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https://www.readbyqxmd.com/read/28213976/enhancement-of-%C3%AE-globin-gene-expression-in-thalassemic-ivs2-654-induced-pluripotent-stem-cell-derived-erythroid-cells-by-modified-u7-snrna
#1
Phetcharat Phanthong, Suparerk Borwornpinyo, Narisorn Kitiyanant, Natee Jearawiriyapaisarn, Lalana Nuntakarn, Jirawat Saetan, Tiwaporn Nualkaew, Khanit Sa-Ngiamsuntorn, Usanarat Anurathapan, Andras Dinnyes, Yindee Kitiyanant, Suradej Hongeng
The therapeutic use of patient-specific induced pluripotent stem cells (iPSCs) is emerging as a potential treatment of β-thalassemia. Ideally, patient-specific iPSCs would be genetically corrected by various approaches to treat β-thalassemia including lentiviral gene transfer, lentivirus-delivered shRNA, and gene editing. These corrected iPSCs would be subsequently differentiated into hematopoietic stem cells and transplanted back into the same patient. In this article, we present a proof of principle study for disease modeling and screening using iPSCs to test the potential use of the modified U7 small nuclear (sn) RNA to correct a splice defect in IVS2-654 β-thalassemia...
February 18, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28213671/exome-analysis-of-smith-magenis-like-syndrome-cohort-identifies-de-novo-likely-pathogenic-variants
#2
Seth I Berger, Carla Ciccone, Karen L Simon, May Christine Malicdan, Thierry Vilboux, Charles Billington, Roxanne Fischer, Wendy J Introne, Andrea Gropman, Jan K Blancato, James C Mullikin, William A Gahl, Marjan Huizing, Ann C M Smith
Smith-Magenis syndrome (SMS), a neurodevelopmental disorder characterized by dysmorphic features, intellectual disability (ID), and sleep disturbances, results from a 17p11.2 microdeletion or a mutation in the RAI1 gene. We performed exome sequencing on 6 patients with SMS-like phenotypes but without chromosomal abnormalities or RAI1 variants. We identified pathogenic de novo variants in two cases, a nonsense variant in IQSEC2 and a missense variant in the SAND domain of DEAF1, and candidate de novo missense variants in an additional two cases...
February 17, 2017: Human Genetics
https://www.readbyqxmd.com/read/28212793/mir-634-is-a-pol-iii-dependent-intronic-microrna-regulating-alternative-polyadenylated-isoforms-of-its-host-gene-prkca
#3
Elvezia Maria Paraboschi, Giulia Cardamone, Valeria Rimoldi, Stefano Duga, Giulia Soldà, Rosanna Asselta
BACKGROUND: The protein kinase C alpha (PRKCA) gene, coding for a Th17-cell-selective kinase, shows a complex splicing pattern, with at least 2 stable alternative transcripts characterized by an alternative upstream polyadenylation site. Polymorphisms in this gene were associated with several conditions, including multiple sclerosis, asthma, schizophrenia, and cancer. The presence of a microRNA (miRNA), i.e. miR-634, within intron 15 of the PRKCA gene, suggests the intriguing possibility that this miRNA might play a role in the susceptibility to these pathologies...
February 14, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28210900/false-responses-of-renilla-luciferase-reporter-control-to-nuclear-receptor-tr4
#4
Dongyun Zhang, Sam S Atlasi, Krishna K Patel, Zihao Zhuang, Anthony P Heaney
Renilla luciferase reporter is a widely used internal control in dual luciferase reporter assay system, where its transcription is driven by a constitutively active promoter. However, the authenticity of the Renilla luciferase response in some experimental settings has recently been questioned. Testicular receptor 4 (TR4, also known as NR2C2) belongs to the subfamily 2 of nuclear receptors. TR4 binds to a direct repeat regulatory element in the promoter of a variety of target genes and plays a key role in tumorigenesis, lipoprotein regulation, and central nervous system development...
February 16, 2017: Molecular and Cellular Biochemistry
https://www.readbyqxmd.com/read/28209632/high-resolution-profiling-of-nmd-targets-in-yeast-reveals-translational-fidelity-as-a-basis-for-substrate-selection
#5
Alper Celik, Richard Baker, Feng He, Allan Jacobson
Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we re-evaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-Seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detection, including many intron-containing pre-mRNAs and several non-coding RNAs...
February 16, 2017: RNA
https://www.readbyqxmd.com/read/28209125/the-mitochondrial-genome-sequences-of-the-round-goby-and-the-sand-goby-reveal-patterns-of-recent-evolution-in-gobiid-fish
#6
Irene Adrian-Kalchhauser, Ola Svensson, Verena E Kutschera, Magnus Alm Rosenblad, Martin Pippel, Sylke Winkler, Siegfried Schloissnig, Anders Blomberg, Patricia Burkhardt-Holm
BACKGROUND: Vertebrate mitochondrial genomes are optimized for fast replication and low cost of RNA expression. Accordingly, they are devoid of introns, are transcribed as polycistrons and contain very little intergenic sequences. Usually, vertebrate mitochondrial genomes measure between 16.5 and 17 kilobases (kb). RESULTS: During genome sequencing projects for two novel vertebrate models, the invasive round goby and the sand goby, we found that the sand goby genome is exceptionally small (16...
February 16, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28207947/association-and-expression-of-antigen-processing-gene-psmb8-coding-for-low-molecular-mass-protease-7-lmp7-with-vitiligo-in-north-india-case-control-study
#7
P Dani, N Patnaik, A Singh, A Jaiswal, B Agrawal, A A Kumar, S R Varkhande, A Sharma, U Vaish, P Ghosh, V K Sharma, P Sharma, G Verma, H K Kar, S Gupta, V T Natarajan, R S Gokhale, R Rani
BACKGROUND: Vitiligo is a multifactorial, autoimmune, depigmenting disorder of the skin where aberrant presentation of auto antigens may have a role to play. OBJECTIVES: To study the association of antigen processing genes, PSMB8 and PSMB9 with vitiligo. METHODS: 1320 vitiligo cases (1050 generalized and 270 localized) and 752 normal healthy controls were studied for PSMB9 exon 3 G/A SNP, PSMB8 exon 2 C/A SNP and PSMB8 Intron 6 G/T at 37360 site using PCR-RFLP...
February 16, 2017: British Journal of Dermatology
https://www.readbyqxmd.com/read/28207183/combining-the-auxin-inducible-degradation-system-with-crispr-cas9-based-genome-editing-for-the-conditional-depletion-of-endogenous-drosophila-melanogaster-proteins
#8
Melinda Bence, Ferenc Jankovics, Tamás Lukácsovich, Miklós Erdélyi
Inducible protein degradation techniques have considerable advantages over classical genetic approaches, which generate loss-of-function phenotypes at the gene or mRNA level. The plant-derived auxin-inducible degradation system (AID) is a promising technique which enables the degradation of target proteins tagged with the AID motif in non-plant cells. Here, we present a detailed characterization of this method employed during the adult oogenesis of Drosophila. Furthermore, with the help of CRISPR/Cas9-based genome editing, we improve the utility of the AID system in the conditional elimination of endogenously expressed proteins...
February 16, 2017: FEBS Journal
https://www.readbyqxmd.com/read/28203040/a-case-control-study-of-the-association-between-polymorphisms-in-the-fibrinogen-alpha-chain-gene-and-schizophrenia
#9
Wenwang Rao, Na Zhou, Huiping Zhang, Rui Liu, Shangchao Zhang, Yingying Su, Guang Yang, Yue Ma, Jieping Shi, Yaqin Yu, Qiong Yu
Our previous studies using the mass spectrum analysis provided evidence that fibrinopeptide A (FPA) could be a potential biomarker for schizophrenia diagnosis. We sought further to demonstrate that variants in the fibrinogen alpha chain gene (FGA) coded FPA might confer vulnerability to schizophrenia. 1,145 patients with schizophrenia and 1,016 healthy volunteers from the Han population in Northeast China were recruited. The association of three tag single nucleotide polymorphisms (SNPs) (rs2070011 in the 5'UTR, rs2070016 in intron 4, and rs2070022 in the 3'UTR) in FGA and schizophrenia was examined using a case-control study design...
2017: Disease Markers
https://www.readbyqxmd.com/read/28202009/development-of-intron-targeting-it-markers-specific-for-chromosome-arm-4vs-of-haynaldia-villosa-by-chromosome-sorting-and-next-generation-sequencing
#10
Haiyan Wang, Keli Dai, Jin Xiao, Chunxia Yuan, Renhui Zhao, Jaroslav Doležel, Yufeng Wu, Aizhong Cao, Peidu Chen, Shouzhong Zhang, Xiue Wang
BACKGROUND: Haynaldia villosa (L.) Schur (syn. Dasypyrum villosum L. Candargy, 2n = 14, genome VV) is the tertiary gene pool of wheat, and thus a potential resource of genes for wheat improvement. Among other, wheat yellow mosaic (WYM) resistance gene Wss1 and a take-all resistance gene were identified on the short arm of chromosome 4 V (4VS) of H. villosa. We had obtained introgressions on 4VS chromosome arm, with the objective of utilizing the target genes. However, monitoring these introgressions has been a daunting task because of inadequate knowledge as to H...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28201988/molecular-characterization-of-mhc-class-iib-genes-of-sympatric-neotropical-cichlids
#11
Melinda J Hofmann, Seraina E Bracamonte, Christophe Eizaguirre, Marta Barluenga
BACKGROUND: The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC remains to be characterized in many species including any Neotropical cichlid fish. Neotropical crater lake cichlids are ideal models to study evolutionary processes as they display one of the most convincing examples of sympatric and repeated parallel radiation events within and among isolated crater lakes...
February 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28201983/comparative-analysis-of-the-mitochondrial-genomes-of-colletotrichum-gloeosporioides-sensu-lato-insights-into-the-evolution-of-a-fungal-species-complex-interacting-with-diverse-plants
#12
Xiaofei Liang, Xianglin Tian, Wenkui Liu, Tingyu Wei, Wei Wang, Qiuyue Dong, Bo Wang, Yanan Meng, Rong Zhang, Mark L Gleason, Guangyu Sun
BACKGROUND: The fungal species complex Colletotrichum gloeosporioides sensu lato contains over 20 plant-interacting species. These species exhibit different life styles (e.g., endophytes, foliar and fruit pathogens) and show considerable variation in host and tissue adaptation strategies. Accurate species delimitation in C. gloeosporioides s.l. is very challenging due to nascent lineage boundaries and phenotypic plasticity, which strongly impedes studies of the complex's host-interaction biology...
February 15, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28199328/association-of-pvuii-and-xbai-polymorphisms-on-estrogen-receptor-alpha-esr1-gene-to-changes-into-serum-lipid-profile-of-post-menopausal-women-effects-of-aging-body-mass-index-and-breast-cancer-incidence
#13
Neuza Felix Gomes-Rochette, Letícia Soncini Souza, Bruno Otoni Tommasi, Diego França Pedrosa, Sérgio Ragi Eis, Irani do Carmo Francischetto Fin, Fernando Luiz Herkenhoff Vieira, Jones Bernardes Graceli, Letícia Batista Azevedo Rangel, Ian Victor Silva
Estrogen is a steroidal hormone involved in several physiological functions in the female body including regulation of serum lipid metabolism and breast cancer (BC). Estrogen actions on serum lipids mostly occur through its binding to intracellular Estrogen Receptor alpha (ERalpha) isoform, expressed in most of tissues. This gene (ESR1) exhibit many polymorphic sites (SNPs) located either on translated and non-translated regions that regulate ERalpha protein expression and function. This paper aimed to investigate the association of two intronic SNPs of ESR1 gene, namely c454-397T>C (PvuII) and c454-351A>G (XbaI) to alterations in serum levels of total cholesterol (T-chol), total lipid (TL), low density lipoprotein cholesterol (LDL), high density lipoprotein (HDL), and triglycerides (TG) in a cohort of post-menopausal women...
2017: PloS One
https://www.readbyqxmd.com/read/28198448/influence-of-fkbp5-polymorphism-and-dna-methylation-on-structural-changes-of-the-brain-in-major-depressive-disorder
#14
Kyu-Man Han, Eunsoo Won, Youngbo Sim, June Kang, Changsu Han, Yong-Ku Kim, Seung-Hyun Kim, Sook-Haeng Joe, Min-Soo Lee, Woo-Suk Tae, Byung-Joo Ham
A single nucleotide polymorphism of rs1360780 in the FKBP5 gene is associated with a predisposition to developing major depressive disorder (MDD). We investigated the interactive effects of FKBP5 rs1360780 allelic variants, DNA methylation, and the diagnosis of MDD on structural changes of the entire brain. One hundred and fourteen patients with MDD and eighty-eight healthy controls underwent T1-weighted structural magnetic resonance imaging and FKBP5 rs1360780 genotyping, including DNA methylation of intron 7...
February 15, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28197542/the-proline-arginine-dipeptide-from-hexanucleotide-repeat-expanded-c9orf72-inhibits-the-proteasome
#15
Rahul Gupta, Matthews Lan, Jelena Mojsilovic-Petrovic, Won Hoon Choi, Nathaniel Safren, Sami Barmada, Min Jae Lee, Robert Kalb
An intronic hexanucleotide repeat expansion (HRE) mutation in the C9ORF72 gene is the most common cause of familial ALS and frontotemporal dementia (FTD) and is found in ∼7% of individuals with apparently sporadic disease. Several different diamino acid peptides can be generated from the HRE by noncanonical translation (repeat-associated non-ATG translation, or RAN translation), and some of these peptides can be toxic. Here, we studied the effects of two arginine containing RAN translation products [proline/arginine repeated 20 times (PR20) and glycine/arginine repeated 20 times (GR20)] in primary rat spinal cord neuron cultures grown on an astrocyte feeder layer...
January 2017: ENeuro
https://www.readbyqxmd.com/read/28196451/phenotypic-and-genetic-analysis-of-dysprothrombinemia-due-to-a-novel-homozygous-mutation
#16
Kankan Su, Yanhui Jin, Zhihai Miao, Xiaoli Cheng, Lihong Yang, Mingshan Wang
OBJECTIVE: We study the phenotype and genotype of a novel gene mutation of factor II (FII) that leads to dysprothrombinemia, and do the meta-analysis to illuminate its molecular pathogenesis. It will further contribute to our comprehension of the pathogenesis of this type of disease. METHODS: The prothrombin time (PT), activated partial thromboplastin time (APTT) and the activities of other factors were determined by the one-stage clotting method. The prothrombin antigen was measured with enzyme-linked immunosorbent assay (ELISA)...
February 14, 2017: Hematology (Amsterdam, Netherlands)
https://www.readbyqxmd.com/read/28196413/alu-derived-alternative-splicing-events-specific-to-macaca-lineages-in-ctsf-gene
#17
Ja-Rang Lee, Sang-Je Park, Young-Hyun Kim, Se-Hee Choe, Hyeon-Mu Cho, Sang-Rae Lee, Sun-Uk Kim, Ji-Su Kim, Bo-Woong Sim, Bong-Seok Song, Kang-Jin Jeong, Youngjeon Lee, Yeung Bae Jin, Philyong Kang, Jae-Won Huh, Kyu-Tae Chang
Cathepsin F, which is encoded by CTSF, is a cysteine proteinase ubiquitously expressed in several tissues. In a previous study, novel transcripts of the CTSF gene were identified in the crab-eating monkey deriving from the integration of an Alu element-AluYRa1. The occurrence of AluYRa1-derived alternative transcripts and the mechanism of exonization events in the CTSF gene of human, rhesus monkey, and crabeating monkey were investigated using PCR and reverse transcription PCR on the genomic DNA and cDNA isolated from several tissues...
February 14, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/28196140/hypoxia-inducible-factors-regulate-the-transcription-of-the-sprouty2-gene-and-expression-of-the-sprouty2-protein
#18
Xianlong Gao, Kristin C Hicks, Paul Neumann, Tarun B Patel
Receptor Tyrosine Kinase (RTK) signaling plays a major role in tumorigenesis and normal development. Sprouty2 (Spry2) attenuates RTK signaling and inhibits processes such as angiogenesis, cell proliferation, migration and survival, which are all upregulated in tumors. Indeed in cancers of the liver, lung, prostate and breast, Spry2 protein levels are markedly decreased correlating with poor patient prognosis and shorter survival. Thus, it is important to understand how expression of Spry2 is regulated. While prior studies have focused on the post-translation regulation of Spry2, very few studies have focused on the transcriptional regulation of SPRY2 gene...
2017: PloS One
https://www.readbyqxmd.com/read/28193846/protein-4-1r-exon-16-3-splice-site-activation-requires-coordination-among-tia1-pcbp1-and-rbm39-during-terminal-erythropoiesis
#19
Shu-Ching Huang, Henry S Zhang, Brian Yu, Ellen McMahon, Dan T Nguyen, Faye H Yu, Alexander C Ou, Jennie Park Ou, Edward J Benz
Exon 16 of protein 4.1R encodes a spectrin/actin-binding peptide critical for erythrocyte membrane stability. Its expression during erythroid differentiation is regulated by alternative pre-mRNA splicing. A UUUUCCCCCC-motif situated between the branch point and the 3' splice site is crucial for inclusion. We show that the "UUUU" region and the last 3 C's in this motif are necessary for the binding of splicing factors TIA1 and Pcbp1, and that these proteins appear to act in a collaborative manner to enhance exon 16 inclusion...
February 13, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28193834/genome-wide-analysis-of-the-circulating-mirnome-after-cerebral-ischemia-reveals-a-reperfusion-induced-microrna-cluster
#20
Stefan Uhlmann, Eva Mracsko, Ehsan Javidi, Sarah Lamble, Ana Teixeira, Agnes Hotz-Wagenblatt, Karl-Heinz Glatting, Roland Veltkamp
BACKGROUND AND PURPOSE: Circulating microRNAs (miRNAs) are emerging biomarkers for stroke because of their high stability in the bloodstream and association with pathophysiologic conditions. However, the circulating whole-genome miRNAs (miRNome) has not been characterized comprehensively in the acute phase of stroke. METHODS: We profiled the circulating miRNome in mouse models of acute ischemic and hemorrhagic stroke by next-generation sequencing. Stroke models were compared with sham-operated and naive mice to identify deregulated circulating miRNAs...
February 13, 2017: Stroke; a Journal of Cerebral Circulation
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