Complexity and species variation of the kidney-type glutaminase gene

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.

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Animal-APAdb: a comprehensive animal alternative polyadenylation database

Nucleic Acids Research ◽

10.1093/nar/gkaa778 ◽

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.

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SRSF3 and SRSF7 modulate 3′UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels

Genome Biology ◽

10.1186/s13059-021-02298-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Oliver Daniel Schwich ◽

Nicole Blümel ◽

Mario Keller ◽

Marius Wegener ◽

Samarth Thonta Setty ◽

...

Keyword(s):

Alternative Splicing ◽

Mrna Export ◽

Domain Architecture ◽

Alternative Polyadenylation ◽

Sr Proteins ◽

Untranslated Regions ◽

Dual Function ◽

Independent Manner ◽

Polyadenylation Sites ◽

Selection Of

Abstract Background Alternative polyadenylation (APA) refers to the regulated selection of polyadenylation sites (PASs) in transcripts, which determines the length of their 3′ untranslated regions (3′UTRs). We have recently shown that SRSF3 and SRSF7, two closely related SR proteins, connect APA with mRNA export. The mechanism underlying APA regulation by SRSF3 and SRSF7 remained unknown. Results Here we combine iCLIP and 3′-end sequencing and find that SRSF3 and SRSF7 bind upstream of proximal PASs (pPASs), but they exert opposite effects on 3′UTR length. SRSF7 enhances pPAS usage in a concentration-dependent but splicing-independent manner by recruiting the cleavage factor FIP1, generating short 3′UTRs. Protein domains unique to SRSF7, which are absent from SRSF3, contribute to FIP1 recruitment. In contrast, SRSF3 promotes distal PAS (dPAS) usage and hence long 3′UTRs directly by counteracting SRSF7, but also indirectly by maintaining high levels of cleavage factor Im (CFIm) via alternative splicing. Upon SRSF3 depletion, CFIm levels decrease and 3′UTRs are shortened. The indirect SRSF3 targets are particularly sensitive to low CFIm levels, because here CFIm serves a dual function; it enhances dPAS and inhibits pPAS usage by binding immediately downstream and assembling unproductive cleavage complexes, which together promotes long 3′UTRs. Conclusions We demonstrate that SRSF3 and SRSF7 are direct modulators of pPAS usage and show how small differences in the domain architecture of SR proteins can confer opposite effects on pPAS regulation.

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The landscape of alternative polyadenylation in single cells of the developing mouse embryo

Nature Communications ◽

10.1038/s41467-021-25388-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Vikram Agarwal ◽

Sereno Lopez-Darwin ◽

David R. Kelley ◽

Jay Shendure

Keyword(s):

Rna Binding ◽

Developmental Stages ◽

Single Cells ◽

Neuronal Cell ◽

Alternative Polyadenylation ◽

Cell Types ◽

Untranslated Regions ◽

Mammalian Development ◽

Translation Rate ◽

Dynamic Landscape

Abstract3′ untranslated regions (3′ UTRs) post-transcriptionally regulate mRNA stability, localization, and translation rate. While 3′-UTR isoforms have been globally quantified in limited cell types using bulk measurements, their differential usage among cell types during mammalian development remains poorly characterized. In this study, we examine a dataset comprising ~2 million nuclei spanning E9.5–E13.5 of mouse embryonic development to quantify transcriptome-wide changes in alternative polyadenylation (APA). We observe a global lengthening of 3′ UTRs across embryonic stages in all cell types, although we detect shorter 3′ UTRs in hematopoietic lineages and longer 3′ UTRs in neuronal cell types within each stage. An analysis of RNA-binding protein (RBP) dynamics identifies ELAV-like family members, which are concomitantly induced in neuronal lineages and developmental stages experiencing 3′-UTR lengthening, as putative regulators of APA. By measuring 3′-UTR isoforms in an expansive single cell dataset, our work provides a transcriptome-wide and organism-wide map of the dynamic landscape of alternative polyadenylation during mammalian organogenesis.

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Aptardi predicts polyadenylation sites in sample-specific transcriptomes using high-throughput RNA sequencing and DNA sequence

Nature Communications ◽

10.1038/s41467-021-21894-x ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Ryan Lusk ◽

Evan Stene ◽

Farnoush Banaei-Kashani ◽

Boris Tabakoff ◽

Katerina Kechris ◽

...

Keyword(s):

Rna Sequencing ◽

Dna Sequence ◽

Mammalian Species ◽

Alternative Polyadenylation ◽

Sequence Information ◽

Rna Seq ◽

Average Precision ◽

Polyadenylation Sites ◽

Dna Nucleotide Sequence

AbstractAnnotation of polyadenylation sites from short-read RNA sequencing alone is a challenging computational task. Other algorithms rooted in DNA sequence predict potential polyadenylation sites; however, in vivo expression of a particular site varies based on a myriad of conditions. Here, we introduce aptardi (alternative polyadenylation transcriptome analysis from RNA-Seq data and DNA sequence information), which leverages both DNA sequence and RNA sequencing in a machine learning paradigm to predict expressed polyadenylation sites. Specifically, as input aptardi takes DNA nucleotide sequence, genome-aligned RNA-Seq data, and an initial transcriptome. The program evaluates these initial transcripts to identify expressed polyadenylation sites in the biological sample and refines transcript 3′-ends accordingly. The average precision of the aptardi model is twice that of a standard transcriptome assembler. In particular, the recall of the aptardi model (the proportion of true polyadenylation sites detected by the algorithm) is improved by over three-fold. Also, the model—trained using the Human Brain Reference RNA commercial standard—performs well when applied to RNA-sequencing samples from different tissues and different mammalian species. Finally, aptardi’s input is simple to compile and its output is easily amenable to downstream analyses such as quantitation and differential expression.

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Calcitonin/calcitonin gene-related peptide transcription unit: tissue-specific expression involves selective use of alternative polyadenylation sites

Molecular and Cellular Biology ◽

10.1128/mcb.4.10.2151-2160.1984 ◽

1984 ◽

Vol 4 (10) ◽

pp. 2151-2160

Author(s):

S G Amara ◽

R M Evans ◽

M G Rosenfeld

Keyword(s):

Regulation Of Gene Expression ◽

Alternative Polyadenylation ◽

Calcitonin Gene Related Peptide ◽

Transcription Unit ◽

Specific Expression ◽

Tissue Specific ◽

Related Peptide ◽

Calcitonin Gene ◽

Polyadenylation Sites ◽

Specific Regulation

Different 3' coding exons in the rat calcitonin gene are used to generate distinct mRNAs encoding either the hormone calcitonin in thyroidal C-cells or a new neuropeptide referred to as calcitonin gene-related peptide in neuronal tissue, indicating the RNA processing regulation is one strategy used in tissue-specific regulation of gene expression in the brain. Although the two mRNAs use the same transcriptional initiation site and have identical 5' terminal sequences, their 3' termini are distinct. The polyadenylation sites for calcitonin and calcitonin gene-related peptide mRNAs are located at the end of the exons 4 and 6, respectively. Termination of transcription after the calcitonin exon does not dictate the production of calcitonin mRNA, because transcription proceeds through both calcitonin and calcitonin gene-related peptide exons irrespective of which mRNA is ultimately produced. In isolated nuclei, both polyadenylation sites appear to be utilized; however, the proximal (calcitonin) site is preferentially used in nuclei from tissues producing calcitonin mRNA. These data suggest that the mechanism dictating production of each mRNA involves the selective use of alternative polyadenylation sites.

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Structure and expression of histone H3.3 genes in Drosophila melanogaster and Drosophila hydei

Genome ◽

10.1139/g95-075 ◽

1995 ◽

Vol 38 (3) ◽

pp. 586-600 ◽

Cited By ~ 35

Author(s):

Anna S. Akhmanova ◽

Petra C. T. Bindels ◽

Jie Xu ◽

Koos Miedema ◽

Hannie Kremer ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Sequence Similarity ◽

Expression Patterns ◽

Alternative Polyadenylation ◽

Cdna Clones ◽

Drosophila Hydei ◽

Histone H3.3 ◽

Somatic Tissues ◽

Polyadenylation Sites ◽

Limited Sequence

We demonstrate that in Drosophila melanogaster the histone H3.3 replacement variant is encoded by two genes, H3.3A and H3.3B. We have isolated cDNA clones for H3.3A and cDNA and genomic clones for H3.3B. The genes encode exactly the same protein but are widely divergent in their untranslated regions (UTR). Both genes are expressed in embryos and adults; they are expressed in the gonads as well as in somatic tissues of the flies. However, only one of them, H3.3A, shows strong testes expression. The 3′ UTR of the H3.3A gene is relatively short (~250 nucleotides (nt)). H3.3B transcripts can be processed at several polyadenylation sites, the longest with a 3′ UTR of more than 1500 nt. The 3′ processing sites, preferentially used in the gonads and somatic tissues, are different. We have also isolated the Drosophila hydei homologues of the two H3.3 genes. They are quite similar to the D. melanogaster genes in their expression patterns. However, in contrast to their vertebrate counterparts, which are highly conserved in their noncoding regions, the Drosophila genes display only limited sequence similarity in these regions.Key words: H3.3 histone variant, Drosophila, sequence comparison, alternative polyadenylation, testis expression.

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TSAPA: identification of tissue-specific alternative polyadenylation sites in plants

Bioinformatics ◽

10.1093/bioinformatics/bty044 ◽

2018 ◽

Vol 34 (12) ◽

pp. 2123-2125 ◽

Cited By ~ 3

Author(s):

Guoli Ji ◽

Moliang Chen ◽

Wenbin Ye ◽

Sheng Zhu ◽

Congting Ye ◽

...

Keyword(s):

Alternative Polyadenylation ◽

Tissue Specific ◽

Specific Alternative ◽

Polyadenylation Sites

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Genome-wide profiling reveals cancer-related genes with switched alternative polyadenylation sites in colorectal cancer

OncoTargets and Therapy ◽

10.2147/ott.s164233 ◽

2018 ◽

Vol Volume 11 ◽

pp. 5349-5357 ◽

Cited By ~ 3

Author(s):

Xiaochen Yang ◽

Jun Wu ◽

Wei Xu ◽

Sheng Tan ◽

Changyu Chen ◽

...

Keyword(s):

Colorectal Cancer ◽

Alternative Polyadenylation ◽

Genome Wide ◽

Polyadenylation Sites

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NP1 Protein of the Bocaparvovirus Minute Virus of Canines Controls Access to the Viral Capsid Genes via Its Role in RNA Processing

Journal of Virology ◽

10.1128/jvi.02618-15 ◽

2015 ◽

Vol 90 (4) ◽

pp. 1718-1728 ◽

Cited By ~ 19

Author(s):

Olufemi O. Fasina ◽

Yanming Dong ◽

David J. Pintel

Keyword(s):

Rna Processing ◽

Alternative Polyadenylation ◽

Genome Replication ◽

Coding Region ◽

Content Type ◽

Mrna Transcripts ◽

Viral Genome Replication ◽

Minute Virus ◽

Polyadenylation Sites ◽

The Right

ABSTRACTMinute virus of canines (MVC) is an autonomous parvovirus in the genusBocaparvovirus. It has a single promoter that generates a single pre-mRNA processed via alternative splicing and alternative polyadenylation to produce at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another complex site, (pA)p, within the capsid-coding region. During viral infection, the mRNAs must extend through (pA)p and undergo additional splicing of the immediately upstream 3D∕3A intron to access the capsid gene. MVC NP1 is a 22-kDa nuclear phosphoprotein unique to the genusBocaparvovirusof theParvovirinaewhich we have shown governs suppression of (pA)p independently of viral genome replication. We show here that in addition to suppression of (pA)p, NP1 is also required for the excision of the MVC 3D∕3A intron, independently of its effect on alternative polyadenylation. Mutations of the arginine∕serine (SR) di-repeats within the intrinsically disordered amino terminus of NP1 are required for splicing of the capsid transcript but not suppression of polyadenylation at (pA)p. 3′-end processing of MVC mRNAs at (pA)p is critical for viral genome replication and the optimal expression of NP1 and NS1. Thus, a finely tuned balance between (pA)p suppression and usage is necessary for efficient virus replication. NP1 is the first parvovirus protein implicated in RNA processing. Its characterization reveals another way that parvoviruses govern access to their capsid protein genes, namely, at the RNA level, by regulating the essential splicing of an intron and the suppression of an internal polyadenylation site.IMPORTANCETheParvovirinaeare small nonenveloped icosahedral viruses that are important pathogens in many animal species, including humans. Although parvoviruses have only subtle early-to-late expression shifts, they all regulate access to their capsid genes. Minute virus of canines (MVC) is an autonomous parvovirus in the genusBocaparvovirus. It has a single promoter generating a single pre-mRNA which is processed via alternative splicing and alternative polyadenylation to generate at least 8 mRNA transcripts. MVC contains two polyadenylation sites, one at the right-hand end of the genome, (pA)d, and another, (pA)p, within the capsid-coding region. It had not been clear how the potent internal polyadenylation motif is suppressed to allow processing, export, and accumulation of the spliced capsid protein-encoding mRNAs. We show here that MVC NP1, the first parvovirus protein to be implicated in RNA processing, governs access to the MVC capsid gene by facilitating splicing and suppressing internal polyadenylation of MVC pre-mRNAs.

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