scholarly journals Animal-APAdb: a comprehensive animal alternative polyadenylation database

2020 ◽  
Vol 49 (D1) ◽  
pp. D47-D54
Author(s):  
Weiwei Jin ◽  
Qizhao Zhu ◽  
Yanbo Yang ◽  
Wenqian Yang ◽  
Dongyang Wang ◽  
...  
Keyword(s):  
Gene Expression Regulation ◽  
Alternative Polyadenylation ◽  
Untranslated Regions ◽  
Sequencing Data ◽  
Comprehensive Information ◽  
Transcriptional Regulatory Mechanism ◽  
Transcriptional Regulatory ◽  
Polyadenylation Sites ◽  
User Friendly ◽  
Polyadenylation Signals

Abstract Alternative polyadenylation (APA) is an important post-transcriptional regulatory mechanism that recognizes different polyadenylation signals on transcripts, resulting in transcripts with different lengths of 3′ untranslated regions and thereby influencing a series of biological processes. Recent studies have highlighted the important roles of APA in human. However, APA profiles in other animals have not been fully recognized, and there is no database that provides comprehensive APA information for other animals except human. Here, by using the RNA sequencing data collected from public databases, we systematically characterized the APA profiles in 9244 samples of 18 species. In total, we identified 342 952 APA events with a median of 17 020 per species using the DaPars2 algorithm, and 315 691 APA events with a median of 17 953 per species using the QAPA algorithm in these 18 species, respectively. In addition, we predicted the polyadenylation sites (PAS) and motifs near PAS of these species. We further developed Animal-APAdb, a user-friendly database (http://gong_lab.hzau.edu.cn/Animal-APAdb/) for data searching, browsing and downloading. With comprehensive information of APA events in different tissues of different species, Animal-APAdb may greatly facilitate the exploration of animal APA patterns and novel mechanisms, gene expression regulation and APA evolution across tissues and species.

scholarly journals The length of the expressed 3’ UTR is an intermediate molecular phenotype linking genetic variants to complex diseases

2019 ◽  
Author(s):  
Elisa Mariella ◽  
Federico Marotta ◽  
Elena Grassi ◽  
Stefano Gilotto ◽  
Paolo Provero
Keyword(s):  
Genetic Variants ◽  
Association Studies ◽  
Alternative Polyadenylation ◽  
Complex Diseases ◽  
Genome Wide Association Studies ◽  
Sequencing Data ◽  
Transcriptional Regulatory Mechanism ◽  
Transcriptional Regulatory ◽  
Common Genetic Variants ◽  
Molecular Phenotypes

AbstractIn the last decades, genome wide association studies (GWAS) have uncovered tens of thousands of associations between common genetic variants and complex diseases. However, these statistical associations can rarely be interpreted functionally and mechanistically. As the majority of the disease-associated variants are located far from coding sequences, even the relevant gene is often unclear. A way to gain insight into the relevant mechanisms is to study the genetic determinants of intermediate molecular phenotypes, such as gene expression and transcript structure. We propose a computational strategy to discover genetic variants affecting the relative expression of alternative 3’ untranslated region (UTR) isoforms, generated through alternative polyadenylation, a widespread post-transcriptional regulatory mechanism known to have relevant functional consequences. When applied to a large dataset in which whole genome and RNA sequencing data are available for 373 European individuals, 2,530 genes with alternative polyadenylation quantitative trait loci (apaQTL) were identified. We analyze and discuss possible mechanisms of action of these variants, and we show that they are significantly enriched in GWAS hits, in particular those concerning immune-related and neurological disorders. Our results point to an important role for genetically determined alternative polyadenylation in affecting predisposition to complex diseases, and suggest new ways to extract functional information from GWAS data.

scholarly journals The RNA-Binding Protein HuD Regulates Alternative Splicing and Alternative Polyadenylation in the Mouse Neocortex

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2836
Author(s):  
Rebecca M. Sena ◽  
Jeffery L. Twiss ◽  
Amy S. Gardiner ◽  
Michela Dell’Orco ◽  
David N. Linsenbardt ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Rna Binding ◽  
Rna Binding Proteins ◽  
Alternative Polyadenylation ◽  
Untranslated Regions ◽  
Sequencing Data ◽  
Hu Proteins ◽  
Nuclear Events ◽  
Neuronal Functions ◽  
Polyadenylation Signals

The neuronal Hu/ELAV-like proteins HuB, HuC and HuD are a class of RNA-binding proteins that are crucial for proper development and maintenance of the nervous system. These proteins bind to AU-rich elements (AREs) in the untranslated regions (3′-UTRs) of target mRNAs regulating mRNA stability, transport and translation. In addition to these cytoplasmic functions, Hu proteins have been implicated in alternative splicing and alternative polyadenylation in the nucleus. The purpose of this study was to identify transcriptome-wide effects of HuD deletion on both of these nuclear events using RNA sequencing data obtained from the neocortex of Elavl4–/– (HuD KO) mice. HuD KO affected alternative splicing of 310 genes, including 17 validated HuD targets such as Cbx3, Cspp1, Snap25 and Gria2. In addition, deletion of HuD affected polyadenylation of 53 genes, with the majority of significantly altered mRNAs shifting towards usage of proximal polyadenylation signals (PAS), resulting in shorter 3′-UTRs. None of these genes overlapped with those showing alternative splicing events. Overall, HuD KO had a greater effect on alternative splicing than polyadenylation, with many of the affected genes implicated in several neuronal functions and neuropsychiatric disorders.

scholarly journals Template-switching artifacts resemble alternative polyadenylation

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zsolt Balázs ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Template Switching ◽  
Cdna Sequencing ◽  
Sequencing Data ◽  
Filtering Algorithm ◽  
Long Read ◽  
Polyadenylation Sites ◽  
Sequencing Platforms

Abstract Background Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. Results Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. Conclusions Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.

scholarly journals PolyASite 2.0: a consolidated atlas of polyadenylation sites from 3′ end sequencing

2019 ◽  
Author(s):  
Christina J Herrmann ◽  
Ralf Schmidt ◽  
Alexander Kanitz ◽  
Panu Artimo ◽  
Andreas J Gruber ◽  
...  
Keyword(s):  
Alternative Polyadenylation ◽  
Quality Measures ◽  
Cell Types ◽  
Cell Type ◽  
Transcript Isoforms ◽  
Cleavage And Polyadenylation ◽  
Integrated Processing ◽  
Cell Type Specific ◽  
Polyadenylation Sites ◽  
Polyadenylation Signals

Abstract Generated by 3′ end cleavage and polyadenylation at alternative polyadenylation (poly(A)) sites, alternative terminal exons account for much of the variation between human transcript isoforms. More than a dozen protocols have been developed so far for capturing and sequencing RNA 3′ ends from a variety of cell types and species. In previous studies, we have used these data to uncover novel regulatory signals and cell type-specific isoforms. Here we present an update of the PolyASite (https://polyasite.unibas.ch) resource of poly(A) sites, constructed from publicly available human, mouse and worm 3′ end sequencing datasets by enforcing uniform quality measures, including the flagging of putative internal priming sites. Through integrated processing of all data, we identified and clustered sites that are closely spaced and share polyadenylation signals, as these are likely the result of stochastic variations in processing. For each cluster, we identified the representative - most frequently processed - site and estimated the relative use in the transcriptome across all samples. We have established a modern web portal for efficient finding, exploration and export of data. Database generation is fully automated, greatly facilitating incorporation of new datasets and the updating of underlying genome resources.

Regulation of the expression of histone H3.3 by differential polyadenylation

Genome ◽  
2005 ◽  
Vol 48 (3) ◽  
pp. 503-510 ◽  
Author(s):  
Rongrong Feng ◽  
Xiaoying Tang ◽  
Angela Becker ◽  
Anja Berger ◽  
Jing Ye ◽  
...  
Keyword(s):  
Germ Line ◽  
Evolutionary Conservation ◽  
Untranslated Regions ◽  
Histone Genes ◽  
Marker Protein ◽  
Male Germ Line ◽  
Histone H3.3 ◽  
Polyadenylation Sites ◽  
Functional Relevance ◽  
Polyadenylation Signals

Previously we have shown that the 3' untranslated regions (UTRs) of the replacement histone genes H3.3.A and H3.3B of Drosophila melanogaster differ in their nucleotide sequences and have different polyadenylation sites. To understand their functional relevance, which might explain the presence and evolutionary conservation of 2 different H3.3 genes, green flourescent protein (GFP) constructs with different 3' UTR sections were studied by the expression of GFP as a marker protein. Here we show that the polyadenylation signals modify the cell-specific translation of the histone replacement variants in testes and ovaries. The H3.3A gene may be required to provide postmeiotic histone H3.3 in the male germ line in transition to chromatin packaging in sperm.Key words: histone H3.3, polyadenylation, oogenesis, spermatogenesis, histone translation.

scholarly journals APA-Scan: Detection and Visualization of 3’-UTR APA with RNA-seq and 3’-end-seq Data

2020 ◽  
Author(s):  
Naima Ahmed Fahmi ◽  
Jae-Woong Chang ◽  
Heba Nassereddeen ◽  
Khandakar Tanvir Ahmed ◽  
Deliang Fan ◽  
...  
Keyword(s):  
Rna Binding ◽  
Rna Binding Proteins ◽  
Alternative Polyadenylation ◽  
Transcriptional Level ◽  
Cleavage Sites ◽  
Read Coverage ◽  
Rna Seq ◽  
Regulate Gene Expression ◽  
Polyadenylation Sites ◽  
Polyadenylation Signals

AbstractThe eukaryotic genome is capable of producing multiple isoforms from a gene by alternative polyadenylation (APA) during pre-mRNA processing. APA in the 3’-untranslated region (3’-UTR) of mRNA produces transcripts with shorter 3’-UTR. Often, 3’-UTR serves as a binding platform for microRNAs and RNA-binding proteins, which affect the fate of the mRNA transcript. Thus, 3’-UTR APA provides a means to regulate gene expression at the post-transcriptional level and is known to promote translation. Current bioinformatics pipelines have limited capability in profiling 3’-UTR APA events due to incomplete annotations and a low-resolution analyzing power: widely available bioinformatics pipelines do not reference actionable polyadenylation (cleavage) sites but simulate 3’-UTR APA only using RNA-seq read coverage, causing false positive identifications. To overcome these limitations, we developed APA-Scan, a robust program that identifies 3’-UTR APA events and visualizes the RNA-seq short-read coverage with gene annotations. APA-Scan utilizes either predicted or experimentally validated actionable polyadenylation signals as a reference for polyadenylation sites and calculates the quantity of long and short 3’-UTR transcripts in the RNA-seq data. The performance of APA-Scan was validated by qPCR.ImplementationAPA-Scan is implemented in Python. Source code and a comprehensive user’s manual are freely available at https://github.com/compbiolabucf/APA-Scan

scholarly journals Is this really the end? Template-switching artifacts resemble alternative polyadenylation

2019 ◽  
Author(s):  
Zsolt Balázs ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Template Switching ◽  
Cdna Sequencing ◽  
Sequencing Data ◽  
Filtering Algorithm ◽  
Long Read ◽  
Polyadenylation Sites ◽  
Sequencing Platforms

Abstract Background: Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. Results: Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. Conclusions: Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.

Complexity and species variation of the kidney-type glutaminase gene

2002 ◽  
Vol 9 (3) ◽  
pp. 157-166 ◽  
Author(s):  
L. David Porter ◽  
Hend Ibrahim ◽  
Lynn Taylor ◽  
Norman P. Curthoys
Keyword(s):  
Rat Kidney ◽  
Alternative Polyadenylation ◽  
Rnase H ◽  
Untranslated Regions ◽  
Species Variation ◽  
Pcr Cloning ◽  
Mrna Stabilization ◽  
Ph Response ◽  
Untranslated Sequence ◽  
Polyadenylation Sites

Increased expression of rat kidney-type glutaminase (KGA) during metabolic acidosis results from selective mRNA stabilization. This process is mediated by an 8-base AU-sequence that functions as a pH-response element (pHRE). LLC-PK1-FBPase+ cells, a pH-responsive porcine kidney cell line, express four distinct GA mRNAs. RNase H mapping indicated that three of the GA mRNAs are generated by use of alternative polyadenylation sites and are homologs of the rat KGA mRNA, while the fourth contains a different COOH-terminal coding and 3′-untranslated sequence. PCR cloning and sequencing established that the latter GA mRNA is the homolog of the human GAC mRNA. A rat GAC cDNA was also cloned from a rat kidney library. The 3′-untranslated regions of the GAC mRNAs, but not the porcine or human KGA mRNAs, contain identifiable pHREs. The human KGA gene spans 82 kb and is composed of 19 exons. The unique sequence from the hGAC cDNA is contained in a single exon. Thus in humans, alternative splicing of the initial transcript could produce two GA mRNAs, only one of which may be increased during acidosis.

scholarly journals Template-switching artifacts resemble alternative polyadenylation

2019 ◽  
Author(s):  
Zsolt Balázs ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Template Switching ◽  
Cdna Sequencing ◽  
Sequencing Data ◽  
Filtering Algorithm ◽  
Long Read ◽  
Polyadenylation Sites ◽  
Sequencing Platforms

Abstract Background: Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. Results: Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. Conclusions: Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.

scholarly journals Template-switching artifacts resemble alternative polyadenylation

2019 ◽  
Author(s):  
Zsolt Balázs ◽  
Dóra Tombácz ◽  
Zsolt Csabai ◽  
Norbert Moldován ◽  
Michael Snyder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Alternative Polyadenylation ◽  
Template Switching ◽  
Cdna Sequencing ◽  
Sequencing Data ◽  
Filtering Algorithm ◽  
Long Read ◽  
Polyadenylation Sites ◽  
Sequencing Platforms

Abstract Background: Alternative polyadenylation is commonly examined using cDNA sequencing, which is known to be affected by template-switching artifacts. However, the effects of such template-switching artifacts on alternative polyadenylation are generally disregarded, while alternative polyadenylation artifacts are attributed to internal priming. Results: Here, we analyzed both long-read cDNA sequencing and direct RNA sequencing data of two organisms, generated by different sequencing platforms. We developed a filtering algorithm which takes into consideration that template-switching can be a source of artifactual polyadenylation when filtering out spurious polyadenylation sites. The algorithm outperformed the conventional internal priming filters based on comparison to direct RNA sequencing data. We also showed that the polyadenylation artifacts arise in cDNA sequencing at consecutive stretches of as few as three adenines. There was no substantial difference between the lengths of poly(A) tails at the artifactual and the true transcriptional end sites even though it is expected that internal priming artifacts have shorter poly(A) tails than genuine polyadenylated reads. Conclusions: Our findings suggest that template switching plays an important role in the generation of spurious polyadenylation and support the need for more rigorous filtering of artifactual polyadenylation sites in cDNA data, or that alternative polyadenylation should be annotated using native RNA sequencing.

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