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https://www.readbyqxmd.com/read/29236260/generation-of-cell-lines-stably-expressing-a-fluorescent-reporter-of-nonsense-mediated-mrna-decay-activity
#1
Nadezhda M Markina, Anton P Pereverzev, Dmitry B Staroverov, Konstantin A Lukyanov, Nadya G Gurskaya
Nonsense-mediated mRNA decay (NMD) is a mechanism of mRNA surveillance ubiquitous among eukaryotes. Importantly, NMD not only removes aberrant transcripts with premature stop codons, but also regulates expression of many normal genes. A recently introduced dual-color fluorescent protein-based reporter enables analysis of NMD activity in live cells. In this chapter we describe the method to generate stable transgenic cell lines expressing the splicing-dependent NMD reporter using consecutive steps of lentivirus transduction and Tol2 transposition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235495/identification-of-nonsense-mediated-mrna-decay-pathway-as-a-critical-regulator-of-p53-isoform-%C3%AE
#2
Lauren E Cowen, Yi Tang
Human TP53 gene encodes the tumor suppressor p53 and, via alternative splicing, the p53β and γ isoforms. Numerous studies have shown that p53β/γ can modulate p53 functions and are critically involved in regulation of cellular response to stress conditions. However, it is not fully understood how the β and γ isoforms are regulated following splicing. Using gene targeting and RNAi, we showed that depletion of the nonsense-mediated mRNA decay (NMD) factor SMG7 or UPF1 significantly induced p53β but had minimal effect on p53γ...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235465/molecular-basis-of-differential-3-splice-site-sensitivity-to-anti-tumor-drugs-targeting-u2-snrnp
#3
Luisa Vigevani, André Gohr, Thomas Webb, Manuel Irimia, Juan Valcárcel
Several splicing-modulating compounds, including Sudemycins and Spliceostatin A, display anti-tumor properties. Combining transcriptome, bioinformatic and mutagenesis analyses, we delineate sequence determinants of the differential sensitivity of 3' splice sites to these drugs. Sequences 5' from the branch point (BP) region strongly influence drug sensitivity, with additional functional BPs reducing, and BP-like sequences allowing, drug responses. Drug-induced retained introns are typically shorter, displaying higher GC content and weaker polypyrimidine-tracts and BPs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29235382/exploiting-differential-rna-splicing-patterns-a-potential-new-group-of-therapeutic-targets-in-cancer
#4
Nidhi Jyotsana, Michael Heuser
Mutations in genes associated with splicing have been found in hematologic malignancies, but also in solid cancers. Aberrant cancer specific RNA splicing either results from mutations or misexpression of the spliceosome genes directly, or from mutations in splice sites of oncogenes or tumor suppressors. Areas covered: In this review, we present molecular targets of aberrant splicing in various malignancies, information on existing and emerging therapeutics against such targets, and strategies for future drug development...
December 13, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/29234324/long-non-coding-rnas-emerging-and-versatile-regulators-in-host-virus-interactions
#5
REVIEW
Xing-Yu Meng, Yuzi Luo, Muhammad Naveed Anwar, Yuan Sun, Yao Gao, Huawei Zhang, Muhammad Munir, Hua-Ji Qiu
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29234285/a-microarray-study-of-carpet-shell-clam-ruditapes-decussatus-shows-common-and-organ-specific-growth-related-gene-expression-differences-in-gills-and-digestive-gland
#6
Carlos Saavedra, Massimo Milan, Ricardo B Leite, David Cordero, Tomaso Patarnello, M Leonor Cancela, Luca Bargelloni
Growth rate is one of the most important traits from the point of view of individual fitness and commercial production in mollusks, but its molecular and physiological basis is poorly known. We have studied differential gene expression related to differences in growth rate in adult individuals of the commercial marine clam Ruditapes decussatus. Gene expression in the gills and the digestive gland was analyzed in 5 fast-growing and five slow-growing animals by means of an oligonucleotide microarray containing 14,003 probes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29233978/an-oomycete-plant-pathogen-reprograms-host-pre-mrna-splicing-to-subvert-immunity
#7
Jie Huang, Lianfeng Gu, Ying Zhang, Tingxiu Yan, Guanghui Kong, Liang Kong, Baodian Guo, Min Qiu, Yang Wang, Maofeng Jing, Weiman Xing, Wenwu Ye, Zhe Wu, Zhengguang Zhang, Xiaobo Zheng, Mark Gijzen, Yuanchao Wang, Suomeng Dong
The process of RNA splicing influences many physiological processes, including plant immunity. However, how plant parasites manipulate host RNA splicing process remains unknown. Here we demonstrate that PsAvr3c, an avirulence effector from oomycete plant pathogen Phytophthora sojae, physically binds to and stabilizes soybean serine/lysine/arginine-rich proteins GmSKRPs. The SKRPs are novel proteins that associate with a complex that contains plant spliceosome components, and are negative regulators of plant immunity...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233922/deep-experimental-profiling-of-microrna-diversity-deployment-and-evolution-across-the-drosophila-genus
#8
Jaaved Mohammed, Alex S Flynt, Alexandra M Panzarino, Md Mosharrof Hussein Mondal, Matthew DeCruz, Adam Siepel, Eric C Lai
To assess miRNA evolution across the Drosophila genus, we analyzed several billion small RNA reads across 12 fruit fly species. These data permit comprehensive curation of species- and clade-specific variation in miRNA identity, abundance, and processing. Among well-conserved miRNAs, we observed unexpected cases of clade-specific variation in 5' end precision, occasional antisense loci, and putatively noncanonical loci. We also used strict criteria to identify a large set (649) of novel, evolutionarily restricted miRNAs...
December 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29233683/caspase-mediated-cleavage-of-x-ray-repair-cross-complementing-group-4-promotes-apoptosis-by-enhancing-nuclear-translocation-of-caspase-activated-dnase
#9
Yumi Sunatani, Radhika Pankaj Kamdar, Mukesh Kumar Sharma, Tadashi Matsui, Ryo Sakasai, Mitsumasa Hashimoto, Yasuhito Ishigaki, Yoshihisa Matsumoto, Kuniyoshi Iwabuchi
X-ray repair cross-complementing group 4 (XRCC4), a repair protein for DNA double-strand breaks, is cleaved by caspases during apoptosis. In this study, we examined the role of XRCC4 in apoptosis. Cell lines, derived from XRCC4-deficient M10 mouse lymphoma cells and stably expressing wild-type XRCC4 or caspase-resistant XRCC4, were established and treated with staurosporine (STS) to induce apoptosis. In STS-induced apoptosis, expression of wild-type, but not caspase-resistant, XRCC4 in XRCC4-deficient cells enhanced oligonucleosomal DNA fragmentation and the appearance of TUNEL-positive cells by promoting nuclear translocation of caspase-activated DNase (CAD), a major nuclease for oligonucleosomal DNA fragmentation...
December 9, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/29232016/characterization-of-h3-3-and-hira-expression-and-function-in-bovine-early-embryos
#10
Kun Zhang, Han Wang, Sandeep K Rajput, Joseph K Folger, George W Smith
Histone variant H3.3 is encoded by two distinct genes, H3F3A and H3F3B, that are closely associated with actively transcribed genes. H3.3 replacement is continuous and essential for maintaining correct chromatin structure during mouse oogenesis. Upon fertilization, H3.3 is incorporated to parental chromatin, and is required for blastocyst formation in mice. The H3.3 exchange process is facilitated by the chaperone HIRA, particularly during zygote development. We previously demonstrated that H3.3 is required for bovine early embryonic development; here, we explored the mechanisms of its functional requirement...
December 12, 2017: Molecular Reproduction and Development
https://www.readbyqxmd.com/read/29232014/mutations-of-the-glycine-cleavage-system-genes-possibly-affect-the-negative-symptoms-of-schizophrenia-through-metabolomic-profile-changes
#11
Akane Yoshikawa, Fumichika Nishimura, Aya Inai, Yosuke Eriguchi, Masaki Nishioka, Atsuhiko Takaya, Mamoru Tochigi, Yoshiya Kawamura, Tadashi Umekage, Kayoko Kato, Tsukasa Sasaki, Yoshiaki Ohashi, Kazuya Iwamoto, Kiyoto Kasai, Chihiro Kakiuchi
AIM: Hypofunction of N-methyl-D-aspartate receptors (NMDARs) may contribute to the pathophysiology of schizophrenia (SCZ). Recently, the glycine cleavage system (GCS) was shown to affect NMDAR function in the brain. GCS functional defects cause nonketotic hyperglycinemia (NKH), the atypical phenotype of which presents psychiatric symptoms similar to SCZ. Here, we examined the involvement of GCS in SCZ. METHODS: First, to identify the rare variants and the exonic deletions, we re-sequenced all the coding exons and the splice sites of four GCS genes (GLDC, AMT, GCSH, DLD) in 474 patients with SCZ and 475 controls and performed multiplex ligation-dependent probe amplification (MLPA) analysis in SCZ...
December 12, 2017: Psychiatry and Clinical Neurosciences
https://www.readbyqxmd.com/read/29231888/analysis-and-prediction-of-exon-skipping-events-from-rna-seq-with-sequence-information-using-rotation-forest
#12
Xiuquan Du, Changlin Hu, Yu Yao, Shiwei Sun, Yanping Zhang
In bioinformatics, exon skipping (ES) event prediction is an essential part of alternative splicing (AS) event analysis. Although many methods have been developed to predict ES events, a solution has yet to be found. In this study, given the limitations of machine learning algorithms with RNA-Seq data or genome sequences, a new feature, called RS (RNA-seq and sequence) features, was constructed. These features include RNA-Seq features derived from the RNA-Seq data and sequence features derived from genome sequences...
December 12, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29231014/-correlation-between-genetic-variants-and-polymorphism-of-caveolin-and-sudden-unexplained-death
#13
F Y Wu, X H Tang, L L Gai, X P Kong, B Hao, E W Huang, H Shi, L H Sheng, L Quan, S P Liu, B Luo
OBJECTIVES: To explore the genetic variation sites of caveolin (CAV) and their correlation with sudden unexplained death (SUD). METHODS: The blood samples were collected from SUD group (71 cases), coronary artery disease (CAD) group (62 cases) and control group (60 cases), respectively. The genome DNA were extracted and sequencing was performed directly by amplifying gene coding region and exon-intron splicing region of CAV1 and CAV3 using PCR...
April 2017: Fa Yi Xue za Zhi
https://www.readbyqxmd.com/read/29230626/efficient-one-step-fusion-pcr-based-on-dual-asymmetric-primers-and-two-step-annealing
#14
Yilan Liu, Jinjin Chen, Anders Thygesen
Gene splicing by fusion PCR is a versatile and widely used methodology, especially in synthetic biology. We here describe a rapid method for splicing two fragments by one-round fusion PCR with a dual-asymmetric primers and two-step annealing (ODT) method. During the process, the asymmetric intermediate fragments were generated in the early stage. Thereafter, they were hybridized in the subsequent cycles to serve as template for the target full-length product. The process parameters such as primer ratio, elongation temperature and cycle numbers were optimized...
December 11, 2017: Molecular Biotechnology
https://www.readbyqxmd.com/read/29230609/comparative-assessment-of-chloroplast-transcriptional-responses-highlights-conserved-and-unique-patterns-across-triticeae-members-under-salt-stress
#15
Saeid Mirzaei, Mehdi Mansouri, Ghasem Mohammadi-Nejad, Gaurav Sablok
Chloroplast functional genomics, in particular understanding the chloroplast transcriptional response is of immense importance mainly due to its role in oxygenic photosynthesis. As a photosynthetic unit, its efficiency and transcriptional activity is directly regulated by reactive oxygen species during abiotic and biotic stress and subsequently affects carbon assimilation, and plant biomass. In crops, understanding photosynthesis is crucial for crop domestication by identifying the traits that could be exploited for crop improvement...
December 11, 2017: Photosynthesis Research
https://www.readbyqxmd.com/read/29230098/circular-rnas-a-novel-type-of-non-coding-rna-and-their-potential-implications-in-antiviral-immunity
#16
REVIEW
Man Wang, Fei Yu, Wei Wu, Yuan Zhang, Wenguang Chang, Murugavel Ponnusamy, Kun Wang, Peifeng Li
Circular RNAs (circRNAs), a novel type of non-coding RNAs (ncRNAs), are ubiquitously expressed in eukaryotic cells during post-transcriptional processes. Unlike linear RNAs, circRNAs form covalent-closed continuous loops without 5' to 3' polarities and poly (A) tails. With advances in high-throughput sequencing technology, numerous circRNAs have been identified in plants, animals and humans. Notably, circRNAs display cell-type, tissue-type and developmental-stage specific expression patterns in eukaryotic transcriptome, which reveals their significant regulatory functions in gene expression...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29230097/the-molecular-mechanisms-of-regulation-on-usp2-s-alternative-splicing-and-the-significance-of-its-products
#17
REVIEW
Han-Qing Zhu, Feng-Hou Gao
Ubiquitin-specific protease 2 (USP2) has a regulatory function in cell growth or death and is involved in the pathogenesis of various diseases. USP2 gene can generate 7 splicing variants through alternative splicing, and 5 variants respectively as USP2-201, USP2-202, USP2-204, USP2-205, USP2-206 can encode proteins. The influence of circadian rhythm, nutrition and androgen on specific signaling molecules or cytokines can regulate the alternative splicing of USP2. Specifically, PKC activator, IL-1β, TNF-α, PDGF-BB, TGF-β1 are all regulatory factors for USP2's alternative splicing...
2017: International Journal of Biological Sciences
https://www.readbyqxmd.com/read/29229984/molecular-and-functional-variation-in-ipsc-derived-sensory-neurons
#18
Jeremy Schwartzentruber, Stefanie Foskolou, Helena Kilpinen, Julia Rodrigues, Kaur Alasoo, Andrew J Knights, Minal Patel, Angela Goncalves, Rita Ferreira, Caroline Louise Benn, Anna Wilbrey, Magda Bictash, Emma Impey, Lishuang Cao, Sergio Lainez, Alexandre Julien Loucif, Paul John Whiting, Alex Gutteridge, Daniel J Gaffney
Induced pluripotent stem cells (iPSCs), and cells derived from them, have become key tools for modeling biological processes, particularly in cell types that are difficult to obtain from living donors. Here we present a map of regulatory variants in iPSC-derived neurons, based on 123 differentiations of iPSCs to a sensory neuronal fate. Gene expression was more variable across cultures than in primary dorsal root ganglion, particularly for genes related to nervous system development. Using single-cell RNA-sequencing, we found that the number of neuronal versus contaminating cells was influenced by iPSC culture conditions before differentiation...
December 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29229983/annotation-free-quantification-of-rna-splicing-using-leafcutter
#19
Yang I Li, David A Knowles, Jack Humphrey, Alvaro N Barbeira, Scott P Dickinson, Hae Kyung Im, Jonathan K Pritchard
The excision of introns from pre-mRNA is an essential step in mRNA processing. We developed LeafCutter to study sample and population variation in intron splicing. LeafCutter identifies variable splicing events from short-read RNA-seq data and finds events of high complexity. Our approach obviates the need for transcript annotations and circumvents the challenges in estimating relative isoform or exon usage in complex splicing events. LeafCutter can be used both to detect differential splicing between sample groups and to map splicing quantitative trait loci (sQTLs)...
December 11, 2017: Nature Genetics
https://www.readbyqxmd.com/read/29229980/molecular-cloning-of-novel-transcripts-of-human-kallikrein-related-peptidases-5-6-7-8-and-9-klk5-klk9-using-next-generation-sequencing
#20
Panagiotis G Adamopoulos, Christos K Kontos, Andreas Scorilas
Alternative splicing of cancer-related genes is a common cellular mechanism accounting for cancer cell transcriptome complexity and affecting cell cycle control, proliferation, apoptosis, angiogenesis, invasion, and metastasis. In this study, we describe the discovery and molecular cloning of thirty novel transcripts of the human KLK5, KLK6, KLK7, KLK8 and KLK9 genes, using 3' rapid amplification of cDNA ends (3' RACE) and NGS technology, as well as their expression analysis in many established cell lines, originating from several distinct cancerous and normal tissues...
December 11, 2017: Scientific Reports
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