scholarly journals The Transcription Profile of Aleutian Mink Disease Virus in CRFK Cells Is Generated by Alternative Processing of Pre-mRNAs Produced from a Single Promoter

2006 ◽  
Vol 80 (2) ◽  
pp. 654-662 ◽  
Author(s):  
Jianming Qiu ◽  
Fang Cheng ◽  
Lisa R. Burger ◽  
David Pintel
Keyword(s):  
Alternative Polyadenylation ◽  
Transcription Profile ◽  
Coding Region ◽  
Alternative Processing ◽  
Proximal Site ◽  
A Site ◽  
Splicing Patterns ◽  
Viral Capsid Proteins ◽  
Distal Site ◽  
Single Promoter

ABSTRACT A reevaluation of the transcription profile of Aleutian mink disease parvovirus (AMDV)-infected CRFK cells at either 32°C or 37°C has determined that strain AMDV-G encodes six species of mRNAs produced by alternative splicing and alternative polyadenylation of a pre-mRNA generated by a single promoter at the left end of the genome. Three different splicing patterns are used, and each type is found polyadenylated at either the 3′ end of the genome (the distal site) or at a site in the center of the genome (the proximal site). All spliced species accumulate similarly over the course of infection, with the R2 RNA predominant throughout. The R2 RNA, which contains and can express the NS2 coding region, encodes the viral capsid proteins VP1 and VP2.

scholarly journals Block to the Production of Full-Length B19 Virus Transcripts by Internal Polyadenylation Is Overcome by Replication of the Viral Genome

2008 ◽  
Vol 82 (20) ◽  
pp. 9951-9963 ◽  
Author(s):  
Wuxiang Guan ◽  
Fang Cheng ◽  
Yuko Yoto ◽  
Steve Kleiboeker ◽  
Susan Wong ◽  
...  
Keyword(s):  
Nonstructural Protein ◽  
Infectious Clone ◽  
Alternative Polyadenylation ◽  
Virus Genome ◽  
Full Length ◽  
Genome Replication ◽  
Limiting Step ◽  
Replication Systems ◽  
Viral Capsid Proteins ◽  
Distal Site

ABSTRACT The pre-mRNA processing strategy of the B19 virus is unique among parvoviruses. B19 virus-generated pre-mRNAs are transcribed from a single promoter and are extensively processed by alternative splicing and alternative polyadenylation to generate 12 transcripts. Blockage of the production of full-length B19 virus transcripts at the internal polyadenylation site [(pA)p] was previously reported to be a limiting step in B19 virus permissiveness. We show here that in the absence of genome replication, internal polyadenylation of B19 virus RNAs at (pA)p is favored in cells which are both permissive and nonpermissive for B19 viral replication. Replication of the B19 virus genome, however, introduced either by viral infection or by transfection of an infectious clone into permissive cells or forced by heterologous replication systems in nonpermissive cells, enhanced readthrough of (pA)p and the polyadenylation of B19 virus transcripts at the distal site [(pA)d]. Therefore, replication of the genome facilitates the generation of sufficient full-length transcripts that encode the viral capsid proteins and the essential 11-kDa nonstructural protein. Furthermore, we show that polyadenylation of B19 viral RNA at (pA)p likely competes with splicing at the second intron. Thus, we conclude that replication of the B19 virus genome is the primary limiting step governing B19 virus tropism.

movAPA: modeling and visualization of dynamics of alternative polyadenylation across biological samples

2020 ◽  
Author(s):  
Wenbin Ye ◽  
Tao Liu ◽  
Hongjuan Fu ◽  
Congting Ye ◽  
Guoli Ji ◽  
...  
Keyword(s):  
Biological Samples ◽  
Tissue Specificity ◽  
Single Cells ◽  
Alternative Polyadenylation ◽  
R Package ◽  
Supplementary Information ◽  
Rna Seq ◽  
Mouse Sperm ◽  
High Scalability ◽  
A Site

Abstract Motivation Alternative polyadenylation (APA) has been widely recognized as a widespread mechanism modulated dynamically. Studies based on 3′ end sequencing and/or RNA-seq have profiled poly(A) sites in various species with diverse pipelines, yet no unified and easy-to-use toolkit is available for comprehensive APA analyses. Results We developed an R package called movAPA for modeling and visualization of dynamics of alternative polyadenylation across biological samples. movAPA incorporates rich functions for preprocessing, annotation and statistical analyses of poly(A) sites, identification of poly(A) signals, profiling of APA dynamics and visualization. Particularly, seven metrics are provided for measuring the tissue-specificity or usages of APA sites across samples. Three methods are used for identifying 3′ UTR shortening/lengthening events between conditions. APA site switching involving non-3′ UTR polyadenylation can also be explored. Using poly(A) site data from rice and mouse sperm cells, we demonstrated the high scalability and flexibility of movAPA in profiling APA dynamics across tissues and single cells. Availability and implementation https://github.com/BMILAB/movAPA. Supplementary information Supplementary data are available at Bioinformatics online.

The regulated production of mu m and mu s mRNA is dependent on the relative efficiencies of mu s poly(A) site usage and the c mu 4-to-M1 splice

1989 ◽  
Vol 9 (2) ◽  
pp. 726-738
Author(s):  
M L Peterson ◽  
R P Perry
Keyword(s):  
B Cells ◽  
Consensus Sequence ◽  
Splice Junction ◽  
Detectable Effect ◽  
Small Nuclear Rna ◽  
Site Model ◽  
Proximal Site ◽  
Precursor Rna ◽  
Immunoglobulin Mu ◽  
A Site

The relative abundance of the mRNAs encoding the membrane (mu m) and secreted (mu s) forms of immunoglobulin mu heavy chain is regulated during B-cell maturation by a change in the mode of RNA processing. Current models to explain this regulation involve either competition between cleavage-polyadenylation at the proximal (mu s) poly(A) site and cleavage-polyadenylation at the distal (mu m) poly(A) site [poly(A) site model] or competition between cleavage-polyadenylation at the mu s poly(A) site and splicing of the C mu 4 and M1 exons, which eliminates the mu s site (mu s site-splice model). To test certain predictions of these models and to determine whether there is a unique structural feature of the mu s poly(A) site that is essential for regulation, we constructed modified mu genes in which the mu s or mu m poly(A) site was replaced by other poly(A) sites and then studied the transient expression of these genes in cells representative of both early- and late-stage lymphocytes. Substitutions at the mu s site dramatically altered the relative usage of this site and caused corresponding reciprocal changes in the usage of the mu m site. Despite these changes, use of the proximal site was still usually higher in plasmacytomas than in pre-B cells, indicating that regulation does not depend on a unique feature of the mu s poly(A) site. Replacement of the distal (mu m) site had no detectable effect on the usage of the mu s site in either plasmacytomas or pre-B cells. These findings are inconsistent with the poly(A) site model. In addition, we noted that in a wide variety of organisms, the sequence at the 5' splice junction of the C mu 4-to-M1 intron is significantly different from the consensus 5' splice junction sequence and is therefore suboptimal with respect to its complementary base pairing with U1 small nuclear RNA. When we mutated this suboptimal sequence into the consensus sequence, the mu mRNA production in plasmacytoma cells was shifted from predominantly mu s to exclusively mu m. This result unequivocally demonstrated that splicing of the C mu 4-to-M1 exon is in competition with usage of the mu s poly(A) site. A key feature of this regulatory phenomenon appears to be the appropriately balanced efficiencies of these two processing reactions. Consistent with predictions of the mu s site-splice model, B cells were found to contain mu m precursor RNA that had undergone the C mu 4-to-M1 splice but had not yet been polyadenylated at the mu m site.

scholarly journals The Transcription Profile of the Bocavirus Bovine Parvovirus Is Unlike Those of Previously Characterized Parvoviruses

2007 ◽  
Vol 81 (21) ◽  
pp. 12080-12085 ◽  
Author(s):  
Jianming Qiu ◽  
Fang Cheng ◽  
F. Brent Johnson ◽  
David Pintel
Keyword(s):  
Nonstructural Protein ◽  
Alternative Polyadenylation ◽  
Open Reading Frame ◽  
Capsid Proteins ◽  
Transcription Profile ◽  
Reading Frame ◽  
Left Hand ◽  
The Right ◽  
Bovine Parvovirus ◽  
Transcription Map

ABSTRACT The Bocavirus bovine parvovirus generated a single pre-mRNA from a promoter at its left-hand end; however, the pattern of its alternative polyadenylation and splicing was different from that of other parvoviruses. A large left-hand-end open reading frame (ORF) encoded a nonstructural protein of approximately 95 kDa. An abundant, spliced, internally polyadenylated transcript encoded the viral NP1 protein from an ORF in the center of the genome. Transcripts encoding the capsid proteins were polyadenylated in the right-hand terminal palindrome. This is the first published transcription map of a member of the Bocavirus genus of the Parvovirinae.

Prolonged aspirin inhibition of anodal vasodilation is not due to the trafficking delay of neural mediators

2003 ◽  
Vol 285 (1) ◽  
pp. R155-R161 ◽  
Author(s):  
S. Durand ◽  
B. Fromy ◽  
M. Tartas ◽  
A. Jardel ◽  
J. L. Saumet ◽  
...  
Keyword(s):  
Time Course ◽  
Nerve Endings ◽  
High Dose ◽  
Current Application ◽  
Cutaneous Vasodilation ◽  
Dose Aspirin ◽  
Proximal Site ◽  
Time Required ◽  
Distal Site ◽  
High Dose Aspirin

We previously reported that forearm vasodilation to a delivered all-at-once over 5 min or a 1-min repeated monopolar anodal 0.10-mA current application is aspirin sensitive and that a single high-dose aspirin exerts a long-lived effect in the former case. We hypothesized that 1) in the latter case, the effect of aspirin would also be long lived and 2) the time required to resupply nerve endings with unblocked cyclooxygenase through axonal transport could explain this phenomenon. We studied the time course for the recovery of vasodilation to repeated current application after placebo or 1-g aspirin treatment. We then searched for a difference at a proximal vs. distal site in the recovery of the response. Aspirin abolished current-induced vasodilation at 2 h, 10 h, and 3 days, with a progressive recovery thereafter, but no difference between distal and proximal site was observed for the recovery of the response. This suggests that, although neural cyclooxygenase could participate in the response, the time course of aspirin inhibition of current-induced cutaneous vasodilation is not due to the time required through neural transport to resupply nerve endings with unblocked proteins.

Gastric cancer in proximal site exerts poorer survival outcome with divergent genetic features than distal site

2020 ◽  
Vol 88 ◽  
pp. 107360
Author(s):  
Qingchao Zhao ◽  
Ke Chen ◽  
Weiwei Tong ◽  
Changqing Ge ◽  
Dongqiang Zhao
Keyword(s):  
Gastric Cancer ◽  
Survival Outcome ◽  
Proximal Site ◽  
Genetic Features ◽  
Distal Site

scholarly journals Single-Molecule Long-Read Sequencing Reveals the Diversity of Full-Length Transcripts in Leaves of Gnetum (Gnetales)

2019 ◽  
Vol 20 (24) ◽  
pp. 6350 ◽  
Author(s):  
Nan Deng ◽  
Chen Hou ◽  
Fengfeng Ma ◽  
Caixia Liu ◽  
Yuxin Tian
Keyword(s):  
Single Molecule ◽  
Developmental Stages ◽  
Alternative Polyadenylation ◽  
Full Length ◽  
Stomatal Development ◽  
Rna Seq ◽  
Leaf Transcriptome ◽  
Long Read ◽  
Non Coding Rnas ◽  
A Site

The limitations of RNA sequencing make it difficult to accurately predict alternative splicing (AS) and alternative polyadenylation (APA) events and long non-coding RNAs (lncRNAs), all of which reveal transcriptomic diversity and the complexity of gene regulation. Gnetum, a genus with ambiguous phylogenetic placement in seed plants, has a distinct stomatal structure and photosynthetic characteristics. In this study, a full-length transcriptome of Gnetum luofuense leaves at different developmental stages was sequenced with the latest PacBio Sequel platform. After correction by short reads generated by Illumina RNA-Seq, 80,496 full-length transcripts were obtained, of which 5269 reads were identified as isoforms of novel genes. Additionally, 1660 lncRNAs and 12,998 AS events were detected. In total, 5647 genes in the G. luofuense leaves had APA featured by at least one poly(A) site. Moreover, 67 and 30 genes from the bHLH gene family, which play an important role in stomatal development and photosynthesis, were identified from the G. luofuense genome and leaf transcripts, respectively. This leaf transcriptome supplements the reference genome of G. luofuense, and the AS events and lncRNAs detected provide valuable resources for future studies of investigating low photosynthetic capacity of Gnetum.

scholarly journals Intronic Alternative Polyadenylation in the Middle of the DMD Gene Produces Half-Size N-Terminal Dystrophin with a Potential Implication of ECG Abnormalities of DMD Patients

2020 ◽  
Vol 21 (10) ◽  
pp. 3555
Author(s):  
Abdul Qawee Mahyoob Rani ◽  
Tetsushi Yamamoto ◽  
Tatsuya Kawaguchi ◽  
Kazuhiro Maeta ◽  
Hiroyuki Awano ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Alternative Polyadenylation ◽  
Coding Region ◽  
Terminal Exon ◽  
Potential Implication ◽  
Human Genes ◽  
Cardiac Muscles ◽  
Rapid Amplification ◽  
Dmd Gene ◽  
Ecg Abnormalities

The DMD gene is one of the largest human genes, being composed of 79 exons, and encodes dystrophin Dp427m which is deficient in Duchenne muscular dystrophy (DMD). In some DMD patient, however, small size dystrophin reacting with antibody to N-terminal but not to C-terminal has been identified. The mechanism to produce N-terminal small size dystrophin remains unknown. Intronic polyadenylation is a mechanism that produces a transcript with a new 3′ terminal exon and a C-terminal truncated protein. In this study, intronic alternative polyadenylation was disclosed to occur in the middle of the DMD gene and produce the half-size N-terminal dystrophin Dp427m, Dpm234. The 3′-rapid amplification of cDNA ends revealed 421 bp sequence in the downstream of DMD exon 41 in U-251 glioblastoma cells. The cloned sequence composing of the 5′ end sequence of intron 41 was decided as the terminal exon, since it encoded poly (A) signal followed by poly (A) stretch. Subsequently, a fragment from DMD exon M1 to intron 41 was obtained by PCR amplification. This product was named Dpm234 after its molecular weight. However, Dpm234 was not PCR amplified in human skeletal and cardiac muscles. Remarkably, Dpm234 was PCR amplified in iPS-derived cardiomyocytes. Accordingly, Western blotting of cardiomyocyte proteins showed a band of 234 kDa reacting with dystrophin antibody to N-terminal, but not C-terminal. Clinically, DMD patients with mutations in the Dpm234 coding region were found to have a significantly higher likelihood of two ECG abnormal findings. Intronic alternative splicing was first revealed in Dp427m to produce small size dystrophin.

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

2015 ◽  
Vol 90 (4) ◽  
pp. 1718-1728 ◽  
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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