals that PTB competes with CstF for recognition of the pA signal's pyrimidine-rich downstream sequence element. This may be analogous to its role in alternative splicing, where PTB competes with U2AF for binding to pyrimidine-rich intronic sequences. The pA signal of the C2 complement gene unusually possesses a PTB-dependent upstream sequence, so that knockdown of PTB expression by RNA interference reduces C2 mRNA expression even though PTB overexpression still inhibits polyadenylation. Consequently, we show that PTB can act as a regulator of mRNA expression through both its negative and positive effects on mRNA 3′ end processing.

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Dissertations / Theses on the topic "RNA 3' Polyadenylation Signals"

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Holec, Sarah Gagliardi Dominique. "Polyadenylation and RNA degradation." Strasbourg : Université Louis Pasteur, 2008. http://eprints-scd-ulp.u-strasbg.fr:8080/987/01/HOLEC_Sarah_2008.pdf.

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Sheppard, Sarah E. "Application of a Naïve Bayes Classifier to Assign Polyadenylation Sites from 3' End Deep Sequencing Data: A Dissertation." eScholarship@UMMS, 2013. http://escholarship.umassmed.edu/gsbs_diss/653.

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Cleavage and polyadenylation of a precursor mRNA is important for transcription termination, mRNA stability, and regulation of gene expression. This process is directed by a multitude of protein factors and cis elements in the pre-mRNA sequence surrounding the cleavage and polyadenylation site. Importantly, the location of the cleavage and polyadenylation site helps define the 3’ untranslated region of a transcript, which is important for regulation by microRNAs and RNA binding proteins. Additionally, these sites have generally been poorly annotated. To identify 3’ ends, many techniques utilize an oligo-dT primer to construct deep sequencing libraries. However, this approach can lead to identification of artifactual polyadenylation sites due to internal priming in homopolymeric stretches of adenines. Previously, simple heuristic filters relying on the number of adenines in the genomic sequence downstream of a putative polyadenylation site have been used to remove these sites of internal priming. However, these simple filters may not remove all sites of internal priming and may also exclude true polyadenylation sites. Therefore, I developed a naïve Bayes classifier to identify putative sites from oligo-dT primed 3’ end deep sequencing as true or false/internally primed. Notably, this algorithm uses a combination of sequence elements to distinguish between true and false sites. Finally, the resulting algorithm is highly accurate in multiple model systems and facilitates identification of novel polyadenylation sites.

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Chambers, A. "RNA 3' cleavage and polyadenylation in oocytes, eggs and embryos of Xenopus laevis." Thesis, University of Warwick, 1986. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.380275.

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Shen, Yingjia. "Genome wide studies of mRNA 3'-end processing signals and alternative polyadenylation in plants." Miami University / OhioLINK, 2009. http://rave.ohiolink.edu/etdc/view?acc_num=miami1260664627.

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Forbes, Kevin Patrick. "Characterization of plant polyadenylation transacting factors--factors that modify poly(A)polymerse activity." Lexington, Ky. : [University of Kentucky Libraries], 2005. http://lib.uky.edu/ETD/ukyplph2005d00278/etd.pdf.

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Thesis (Ph. D.)--University of Kentucky, 2005.
Title from document title page (viewed on November 7, 2005). Document formatted into pages; contains vi, 135 p. : ill. Includes abstract and vita. Includes bibliographical references (p. 113-133).

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Loke, Johnny Chee Heng. "COMPILATION OF mRNA POLYADENYLATION SIGNALS IN ARABIDOPSIS THALIANA REVEALED NEW SIGNAL ELEMENTS AND POTENTIAL SECONDARY STRUCTURES." Miami University / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=miami1103223217.

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Nadimpalli, Hima Priyanka 1988. "Insights into cytoplasmatic polyadenylation mediated by Drosophila Dicer-2." Doctoral thesis, Universitat Pompeu Fabra, 2017. http://hdl.handle.net/10803/664810.

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Cytoplasmic polyadenylation is a widespread mechanism to control mRNA translation. In vertebrates, this mechanism requires two sequence elements in the 3’ UTR of substrate mRNAs, the U-rich Cytoplasmic Polyadenylation Element (CPE) and the AAUAAA polyadenylation hexanucleotide (HN). In Drosophila early embryos, the cytoplasmic polyadenylation of Toll mRNA occurs independently of these elements, and requires Dicer-2, a factor previously known for its functions in RNA interference (RNAi), in addition to the poly(A) polymerase Wispy. To understand this novel function of Dicer-2 in cytoplasmic polyadenylation and translation, we aimed to dissect the required cisacting requirements in Toll mRNA, and to identify Dicer-2 protein partners and mRNA targets. We found that multiple signals in the 3’ UTR of Toll cooperate for polyadenylation, and that in early embryos the non-canonical signals dominate, probably due to the presence of inhibitory elements for canonical polyadenylation. Interactome analysis using affinity purification of Dicer-2 and mass spectrometry revealed that Dicer-2 interacts with multiple proteins outside the RNAi pathway. Importantly, proteins involved in poly(A) tailmediated translational regulation and PABP binding were identified, suggesting potential co-factors of Dicer-2 in polyadenylation. Furthermore, RIP-Seq analysis of Dicer-2 revealed enrichment of mRNAs which were previously found downregulated in wispy mutants. These results suggest that the role of Dicer-2 in cytoplasmic viii polyadenylation might be widespread, and provide the basis for future investigation.
La poliadenilación citoplasmática es un mecanismo de control de la traducción extendido a lo largo de la escala animal. En vertebrados, este mecanismo requiere dos secuencias en el extremo 3’ no traducido (UTR) del mRNA, el elemento de poliadenilación citoplasmática rico en uridinas (CPE) y el hexanucleótido de poliadenilación AAUAAA (HN). En embriones tempranos de Drosophila, la poliadenilación de Toll, sin embargo, ocurre independientemente de estas secuencias, y requiere al menos dos factores: Dicer-2, una proteína previamente implicada en interferencia de RNA (RNAi), y la poly(A) polimerasa Wispy. Para entender esta nueva función de Dicer-2 en poliadenilación citoplasmática y traducción, nos propusimos diseccionar los elementos en el extremo 3’ UTR de Toll relevantes para este mecanismo de poliadenilación no canónica, así como identificar proteínas y mRNAs que interaccionan con Dicer-2 a gran escala. Nuestros resultados indican que el extremo 3’ UTR de Toll contiene varias secuencias implicadas en poliadenilación, y que el mecanismo no canónico es dominante en embriones tempranos, probablemente porque los elementos canónicos (CPE y HN) se encuentran activamente reprimidos. El estudio del interactoma de Dicer-2, realizado por purificación por afinidad e identificación por espectrometría de masas, reveló numerosas proteínas que no están implicadas en RNAi. Entre ellas, encontramos factores previamente relacionados con control de la longitud del poly(A) o con interacción con PABP y traducción, sugiriendo que estos factores podrían actuar x como co-factores de Dicer-2 en poliadenilación citoplasmática. Análisis de mRNA targets mediante RIP-Seq reveló multiples tránscritos que previamente fueron identificados como targets de Wispy. Estos resultados sugieren una función extendida de Dicer-2 en poliadenilación citoplasmática, y establecen una base sólida para investigaciones futuras.

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Braz, Sandra Catarina Oliveira. "Alternative polyadenylation of Rho GTPases : a gene/cell specific process." Master's thesis, Universidade de Aveiro, 2014. http://hdl.handle.net/10773/14865.

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Mestrado em Biologia Molecular e Celular
Alternative polyadenylation (APA) is an important mechanism of gene regulation that occurs in 70% of eukaryotic organisms. This process comprises the formation of alternative 3’ ends of an mRNA by cleavage of the pre-mRNA and polyadenylation at different sites according to the polyadenylation signals (pAs). The choice of pAs in APA is a co-transcriptional mechanism that depends on auxiliary cis- and trans-acting factors. The usage of the proximal or the distal pAs has been related to global physiologic events. It is consensually assumed that in proliferative conditions there is preferential usage of proximal pAs, while during development and in differentiated cellular states occurs lengthening of the 3’UTRs by selection of the distal pAs. This pattern is also confirmed in brain tissues, where most of the cells are differentiated, and where it was observed a lengthening of the 3’ UTRs. However, there is not a complete switch for the distal pA, since the shortest mRNA is still expressed. Rho GTPases are key molecular switchers essential for several cellular processes, including differentiation, however nothing is known about transcriptional regulation in these genes. Therefore, we started to explore if Rho GTPases genes undergo APA. We found by 3’RACE analyses, that classical Rho GTPAses express two alternative mRNA isoforms. However during oligodendrocytes differentiation, they preferentially express the shortest mRNA isoform, and we did not observe a switch towards the distal pA usage, in contrast with the published genome-wide data obtained from brain tissues. Since Rho GTPases are tightly regulated at the protein level by GEFs and GAPs, they may not require this mode of co-transcriptional regulation. The atypical RhoBTB2, which is constitutively active, present a global induction of distal pA sites, distinct from the classical Rho GTPases. Interestingly, this pattern suggests that APA is a gene specific mechanism. As longer 3'UTRs contain more binding sites for miRNAs and RNA binding proteins (RBPs) this suggests that atypical Rho GTPases require a fine-tune regulation at the co-transcriptional level, by APA. Additionally, we showed that APA is also cell-specific, by analyzing the expression of the different mRNA isoforms of Rho GTPases in other glial cells (microglia, astrocytes) and different types of neurons (cortical, striatal and hippocampal). We observed the same APA profile for the selected Rho GTPases in all glial cells types. However, in cortical and striatal neurons we observed a lengthening in the 3’UTR Rac1 mRNA during axonal growth, which results in the increase of the total protein levels. Taken together, our results indicate for the first time that APA is a gene- and cell- specific mechanism. In addition, we have found a differential expression of both Cdc42 isoforms during OL and sciatic nerve differentiation. During in vitro OL and in vivo sciatic nerve differentiation we observed an increase in the expression ratio between Cdc42 Iso1/Cdc42 Iso2. Further, constitutive expression of Cdc42 Iso2 in OLs induces a delay in differentiation, whereas constitutive expression of Cdc42 Iso1 induces an increase in OL branching, suggesting an exacerbation of the differentiated phenotype. Thus, these observations suggest a distinct role for the different Cdc42 isoforms during OL differentiation. Overall, this thesis opens new avenues to explore in the future that can impact our understanding on the regulation of the myelination/remyelination processes.
A poliadenilação alternativa (APA) é um mecanismo importante de regulação genética que ocorre em 70% dos organismos eucariotas. Este mecanismo compreende a formação de extremidades 3’ alternativas por poliadenilação em diferentes locais do mRNA, de acordo com os sinais de poliadenilação (pAs). Na APA, a escolha dos pAs é um mecanismo co-transcripcional que depende de factores auxiliares cis e trans necessários para os processos de clivagem e poliadenilação de todos os pré-mRNAs. Além disso, o uso dos pAs proximais ou distais está relacionado com eventos fisiológicos gerais. Consensualmente assume-se que em estados de proliferação ocorre o encurtamento, enquanto em estados de desenvolvimento e diferenciação ocorre o alongamento das extremidades 3’ não traduzidas (3’UTRs). Este padrão de APA é confirmado em tecidos cerebrais, onde a maior parte das células são diferenciadas, no entanto não existe uma alteração completa para a isoforma de mRNA longa uma vez que a isoforma curta continua a ser expressa. As Rho GTPases são ‘interruptores’ moleculares essenciais a vários processos celulares, incluindo a diferenciação, no entanto nada é conhecido sobre a sua regulação transcripcional. Assim, começamos a explorar se estes genes são regulados por APA. Descobrimos por análise de 3´RACE que, as Rho GTPases clássicas, expressam duas formas alternativas de mRNA. Contudo durante a diferenciação dos oligodendrócitos (OLs), eles expressam preferencialmente a isoforma mRNA mais curta, e não se observou uma alteração para a escolha da isoforma mais longa, em contraste com os dados de estudos globais do genoma em tecido cerebral. Uma vez que estas proteínas são altamente reguladas por GEFs e por GAPs, provavelmente não necessitam de regulação a nível transcripcional. As Rho GTPases atípicas, que estão constitutivamente activas, apresentam um indução global dos pAs distais, distintas das Rho GTPases clássicas. Curiosamente, este padrão sugere que APA é um mecanismo específico do gene. Como 3’UTRs mais longas providenciam mais locais de ligação para microRNA ou proteínas de ligação ao RNA (RBPs), isto sugere que as Rho GTPases atípicas requerem uma regulação mais fina ao nível co-transcriptional, por APA. Adicionalmente, mostramos que a APA é também específica de cada tipo celular, pela análise da expressão do mRNA em outras células da glia (microglia, astrócitos), e em diferentes tipos de neurónios (corticais, estriatais e hipocampais). Nós observamos o mesmo padrão de APA para as Rho GTPases selecionadas em todas as células da glia. No entanto, em neurónios corticais e do estriado, observámos a existência do alongamento do 3’UTR no mRNA da Rac1 durante o crescimento axonal, o que resulta num aumento da quantidade total de proteína. Em resumo, estes resultados indicam, pela primeira vez, que a APA é um mecanismo específico de cada gene e de cada tipo celular. Para além disso, descobrimos uma expressão diferencial de ambas as isoformas da Cdc42 durante a diferenciação dos OLs e do nervo ciático. Durante a diferenciação in vitro de OLs e in vivo do nervo ciático, observámos um aumento do rácio da expressão entre Cdc42 Iso1/Cdc42 Iso2. Mais ainda, a expressão constitutiva de Cdc42 Iso2 em OLs induz um atraso na diferenciação, enquanto a expressão constitutiva da Cdc42 Iso1 induz um aumento das ramificações, sugerindo uma exacerbação do fenótipo de diferenciação. Assim, estas observações sugerem um papel distinto para as diferentes isoformas de Cdc42 durante a diferenciação de OLs. Globalmente, esta tese abre novos caminhos para explorar no futuro, que podem ter um impacto no nosso conhecimento, na regulação do processo de mielinização/remielinização.

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Dalgleish, Gillian Denise. "Localisation signals within the c-myc and c-fos 3'untranslated regions." Thesis, University of Aberdeen, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.481826.

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Da, Rocha Oliveira Nunes Nuno Miguel. "Analysis of human non-canonical 3’end formation signals." Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:f77c04f1-7530-442d-8654-81ccb6d0e362.

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Abstract:

Cleavage and polyadenylation are essential pre-mRNA processing reactions maturing the 3’end of almost all protein encoding eukaryotic mRNAs. Analysis of the sequences required for cleavage and polyadenylation in the human melanocortin 4 receptor (MC4R) and the human transcription factors JUNB and JUND pre-mRNAs revealed that, at least for some mammalian genes, 3’end processing of the primary transcript is independent of previously described auxiliary sequence elements located upstream or downstream of the core poly(A) sequences. The analysis of the MC4R poly(A) site, contrary to the current understanding of mammalian poly(A) sites, showed that mutations of the AUUAAA hexamer sequence had no effect on 3’end processing levels while mutations in the short DSE severely reduced cleavage efficiency. The MC4R poly(A) site uses a potent DSE and to direct maximal cleavage efficiency requires only a short upstream adenosine rich sequence. Furthermore, analysis of the endogenous A-rich human JUNB poly(A) signal validated upstream A-rich core sequences as genuine 3’end formation directing sequences in human non-canonical 3’end formation signals. The results show that a minimal human poly(A) site, similar to yeast and plants, can be defined by an adenosine rich sequence adjacent to a U/GU-rich sequence element and a cleavage site. These findings further imply that some human non-canonical poly(A) sites may be recognised via a similar DSE-dependent mechanism and may not require additional auxiliary sequence elements. Finally, results on the analysis of the EDF1 poly(A) signal show that, in a spliced environment, A-rich sequences are also 3’end formation effectors but depend on an competent upstream splicing reaction for efficient definition of the 3’end processing site.

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Books on the topic "RNA 3' Polyadenylation Signals"

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Chambers, Alistair. RNA 3' cleavage and polyadenylation in oocytes, eggs and embryos of "Xenopus laevis". [s.l.]: typescript, 1986.

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Book chapters on the topic "RNA 3' Polyadenylation Signals"

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Osborne, H. B., and J. D. Richter. "Translational Control by Polyadenylation During Early Development." In Cytoplasmic fate of messenger RNA, 173–98. Berlin, Heidelberg: Springer Berlin Heidelberg, 1997. http://dx.doi.org/10.1007/978-3-642-60471-3_8.

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Lange, Heike, and Dominique Gagliardi. "Polyadenylation in RNA Degradation Processes in Plants." In Non Coding RNAs in Plants, 209–25. Berlin, Heidelberg: Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-19454-2_13.

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Schöning, Uwe, Thomas Schnattinger, Hans A. Kestler, Britta Stoll, and Anita Marchfelder. "RNA Structures as Processing Signals." In Information- and Communication Theory in Molecular Biology, 367–74. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-54729-9_17.

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Keller, Walter. "3′-End Cleavage and polyadenylation of nuclear Messenger RNA Precursors." In Pre-mRNA Processing, 113–34. Berlin, Heidelberg: Springer Berlin Heidelberg, 1995. http://dx.doi.org/10.1007/978-3-662-22325-3_7.

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Ji, Guoli, Xiaohui Wu, Qingshun Quinn Li, and Jianti Zheng. "Messenger RNA Polyadenylation Site Recognition in Green Alga Chlamydomonas Reinhardtii." In Advances in Neural Networks - ISNN 2010, 17–26. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-13278-0_3.

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Sanfaçon, Hélène, Peter Brodman, and Thomas Hohn. "Polyadenylation of Cauliflower Mosaic Virus RNA is Controlled by Promoter Proximity." In Post-Transcriptional Control of Gene Expression, 359–65. Berlin, Heidelberg: Springer Berlin Heidelberg, 1990. http://dx.doi.org/10.1007/978-3-642-75139-4_33.

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Timmons, Lisa. "Systemic RNAi in C. elegans from the Viewpoint of RNA as Extracellular Signals." In Nucleic Acids and Molecular Biology, 69–92. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-12617-8_6.

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Bujarski, Jozef J., and Paul Kaesberg. "Insertion of Signals for Autolytic Cleavage in Viral cDNAs Provides Nearly Correct 3’ Ends of Viral RNA Transcripts." In Plant Molecular Biology, 632. Boston, MA: Springer US, 1987. http://dx.doi.org/10.1007/978-1-4615-7598-6_67.

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Lamas-Maceiras, Monica, Silvia Seoane, and Maria A. "Alternative Polyadenylation in Yeast: 3 ́-UTR Elements and Processing Factors Acting at a Distance." In RNA Processing. InTech, 2011. http://dx.doi.org/10.5772/21151.

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Ogorodnikov, Anton, and Sven Danckwardt. "TRENDseq—A highly multiplexed high throughput RNA 3′ end sequencing for mapping alternative polyadenylation." In Methods in Enzymology, 37–72. Elsevier, 2021. http://dx.doi.org/10.1016/bs.mie.2021.03.022.

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Conference papers on the topic "RNA 3' Polyadenylation Signals"

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Fu, Hongjuan, Yibo Zhuang, Xiaohui Wu, and Guoli Ji. "A Pipeline to Identify Novel 3’ UTRs and Widespread Intergenic Transcription by Combination of Polyadenylation Sites and RNA-seq Data." In ICBBS '20: 2020 9th International Conference on Bioinformatics and Biomedical Science. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3431943.3432289.

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