Relevant bibliographies by topics / Cotranscriptionality

Academic literature on the topic 'Cotranscriptionality'

Author: Grafiati
Published: 9 March 2023

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Journal articles on the topic "Cotranscriptionality"

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Aslanzadeh, Vahid, Yuanhua Huang, Guido Sanguinetti, and Jean D. Beggs. "Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast." Genome Research 28, no. 2 (December 18, 2017): 203–13. http://dx.doi.org/10.1101/gr.225615.117.

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2

Perales, Roberto, and David Bentley. "“Cotranscriptionality”: The Transcription Elongation Complex as a Nexus for Nuclear Transactions." Molecular Cell 36, no. 2 (October 2009): 178–91. http://dx.doi.org/10.1016/j.molcel.2009.09.018.

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Aslanzadeh, Vahid, Yuanhua Huang, Guido Sanguinetti, and Jean D. Beggs. "Corrigendum: Transcription rate strongly affects splicing fidelity and cotranscriptionality in budding yeast." Genome Research 28, no. 4 (April 2018): 606.2. http://dx.doi.org/10.1101/gr.236265.118.

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Koš, Martin, and David Tollervey. "Yeast Pre-rRNA Processing and Modification Occur Cotranscriptionally." Molecular Cell 37, no. 6 (March 2010): 809–20. http://dx.doi.org/10.1016/j.molcel.2010.02.024.

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Nawroth, I., F. Mueller, E. Basyuk, N. Beerens, U. L. Rahbek, X. Darzacq, E. Bertrand, J. Kjems, and U. Schmidt. "Stable assembly of HIV-1 export complexes occurs cotranscriptionally." RNA 20, no. 1 (November 19, 2013): 1–8. http://dx.doi.org/10.1261/rna.038182.113.

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Pendleton, Kathryn E., Sung-Kyun Park, Olga V. Hunter, Stefan M. Bresson, and Nicholas K. Conrad. "Balance between MAT2A intron detention and splicing is determined cotranscriptionally." RNA 24, no. 6 (March 21, 2018): 778–86. http://dx.doi.org/10.1261/rna.064899.117.

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Li, Jiang, Jie Chao, Jiye Shi, and Chunhai Fan. "Cotranscriptionally Folded RNA Nanostructures Pave the Way to Intracellular Nanofabrication." ChemBioChem 16, no. 1 (November 21, 2014): 39–41. http://dx.doi.org/10.1002/cbic.201402627.

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Schmidt, Ute, Eugenia Basyuk, Marie-Cécile Robert, Minoru Yoshida, Jean-Philippe Villemin, Didier Auboeuf, Stuart Aitken, and Edouard Bertrand. "Real-time imaging of cotranscriptional splicing reveals a kinetic model that reduces noise: implications for alternative splicing regulation." Journal of Cell Biology 193, no. 5 (May 30, 2011): 819–29. http://dx.doi.org/10.1083/jcb.201009012.

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Splicing is a key process that expands the coding capacity of genomes. Its kinetics remain poorly characterized, and the distribution of splicing time caused by the stochasticity of single splicing events is expected to affect regulation efficiency. We conducted a small-scale survey on 40 introns in human cells and observed that most were spliced cotranscriptionally. Consequently, we constructed a reporter system that splices cotranscriptionally and can be monitored in live cells and in real time through the use of MS2–GFP. All small nuclear ribonucleoproteins (snRNPs) are loaded on nascent pre-mRNAs, and spliceostatin A inhibits splicing but not snRNP recruitment. Intron removal occurs in minutes and is best described by a model where several successive steps are rate limiting. Each pre-mRNA molecule is predicted to require a similar time to splice, reducing kinetic noise and improving the regulation of alternative splicing. This model is relevant to other kinetically controlled processes acting on few molecules.
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9

Wuarin, J., and U. Schibler. "Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing." Molecular and Cellular Biology 14, no. 11 (November 1994): 7219–25. http://dx.doi.org/10.1128/mcb.14.11.7219-7225.1994.

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In order to examine whether splicing can occur cotranscriptionally in mammalian nuclei, we mapped exon-intron boundaries on nascent RNA chains transcribed by RNA polymerase II. A procedure that allows fractionation of nuclei into a chromatin pellet containing DNA, histones, and ternary transcription complexes and a supernatant containing the bulk of the nonhistone proteins and RNAs that are released from their DNA templates was developed. The transcripts of the genes encoding DBP, a transcriptional activator protein, and HMG coenzyme A reductase recovered from the chromatin pellet and the supernatant were analyzed by S1 nuclease mapping. The large majority of the RNA molecules from the pellet appeared to be nascent transcripts, since, in contrast to the transcripts present in the supernatant, they were not cleaved at the polyadenylation site but rather contained heterogeneous 3' termini encompassing this site. Splicing intermediates could be detected among nascent and released transcripts, suggesting that splicing occurs both cotranscriptionally and posttranscriptionally. Our results also indicate that polyadenylation is not required for the splicing of the last DBP intron. In addition to allowing detailed structural analysis of nascent RNA chains, the physical isolation of nascent transcripts also yields reliable measurements of relative transcription rates.
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Wuarin, J., and U. Schibler. "Physical isolation of nascent RNA chains transcribed by RNA polymerase II: evidence for cotranscriptional splicing." Molecular and Cellular Biology 14, no. 11 (November 1994): 7219–25. http://dx.doi.org/10.1128/mcb.14.11.7219.

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Abstract:
In order to examine whether splicing can occur cotranscriptionally in mammalian nuclei, we mapped exon-intron boundaries on nascent RNA chains transcribed by RNA polymerase II. A procedure that allows fractionation of nuclei into a chromatin pellet containing DNA, histones, and ternary transcription complexes and a supernatant containing the bulk of the nonhistone proteins and RNAs that are released from their DNA templates was developed. The transcripts of the genes encoding DBP, a transcriptional activator protein, and HMG coenzyme A reductase recovered from the chromatin pellet and the supernatant were analyzed by S1 nuclease mapping. The large majority of the RNA molecules from the pellet appeared to be nascent transcripts, since, in contrast to the transcripts present in the supernatant, they were not cleaved at the polyadenylation site but rather contained heterogeneous 3' termini encompassing this site. Splicing intermediates could be detected among nascent and released transcripts, suggesting that splicing occurs both cotranscriptionally and posttranscriptionally. Our results also indicate that polyadenylation is not required for the splicing of the last DBP intron. In addition to allowing detailed structural analysis of nascent RNA chains, the physical isolation of nascent transcripts also yields reliable measurements of relative transcription rates.
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Dissertations / Theses on the topic "Cotranscriptionality"

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FONTANA, GABRIELE ALESSANDRO. "Mitochondrial stress deregulates the expression of Brahma, a chromatin - remodeling factor that controls transcription and splicing of genes involved in axon growth and guidance." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2012. http://hdl.handle.net/10281/29856.

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The human protein Brahma (Brm), encoded by the SMARCA2 gene, is one of the two mutually exclusive ATPase subunits of the mammalian SWI/SNF-BAF chromatin-remodelling complex. Brm-containing BAF complexes are enriched in neurons, where they play crucial roles in the regulation of genes involved in neuronal differentiation. Moreover, it has been reported that Brm associates with components of the spliceosome to regulate the inclusion of alternative internal exons. While investigating with splicing-sensitive microarrays the gene expression changes triggered by mitochondrial stress, I found that Brm is strongly downregulated in SH-SY5Y human neuroblastoma cells overexpressing the SOD1 (G93A) protein, one of the genetic causes of Amyotrophic Lateral Sclerosis (ALS). I found that this downregulation is due to a mitochondrial stress-induced impairment in the SMARCA2 promoter activity. Among the genes deregulated at the splicing level by SOD1 (G93A) expression, I identified several targets that are regulated by alternative 3’ terminal exon usage in a Brm-dependent manner. Specifically, I found that Brm promotes the skipping of the proximal terminal exon in five out of six genes that were analyzed. In order to define the molecular mechanism that allow to Brm to modulate the choice of alternative 3’ terminal exons, I used one of these genes, RPRD1A, as a model. I found that Brm inhibits the choice of the proximal RPRD1A last exon by directly localizing in its genomic region. In turn, the absence of Brm at the level of the proximal last exon is concomitant with a change in the processivity of the RNA Polymerase II, an observation consistent with the “terminal exon pausing” event. I hypothesized a model where Brahma may recruit the Bard1-Cstf complex on the RPRD1A proximal last exon, a complex known to inhibit the 3’ end processing of the pre-mRNA. These observations suggest an inhibitory role for Brm, which is exerted both at the level of the cotranscriptional choice of the proximal last exon and at the level of the 3’ end pre-mRNA processing.
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Book chapters on the topic "Cotranscriptionality"

1

Mohammed, Abdulmelik, Pekka Orponen, and Sachith Pai. "Algorithmic Design of Cotranscriptionally Folding 2D RNA Origami Structures." In Unconventional Computation and Natural Computation, 159–72. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-92435-9_12.

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