Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals

Li, Xiuqing; Du, Donglei

doi:10.1186/s12862-014-0162-7

Cited by 29 publications

(32 citation statements)

References 59 publications

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“…By contrast, we did observe a significant enrichment of predicted 3'-splice sites (Kolmogorov-Smirnoff test, D = 0.33, P = 0.0009) ( Supplementary Figure 1C ), although the underlying mechanistic cause of this enrichment remains unclear. The modest enrichment in poly(A) sites may in part be due to the fact that plants use more diverse, and less well characterized, poly(A) sites than mammals (Li and Du, 2014) . Third, we asked whether there was any relation between PROMPT-producing regions and the UNT-producing genes identified by (Chekanova et al, 2007) .…”

Section: Properties Of Prompts and Their Associated Genesmentioning

confidence: 99%

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Thieffry

Bornholdt

Ivanov

et al. 2019

Preprint

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In animals, transcription by RNA polymerase II initiates bidirectionally from gene promoters to produce pre-mRNAs on the forward strand and promoter upstream transcripts (PROMPTs) on the reverse strand. PROMPTs are rapidly degraded by the nuclear exosome. Similarly, active enhancer regions in animals initiate transcription of exosome-sensitive enhancer RNAs (eRNAs). Previous studies based on nascent RNA approaches concluded that Arabidopsis thaliana does not produce PROMPTs . Here, we used steady-state RNA sequencing methods in mutants defective in nuclear RNA decay, including by the exosome, to reassess the existence of PROMPTs and eRNAs in A. thaliana . While PROMPTs are overall rare in A. thaliana , about 100 clear cases of exosome-sensitive PROMPTs and 113 loci producing eRNA-like transcripts were identified. In addition, we found~200 transcription start sites within 3'-UTR-encoding regions that produce unspliced exosome-sensitive antisense RNAs covering much of the cognate pre-mRNA. A typical representative of this class of RNAs is the previously characterized non-coding RNA controlling the expression of the key seed dormancy regulator, DELAY OF GERMINATION1 . Exosome-sensitive antisense RNAs are overrepresented in transcription factor genes, suggesting a potential for widespread control of gene expression.Lastly, we assess the use of alternative promoters in A. thaliana and compare the accuracy of existing TSS annotations.

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Section: Properties Of Prompts and Their Associated Genesmentioning

confidence: 99%

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Thieffry

Bornholdt

Ivanov

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…However, other reports suggest that the process of polyadenylation may accommodate a great deal of variability or flexibility, in terms both of the nature of the cis elements that guide polyadenylation and the complex that mediates the process. For example, in studies of poly(A) signals in green algae, motifs related to UGUAA (and not AAUAAA) were found to be most often associated with poly(A) sites [ 19 – 22 ]; in these organisms, there was little indication that an A-rich motif analogous to the mammalian is involved in polyadenylation. In Giardia lamblia , variations of the motif GUAA were among the most prominent in regions nearby poly(A) sites; the motif was also a frequent occurrence in this region [ 23 ].…”

Section: Introductionmentioning

confidence: 99%

“…In Trichomonas vaginalis , the motif UAAA functions as a poly(A) signal [ 24 ]. U-rich motifs, typified by and , have been proposed to serve as poly(A) signals in Trypanosoma cruzi and Blastocystis hominis , respectively [ 19 ]. Polyadenylation in these latter organisms has additional special features or aspects.…”

Section: Introductionmentioning

confidence: 99%

Characterization of mRNA polyadenylation in the apicomplexa

2018

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Messenger RNA polyadenylation is a universal aspect of gene expression in eukaryotes. In well-established model organisms, this process is mediated by a conserved complex of 15–20 subunits. To better understand this process in apicomplexans, a group of unicellular parasites that causes serious disease in humans and livestock, a computational and high throughput sequencing study of the polyadenylation complex and poly(A) sites in several species was conducted. BLAST-based searches for orthologs of the human polyadenylation complex yielded clear matches to only two—poly(A) polymerase and CPSF73—of the 19 proteins used as queries in this analysis. As the human subunits that recognize the AAUAAA polyadenylation signal (PAS) were not immediately obvious, a computational analysis of sequences adjacent to experimentally-determined apicomplexan poly(A) sites was conducted. The results of this study showed that there exists in apicomplexans an A-rich region that corresponds in position to the AAUAAA PAS. The set of experimentally-determined sites in one species, Sarcocystis neurona, was further analyzed to evaluate the extent and significance of alternative poly(A) site choice in this organism. The results showed that almost 80% of S. neurona genes possess more than one poly(A) site, and that more than 780 sites showed differential usage in the two developmental stages–extracellular merozoites and intracellular schizonts–studied. These sites affected more than 450 genes, and included a disproportionate number of genes that encode membrane transporters and ribosomal proteins. Taken together, these results reveal that apicomplexan species seem to possess a poly(A) signal analogous to AAUAAA even though genes that may encode obvious counterparts of the AAUAAA-recognizing proteins are absent in these organisms. They also indicate that, as is the case in other eukaryotes, alternative polyadenylation is a widespread phenomenon in S. neurona that has the potential to impact growth and development.

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“…The reports to date (e.g., [ 30 – 32 , 39 ]) leave little doubt as to the importance of the UGUAA motif in specifying poly(A) sites in Chlamydomonas. Indeed, if one base substitutions in the motif are allowed, then more than 95% of all sites identified here can be associated with the UGUAA motif.…”

Section: Discussionmentioning

confidence: 99%

Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii

et al. 2016

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The polyadenylation of RNA is a near-universal feature of RNA metabolism in eukaryotes. This process has been studied in the model alga Chlamydomonas reinhardtii using low-throughput (gene-by-gene) and high-throughput (transcriptome sequencing) approaches that recovered poly(A)-containing sequence tags which revealed interesting features of this critical process in Chlamydomonas. In this study, RNA polyadenylation has been studied using the so-called Poly(A) Tag Sequencing (PAT-Seq) approach. Specifically, PAT-Seq was used to study poly(A) site choice in cultures grown in four different media types—Tris-Phosphate (TP), Tris-Phosphate-Acetate (TAP), High-Salt (HS), and High-Salt-Acetate (HAS). The results indicate that: 1. As reported before, the motif UGUAA is the primary, and perhaps sole, cis-element that guides mRNA polyadenylation in the nucleus; 2. The scope of alternative polyadenylation events with the potential to change the coding sequences of mRNAs is limited; 3. Changes in poly(A) site choice in cultures grown in the different media types are very few in number and do not affect protein-coding potential; 4. Organellar polyadenylation is considerable and affects primarily ribosomal RNAs in the chloroplast and mitochondria; and 5. Organellar RNA polyadenylation is a dynamic process that is affected by the different media types used for cell growth.

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Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals

Cited by 29 publications

References 59 publications

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Characterization of Arabidopsis thaliana promoter bidirectionality and antisense RNAs by depletion of nuclear RNA decay enzymes

Characterization of mRNA polyadenylation in the apicomplexa

Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii

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