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https://www.readbyqxmd.com/read/29031100/discovery-of-a-new-mechanism-for-regulation-of-plant-triacylglycerol-metabolism-the-peanut-diacylglycerol-acyltransferase-1-gene-family-transcriptome-is-highly-enriched-in-alternative-splicing-variants
#1
Ling Zheng, Jay Shockey, Feng Guo, Lingmin Shi, Xinguo Li, Lei Shan, Shubo Wan, Zhenying Peng
Triacylglycerols (TAGs) are the most important energy storage form in oilseed crops. Diacylglycerol acyltransferase (DGAT) catalyzes the rate-limiting step of the Kennedy pathway of TAG biosynthesis. To date, little is known about the regulation of DGAT activity in peanut (Arachis hypogaea), an agronomically important oilseed crop that is cultivated in many parts of the world. In this study, seven distinct forms of type 1 DGAT (AhDGAT1.1-AhDGAT1.7) were identified, cloned, and characterized. Comparisons of the nucleotide sequences and gene structures revealed many different splicing variants of AhDGAT1, some of which displayed different organ-specific expression patterns...
October 6, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/29031089/17%C3%AE-estradiol-regulates-the-rna-binding-protein-nova1-which-then-regulates-the-alternative-splicing-of-estrogen-receptor-%C3%AE-in-the-aging-female-rat-brain
#2
Cody L Shults, Caitlin B Dingwall, Chun K Kim, Elena Pinceti, Yathindar S Rao, Toni R Pak
Alternative RNA splicing results in the translation of diverse protein products arising from a common nucleotide sequence. These alternative protein products are often functional and can have widely divergent actions from the canonical protein. Studies in humans and other vertebrate animals have demonstrated that alternative splicing events increase with advanced age, sometimes resulting in pathological consequences. Menopause represents a critical transition for women, where the beneficial effects of estrogens are no longer evident; therefore, factors underlying increased pathological conditions in women are confounded by the dual factors of aging and declining estrogens...
September 14, 2017: Neurobiology of Aging
https://www.readbyqxmd.com/read/29031026/genome-wide-characterization-of-differential-transcript-usage-in-arabidopsis-thaliana
#3
Dries Vaneechoutte, April R Estrada, Ying-Chen Lin, Ann E Loraine, Klaas Vandepoele
Alternative splicing and the usage of alternate transcription start- or stop sites allows a single gene to produce multiple transcript isoforms. Most plant genes express certain isoforms at a significantly higher level than others, but under specific conditions this expression dominance can change, resulting in a different set of dominant isoforms. These events of Differential Transcript Usage (DTU) have been observed for thousands of Arabidopsis thaliana, Zea mays and Vitis vinifera genes and have been linked to development and stress response...
October 14, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29029362/altered-tdp-43-dependent-splicing-in-hspb8-related-distal-hereditary-motor-neuropathy-and-myofibrillar-myopathy
#4
Andrea Cortese, Matilde Laurà, Carlo Casali, Ichizo Nishino, Yukiko K Hayashi, Stefania Magri, Franco Taroni, Cristiana Stuani, Paola Saveri, Maurizio Moggio, Michela Ripolone, A Prelle, C Pisciotta, A Sagnelli, Anna Pichiecchio, Mary M Reilly, Emanuele Buratti, Davide Pareyson
INTRODUCTION: Mutations in the small heat shock protein 22 gene (HSPB8) have been associated with Charcot-Marie-Tooth type 2L, distal hereditary motor neuropathy (dHMN) type IIa and, more recently, distal myopathy/myofibrillar myopathy (MFM) with protein aggregates and TDP-43 inclusions. OBJECTIVE: To report a novel family with HSPB8 (K141E) -related dHMN/MFM and to investigate, in a patient muscle biopsy, whether the presence of protein aggregates was paralleled by altered TDP-43 function...
October 13, 2017: European Journal of Neurology: the Official Journal of the European Federation of Neurological Societies
https://www.readbyqxmd.com/read/29029327/the-exonization-and-functionalization-of-an-alu-j-element-in-the-protein-coding-region-of-glycoprotein-hormone-alpha-gene-represent-a-novel-mechanism-to-the-evolution-of-hemochorial-placentation-in-primates
#5
Haidi Chen, Li Chen, Yune Wu, Hao Shen, Guang Yang, Cheng Deng
Alu elements contribute considerably to gene regulation and genome evolution in primates. The generation of new exons from Alu elements has been found in various human genes, and the regulatory function of the Alu exon has been investigated in many studies. However, the functionalization of Alu elements in protein coding regions remains unknown. Here, we reported that an Alu-J element exonized in the glycoprotein hormone alpha (GPHA) gene and encoded an additional N-terminal peptide (Alu-J encoding peptide) of the mature GPHA peptide, leading to a splicing variant of Alu-GPHA in anthropoid primates approximately 35 million years ago...
September 26, 2017: Molecular Biology and Evolution
https://www.readbyqxmd.com/read/29029073/clinical-genetics-and-outcome-of-left-ventricular-non-compaction-cardiomyopathy
#6
Farbod Sedaghat-Hamedani, Jan Haas, Feng Zhu, Christian Geier, Elham Kayvanpour, Martin Liss, Alan Lai, Karen Frese, Regina Pribe-Wolferts, Ali Amr, Daniel Tian Li, Omid Shirvani Samani, Avisha Carstensen, Diana Martins Bordalo, Marion Müller, Christine Fischer, Jing Shao, Jing Wang, Ming Nie, Li Yuan, Sabine Haßfeld, Christine Schwartz, Min Zhou, Zihua Zhou, Yanwen Shu, Min Wang, Kai Huang, Qiutang Zeng, Longxian Cheng, Tobias Fehlmann, Philipp Ehlermann, Andreas Keller, Christoph Dieterich, Katrin Streckfuß-Bömeke, Yuhua Liao, Michael Gotthardt, Hugo A Katus, Benjamin Meder
Aims: In this study, we aimed to clinically and genetically characterize LVNC patients and investigate the prevalence of variants in known and novel LVNC disease genes. Introduction: Left ventricular non-compaction cardiomyopathy (LVNC) is an increasingly recognized cause of heart failure, arrhythmia, thromboembolism, and sudden cardiac death. We sought here to dissect its genetic causes, phenotypic presentation and outcome. Methods and results: In our registry with follow-up of in the median 61 months, we analysed 95 LVNC patients (68 unrelated index patients and 27 affected relatives; definite familial LVNC = 23...
October 6, 2017: European Heart Journal
https://www.readbyqxmd.com/read/29028823/novel-mutations-in-darier-disease-and-association-to-self-reported-disease-severity
#7
Ivone U S Leong, Alexander Stuckey, Tara Ahanian, Martin Cederlöf, Jakob D Wikstrom
Darier disease is a rare and severe autosomal dominant skin disease characterised by malodorous keratotic papules in seborrheic areas of the skin. Darier disease affects up to 1 in 30 000 people and is caused by mutations in the ATP2A2 gene, which encodes to the sarco/endoplasmic reticulum calcium-ATPase isoform 2 that pumps calcium into the endoplasmic reticulum. Although many ATP2A2 variants have been described, it is not known if genotype correlates with phenotype, which could be important for prognosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29028476/differential-interaction-between-human-and-murine-crm1-and-lentiviral-rev-proteins
#8
Yan Yue, Ayse K Coskun, Navneet Jawanda, Jim Auer, Richard E Sutton
Mice have multiple obstacles to HIV replication, including a block of unspliced and partially spliced viral mRNA nuclear export. In human, Rev binds to the Rev-response element and human (h) Crm1, facilitating nuclear export of RRE-containing viral RNAs. Murine (m) Crm1 is less functional than hCrm1 in this regard. Here we demonstrated that in biochemical experiments mCrm1 failed to interact with HIV Rev whereas hCrm1 did. In genetic experiments in human cells, we observed a modest but significant differential effect between mCrm1 and hCrm1, which was also true of other lentiviral Revs tested...
October 10, 2017: Virology
https://www.readbyqxmd.com/read/29028266/circpro-an-integrated-tool-for-the-identification-of-circrnas-with-protein-coding-potential
#9
Xianwen Meng, Qi Chen, Peijing Zhang, Ming Chen
Summary: Circular RNAs (circRNAs), a novel class of endogenous RNAs, are widespread in eukaryotic cells. Emerging roles in diverse biological processes suggest that circRNA is a promising key player in RNA world. Most circRNAs are generated through back-splicing of pre-mRNAs, forming a covalently closed loop structure with no 5' caps or 3' polyadenylated tails. In addition, most circRNAs were not associated with translating ribosomes, therefore, circRNAs were deemed to be noncoding. However, the latest research findings revealed that some circRNAs could generate proteins in vivo, which expands the landscape of transcriptome and proteome...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028265/stereogene-rapid-estimation-of-genome-wide-correlation-of-continuous-or-interval-feature-data
#10
Elena D Stavrovskaya, Tejasvi Niranjan, Elana J Fertig, Sarah J Wheelan, Alexander V Favorov, Andrey A Mironov
Motivation: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. Results: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29028262/tsis-an-r-package-to-infer-alternative-splicing-isoform-switches-for-time-series-data
#11
Wenbin Guo, Cristiane P G Calixto, John W S Brown, Runxuan Zhang
Summary: An alternative splicing isoform switch is where a pair of transcript isoforms reverse their relative expression abundances in response to external or internal stimuli. Although computational methods are available to study differential alternative splicing, few tools for detection of isoform switches exist and these are based on pairwise comparisons. Here, we provide the TSIS R package, which is the first tool for detecting significant transcript isoform switches in time-series data...
October 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29027900/rna-polymerase-ii-stalling-at-pre-mrna-splice-sites-is-enforced-by-ubiquitination-of-the-catalytic-subunit
#12
Laura Milligan, Camille Sayou, Alex Tuck, Tatsiana Auchynnikava, Jane E A Reid, Ross Alexander, Flavia de Lima Alves, Robin Allshire, Christos Spanos, Juri Rappsilber, Jean D Beggs, Grzegorz Kudla, David Tollervey
Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex. Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. Ubiquitinated RNAPII showed similar enrichment...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/29027761/oxidative-stress-and-mitochondrial-dynamics-malfunction-are-linked-in-pelizaeus-merzbacher-disease
#13
Montserrat Ruiz, Mélina Bégou, Nathalie Launay, Pablo Ranea-Robles, Patrizia Bianchi, Jone López-Erauskin, Laia Morató, Cristina Guilera, Bérengère Petit, Catherine Vaurs-Barriere, Céline Guéret-Gonthier, Marie-Noëlle Bonnet-Dupeyron, Stéphane Fourcade, Johan Auwerx, Odile Boespflug-Tanguy, Aurora Pujol
Pelizaeus-Merzbacher disease (PMD) is a fatal hypomyelinating disorder characterized by early impairment of motor development, nystagmus, choreoathetotic movements, ataxia and progressive spasticity. PMD is caused by variations in the proteolipid protein gene PLP1, which encodes the two major myelin proteins of the central nervous system, PLP and its spliced isoform DM20, in oligodendrocytes. Large duplications including the entire PLP1 gene are the most frequent causative mutation leading to the classical form of PMD...
October 13, 2017: Brain Pathology
https://www.readbyqxmd.com/read/29026277/novel-splice-site-mutation-in-gata3-in-a-patient-with-hdr-syndrome
#14
Kumihiro Matsuo, Arisa Kobayashi, Yusuke Tanahashi, Satoko Maruyama, Yoshihiro Niitsu, Hidenori Katsuta, Akiko Furuya, Shigeru Suzuki, Mitsunobu Kawamura, Hiroshi Azuma
No abstract text is available yet for this article.
2017: Clinical Pediatric Endocrinology: Case Reports and Clinical Investigations: Official Journal of the Japanese Society for Pediatric Endocrinology
https://www.readbyqxmd.com/read/29025893/disease-specific-biases-in-alternative-splicing-and-tissue-specific-dysregulation-revealed-by-multitissue-profiling-of-lymphocyte-gene-expression-in-type-1-diabetes
#15
Jeremy R B Newman, Ana Conesa, Matthew Mika, Felicia N New, Suna Onengut-Gumuscu, Mark A Atkinson, Stephen S Rich, Lauren M McIntyre, Patrick Concannon
Genome-wide association studies (GWAS) have identified multiple, shared allelic associations with many autoimmune diseases. However, the pathogenic contributions of variants residing in risk loci remain unresolved. The location of the majority of shared disease-associated variants in noncoding regions suggests they contribute to risk of autoimmunity through effects on gene expression in the immune system. In the current study, we test this hypothesis by applying RNA sequencing to CD4(+), CD8(+), and CD19(+) lymphocyte populations isolated from 81 subjects with type 1 diabetes (T1D)...
October 12, 2017: Genome Research
https://www.readbyqxmd.com/read/29025584/regulatory-mechanisms-of-long-noncoding-rnas-on-gene-expression-in-cancers
#16
REVIEW
Weiliang Sun, Yunben Yang, Chunjing Xu, Junming Guo
Long non-coding RNAs (lncRNAs) are a heterogeneous class of RNAs that are non-protein coding transcripts longer than 200 nucleotides. In this review, we introduce the mechanisms by which lncRNAs regulate gene expression in four parts, epigenetic regulation (genetic imprinting and chromatin remodeling), transcriptional regulation (molecular decoy), post-transcriptional regulation (splicing and mRNA decay), and translational regulation. H19, Xist, and others are involved in genomic imprinting. HOTAIR and ANRIL function in chromatin remodeling...
October 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29024828/a-classical-ehlers-danlos-syndrome-family-with-incomplete-presentation-diagnosed-by-molecular-testing
#17
Marina Colombi, Chiara Dordoni, Valeria Cinquina, Marina Venturini, Marco Ritelli
The 2017 EDS revised nosology indicates that minimal criteria suggestive for classical Ehlers-Danlos syndrome (cEDS) are skin hyperextensibility plus atrophic scarring together with either generalized joint hypermobility (gJHM) and/or at least three minor criteria that include cutaneous features and gJHM complications. Confirmatory molecular testing is obligatory to reach a final diagnosis. Although the large majority of the patients presents with these clinical features, some do not and might remain undiagnosed or misdiagnosed...
October 9, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/29024760/rna-processing-in-the-male-germline-mechanisms-and-implications-for-fertility
#18
REVIEW
Julien M D Legrand, Robin M Hobbs
Mammalian spermatogenesis is a tightly coordinated process that gives rise to mature spermatozoa capable of fertilising an ovum during sexual reproduction. A population of stem and progenitor cells known as undifferentiated spermatogonia enables continual spermatogenesis throughout life. A complex transcriptional network that balances self-renewal of spermatogonia with their timely differentiation in order to maintain constant fertility regulates this process. Importantly, post-transcriptional regulation of gene expression plays a critical role in spermatogenesis, necessitated by the profound genetic and morphological changes that occur during meiosis and sperm maturation...
October 9, 2017: Seminars in Cell & Developmental Biology
https://www.readbyqxmd.com/read/29024628/biologico-clinical-significance-of-dnmt3a-variants-expression-in-acute-myeloid-leukemia
#19
Na Lin, Wei Fu, Chen Zhao, Bixin Li, Xiaojing Yan, Yan Li
DNA methyltransferase 3A (DNMT3A) catalyzes de novo DNA methylation and plays important roles in the pathogenesis of acute myeloid leukemia. However, the expression status of DNMT3A variants in acute myeloid leukemia remains obscure. This study aimed to assess the expression levels of alternative splicing of DNMT3A variants and explore their roles in acute myeloid leukemia (AML). DNMT3A variants gene expression were assessed, measuring their effects on cell proliferation. In addition, the expression of DNMT3A variants were evaluated in acute myeloid leukemia patients...
October 9, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/29024003/molecular-characterization-of-the-llama-fgf5-gene-and-identification-of-putative-loss-of-function-mutations
#20
M S Daverio, L Vidal-Rioja, E N Frank, F Di Rocco
Llama, the most numerous domestic camelid in Argentina, has good fiber-production ability. Although a few genes related to other productive traits have been characterized, the molecular genetic basis of fiber growth control in camelids is still poorly understood. Fibroblast growth factor 5 (FGF5) is a secreted signaling protein that controls hair growth in humans and other mammals. Mutations in the FGF5 gene have been associated with long-hair phenotypes in several species. Here, we sequenced the llama FGF5 gene, which consists of three exons encoding 813 bp...
October 11, 2017: Animal Genetics
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