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https://www.readbyqxmd.com/read/29908124/modifications-in-small-nuclear-rnas-and-their-roles-in-spliceosome-assembly-and-function
#1
Markus T Bohnsack, Katherine E Sloan
Modifications in cellular RNAs have emerged as key regulators of all aspects of gene expression, including pre-mRNA splicing. During spliceosome assembly and function, the small nuclear RNAs (snRNAs) form numerous dynamic RNA-RNA and RNA-protein interactions, which are required for spliceosome assembly, correct positioning of the spliceosome on substrate pre-mRNAs and catalysis. The human snRNAs contain several base methylations as well as a myriad of pseudouridines and 2'-O-methylated nucleotides, which are largely introduced by small Cajal body-specific-RNPs...
June 1, 2018: Biological Chemistry
https://www.readbyqxmd.com/read/29907768/hmena-isoforms-impact-nsclc-patient-outcome-through-fibronectin-%C3%AE-1-integrin-axis
#2
Francesca Di Modugno, Sheila Spada, Belinda Palermo, Paolo Visca, Pierluigi Iapicca, Anna Di Carlo, Barbara Antoniani, Isabella Sperduti, Anna Di Benedetto, Irene Terrenato, Marcella Mottolese, Francesco Gandolfi, Francesco Facciolo, Emily I Chen, Martin A Schwartz, Angela Santoni, Mina J Bissell, Paola Nisticò
We demonstrated previously that the splicing of the actin regulator, hMENA, generates two alternatively expressed isoforms, hMENA11a and hMENAΔv6, which have opposite functions in cell invasiveness. Their mechanisms of action have remained unclear. Here we report two major findings: (i) hMENA regulates β1 integrin expression. This was shown by depleting total hMENA, which led to loss of nuclear expression of serum response factor (SRF)-coactivator myocardin-related transcription factor 1 (MRTF-A), leading to an increase in the G-actin/F-actin ratio crucial for MRTF-A localization...
June 15, 2018: Oncogene
https://www.readbyqxmd.com/read/29905149/group-ii-intron-inhibits-conjugative-relaxase-expression-in-bacteria-by-mrna-targeting
#3
Guosheng Qu, Carol Lyn Piazza, Dorie Smith, Marlene Belfort
Group II introns are mobile ribozymes that are rare in bacterial genomes, often cohabiting with various mobile elements, and seldom interrupting housekeeping genes. What accounts for this distribution has not been well understood. Here, we demonstrate that Ll.LtrB, the group II intron residing in a relaxase gene on a conjugative plasmid from Lactococcus lactis , inhibits its host gene expression and restrains the naturally cohabiting mobile element from conjugative horizontal transfer. We show that reduction in gene expression is mainly at the mRNA level, and results from the interaction between exon-binding sequences (EBSs) in the intron and intron-binding sequences (IBSs) in the mRNA...
June 15, 2018: ELife
https://www.readbyqxmd.com/read/29905030/decreased-expression-of-serine-arginine-rich-splicing-factor-1-in-t-cells-from-patients-with-active-systemic-lupus-erythematosus-accounts-for-reduced-expression-of-rasgrp1-and-dna-methyltransferase-1
#4
Michihiro Kono, Takashi Kurita, Shinsuke Yasuda, Michihito Kono, Yuichiro Fujieda, Toshiyuki Bohgaki, Takayuki Katsuyama, George C Tsokos, Vaishali R Moulton, Tatsuya Atsumi
OBJECTIVE: T cells from SLE patients have reduced protein levels of RasGRP1, a guanine nucleotide exchange factor for Ras, and increased transcript of alternatively spliced (AS) forms lacking exon 11. Serine/arginine-rich splicing factor 1 (SRSF1) binds pre-mRNA to regulate AS forms of several genes, including CD3ζ in SLE T cells. This study aimed to assess whether SRSF1 controls the expression of RasGRP1 in T cells from SLE patients. METHODS: We studied T cells from 45 SLE and 18 healthy subjects...
June 14, 2018: Arthritis & Rheumatology
https://www.readbyqxmd.com/read/29904728/transcriptomic-profiling-of-human-skin-biopsies-in-the-clinical-trial-setting-a-protocol-for-high-quality-rna-extraction-from-skin-tumours
#5
Marina Danilenko, Robert Stones, Neil Rajan
Transcriptomic profiling of skin disease using next generation sequencing allows for detailed information on aspects of RNA biology including gene expression, non-coding regulatory elements and gene splicing. The application of RNA sequencing to human skin disease and cancer is often hampered by degraded RNA. Here we describe a protocol that allows for consistently intact RNA to be extracted from snap frozen skin biopsy samples, which has been validated in a clinical trial setting. Human skin tumour punch biopsies (n=28) ranging from 4-6mm in diameter were obtained from 14 patients with an inherited skin tumour syndrome (CYLD cutaneous syndrome) and frozen in liquid nitrogen prior to being stored at -80°C...
2018: Wellcome Open Research
https://www.readbyqxmd.com/read/29904576/genomics-of-autism-spectrum-disorder-approach-to-therapy
#6
REVIEW
Fatma Ayhan, Genevieve Konopka
Autism spectrum disorder (ASD) is a highly prevalent neurodevelopmental condition with no current treatment available. Although advances in genetics and genomics have identified hundreds of genes associated with ASD, very little is known about the pathophysiology of ASD and the functional contribution of specific genes to ASD phenotypes. Improved understanding of the biological function of ASD-associated genes and how this heterogeneous group of genetic variants leads to the disease is needed in order to develop therapeutic strategies...
2018: F1000Research
https://www.readbyqxmd.com/read/29904030/unconventional-secretion-and-intercellular-transfer-of-mutant-huntingtin
#7
REVIEW
Bor Luen Tang
The mechanism of intercellular transmission of pathological agents in neurodegenerative diseases has received much recent attention. Huntington's disease (HD) is caused by a monogenic mutation in the gene encoding Huntingtin (HTT). Mutant HTT (mHTT) harbors a CAG repeat extension which encodes an abnormally long polyglutamine (polyQ) repeat at HTT's N-terminus. Neuronal pathology in HD is largely due to the toxic gain-of-function by mHTT and its proteolytic products, which forms both nuclear and cytoplasmic aggregates that perturb nuclear gene transcription, RNA splicing and transport as well cellular membrane dynamics...
June 14, 2018: Cells
https://www.readbyqxmd.com/read/29903725/human-primitive-brain-displays-negative-mitochondrial-nuclear-expression-correlation-of-respiratory-genes
#8
Gilad Barshad, Amit Blumberg, Tal Cohen, Dan Mishmar
Oxidative phosphorylation (OXPHOS), a fundamental energy source in all human tissues, requires interactions between mitochondrial (mtDNA) and nuclear (nDNA)-encoded protein subunits. Although such interactions are fundamental to OXPHOS, bi-genomic co-regulation is poorly understood. To address this question, we analyzed ~8,500 RNA-seq experiments from 48 human body sites. Despite well-known variation in mitochondrial activity, quantity and morphology, we found overall positive mtDNA-nDNA OXPHOS genes' co-expression across human tissues...
June 14, 2018: Genome Research
https://www.readbyqxmd.com/read/29903723/long-read-sequencing-of-nascent-rna-reveals-coupling-among-rna-processing-events
#9
Lydia Herzel, Korinna Straube, Karla M Neugebauer
Pre-mRNA splicing is accomplished by the spliceosome, a megadalton complex that assembles de novo on each intron. Because spliceosome assembly and catalysis occur cotranscriptionally, we hypothesized that introns are removed in the order of their transcription in genomes dominated by constitutive splicing. Remarkably little is known about splicing order and the regulatory potential of nascent transcript remodeling by splicing, due to the limitations of existing methods that focus on analysis of mature splicing products (mRNAs) rather than substrates and intermediates...
June 14, 2018: Genome Research
https://www.readbyqxmd.com/read/29902889/-synthesis-and-regulation-of-secondary-metabolites-by-microrna-in-medicinal-plants
#10
REVIEW
Yun Lu, Wei Gao, Lu-Qi Huang
miRNA (microRNA) is a kind of important endogenous non-coding small RNA, which mainly regulates the expression of target gene at the post-transcriptional level by splicing and translation inhibition and it plays an important role in the synthesis of plant secondary metabolites, especially for medicinal plants, the secondary metabolites are mostly active ingredients, which are the basis of medicinal effects. It is of great significance to study the biosynthetic pathways and complex regulatory networks of secondary metabolites of medicinal plants...
May 2018: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29902268/axon-outgrowth-and-neuronal-differentiation-defects-after-a-smn-and-fl-smn-silencing-in-primary-hippocampal-cultures
#11
Daniela Pletto, Silvia Capra, Adele Finardi, Francesca Colciaghi, Paola Nobili, Giorgio Stefano Battaglia, Denise Locatelli, Cinzia Cagnoli
Spinal Muscular Atrophy (SMA) is a severe autosomal recessive disease characterized by selective motor neuron degeneration, caused by disruptions of the Survival of Motor Neuron 1 (Smn1) gene. The main product of SMN1 is the full-length SMN protein (FL-SMN), that plays an established role in mRNA splicing. FL-SMN is also involved in neurite outgrowth and axonal transport. A shorter SMN isoform, axonal-SMN or a-SMN, displays a more specific axonal localization and has remarkable axonogenic properties in NSC-34...
2018: PloS One
https://www.readbyqxmd.com/read/29901772/sox9-has-distinct-regulatory-roles-in-alternative-splicing-and-transcription
#12
Michael Girardot, Elsa Bayet, Justine Maurin, Philippe Fort, Pierre Roux, Peggy Raynaud
SOX9 is known as a crucial transcription factor for various developmental processes and for tissue homeostasis. We examined here its potential role in alternative splicing by analyzing global splicing changes, using RNA-seq of colon tumor cells. We show that SOX9 knockdown alters the splicing of hundreds of genes without affecting their expression levels, revealing that SOX9 controls distinct splicing and transcriptional programs. SOX9 does not affect splicing patterns through the control of splicing factors expression...
June 13, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29901616/a-novel-dmd-splicing-mutation-found-in-a-family-responsible-for-x-linked-dilated-cardiomyopathy-with-hyper-ckemia
#13
Jin Tang, Xueqin Song, Guang Ji, Hongran Wu, Shuyan Sun, Shan Lu, Yuan Li, Chi Zhang, Huiqing Zhang
This study was aimed to detect a new mutation responsible for X-linked dilated cardiomyopathy with hyper-CKemia.We studied a proband who presented with cardiac symptoms with hyper-CKemia, but no clinical skeletal involvement in physical examination, laboratory tests, electromyography, echocardiography, and magnetic resonance imaging (MRI) of cardiac muscles. Muscle biopsy for histopathology and immunohistochemistry for accessing sarcolemma changes. The next-generation sequencing and bioinformatics analysis were performed on the patient and Sanger sequencing was confirmed on the other 6 unaffected families...
June 2018: Medicine (Baltimore)
https://www.readbyqxmd.com/read/29900613/germline-variation-in-the-oxidative-dna-repair-genes-nudt1-and-ogg1-is-not-associated-with-hereditary-colorectal-cancer-or-polyposis
#14
Pilar Mur, Ann-Sofie Jemth, Luka Bevc, Nuno Amaral, Matilde Navarro, Rafael Valdés-Mas, Tirso Pons, Gemma Aiza, Miguel Urioste, Alfonso Valencia, Conxi Lázaro, Victor Moreno, Xose S Puente, Pål Stenmark, Ulrika Warpman-Berglund, Gabriel Capellá, Thomas Helleday, Laura Valle
The causal association of NUDT1 ( = MTH1) and OGG1 with hereditary colorectal cancer (CRC) remains unclear. Here we sought to provide additional evidence for or against the causal contribution of NUDT1 and OGG1 mutations to hereditary CRC and/or polyposis. Mutational screening was performed using pooled DNA amplification and targeted next generation sequencing in 529 families (441 uncharacterized MMR-proficient familial non-polyposis colorectal cancer and 88 polyposis cases). Co-segregation, in silico analyses, in vitro functional assays and case-control associations, were carried out to characterize the identified variants...
June 13, 2018: Human Mutation
https://www.readbyqxmd.com/read/29898953/recapitulating-muscle-disease-phenotypes-with-myotonic-dystrophy-1-ips-cells-a-tool-for-disease-modeling-and-drug-discovery
#15
Ricardo Mondragon-Gonzalez, Rita C R Perlingeiro
Myotonic Dystrophy 1 (DM1) is a multi-system disorder primarily affecting the central nervous system, heart and skeletal muscle. It is caused by an expansion of the CTG trinucleotide repeats in the 3' untranslated region of the DMPK gene. Although patient myoblasts have been used for studying the disease in vitro , the invasiveness as well as the low accessibility to muscle biopsies motivate the development of alternative reliable myogenic models. Here, we established two DM1 iPS cell lines from patient-derived fibroblasts, and using the PAX7 conditional expression system, differentiated these into myogenic progenitors, and subsequently, terminally differentiated myotubes...
June 13, 2018: Disease Models & Mechanisms
https://www.readbyqxmd.com/read/29898370/post-transcriptional-regulation-in-hematopoiesis-rna-binding-proteins-take-control
#16
Laura P M H de Rooij, Derek C H Chan, Ava Keyvani Chahi, Kristin J Hope
Normal hematopoiesis is sustained through a carefully orchestrated balance between hematopoietic stem cell (HSC) self-renewal and differentiation. The functional importance of this axis is underscored by the severity of disease phenotypes initiated by abnormal HSC function, including myelodysplastic syndromes and hematopoietic malignancies. Major advances in the understanding of transcriptional regulation of primitive hematopoietic cells have been achieved, however, the post-transcriptional regulatory layer that may impinge on their behavior remains underexplored by comparison...
June 13, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
https://www.readbyqxmd.com/read/29897997/the-exposure-to-uteroplacental-insufficiency-is-associated-with-activation-of-unfolded-protein-response-in-postnatal-life
#17
Annalisa Deodati, Josepmaría Argemí, Daniela Germani, Antonella Puglianiello, Anna Alisi, Cristiano De Stefanis, Roberto Ferrero, Valerio Nobili, Tomás Aragón, Stefano Cianfarani
Early life events are associated with the susceptibility to chronic diseases in adult life. Perturbations of endoplasmic reticulum (ER) homeostasis activate the unfolded protein response (UPR), which contributes to the development of metabolic alterations. Our aim was to evaluate liver UPR in an animal model of intrauterine growth restriction (IUGR). A significantly increased expression of X-box binding protein-1 spliced (XBP1s) mRNA (p<0.01), Endoplasmic Reticulum-localized DnaJ homologue (Erdj4) mRNA (p<0...
2018: PloS One
https://www.readbyqxmd.com/read/29897575/the-structure-of-salm5-suggests-a-dimeric-assembly-for-the-presynaptic-rptp-ligand-recognition
#18
Sudeep Karki, Prodeep Paudel, Celeste Sele, Alexander V Shkumatov, Tommi Kajander
Synaptic adhesion molecules play a crucial role in the regulation of synapse development and maintenance. Recently, several families of leucine-rich repeat (LRR) domain-containing neuronal adhesion molecules have been characterised, including netrin-G ligands, LRRTMs and the synaptic adhesion-like molecule (SALM) family proteins. Most of these are expressed at the excitatory glutamatergic synapses, and dysfunctions of these genes are genetically linked with cognitive disorders, such as autism spectrum disorders and schizophrenia...
June 12, 2018: Protein Engineering, Design & Selection: PEDS
https://www.readbyqxmd.com/read/29897102/genotyping-analysis-of-mns-blood-group-gp-b-a-b-hybrid-glycophorins-in-the-chinese-southern-han-population-using-a-high-resolution-melting-assay
#19
Ling Wei, Genghis H Lopez, Yang Zhang, Jizhi Wen, Zhen Wang, Yongshui Fu, Catherine A Hyland, Robert L Flower, Guangping Luo, Yanli Ji
BACKGROUND: MNS hybrid GP(B-A-B) glycophorins are more commonly found in Southeast Asians and alloantibodies to antigens they carry are clinically significant. Detection of hybrid glycophorins by serologic techniques is limited due to lack of commercial reagents. In this study, a genotyping method for GP(B-A-B) hybrid glycophorins based on high-resolution melting (HRM) analysis was applied for genotyping analysis in the Chinese Southern Han population. STUDY DESIGN AND METHODS: DNA samples from 3104 Chinese Southern Han blood donors were collected...
June 13, 2018: Transfusion
https://www.readbyqxmd.com/read/29896748/-identification-of-a-homozygous-ass1-mutation-in-a-child-with-citrullinemia-type-%C3%A2-with-high-melting-curve-method
#20
Jingjing Sun, Yunlin Shen, Chongbing Yan, Xiaohui Gong
OBJECTIVE: To carry out rapid genetic diagnosis for a child affected with citrullinemia type Ⅰ. METHODS: Peripheral venous blood samples were obtained from the two-day-old child and his parents as well as 100 healthy controls. Serum ammonia and citrulline was determined by biochemical test and tandem mass spectrometry. Sixteen pairs of primers were designed for high-resolution melting (HRM) analysis of all exons and adjacent intronic sequences of the ASS1 gene in the proband, parents and healthy controls...
June 10, 2018: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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