Involvement of Pta1, Pcf11 and a <i>KlCYC1</i> AU‐rich element in alternative RNA 3′‐end processing selection in yeast

Seoane, Silvia; Lamas-Maceiras, Mónica; Rodríguez-Torres, Ana María; Freire-Picos, María Ángeles

doi:10.1016/j.febslet.2009.07.042

Cited by 13 publications

(13 citation statements)

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“…growth phase affects KlCYC1 3Ј-end formation. The mechanism by which the 3Ј-end processing machinery differentially selects the poly(A)-1 versus poly(A)-2 site to generate the S versus L forms is related to the interplay between the proximal AU-rich element and the 3Ј-end processing machinery (17). RT-PCR analyses of the transcript isoforms under different regulatory conditions are shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…The strain ZW13 was used to study KlCYC1 DNA loops in S. cerevisiae (32). The S. cerevisiae isogenic strain pair XH6 (WT) and POC8-23d (pta1-1), described previously (17), was used to analyze the effects of Pta1 on alternative gene loops. Cells were grown in YPD medium (33) to early logarithmic phase (A 600 ϭ 0.6) or to mid-logarithmic phase (A 600 ϭ 1.5), denoted E or M, respectively, in all experiments.…”

Section: Methodsmentioning

confidence: 99%

“…The proximal site yields a transcript of 1.1-kb (S), whereas the distal site is 394 nucleotides downstream, producing a 1.5-kb transcript (L) (Fig. 1A) (15,17). Alternative KlCYC1 processing is growth phase-dependent and is readily distinguished by changes in the ratio of short/long transcripts (15,18).…”

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confidence: 99%

“…Alternative KlCYC1 processing is growth phase-dependent and is readily distinguished by changes in the ratio of short/long transcripts (15,18). Components of Saccharomyces cerevisiae 3Ј-end processing complexes CF-1A and CPF affect proximal versus distal processing (17,18).…”

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confidence: 99%

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Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast

Lamas-Maceiras

Singh

Hampsey

et al. 2016

Journal of Biological Chemistry

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast

Lamas-Maceiras

Singh

Hampsey

et al. 2016

Journal of Biological Chemistry

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“…One of these genes is the yeast KlCYC1 gene [14,15]. The regulated APA for this gene causes two transcripts with different 3´-UTR lengths.…”

Section: Commentmentioning

confidence: 99%

RNA Polymerase II: Reading in Loops to get Different Tails

Freire-Picos¹

2016

Biochem Mol Biol J

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CommentThe RNA polymerase II is the multi-subunit enzyme able to transcribe the protein-encoding genes in eukaryotic cells producing the messenger RNA (mRNA). Two critical steps in eukaryotic mRNA biogenesis, for its correct 3´-end processing are: cleavage and polyadenylation. This is necessary to achieve a message that can be recognized by the proteins that properly export it to the cytosol and so that it can be efficiently translated by the ribosomes or mediate its turnover [1,2].But what happens with the RNA polymerase after a first round of transcription? It is necessary to recycle the RNA polymerase back to the promoter for a new round of transcription. For this last purpose, the formation of DNA-loops, establishing physical interactions between the promoter and the sequences downstream from the coding region, are necessary [3][4][5][6]. The current view is that these loops are transcriptional memories for the cells.However, it is not that simple, the major subunit of the RNA polymerase II has a Carboxy-Terminal Domain (CTD) with multiple repeats of a seven amino-acid sequence (YSTPSPS), each position can be covalently modified and there are multiple combinations possible. This was named as the CTD Code by Buratowski, a term currently in use [7][8][9][10]. CTD is considered as a recruitment platform for the different factors that are associated to the enzyme during initiation, elongation or the steps related to splicing, transcriptional termination and RNA processing. While riding the loop the polymerase will undergo multiple changes in the CTD Code and, to finally be recycled back to the promoter, its CTD must be hypo-phosphorylated.Things become more complicated by the fact that many genes are under alternative 3´-end processing (alternative polyadenylation, APA) [11][12][13]. One of these genes is the yeast KlCYC1 gene [14,15]. The regulated APA for this gene causes two transcripts with different 3´-UTR lengths. We have recently shown in the related article of this comment that for genes with regulated APA there is alternative DNA-loops formation also. Moreover, the predominant processing region is included in the predominant loop. Changes in RNA polymerase II positioning or the CTD phosphatase Ssu72 also correlate with both, the loop and APA predominance [16]. From the data attained for a gene with APA, it is clear the dependence of RNA processing in DNA-loop formation and, as indicated in the title, the RNA polymerase has to read the different loops in order to get messages with different tails which will depend on the cellular requirements. RNA Polymerase II: Reading in Loops to get Different Tails AbstractThe DNA-loops are necessary to recycle the RNA polymerase for the multiple transcription rounds of a gene. The nascent transcript needs to be 3'-end processed: cleaved in a specific position and added a 3´-end poly-(A)-tail to become an mRNA. Under regulated conditions, genes undergo 3´-end RNA processing at different positions. This is called alternative polyadenylation (APA) and, as a consequence,...

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Current awareness on yeast

2010

Yeast

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In order to keep subscribers up‐to‐date with the latest developments in their field, this current awareness service is provided by John Wiley & Sons and contains newly‐published material on yeasts. Each bibliography is divided into 10 sections. 1 Reviews; 2 General; 3 Biochemistry; 4 Biotechnology; 5 Cell Biology; 6 Gene Expression; 7 Genetics; 8 Physiology; 9 Medical Mycology; 10 Recombinant DNA Technology. Within each section, articles are listed in alphabetical order with respect to author. If, in the preceding period, no publications are located relevant to any one of these headings, that section will be omitted. (4 weeks journals ‐ search completed 31st. Dec. 2009)

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Involvement of Pta1, Pcf11 and a KlCYC1 AU‐rich element in alternative RNA 3′‐end processing selection in yeast

Cited by 13 publications

References 45 publications

Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast

Promoter-Terminator Gene Loops Affect Alternative 3′-End Processing in Yeast

RNA Polymerase II: Reading in Loops to get Different Tails

Current awareness on yeast

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