Processing Factors
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2021 ◽  
Author(s):  
Ping Lu ◽  
Daipeng Chen ◽  
Zhaomei Qi ◽  
Haoming Wang ◽  
Yitong Chen ◽  
...  

Alternative splicing (AS) and alternative polyadenylation (APA) of pre-mRNAs contribute greatly to transcriptome complexity and gene expression regulation in higher eukaryotes. Their biological impact in filamentous fungi, however, has been poorly studied. Here we combine PacBio Isoform Sequencing and strand-specific RNA-Seq of multiple tissues together with mutant characterization to reveal the landscape, complexity and regulation of AS and APA in the filamentous plant pathogenic fungus Fusarium graminearum. We updated the reference genome and generated a comprehensive annotation comprising 51,617 transcript isoforms from 17,189 genes. Majority of the transcripts represent novel isoforms, including 2,998 undiscovered protein-coding genes. In total, 42.7% of multi-exonic genes and 64.8% of genes have AS and APA isoforms, respectively, suggesting AS and APA increase previously unrecognized transcriptome complexity in fungi. Nonsense-mediated mRNA decay factor FgUPF1 may not degrade AS transcripts with premature-stop codons but regulate ribosome biogenesis. Distal polyadenylation sites have a strong signal but proximal polyadenylation isoforms are high expressed. The core 3′-end processing factors FgRNA15, FgHRP1, and FgFIP1 play important roles in promoting proximal polyadenylation site usage and also intron splicing. Genome-wide increase in the abundance of transcripts with retained introns and long 3′-UTRs and downregulation of the spliceosomal and 3′-end processing factors are found in older tissues and quiescent conidia, indicating that intron retention and 3′-UTR lengthening may be a transcriptional signature of aging and dormancy in fungi. Overall, our study generates a comprehensive full-length transcript annotation for F. graminearum and provides new insights into the complexity and regulation of transcriptome in filamentous fungi


2021 ◽  
Vol MA2021-02 (30) ◽  
pp. 906-906
Author(s):  
Eddy Simoen ◽  
Anabela Veloso ◽  
Philippe Matagne ◽  
Cor Claeys

2021 ◽  
Vol 104 (4) ◽  
pp. 3-13
Author(s):  
Eddy Simoen ◽  
Anabela Veloso ◽  
Philippe Matagne ◽  
Cor Claeys

Energies ◽  
2021 ◽  
Vol 14 (16) ◽  
pp. 4737
Author(s):  
Sarallah Hamtaei ◽  
Guy Brammertz ◽  
Marc Meuris ◽  
Jef Poortmans ◽  
Bart Vermang

Pure sulfide CIGS solar cells are interesting candidates for standalone solar cells or top cells in a tandem configuration. To understand the limits and improve the power conversion efficiency of these devices, a comprehensive approach aimed at composition, interface, and process engineering should be employed. Here, the latter was explored. Using a two-step fabrication technique and one-variable-at-a-time methodology, we found the four processing factors affecting the absorber the most. While two were already backed by the previous literature, we found new and statistical evidence for two other important factors as well. The impact of alkali barrier diffusion was also established with statistical significance and under various processing conditions. Furthermore, the absorber roughness for samples without a barrier indicated a significant negative linear correlation with the devices’ efficiency. This contribution could aid engineers in more efficient process designs.


2021 ◽  
Vol 12 ◽  
Author(s):  
Shenghan Lou ◽  
Fanzheng Meng ◽  
Xin Yin ◽  
Yao Zhang ◽  
Bangling Han ◽  
...  

RNA processing converts primary transcript RNA into mature RNA. Altered RNA processing drives tumor initiation and maintenance, and may generate novel therapeutic opportunities. However, the role of RNA processing factors in gastric cancer (GC) has not been clearly elucidated. This study presents a comprehensive analysis exploring the clinical, molecular, immune, and drug response features underlying the RNA processing factors in GC. This study included 1079 GC cases from The Cancer Genome Atlas (TCGA, training set), our hospital cohort, and two other external validation sets (GSE15459, GSE62254). We developed an RNA processing-related prognostic signature using Cox regression with the least absolute shrinkage and selection operator (LASSO) penalty. The prognostic value of the signature was evaluated using a multiple-method approach. The genetic variants, pathway activation, immune heterogeneity, drug response, and splicing features associated with the risk signature were explored using bioinformatics methods. Among the tested 819 RNA processing genes, we identified five distinct RNA processing patterns with specific clinical outcomes and biological features. A 10-gene RNA processing-related prognostic signature, involving ZBTB7A, METTL2B, CACTIN, TRUB2, POLDIP3, TSEN54, SUGP1, RBMS1, TGFB1, and PWP2, was further identified. The signature was a powerful and robust prognosis factor in both the training and validation datasets. Notably, it could stratify the survival of patients with GC in specific tumor-node-metastasis (TNM) classification subgroups. We constructed a composite prognostic nomogram to facilitate clinical practice by integrating this signature with other clinical variables (TNM stage, age). Patients with low-risk scores were characterized with good clinical outcomes, proliferation, and metabolism hallmarks. Conversely, poor clinical outcome, invasion, and metastasis hallmarks were enriched in the high-risk group. The RNA processing signature was also involved in tumor microenvironment reprogramming and regulating alternative splicing, causing different drug response features between the two risk groups. The low-risk subgroup was characterized by high genomic instability, high alternative splicing and might benefit from the immunotherapy. Our findings highlight the prognostic value of RNA processing factors for patients with GC and provide insights into the specific clinical and molecular features underlying the RNA processing-related signature, which may be important for patient management and targeting treatment.


Author(s):  
Chunbo Yang ◽  
Maria Georgiou ◽  
Robert Atkinson ◽  
Joseph Collin ◽  
Jumana Al-Aama ◽  
...  

Retinitis pigmentosa (RP) is the most common inherited retinal disease characterized by progressive degeneration of photoreceptors and/or retinal pigment epithelium that eventually results in blindness. Mutations in pre-mRNA processing factors (PRPF3, 4, 6, 8, 31, SNRNP200, and RP9) have been linked to 15–20% of autosomal dominant RP (adRP) cases. Current evidence indicates that PRPF mutations cause retinal specific global spliceosome dysregulation, leading to mis-splicing of numerous genes that are involved in a variety of retina-specific functions and/or general biological processes, including phototransduction, retinol metabolism, photoreceptor disk morphogenesis, retinal cell polarity, ciliogenesis, cytoskeleton and tight junction organization, waste disposal, inflammation, and apoptosis. Importantly, additional PRPF functions beyond RNA splicing have been documented recently, suggesting a more complex mechanism underlying PRPF-RPs driven disease pathogenesis. The current review focuses on the key RP-PRPF genes, depicting the current understanding of their roles in RNA splicing, impact of their mutations on retinal cell’s transcriptome and phenome, discussed in the context of model species including yeast, zebrafish, and mice. Importantly, information on PRPF functions beyond RNA splicing are discussed, aiming at a holistic investigation of PRPF-RP pathogenesis. Finally, work performed in human patient-specific lab models and developing gene and cell-based replacement therapies for the treatment of PRPF-RPs are thoroughly discussed to allow the reader to get a deeper understanding of the disease mechanisms, which we believe will facilitate the establishment of novel and better therapeutic strategies for PRPF-RP patients.


2021 ◽  
Vol 14 (2) ◽  
pp. 65-76
Author(s):  
E. El-Sayed ◽  
H. Hassan ◽  
A. Abd El-Raouf ◽  
S.N. Salman

Summary The effect of the household processing on the reduction rate of chlorpyrifos, metalaxyl and diazinon residues in contaminated oranges has been investigated and the processing factors were determined. The evaluation included validation parameters, matrix effect (ME %), reduction behavior and processing factors (PFs). Validation parameters were successfully applied; the three pesticides showed satisfactory recovery (70–120%) and precision (relative standard deviation - RSD<20%); they also exhibited no matrix effect. The most effective process in the pesticide residues reduction was juicing, followed by pulping while the washing process was less efficient in removing all pesticide residues; sonication showed a high reduction rate with both chlorpyrifos and diazinon. The processing factors (PFs) were generally less than one which indicates that all processes can reduce pesticide residues in oranges. The results could guide the safe and reasonable use of chlorpyrifos, diazinon, and metalaxyl. These processes contribute substantially to reduce consumer exposure to pesticide residues in oranges.


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