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https://www.readbyqxmd.com/read/28454421/notch-is-a-critical-regulator-in-cervical-cancer-by-regulating-numb-splicing
#1
Cai Rong, Yu Feng, Zhou Ye
Cervical cancer, which is the second most common female malignancy, is characterized by the consistent presence of human papillomavirus. Inappropriate activation of Notch signaling has been associated with various types of cancer; however, the role of Notch in cervical cancer remains unclear. The present study aimed to investigate the role of Notch in cervical cancer. The methods used included the generation of plasmids, viability assays, polymerase chain reaction and western blotting The present findings demonstrated that cervical cancer samples also consistently exhibit abnormal activation of the Notch pathway...
April 2017: Oncology Letters
https://www.readbyqxmd.com/read/28454348/effects-of-ptcs-on-nonsense-mediated-mrna-decay-are-dependent-on-ptc-location
#2
Heegyum Moon, Xuexiu Zheng, Tiing Jen Loh, Ha Na Jang, Yongchao Liu, Da-Woon Jung, Darren R Williams, Haihong Shen
The récepteur d'origine nantais (RON) gene is a proto-oncogene that is responsible for encoding the human macrophage-stimulating protein (MSP) 1 receptor. MSP activation induces RON-mediated cell dissociation, migration and matrix invasion. Isoforms of RON that exclude exons 5 and 6 encode the RONΔ160 protein, which promotes cell transformation in vitro and tumor metastasis in vivo. Premature termination codons (PTCs) in exons activate the nonsense-mediated mRNA decay (NMD) signaling pathway. The present study demonstrated that PTCs at various locations in the alternative exons 5 and 6 could induce NMD of the majority of the spliced, or partially spliced, isoforms...
March 2017: Oncology Letters
https://www.readbyqxmd.com/read/28453668/a-mass-graph-based-approach-for-the-identification-of-modified-proteoforms-using-top-down-tandem-mass-spectra
#3
Qiang Kou, Si Wu, Nikola Tolic, Ljiljana Paša-Tolic, Yunlong Liu, Xiaowen Liu
Motivation: Although proteomics has rapidly developed in the past decade, researchers are still in the early stage of exploring the world of complex proteoforms, which are protein products with various primary structure alterations resulting from gene mutations, alternative splicing, post-translational modifications, and other biological processes. Proteoform identification is essential to mapping proteoforms to their biological functions as well as discovering novel proteoforms and new protein functions...
May 1, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28449304/a-case-of-familial-transmission-of-the-newly-described-dnmt3a-overgrowth-syndrome
#4
Gabrielle Lemire, Julie Gauthier, Jean-François Soucy, Marie-Ange Delrue
DNMT3A-Overgrowth Syndrome (also known as Tatton-Brown-Rahman Syndrome) (MIM 615879) has recently been described in 13 individuals with de novo heterozygous mutations in DNMT3A gene. This autosomal dominant condition is characterized by overgrowth, dysmorphic facial features and moderate intellectual disability. Missense and truncating point mutations, a small in-frame deletion, as well as microdeletion 2p23 have been reported. Moreover, DNMT3A is commonly somatically mutated in acute myeloid leukemia. We herein report a family with two siblings and their father affected by the syndrome...
April 27, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28448022/development-of-an-economical-dna-delivery-system-by-acufection-and-its-application-to-skin-research
#5
Yu-Jei Lin, Tsung-Lin Lee, Chia-Chi Ku
Dysregulation of immune response in skin is associated with numerous human skin disorders. Direct transfer of immune-related genes into skin tissue is a fascinating approach to investigate immune modulation of cutaneous inflammation in mouse models of human diseases. Here we present a cost-effective protocol that delivered naked DNA in mouse skin and leads to transgene expression. The method is coined "acufection", denoting acupuncture-mediated DNA transfection. To perform acufection, mouse skin was first infused with DNA in phosphate-buffered saline (PBS) and then pricked lightly with a bundle of acupuncture needles to facilitate the absorption of DNA and transfection into cells...
April 19, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/28447221/deleterious-abca7-mutations-and-transcript-rescue-mechanisms-in-early-onset-alzheimer-s-disease
#6
Arne De Roeck, Tobi Van den Bossche, Julie van der Zee, Jan Verheijen, Wouter De Coster, Jasper Van Dongen, Lubina Dillen, Yalda Baradaran-Heravi, Bavo Heeman, Raquel Sanchez-Valle, Albert Lladó, Benedetta Nacmias, Sandro Sorbi, Ellen Gelpi, Oriol Grau-Rivera, Estrella Gómez-Tortosa, Pau Pastor, Sara Ortega-Cubero, Maria A Pastor, Caroline Graff, Håkan Thonberg, Luisa Benussi, Roberta Ghidoni, Giuliano Binetti, Alexandre de Mendonça, Madalena Martins, Barbara Borroni, Alessandro Padovani, Maria Rosário Almeida, Isabel Santana, Janine Diehl-Schmid, Panagiotis Alexopoulos, Jordi Clarimon, Alberto Lleó, Juan Fortea, Magda Tsolaki, Maria Koutroumani, Radoslav Matěj, Zdenek Rohan, Peter De Deyn, Sebastiaan Engelborghs, Patrick Cras, Christine Van Broeckhoven, Kristel Sleegers
Premature termination codon (PTC) mutations in the ATP-Binding Cassette, Sub-Family A, Member 7 gene (ABCA7) have recently been identified as intermediate-to-high penetrant risk factor for late-onset Alzheimer's disease (LOAD). High variability, however, is observed in downstream ABCA7 mRNA and protein expression, disease penetrance, and onset age, indicative of unknown modifying factors. Here, we investigated the prevalence and disease penetrance of ABCA7 PTC mutations in a large early onset AD (EOAD)-control cohort, and examined the effect on transcript level with comprehensive third-generation long-read sequencing...
April 27, 2017: Acta Neuropathologica
https://www.readbyqxmd.com/read/28446598/the-histone-variant-h2a-z-promotes-efficient-cotranscriptional-splicing-in-s-cerevisiae
#7
Lauren T Neves, Stephen Douglass, Roberto Spreafico, Srivats Venkataramanan, Tracy L Kress, Tracy L Johnson
In eukaryotes, a dynamic ribonucleic protein machine known as the spliceosome catalyzes the removal of introns from premessenger RNA (pre-mRNA). Recent studies show the processes of RNA synthesis and RNA processing to be spatio-temporally coordinated, indicating that RNA splicing takes place in the context of chromatin. H2A.Z is a highly conserved histone variant of the canonical histone H2A. In Saccharomyces cerevisiae, H2A.Z is deposited into chromatin by the SWR-C complex, is found near the 5' ends of protein-coding genes, and has been implicated in transcription regulation...
April 1, 2017: Genes & Development
https://www.readbyqxmd.com/read/28446513/frequent-hypomorphic-alleles-account-for-a-significant-fraction-of-abca4-disease-and-distinguish-it-from-age-related-macular-degeneration
#8
Jana Zernant, Winston Lee, Frederick T Collison, Gerald A Fishman, Yuri V Sergeev, Kaspar Schuerch, Janet R Sparrow, Stephen H Tsang, Rando Allikmets
BACKGROUND: Variation in the ABCA4 gene is causal for, or associated with, a wide range of phenotypes from early onset Mendelian retinal dystrophies to late-onset complex disorders such as age-related macular degeneration (AMD). Despite substantial progress in determining the causal genetic variation, even complete sequencing of the entire open reading frame and splice sites of ABCA4 identifies biallelic mutations in only 60%-70% of cases; 20%-25% remain with one mutation and no mutations are found in 10%-15% of cases with clinically confirmed ABCA4 disease...
April 26, 2017: Journal of Medical Genetics
https://www.readbyqxmd.com/read/28446323/-role-of-aberrant-splicing-in-pathogenesis-of-myelodysplastic-syndromes-review
#9
Lin Li, Zhi-Jian Xiao, Xue-Mei Sun
The spectrum of genetic abnormalities in myelodysplastic syndromes(MDS) has been revealed by high-throughput sequencing. However, the functional role of these mutations in occurrence and development of MDS was not delineated. The mutations in splicing factors have been identified as the commonest gene mutations in MDS. Recently, it was reported that the mutated or dysregulated splicing factors, including SF3B1, SRSF2 and U2AF1, attribute to aberrant mRNA splicing, which leads to hematopoietic dysfunction and drives MDS...
April 2017: Zhongguo Shi Yan Xue Ye Xue za Zhi
https://www.readbyqxmd.com/read/28445500/sf3b1-is-a-stress-sensitive-splicing-factor-that-regulates-both-hsf1-concentration-and-activity
#10
Karen S Kim Guisbert, Eric Guisbert
The heat shock response (HSR) is a well-conserved, cytoprotective stress response that activates the HSF1 transcription factor. During severe stress, cells inhibit mRNA splicing which also serves a cytoprotective function via inhibition of gene expression. Despite their functional interconnectedness, there have not been any previous reports of crosstalk between these two pathways. In a genetic screen, we identified SF3B1, a core component of the U2 snRNP subunit of the spliceosome, as a regulator of the heat shock response in Caenorhabditis elegans...
2017: PloS One
https://www.readbyqxmd.com/read/28444304/a-frequent-oligogenic-involvement-in-congenital-hypothyroidism
#11
Tiziana de Filippis, Giulia Gelmini, Elvezia Paraboschi, Maria Cristina Vigone, Marianna Di Frenna, Federica Marelli, Marco Bonomi, Alessandra Cassio, Daniela Larizza, Mirella Moro, Giorgio Radetti, Mariacarolina Salerno, Diego Ardissino, Giovanna Weber, Davide Gentilini, Fabiana Guizzardi, Stefano Duga, Luca Persani
Congenital Hypothyroidism (CH), the most frequent form of preventable mental retardation, is predicted to have a relevant genetic origin. However, CH is frequently reported to be sporadic and candidate gene variations were found in < 10% of the investigated patients. Here, we characterize the involvement of 11 candidate genes through a systematic Next Generation Sequencing (NGS) analysis. The NGS was performed in 177 unrelated CH patients (94 gland-in-situ; 83 dysgenesis) and in 3,538 control subjects...
April 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28444194/evolution-of-the-3r-myb-gene-family-in-plants
#12
Guanqiao Feng, J Gordon Burleigh, Edward L Braun, Wenbin Mei, W Brad Barbazuk
Plant 3R-MYB transcription factors are an important subgroup of the MYB super family in plants; however, their evolutionary history and functions remain poorly understood. We identified 225 3R-MYB proteins from 65 plant species, including algae and all major lineages of land plants. Two segmental duplication events preceding the common ancestor of angiosperms have given rise to three subgroups of the 3R-MYB proteins. Five conserved introns in the domain region of the 3R-MYB genes were identified, which arose through a step-wise pattern of intron gain during plant evolution...
April 20, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28443131/a-bioinformatics-based-alternative-mrna-splicing-code-that-may-explain-some-disease-mutations-is-conserved-in-animals
#13
Wen Qu, Pablo Cingolani, Barry R Zeeberg, Douglas M Ruden
Deep sequencing of cDNAs made from spliced mRNAs indicates that most coding genes in many animals and plants have pre-mRNA transcripts that are alternatively spliced. In pre-mRNAs, in addition to invariant exons that are present in almost all mature mRNA products, there are at least 6 additional types of exons, such as exons from alternative promoters or with alternative polyA sites, mutually exclusive exons, skipped exons, or exons with alternative 5' or 3' splice sites. Our bioinformatics-based hypothesis is that, in analogy to the genetic code, there is an "alternative-splicing code" in introns and flanking exon sequences, analogous to the genetic code, that directs alternative splicing of many of the 36 types of introns...
2017: Frontiers in Genetics
https://www.readbyqxmd.com/read/28442991/a-novel-long-non-coding-rna-durga-modulates-dendrite-density-and-expression-of-kalirin-in-zebrafish
#14
Mayuresh A Sarangdhar, Divya Chaubey, Abhishek Bhatt, Monisha Km, Manish Kumar, Shashi Ranjan, Beena Pillai
Kalirin, a key player in axonal development, nerve growth and synaptic re-modeling, is implicated in many pathological conditions like schizophrenia and autism-spectrum disorders. Alternative promoters and splicing lead to functionally distinct isoforms, but the post-transcriptional regulation of Kalirin has not been studied. Here, we report a novel non-coding RNA, which we name durga, arising from the first exon of kalirin a (kalrna) in the antisense orientation in zebrafish. The kalrna and durga transcripts are barely detectable during early development, but steadily increase by 24 hours post-fertilization (hpf) as the brain develops...
2017: Frontiers in Molecular Neuroscience
https://www.readbyqxmd.com/read/28441933/identification-and-biochemical-characterization-of-the-fructokinase-gene-family-in-arabidopsis-thaliana
#15
John W Riggs, Philip C Cavales, Sonia M Chapiro, Judy Callis
BACKGROUND: Fructose is an abundant sugar in plants as it is a breakdown product of both major sucrose-cleaving enzymes. To enter metabolism, fructose is phosphorylated by a fructokinase (FRK). Known FRKs are members of a diverse family of carbohydrate/purine kinases known as the phosphofructokinase B (pfkB) family. The complete complement of active fructokinases has not been reported for any plant species. RESULTS: Protein sequence analysis of the 22 Arabidopsis thaliana pfkB members identified eight highly related predicted proteins, including one with previously demonstrated FRK activity...
April 26, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28441483/discovery-of-a-novel-class-of-survival-motor-neuron-2-splicing-modifiers-for-the-treatment-of-spinal-muscular-atrophy
#16
Emmanuel Pinard, Luke Green, Michael Reutlinger, Marla Weetall, Nikolai N Naryshkin, John Baird, Karen S Chen, Sergey V Paushkin, Friedrich Metzger, Hasane Ratni
Spinal muscular atrophy (SMA) is caused by mutation or deletion of the survival motor neuron 1 (SMN1) gene, resulting in low levels of functional SMN protein. We have reported recently the identification of small molecules (coumarins, iso-coumarins and pyrido-pyrimidinones) that modify the alternative splicing of SMN2, a paralogous gene to SMN1, restoring the survival motor neuron (SMN) protein level in mouse models of SMA. Herein, we report our efforts to identify a novel chemotype as one strategy to potentially circumvent safety concerns from earlier derivatives, such as in-vitro phototoxicity and in-vitro mutagenicity associated with compounds 1 and 2 or the in-vivo retinal findings observed in a long term chronic tox study with 3 at high exposures only...
April 25, 2017: Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28440507/a-novel-splice-site-mutation-of-wrn-c-ivs28-2t-c-identified-in-a-consanguineous-family-with-werner-syndrome
#17
Pan-Feng Wu, Jie-Yuan Jin, Jing-Jing Li, Ji-Qiang He, Liang-Liang Fan, Min Jin, Hao Huang, Kun Xia, Ju-Yu Tang, Rong Xiang
Werner Syndrome (WS) is a rare, adult‑onset progeroid syndrome that is associated with multiple age‑associated complications and relatively short life expectancy. The characteristics of WS include a 'bird‑like' appearance, canities, cataracts and ulcerations around the ankles. In addition, certain patients develop hypogonadism with atrophic genitalia and infertility. The average life span of affected individuals is 54 years. Previous studies have demonstrated that mutations in the Werner syndrome RecQ like helicase gene (WRN) may contribute to WS...
April 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28440341/quantitative-profiling-of-the-ugt-transcriptome-in-human-drug-metabolizing-tissues
#18
A Tourancheau, M Rouleau, S Guauque-Olarte, L Villeneuve, I Gilbert, A Droit, C Guillemette
Alternative splicing as a mean to control gene expression and diversify function is suspected to considerably influence drug response and clearance. We report the quantitative expression profiles of the human UGT genes including alternatively spliced variants not previously annotated established by deep RNA-sequencing in tissues of pharmacological importance. We reveal a comprehensive quantification of the alternative UGT transcriptome that differ across tissues and among individuals. Alternative transcripts that comprise novel in-frame sequences associated or not with truncations of the 5'- and/or 3'- termini, significantly contribute to the total expression levels of each UGT1 and UGT2 gene averaging 21% in normal tissues, with expression of UGT2 variants surpassing those of UGT1...
April 25, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/28439409/serial-deletion-reveals-structural-basis-and-stability-for-the-core-enzyme-activity-of-human-glutaminase-1-isoforms-relevance-to-excitotoxic-neurodegeneration
#19
Yuju Li, Justin Peer, Runze Zhao, Yinghua Xu, Beiqing Wu, Yi Wang, Changhai Tian, Yunlong Huang, Jialin Zheng
BACKGROUND: Glutaminase 1 is a phosphate-activated metabolic enzyme that catalyzes the first step of glutaminolysis, which converts glutamine into glutamate. Glutamate is the major neurotransmitter of excitatory synapses, executing important physiological functions in the central nervous system. There are two isoforms of glutaminase 1, KGA and GAC, both of which are generated through alternative splicing from the same gene. KGA and GAC both transcribe 1-14 exons in the N-terminal, but each has its unique C-terminal in the coding sequence...
2017: Translational Neurodegeneration
https://www.readbyqxmd.com/read/28439397/transcriptomic-analysis-of-maternally-provisioned-cues-for-phenotypic-plasticity-in-the-annual-killifish-austrofundulus-limnaeus
#20
Amie L Romney, Jason E Podrabsky
BACKGROUND: Genotype and environment can interact during development to produce novel adaptive traits that support life in extreme conditions. The development of the annual killifish Austrofundulus limnaeus is unique among vertebrates because the embryos have distinct cell movements that separate epiboly from axis formation during early development, can enter into a state of metabolic dormancy known as diapause and can survive extreme environmental conditions. The ability to enter into diapause can be maternally programmed, with young females producing embryos that do not enter into diapause...
2017: EvoDevo
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