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Gene splicing

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https://www.readbyqxmd.com/read/27907902/active-5-splice-sites-regulate-the-biogenesis-efficiency-of-arabidopsis-micrornas-derived-from-intron-containing-genes
#1
Katarzyna Knop, Agata Stepien, Maria Barciszewska-Pacak, Michal Taube, Dawid Bielewicz, Michal Michalak, Jan W Borst, Artur Jarmolowski, Zofia Szweykowska-Kulinska
Arabidopsis, miR402 that is encoded within the first intron of a protein-coding gene At1g77230, is induced by heat stress. Its upregulation correlates with splicing inhibition and intronic proximal polyA site selection. It suggests that miR402 is not processed from an intron, but rather from a shorter transcript after selection of the proximal polyA site within this intron. Recently, introns and active 5' splice sites (5'ss') have been shown to stimulate the accumulation of miRNAs encoded within the first exons of intron-containing MIR genes...
October 5, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27907167/infusion-advancing-discovery-of-fusion-genes-and-chimeric-transcripts-from-deep-rna-sequencing-data
#2
Konstantin Okonechnikov, Aki Imai-Matsushima, Lukas Paul, Alexander Seitz, Thomas F Meyer, Fernando Garcia-Alcalde
Analysis of fusion transcripts has become increasingly important due to their link with cancer development. Since high-throughput sequencing approaches survey fusion events exhaustively, several computational methods for the detection of gene fusions from RNA-seq data have been developed. This kind of analysis, however, is complicated by native trans-splicing events, the splicing-induced complexity of the transcriptome and biases and artefacts introduced in experiments and data analysis. There are a number of tools available for the detection of fusions from RNA-seq data; however, certain differences in specificity and sensitivity between commonly used approaches have been found...
2016: PloS One
https://www.readbyqxmd.com/read/27906075/nuclear-bodies-reorganize-during-myogenesis-in-vitro-and-are-differentially-disrupted-by-expression-of-fshd-associated-dux4
#3
Sachiko Homma, Mary Lou Beermann, Bryant Yu, Frederick M Boyce, Jeffrey Boone Miller
BACKGROUND: Nuclear bodies, such as nucleoli, PML bodies, and SC35 speckles, are dynamic sub-nuclear structures that regulate multiple genetic and epigenetic processes. Additional regulation is provided by RNA/DNA handling proteins, notably TDP-43 and FUS, which have been linked to ALS pathology. Previous work showed that mouse cell line myotubes have fewer but larger nucleoli than myoblasts, and we had found that nuclear aggregation of TDP-43 in human myotubes was induced by expression of DUX4-FL, a transcription factor that is aberrantly expressed and causes pathology in facioscapulohumeral dystrophy (FSHD)...
December 1, 2016: Skeletal Muscle
https://www.readbyqxmd.com/read/27905021/netherton-syndrome-a-genotype-phenotype-review
#4
REVIEW
Constantina A Sarri, Angeliki Roussaki-Schulze, Yiannis Vasilopoulos, Efterpi Zafiriou, Aikaterini Patsatsi, Costas Stamatis, Polyxeni Gidarokosta, Dimitrios Sotiriadis, Theologia Sarafidou, Zissis Mamuris
Netherton syndrome (OMIM #256500) is a rare but severe autosomal recessive form of ichthyosis that affects the skin, hair, and immune system. The identification of SPINK5, which encodes for the serine protease inhibitor LEKTI, as the gene responsible for Netherton syndrome, enabled the search for causative mutations in Netherton syndrome patients and families. However, information regarding these mutations and their association with the pathological Netherton syndrome phenotype is scarce. Herein, we provide an up-to-date overview of 80 different mutations in exonic as well as intronic regions that have been currently identified in 172 homozygous or compound heterozygous patients from 144 families...
November 30, 2016: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/27904822/targeted-sequencing-approach-to-identify-genetic-mutations-in-nasu-hakola-disease
#5
Jun-Ichi Satoh, Motoaki Yanaizu, Youhei Tosaki, Kenji Sakai, Yoshihiro Kino
Nasu-Hakola disease (NHD) is a rare autosomal recessive disorder characterized by sclerosing leukoencephalopathy and multifocal bone cysts, caused by a loss-of-function mutation of either TYROBP (DAP12) or TREM2. TREM2 and DAP12 constitute a receptor/adaptor signaling complex expressed exclusively on osteoclasts, dendritic cells, macrophages, and microglia. Premortem molecular diagnosis of NHD requires genetic analysis of both TYROBP and TREM2, in which 20 distinct NHD-causing mutations have been reported. Due to genetic heterogeneity, it is often difficult to identify the exact mutation responsible for NHD...
November 2016: Intractable & Rare Diseases Research
https://www.readbyqxmd.com/read/27903893/identification-of-a-novel-k311-ubiquitination-site-critical-for-androgen-receptor-transcriptional-activity
#6
Urszula L McClurg, David M W Cork, Steven Darby, Claudia A Ryan-Munden, Sirintra Nakjang, Leticia Mendes Côrtes, Achim Treumann, Luke Gaughan, Craig N Robson
The androgen receptor (AR) is the main driver of prostate cancer (PC) development and progression, and the primary therapeutic target in PC. To date, two functional ubiquitination sites have been identified on AR, both located in its C-terminal ligand binding domain (LBD). Recent reports highlight the emergence of AR splice variants lacking the LBD that can arise during disease progression and contribute to castrate resistance. Here, we report a novel N-terminal ubiquitination site at lysine 311. Ubiquitination of this site plays a role in AR stability and is critical for its transcriptional activity...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27903347/-clinical-genetic-and-pathological-features-of-neuronal-ceroid-lipofuscinosis-in-5-chinese-patients
#7
S C Ren, B Q Gao, Y J Wang, X J Wu, Z X Tian, Y L Sun
Objective: To report the clinical, genetic and ultrastructural pathological features of neuronal ceroid lipofuscinosis (NCLs) in 5 Chinese patients. Methods: A total of 5 patients with NCLs were collected from 2013 to 2015 diagnosed by the department of pediatrics of Beijing Tian Tan Hospital. Their clinical, electrophysiological and neuroimaging data of the patients were reviewed.A total of 9 underlying genes of NCLs were tested in 4 cases and their parents.Ultrastructural pathology by skin biopsy was performed in 3 cases respectively...
November 22, 2016: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/27900998/novel-mutations-in-psenen-gene-in-two-chinese-acne-inversa-families-manifested-as-familial-multiple-comedones-and-dowling-degos-disease
#8
Cheng Zhou, Guang-Dong Wen, Lwin Myint Soe, Hong-Jun Xu, Juan Du, Jian-Zhong Zhang
BACKGROUND: Acne inversa (AI), also called hidradenitis suppurativa, is a chronic, inflammatory, recurrent skin disease of the hair follicle. Familial AI shows autosomal-dominant inheritance caused by mutations in the γ-secretase genes. This study was aimed to identify the specific mutations in the γ-secretase genes in two Chinese families with AI. METHODS: In this study, two Chinese families with AI were investigated. All the affected individuals in the two families mainly manifested with multiple comedones, pitted scars, and a few inflammatory nodules on their face, neck, trunk, axilla, buttocks, upper arms, and thighs...
2016: Chinese Medical Journal
https://www.readbyqxmd.com/read/27900551/transcriptional-regulation-of-snrnas-and-its-significance-for-plant-development
#9
Misato Ohtani
Small nuclear RNA (snRNA) represents a distinct class of non-coding RNA molecules. As these molecules have fundamental roles in RNA metabolism, including pre-mRNA splicing and ribosomal RNA processing, it is essential that their transcription be tightly regulated in eukaryotic cells. The genome of each organism contains hundreds of snRNA genes. Although the structures of these genes are highly diverse among organisms, the trans-acting factors that regulate snRNA transcription are evolutionarily conserved. Recent studies of the Arabidopsis thaliana srd2-1 mutant, which is defective in the snRNA transcription factor, provide insight into the physiological significance of snRNA regulation in plant development...
November 29, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27900367/whole-genome-sequencing-of-two-probands-with-hereditary-spastic-paraplegia-reveals-novel-splice-donor-region-variant-and-known-pathogenic-variant-in-spg11
#10
Allen Chi-Shing Yu, Anne Yin-Yan Chan, Wing Chi Au, Yun Shen, Ting Fung Chan, Ho-Yin Edwin Chan
Hereditary spastic paraplegias (HSPs) are a group of heterogeneous neurodegenerative disorders, which are often presented with overlapping phenotypes such as progressive paraparesis and spasticity. To assist the diagnosis of HSP subtypes, next-generation sequencing is often used to provide supporting evidence. In this study, we report the case of two probands from the same family with HSP symptoms, including bilateral lower limb weakness, unsteady gait, cognitive decline, dysarthria, and slurring of speech since the age of 14...
November 2016: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/27899669/an-ultraconserved-element-uce-controls-homeostatic-splicing-of-arglu1-mrna
#11
Stephan P Pirnie, Ahmad Osman, Yinzhou Zhu, Gordon G Carmichael
Arginine and Glutamate-Rich protein 1 (ARGLU1) is a protein whose function is poorly understood, but may act in both transcription and pre-mRNA splicing. We demonstrate that the ARGLU1 gene expresses at least three distinct RNA splice isoforms - a fully spliced isoform coding for the protein, an isoform containing a retained intron that is detained in the nucleus, and an isoform containing an alternative exon that targets the transcript for nonsense mediated decay. Furthermore, ARGLU1 contains a long, highly evolutionarily conserved sequence known as an Ultraconserved Element (UCE) that is within the retained intron and overlaps the alternative exon...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899618/rna-seq-mixology-designing-realistic-control-experiments-to-compare-protocols-and-analysis-methods
#12
Aliaksei Z Holik, Charity W Law, Ruijie Liu, Zeya Wang, Wenyi Wang, Jaeil Ahn, Marie-Liesse Asselin-Labat, Gordon K Smyth, Matthew E Ritchie
Carefully designed control experiments provide a gold standard for benchmarking different genomics research tools. A shortcoming of many gene expression control studies is that replication involves profiling the same reference RNA sample multiple times. This leads to low, pure technical noise that is atypical of regular studies. To achieve a more realistic noise structure, we generated a RNA-sequencing mixture experiment using two cell lines of the same cancer type. Variability was added by extracting RNA from independent cell cultures and degrading particular samples...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899596/chitars-3-1-the-enhanced-chimeric-transcripts-and-rna-seq-database-matched-with-protein-protein-interactions
#13
Alessandro Gorohovski, Somnath Tagore, Vikrant Palande, Assaf Malka, Dorith Raviv-Shay, Milana Frenkel-Morgenstern
Discovery of chimeric RNAs, which are produced by chromosomal translocations as well as the joining of exons from different genes by trans-splicing, has added a new level of complexity to our study and understanding of the transcriptome. The enhanced ChiTaRS-3.1 database (http://chitars.md.biu.ac.il) is designed to make widely accessible a wealth of mined data on chimeric RNAs, with easy-to-use analytical tools built-in. The database comprises 34 922: chimeric transcripts along with 11 714: cancer breakpoints...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899591/modulation-of-nonsense-mediated-decay-by-rapamycin
#14
Rocio T Martinez-Nunez, Andrew Wallace, Doyle Coyne, Linnea Jansson, Miles Rush, Hanane Ennajdaoui, Sol Katzman, Joanne Bailey, Katrin Deinhardt, Tilman Sanchez-Elsner, Jeremy R Sanford
Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regulation in a wide range of species. Despite well-established roles as an inhibitor of cap-dependent mRNA translation, relatively little is known about its effects on other modes of RNA processing. Here, we characterize the landscape of rapamycin-induced post-transcriptional gene regulation. Transcriptome analysis of rapamycin-treated cells reveals genome-wide changes in alternative mRNA splicing and pronounced changes in NMD-sensitive isoforms...
November 28, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899419/progressive-cl-channel-defects-reveal-disrupted-skeletal-muscle-maturation-in-r6-2-huntington-s-mice
#15
Daniel R Miranda, Monica Wong, Shannon H Romer, Cynthia McKee, Gabriela Garza-Vasquez, Alyssa C Medina, Volker Bahn, Andrew D Steele, Robert J Talmadge, Andrew A Voss
Huntington's disease (HD) patients suffer from progressive and debilitating motor dysfunction. Previously, we discovered reduced skeletal muscle chloride channel (ClC-1) currents, inwardly rectifying potassium (Kir) channel currents, and membrane capacitance in R6/2 transgenic HD mice. The ClC-1 loss-of-function correlated with increased aberrant mRNA processing and decreased levels of full-length ClC-1 mRNA (Clcn1 gene). Physiologically, the resulting muscle hyperexcitability may help explain involuntary contractions of HD...
November 29, 2016: Journal of General Physiology
https://www.readbyqxmd.com/read/27899149/the-quality-of-metabolic-pathway-resources-depends-on-initial-enzymatic-function-assignments-a-case-for-maize
#16
Jesse R Walsh, Mary L Schaeffer, Peifen Zhang, Seung Y Rhee, Julie A Dickerson, Taner Z Sen
BACKGROUND: As metabolic pathway resources become more commonly available, researchers have unprecedented access to information about their organism of interest. Despite efforts to ensure consistency between various resources, information content and quality can vary widely. Two maize metabolic pathway resources for the B73 inbred line, CornCyc 4.0 and MaizeCyc 2.2, are based on the same gene model set and were developed using Pathway Tools software. These resources differ in their initial enzymatic function assignments and in the extent of manual curation...
November 29, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/27899133/adaptively-introgressed-neandertal-haplotype-at-the-oas-locus-functionally-impacts-innate-immune-responses-in-humans
#17
Aaron J Sams, Anne Dumaine, Yohann Nédélec, Vania Yotova, Carolina Alfieri, Jerome E Tanner, Philipp W Messer, Luis B Barreiro
BACKGROUND: The 2'-5' oligoadenylate synthetase (OAS) locus encodes for three OAS enzymes (OAS1-3) involved in innate immune response. This region harbors high amounts of Neandertal ancestry in non-African populations; yet, strong evidence of positive selection in the OAS region is still lacking. RESULTS: Here we used a broad array of selection tests in concert with neutral coalescent simulations to demonstrate a signal of adaptive introgression at the OAS locus...
November 29, 2016: Genome Biology
https://www.readbyqxmd.com/read/27898262/characterization-of-genetic-loss-of-function-of-fus-in-zebrafish
#18
Svetlana Lebedeva, António M de Jesus Domingues, Falk Butter, René F Ketting
The RNA-binding protein FUS is implicated in transcription, alternative splicing of neuronal genes and DNA repair. Mutations in FUS have been linked to human neurodegenerative diseases such as ALS (amyotrophic lateral sclerosis). We genetically disrupted fus in zebrafish (Danio rerio) using the CRISPR-Cas9 system. The fus knockout animals are fertile and did not show any distinctive phenotype. Mutation of fus induces mild changes in gene expression on the transcriptome and proteome level in the adult brain...
November 29, 2016: RNA Biology
https://www.readbyqxmd.com/read/27898075/maternal-high-fat-diet-prevents-developmental-programming-by-early-life-stress
#19
M Rincel, A L Lépinay, P Delage, J Fioramonti, V S Théodorou, S Layé, M Darnaudéry
Anxiety disorders and depression are well-documented in subjects exposed to adverse childhood events. Recently, maternal obesity and/or maternal consumption of high-fat diets (HFD) have been also proposed as risk factors for offspring mental health. Here using an animal model in rats, we explored the combinatorial effects of a maternal HFD (40% of energy from fat without impact on maternal weight; during gestation and lactation) and maternal separation (MS) in offspring. In the prefrontal cortex (PFC) of pups, MS led to changes in the expression of several genes such as Bdnf (brain derived neurotrophic factor), 5HT-r1a (serotonin receptor 1a) and Rest4 (neuron-restrictive silencer element, repressor element 1, silencing transcription factor (Rest), splicing variant 4)...
November 29, 2016: Translational Psychiatry
https://www.readbyqxmd.com/read/27897275/an-ex-vivo-model-contributing-to-the-diagnosis-and-evaluation-of-new-drugs-in-cystic-fibrosis
#20
A M Di Lullo, M Scorza, F Amato, M Comegna, V Raia, L Maiuri, G Ilardi, E Cantone, G Castaldo, M Iengo
Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the cystic fibrosis transmembrane regulator (CFTR) gene. About 2000 mutations have been described so far. We setup an ex vivo model of human nasal epithelial cells (HNECs) to study CF patients testing the effect of novel mutations and molecular therapies. We performed the sampling (by brushing), followed by culture and analysis of HNECs using a series of molecular techniques. We performed 50 brushings from CF patients and controls...
November 29, 2016: Acta Otorhinolaryngologica Italica
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