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https://www.readbyqxmd.com/read/28549172/orrm5-an-rna-recognition-motif-containing-protein-has-a-unique-effect-on-mitochondrial-rna-editing
#1
Xiaowen Shi, Benoit Castandet, Arnaud Germain, Maureen R Hanson, Stéphane Bentolila
Plants have an RNA editing mechanism that prevents deleterious organelle mutations from resulting in impaired proteins. A typical flowering plant modifies about 40 cytidines in chloroplast transcripts and many hundreds of cytidines in mitochondrial transcripts. The plant editosome, the molecular machinery responsible for this process, contains members of several protein families, including the organelle RNA recognition motif (ORRM)-containing family. ORRM1 and ORRM6 are chloroplast editing factors, while ORRM2, ORRM3, and ORRM4 are mitochondrial editing factors...
May 26, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28549066/alternative-exon-definition-events-control-the-choice-between-nuclear-retention-and-cytoplasmic-export-of-u11-u12-65k-mrna
#2
Jens Verbeeren, Bhupendra Verma, Elina H Niemelä, Karen Yap, Eugene V Makeyev, Mikko J Frilander
Cellular homeostasis of the minor spliceosome is regulated by a negative feed-back loop that targets U11-48K and U11/U12-65K mRNAs encoding essential components of the U12-type intron-specific U11/U12 di-snRNP. This involves interaction of the U11 snRNP with an evolutionarily conserved splicing enhancer giving rise to unproductive mRNA isoforms. In the case of U11/U12-65K, this mechanism controls the length of the 3' untranslated region (3'UTR). We show that this process is dynamically regulated in developing neurons and some other cell types, and involves a binary switch between translation-competent mRNAs with a short 3'UTR to non-productive isoforms with a long 3'UTR that are retained in the nucleus or/and spliced to the downstream amylase locus...
May 26, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28548211/a-haplotype-block-downstream-of-plasminogen-is-associated-with-chronic-and-aggressive-periodontitis
#3
Matthias Munz, Hong Chen, Yvonne Jockel-Schneider, Knut Adam, Per Hoffman, Klaus Berger, Thomas Kocher, Jörg Meyle, Peter Eickholz, Christof Doerfer, Matthias Laudes, André Uitterlinden, Wolfgang Lieb, Andre Franke, Stefan Schreiber, Steven Offenbacher, Kimon Divaris, Corinna Bruckmann, Bruno G Loos, Soeren Jepsen, Henrik Dommisch, Arne S Schaefer
AIM: The intronic variant rs4252120 in the plasminogen gene (PLG) is known to be associated with aggressive periodontitis (AgP) and atherosclerosis. Here, we examined the chromosomal region spanning PLG for associations with both chronic periodontitis (CP) and AgP. MATERIAL AND METHODS: The association of PLG candidate rs4252120 was tested in a German case-control sample of 1,419 CP cases using the genotyping assay hCV11225947 and 4,562 controls, genotyped with HumanOmni BeadChips...
May 26, 2017: Journal of Clinical Periodontology
https://www.readbyqxmd.com/read/28547825/dual-redundant-sequencing-strategy-full-length-gene-characterisation-of-1056-novel-and-confirmatory-hla-alleles
#4
V Albrecht, C Zweiniger, V Surendranath, K Lang, G Schöfl, A Dahl, S Winkler, V Lange, I Böhme, A H Schmidt
The high-throughput department of DKMS Life Science Lab encounters novel human leukocyte antigen (HLA) alleles on a daily basis. To characterise these alleles, we have developed a system to sequence the whole gene from 5'- to 3'-UTR for the HLA loci A, B, C, DQB1 and DPB1 for submission to the European Molecular Biology Laboratory - European Nucleotide Archive (EMBL-ENA) and the IPD-IMGT/HLA Database. Our workflow is based on a dual redundant sequencing strategy. Using shotgun sequencing on an Illumina MiSeq instrument and single molecule real-time (SMRT) sequencing on a PacBio RS II instrument, we are able to achieve highly accurate HLA full-length consensus sequences...
May 25, 2017: HLA
https://www.readbyqxmd.com/read/28546999/a-birth-of-bipartite-exon-by-intragenic-deletion
#5
Kandai Nozu, Kazumoto Iijima, Toru Igarashi, Shiro Yamada, Jana Kralovicova, Yoshimi Nozu, Tomohiko Yamamura, Shogo Minamikawa, Ichiro Morioka, Takeshi Ninchoji, Hiroshi Kaito, Koichi Nakanishi, Igor Vorechovsky
BACKGROUND: Disease-causing mutations that activate transposon-derived exons without creating a new splice-site consensus have been reported rarely, but they provided unique insights into our understanding of structural motifs required for inclusion of intronic sequences in mature transcripts. METHODS: We employ a combination of experimental and computational techniques to characterize the first de novo bipartite exon activation in genetic disease. RESULTS: The exon originated from two separate introns as a result of an in-frame COL4A5 deletion associated with a typical Alport syndrome...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28546788/dmd-transcripts-in-crl-2061-rhabdomyosarcoma-cells-show-high-levels-of-intron-retention-by-intron-specific-pcr-amplification
#6
Emma Tabe Eko Niba, Ryo Yamanaka, Abdul Qawee Mahyoob Rani, Hiroyuki Awano, Masaaki Matsumoto, Hisahide Nishio, Masafumi Matsuo
BACKGROUND: The DMD gene encoding dystrophin is mutated in Duchenne muscular dystrophy, a fatal progressive muscle wasting disease. DMD has also been shown to act as a tumor suppressor gene. Rhabdomyosarcoma (RMS) is a mesodermal sarcoma that shares characteristics of skeletal muscle precursors. Products of the DMD gene in RMS have not yet been fully clarified. Here, DMD products were analyzed in CRL-2061 cells established from alveolar RMS. METHODS: The 14-kb long DMD cDNA was PCR amplified as 20 separated fragments, as were nine short intron regions...
2017: Cancer Cell International
https://www.readbyqxmd.com/read/28546019/identification-of-2-novel-type-i-ifn-genes-in-japanese-flounder-paralichthys-olivaceus
#7
Yiwen Hu, Takaki Yoshikawa, Seangmin Chung, Ikuo Hirono, Hidehiro Kondo
Two novel type I interferon genes (JfIFN3 and JfIFN4) have been identified in Japanese flounder Paralichthys olivaceus. Open reading frames of JfIFN3 and JfIFN4 were 555bp and 528bp, encoding 184aa and 175aa, respectively. The genomic structures of JfIFN3 and JfIFN4 are composed of 5 exons and 4 introns. JfIFN4 has 2 conserved cysteine residues, while JfIFN3 has 4. JfIFN3 and JfIFN4 showed the highest amino acid sequence identities to turbot IFN1 (74%) and IFN2 (62%), respectively. Interestingly, JfIFN3 and JfIFN4 were clustered in distinct branches with JfIFN1 and JfIFN2, which have reported so far...
May 22, 2017: Fish & Shellfish Immunology
https://www.readbyqxmd.com/read/28546003/thymic-epithelial-cell-specific-deletion-of-jmjd6-reduces-aire-protein-expression-and-exacerbates-disease-development-in-a-mouse-model-of-autoimmune-diabetes
#8
Toyoshi Yanagihara, Takahiro Tomino, Takehito Uruno, Yoshinori Fukui
Thymic epithelial cells (TECs) establish spatially distinct microenvironments in which developing T cells are selected to mature or die. A unique property of medullary TECs is their expression of thousands of tissue-restricted self-antigens that is largely under the control of the transcriptional regulator Aire. We previously showed that Jmjd6, a lysyl hydroxylase for splicing regulatory proteins, is important for Aire protein expression and that transplantation of Jmjd6-deficient thymic stroma into athymic nude mice resulted in multiorgan autoimmunity...
May 22, 2017: Biochemical and Biophysical Research Communications
https://www.readbyqxmd.com/read/28545862/a-novel-pathogenic-variant-in-the-fzd6-gene-causes-recessive-nail-dysplasia-in-a-large-iranian-kindred
#9
Javad Mohammadi-Asl, Mohammad Reza Pourreza, Aliasgar Mohammadi, Ameneh Eskandari, Sima Mozafar-Jalali, Mohammad Amin Tabatabaiefar
BACKGROUND: Nail disorder nonsyndromic congenital (NDNC) is a very rare clinically and genetically heterogeneous disease inherited both in recessive or dominant modes. FZD6 is a component of Wnt-FZD signaling pathway in which recessive loss-of-function variants in the corresponding genes could lead to nail anomalies. OBJECTIVE: A large multiplex family with NDNC was referred for genetic counselling. Thorough genetic evaluation was performed. METHODS: PCR-Sanger sequencing was carried out for the coding exons and exon-intron boundaries of the FZD6 gene...
May 13, 2017: Journal of Dermatological Science
https://www.readbyqxmd.com/read/28545453/genome-wide-methylation-analysis-reveals-differentially-methylated-loci-that-are-associated-with-an-age-dependent-increase-in-bovine-fibroblast-response-to-lps
#10
Filiz T Korkmaz, David E Kerr
BACKGROUND: Differences in DNA methylation are known to contribute to the development of immune-related disorders in humans but relatively little is known about how methylation regulates immune function in cattle. Utilizing whole-transcriptome analyses of bovine dermal fibroblasts, we have previously identified an age and breed-dependent up-regulation of genes within the toll-like receptor 4 (TLR4) pathway that correlates with enhanced fibroblast production of IL-8 in response to lipopolysaccharide (LPS)...
May 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28545234/validation-of-splicing-events-in-transcriptome-sequencing-data
#11
Wolfgang Kaisers, Johannes Ptok, Holger Schwender, Heiner Schaal
Genomic alignments of sequenced cellular messenger RNA contain gapped alignments which are interpreted as consequence of intron removal. The resulting gap-sites, genomic locations of alignment gaps, are landmarks representing potential splice-sites. As alignment algorithms report gap-sites with a considerable false discovery rate, validations are required. We describe two quality scores, gap quality score (gqs) and weighted gap information score (wgis), developed for validation of putative splicing events: While gqs solely relies on alignment data wgis additionally considers information from the genomic sequence...
May 23, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28545148/mitochondrial-genome-evolution-in-alismatales-size-reduction-and-extensive-loss-of-ribosomal-protein-genes
#12
Gitte Petersen, Argelia Cuenca, Athanasios Zervas, Gregory T Ross, Sean W Graham, Craig F Barrett, Jerrold I Davis, Ole Seberg
The order Alismatales is a hotspot for evolution of plant mitochondrial genomes characterized by remarkable differences in genome size, substitution rates, RNA editing, retrotranscription, gene loss and intron loss. Here we have sequenced the complete mitogenomes of Zostera marina and Stratiotes aloides, which together with previously sequenced mitogenomes from Butomus and Spirodela, provide new evolutionary evidence of genome size reduction, gene loss and transfer to the nucleus. The Zostera mitogenome includes a large portion of DNA transferred from the plastome, yet it is the smallest known mitogenome from a non-parasitic plant...
2017: PloS One
https://www.readbyqxmd.com/read/28545024/an-unusual-intragenic-promoter-of-piwil2-contributes-to-aberrant-activation-of-oncogenic-pl2l60
#13
Shan-Shan Liu, Ning Liu, Meng-Yao Liu, Lei Sun, Wu-Yan Xia, Hong-Min Lu, Yu-Jie Fu, Guo-Liang Yang, Juan-Jie Bo, Xiao-Xing Liu, Haizhong Feng, Hailong Wu, Lin-Feng Li, Jian-Xin Gao
PIWIL2-like (PL2L) protein 60 (PL2L60), a product of aberrantly activated PIWIL2 gene, is widely expressed in various types of tumors and may promote tumorigenesis. However, the mechanisms underlying the activation of expression of PL2L60 remain unknown. In this study, an intragenic promoter responsible for the activation of PL2L60 within the human PIWIL2 gene has been identified, cloned and characterized. The promoter of PL2L60 is located in the intron 10 of the host gene PIWIL2. Bioinformatic and mutagenic analysis reveals that this intragenic promoter within the sequence of 50 nucleotides contains two closely arranged cis-acting elements specific for the hepatic leukemia factor (HLF) in the positive strand and signal transducer and activator of transcription 3 (STAT3) in the negative strand...
May 2, 2017: Oncotarget
https://www.readbyqxmd.com/read/28544438/genome-wide-identification-characterization-and-evolution-of-cuticular-protein-genes-in-the-malaria-vector-anopheles-sinensis-diptera-culicidae
#14
Bai-Qi Liu, Liang Qiao, Qi-Yi He, Yong Zhou, Shuang Ren, Bin Chen
Thirteen cuticular proteins (CPs) families have been recognized in arthropods. In this study, 250 Anopheles sinensis CP genes were identified and named based on genome and transcriptome sequences. They were classified into 10 families based on motifs and phylogenetic analyses. In 11 other insect species, 9 had CP numbers > 150 while Apis mellifera and Tribolium castaneum had CP numbers less than 52. The CPs of 8 species occupied > 1.4% of the total genomic gene number whereas in 3 species the CPs occupied < 1%...
May 24, 2017: Insect Science
https://www.readbyqxmd.com/read/28544218/genome-wide-mediation-analysis-of-psychiatric-and-cognitive-traits-through-imaging-phenotypes
#15
Xuan Bi, Liuqing Yang, Tengfei Li, Baisong Wang, Hongtu Zhu, Heping Zhang
Heritability is well documented for psychiatric disorders and cognitive abilities which are, however, complex, involving both genetic and environmental factors. Hence, it remains challenging to discover which and how genetic variations contribute to such complex traits. In this article, they propose to use mediation analysis to bridge this gap, where neuroimaging phenotypes were utilized as intermediate variables. The Philadelphia Neurodevelopmental Cohort was investigated using genome-wide association studies (GWAS) and mediation analyses...
May 22, 2017: Human Brain Mapping
https://www.readbyqxmd.com/read/28543912/association-study-of-interleukin-1-family-interleukin-6-and-its-receptor-gene-polymorphisms-in-patients-with-recurrent-aphthous-stomatitis
#16
Lydie Izakovicova Holla, Simona Valova, Petra Borilova Linhartova, Jirina Bartova, Jitka Petanova, Pavel Kuklinek, Antonin Fassmann
BACKGROUND: Recurrent aphthous stomatitis (RAS) is one of the most common oral chronic ulcerative disease in which proinflammatory cytokines such as interleukin 1 (IL-1) and interleukin 6 (IL-6) are thought to play an important role. The aim of this study was to investigate the possible association between polymorphisms in the IL-1 cytokine family, IL-6 or its receptor and RAS in the Czech population. METHODS: A total of 248 subjects, 184 healthy controls and 64 patients with RAS were genotyped for IL-1A-889C>T, IL-1B-511C>T, IL-1B+3953C>T, IL-1RN86 bp variable number of tandem repeats (VNTR) in intron 2, IL-6-597G>A, IL-6-572G>C, IL-6-174G>C and IL-6R+48992A>C by polymerase chain reaction (PCR) methods...
May 20, 2017: Journal of Oral Pathology & Medicine
https://www.readbyqxmd.com/read/28542872/classification-of-planctonema-like-algae-including-a-new-genus-planctonemopsis-gen-nov-a-new-species-planctonema-gelatinosum-sp-nov-and-a-reinstated-genus-psephonema-trebouxiophyceae-chlorophyta
#17
Xudong Liu, Huan Zhu, Benwen Liu, Guoxiang Liu, Zhengyu Hu
Planctonema-like species consist of planktonic green algae and are found throughout the world. Their characteristic morphology, which includes short and slender filaments consisting of side-by-side or distant cylindrical cells enclosed in a fine and hyaline sheath, makes them easily distinguishable. To date, Planctonema lauterbornii was the only taxon accepted for this group. However, descriptions from different materials have revealed notable morphological differences, including the presence/absence of a pyrenoid, a mucilage sheath and an apical thickening of the cell wall...
May 19, 2017: Journal of Phycology
https://www.readbyqxmd.com/read/28542625/the-identification-of-switch-like-alternative-splicing-exons-among-multiple-samples-with-rna-seq-data
#18
Zhiyi Qin, Xuegong Zhang
Alternative splicing is an ubiquitous phenomenon in most human genes and has important functions. The switch-like exon is the type of exon that has a high level of usage in some tissues, but has a low level of usage in the other tissues. They usually undergo strong tissue-specific regulations. There is still a lack a systematic method to identify switch-like exons from multiple RNA-seq samples. We proposed a novel method called iterative Tertile Absolute Deviation around the mode (iTAD) to profile the distribution of exon relative usages among multiple samples and to identify switch-like exons and other types of exons using a robust statistic estimator...
2017: PloS One
https://www.readbyqxmd.com/read/28542600/snp-in-human-arhgef3-promoter-is-associated-with-dnase-hypersensitivity-transcript-level-and-platelet-function-and-arhgef3-ko-mice-have-increased-mean-platelet-volume
#19
Siying Zou, Alexandra M Teixeira, Myrto Kostadima, William J Astle, Aparna Radhakrishnan, Lukas Mikolaj Simon, Lucy Truman, Jennifer S Fang, John Hwa, Ping-Xia Zhang, Pim van der Harst, Paul F Bray, Willem H Ouwehand, Mattia Frontini, Diane S Krause
Genome-wide association studies have identified a genetic variant at 3p14.3 (SNP rs1354034) that strongly associates with platelet number and mean platelet volume in humans. While originally proposed to be intronic, analysis of mRNA expression in primary human hematopoietic subpopulations reveals that this SNP is located directly upstream of the predominantly expressed ARHGEF3 isoform in megakaryocytes (MK). We found that ARHGEF3, which encodes a Rho guanine exchange factor, is dramatically upregulated during both human and murine MK maturation...
2017: PloS One
https://www.readbyqxmd.com/read/28542515/a-novel-frameshift-mutation-of-smpx-causes-a-rare-form-of-x-linked-nonsyndromic-hearing-loss-in-a-chinese-family
#20
Zhijie Niu, Yong Feng, Lingyun Mei, Jie Sun, Xueping Wang, Juncheng Wang, Zhengmao Hu, Yunpeng Dong, Hongsheng Chen, Chufeng He, Yalan Liu, Xinzhang Cai, Xuezhong Liu, Lu Jiang
X-linked hearing impairment is the rarest form of genetic hearing loss (HL) and represents only a minor fraction of all cases. The aim of this study was to investigate the cause of X-linked inherited sensorineural HL in a four-generation Chinese family. A novel duplication variant (c.217dupA, p.Ile73Asnfs*5) in SMPX was identified by whole-exome sequencing. The frameshift mutation predicted to result in the premature truncation of the SMPX protein was co-segregated with the HL phenotype and was absent in 295 normal controls...
2017: PloS One
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