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Gene splicing

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https://www.readbyqxmd.com/read/29244186/independence-between-pre-mrna-splicing-and-dna-methylation-in-an-isogenic-minigene-resource
#1
Kyster K Nanan, Cody Ocheltree, David Sturgill, Mariana D Mandler, Maria Prigge, Garima Varma, Shalini Oberdoerffer
Actively transcribed genes adopt a unique chromatin environment with characteristic patterns of enrichment. Within gene bodies, H3K36me3 and cytosine DNA methylation are elevated at exons of spliced genes and have been implicated in the regulation of pre-mRNA splicing. H3K36me3 is further responsive to splicing, wherein splicing inhibition led to a redistribution and general reduction over gene bodies. In contrast, little is known of the mechanisms supporting elevated DNA methylation at actively spliced genic locations...
December 15, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29244006/framework-for-reanalysis-of-publicly-available-affymetrix%C3%A2-genechip%C3%A2-data-sets-based-on-functional-regions-of-interest
#2
Ernur Saka, Benjamin J Harrison, Kirk West, Jeffrey C Petruska, Eric C Rouchka
BACKGROUND: Since the introduction of microarrays in 1995, researchers world-wide have used both commercial and custom-designed microarrays for understanding differential expression of transcribed genes. Public databases such as ArrayExpress and the Gene Expression Omnibus (GEO) have made millions of samples readily available. One main drawback to microarray data analysis involves the selection of probes to represent a specific transcript of interest, particularly in light of the fact that transcript-specific knowledge (notably alternative splicing) is dynamic in nature...
December 6, 2017: BMC Genomics
https://www.readbyqxmd.com/read/29243324/validation-of-histone-deacetylase-3-as-a-therapeutic-target-in-castration-resistant-prostate-cancer
#3
Abigail B McLeod, James P Stice, Suzanne E Wardell, Holly M Alley, Ching-Yi Chang, Donald P McDonnell
BACKGROUND: Whereas the androgen receptor (AR) signaling axis remains a therapeutic target in castration-resistant prostate cancer (CRPC), the emergence of AR mutations and splice variants as mechanisms underlying resistance to contemporary inhibitors of this pathway highlights the need for new therapeutic approaches to target this disease. Of significance in this regard is the considerable preclinical data, indicating that histone deacetylase (HDAC) inhibitors may have utility in the treatment of CRPC...
December 15, 2017: Prostate
https://www.readbyqxmd.com/read/29243290/a-non-coding-variant-in-ganab-explains-isolated-polycystic-liver-disease-pcld-in-a-large-family
#4
Whitney Besse, Jungmin Choi, Dina Ahram, Shrikant Mane, Simone Sanna-Cherchi, Vicente Torres, Stefan Somlo
Expanded mutation detection and novel gene discovery for isolated polycystic liver disease (PCLD) are necessary as 50% of cases do not have identified mutations in the seven published disease genes. We investigated a family with 5 affected siblings for which no loss of function variants were identified by whole exome sequencing analysis. SNP genotyping and linkage analysis narrowed the candidate regions to ∼8% of the genome, which included two published PCLD genes in close proximity to each other, GANAB and LRP5...
December 15, 2017: Human Mutation
https://www.readbyqxmd.com/read/29242583/hybrid-splicing-minigene-and-antisense-oligonucleotides-as-efficient-tools-to-determine-functional-protein-rna-interactions
#5
Piotr Cywoniuk, Katarzyna Taylor, Łukasz J Sznajder, Krzysztof Sobczak
Alternative splicing is a complex process that provides a high diversity of proteins from a limited number of protein-coding genes. It is governed by multiple regulatory factors, including RNA-binding proteins (RBPs), that bind to specific RNA sequences embedded in a specific structure. The ability to predict RNA-binding regions recognized by RBPs using whole-transcriptome approaches can deliver a multitude of data, including false-positive hits. Therefore, validation of the global results is indispensable...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242557/the-metabolic-syndrome-associated-small-g-protein-arl15-plays-a-role-in-adipocyte-differentiation-and-adiponectin-secretion
#6
Nuno Rocha, Felicity Payne, Isabel Huang-Doran, Alison Sleigh, Katherine Fawcett, Claire Adams, Anna Stears, Vladimir Saudek, Stephen O'Rahilly, Inês Barroso, Robert K Semple
Common genetic variants at the ARL15 locus are associated with plasma adiponectin, insulin and HDL cholesterol concentrations, obesity, and coronary atherosclerosis. The ARL15 gene encodes a small GTP-binding protein whose function is currently unknown. In this study adipocyte-autonomous roles for ARL15 were investigated using conditional knockdown of Arl15 in murine 3T3-L1 (pre)adipocytes. Arl15 knockdown in differentiated adipocytes impaired adiponectin secretion but not adipsin secretion or insulin action, while in preadipocytes it impaired adipogenesis...
December 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29242366/the-landscape-of-human-mutually-exclusive-splicing
#7
Klas Hatje, Raza-Ur Rahman, Ramon O Vidal, Dominic Simm, Björn Hammesfahr, Vikas Bansal, Ashish Rajput, Michel Edwar Mickael, Ting Sun, Stefan Bonn, Martin Kollmar
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold...
December 14, 2017: Molecular Systems Biology
https://www.readbyqxmd.com/read/29240875/the-expanding-roles-of-argonautes-rna-interference-splicing-and-beyond
#8
Xiaoxia Ma, Ziwei Zuo, Weishan Shao, Yongfeng Jin, Yijun Meng
Argonaute (AGO) protein family is highly conserved in eukaryotes and prokaryotes, reflecting its evolutionarily indispensible role in maintaining normal life cycle of the organisms. Small RNA-guided, AGO-dependent RNA interference (RNAi) is a well-studied pathway for gene expression regulation, which can be performed at transcriptional, posttranscriptional or translational level. In addition to RNAi, growing pieces of evidence point to a novel role of AGOs in pre-mRNA (messenger RNA precursor) splicing in animals...
December 11, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/29240258/dna-and-rna-binding-by-the-wilms-tumour-gene-1-wt1-protein-kts-and-kts-isoforms-from-initial-observations-to-recent-global-genomic-analyses
#9
REVIEW
Tove Ullmark, Giorgia Montano, Urban Gullberg
The Wilms' tumour gene 1 protein (WT1) is a zinc finger transcription factor found indispensable for foetal development. WT1 has also been implicated in the development of tumours in several organ systems, including acute myeloid leukaemia (AML). Four main WT1 isoforms come from two alternative splice events. One alternative splice results in the inclusion or exclusion of three amino acids, KTS, between zinc fingers three and four in the WT1 protein. The KTS insert has been extensively investigated due to the functional implications for DNA and RNA binding...
December 14, 2017: European Journal of Haematology
https://www.readbyqxmd.com/read/29239282/generation-of-human-induced-pluripotent-stem-cells-from-wolfram-syndrome-type-2-patients-bearing-the-c-103-1g-a-cisd2-mutation-for-disease-modeling
#10
Alberto La Spada, Aikaterini Ntai, Stefano Genovese, Maurizio Rondinelli, Pasquale De Blasio, Ida Biunno
Wolfram syndrome (WFS) is a rare autosomal premature aging syndrome that shows signs of diabetes mellitus (DM), optic atrophy (OA) and deafness in addition to central nervous system and endocrine complications. The frequent form of WFS, type 1 (WFS1), harbours causative mutations in the WFS1 gene, while the rare form or type 2 (WFS2), involves CISD2. Mutations in these two genes are recognized by a subset of variable clinical symptoms and a set of overlapping features. Here we report on the generation of stable human induced pluripotent stem cells (hiPSCs) derived from primary fibroblasts of a previously reported Italian family with CISD2 mutation (c...
December 14, 2017: Stem Cells and Development
https://www.readbyqxmd.com/read/29238599/characterization-of-physiological-and-molecular-processes-associated-with-potato-response-to-zebra-chip-disease
#11
Chika C Nwugo, Venkatesan G Sengoda, Li Tian, Hong Lin
Transcriptional analyses identified molecular mechanisms associated with the response of leaf and root potato tissues to 'Candidatus. Liberibacter solanacearum' (Lso) infection, presumptive causal agent of zebra chip disease (ZC). Putative Lso infection affected several host processes including defense response-, regulation-, starch metabolism- and energy production-related processes. Interestingly, while proteinase inhibitors were strongly upregulated in leaf tissues, a concomitant downregulation was observed in root tissues...
2017: Horticulture Research
https://www.readbyqxmd.com/read/29237418/a-donor-splice-site-mutation-in-cisd2-generates-multiple-truncated-non-functional-isoforms-in-wolfram-syndrome-type-2-patients
#12
Monica Cattaneo, Lucia La Sala, Maurizio Rondinelli, Edoardo Errichiello, Orsetta Zuffardi, Annibale Alessandro Puca, Stefano Genovese, Antonio Ceriello
BACKGROUND: Mutations in the gene that encodes CDGSH iron sulfur domain 2 (CISD2) are causative of Wolfram syndrome type 2 (WFS2), a rare autosomal recessive neurodegenerative disorder mainly characterized by diabetes mellitus, optic atrophy, peptic ulcer bleeding and defective platelet aggregation. Four mutations in the CISD2 gene have been reported. Among these mutations, the homozygous c.103 + 1G > A substitution was identified in the donor splice site of intron 1 in two Italian sisters and was predicted to cause a exon 1 to be skipped...
December 13, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/29237010/crispr-cas9-mediated-modulation-of-splicing-efficiency-reveals-short-splicing-isoform-of-xist-rna-is-sufficient-to-induce-x-chromosome-inactivation
#13
Minghui Yue, Yuya Ogawa
Alternative splicing of mRNA precursors results in multiple protein variants from a single gene and is critical for diverse cellular processes and development. Xist encodes a long noncoding RNA which is a central player to induce X-chromosome inactivation in female mammals and has two major splicing variants: long and short isoforms of Xist RNA. Although a differentiation-specific and a female-specific expression of Xist isoforms have been reported, the functional role of each Xist RNA isoform is largely unexplored...
December 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29236940/polyclonal-rb1-mutations-and-acquired-resistance-to-cdk-4-6-inhibitors-in-patients-with-metastatic-breast-cancer
#14
R Condorelli, L Spring, J O'Shaughnessy, L Lacroix, C Bailleux, V Scott, J Dubois, R J Nagy, R B Lanman, A J Iafrate, F Andre, A Bardia
Background: While deregulation of the cyclin D1-CDK4/6-retinoblastoma pathway is common in hormone receptor positive (HR+) breast cancer, Rb is usually intact in HR+ breast cancer, and targeted CDK 4/6 inhibitors that act upstream of Rb, are routinely being utilized in clinical practice. However, factors that can lead to clinical resistance to CDK 4/6 inhibitors are not known. Patients and methods: We identified patients who had pre and post genotyping in tissue and peripheral blood samples after receiving CDK 4/6 inhibitors...
December 11, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29236932/alternative-splicing-originates-different-domain-structure-organization-of-lutzomyia-longipalpis-chitinases
#15
João Ramalho Ortigão-Farias, Tatiana Di-Blasi, Erich Loza Telleria, Ana Carolina Andorinho, Thais Lemos-Silva, Marcelo Ramalho-Ortigão, Antônio Jorge Tempone, Yara Maria Traub-Csekö
BACKGROUND The insect chitinase gene family is composed by more than 10 paralogs, which can codify proteins with different domain structures. In Lutzomyia longipalpis, the main vector of visceral leishmaniasis in Brazil, a chitinase cDNA from adult female insects was previously characterized. The predicted protein contains one catalytic domain and one chitin-binding domain (CBD). The expression of this gene coincided with the end of blood digestion indicating a putative role in peritrophic matrix degradation...
February 2018: Memórias do Instituto Oswaldo Cruz
https://www.readbyqxmd.com/read/29236736/functions-for-fission-yeast-splicing-factors-spslu7-and-spprp18-in-alternative-splice-site-choice-and-stress-specific-regulated-splicing
#16
Geetha Melangath, Titash Sen, Rakesh Kumar, Pushpinder Bawa, Subha Srinivasan, Usha Vijayraghavan
Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3'ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site choice, intron retention and to study the cellular implications of regulated splicing. From our custom microarray data we deduce a stringent reproducible subset of S...
2017: PloS One
https://www.readbyqxmd.com/read/29236260/generation-of-cell-lines-stably-expressing-a-fluorescent-reporter-of-nonsense-mediated-mrna-decay-activity
#17
Nadezhda M Markina, Anton P Pereverzev, Dmitry B Staroverov, Konstantin A Lukyanov, Nadya G Gurskaya
Nonsense-mediated mRNA decay (NMD) is a mechanism of mRNA surveillance ubiquitous among eukaryotes. Importantly, NMD not only removes aberrant transcripts with premature stop codons, but also regulates expression of many normal genes. A recently introduced dual-color fluorescent protein-based reporter enables analysis of NMD activity in live cells. In this chapter we describe the method to generate stable transgenic cell lines expressing the splicing-dependent NMD reporter using consecutive steps of lentivirus transduction and Tol2 transposition...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29235495/identification-of-nonsense-mediated-mrna-decay-pathway-as-a-critical-regulator-of-p53-isoform-%C3%AE
#18
Lauren E Cowen, Yi Tang
Human TP53 gene encodes the tumor suppressor p53 and, via alternative splicing, the p53β and γ isoforms. Numerous studies have shown that p53β/γ can modulate p53 functions and are critically involved in regulation of cellular response to stress conditions. However, it is not fully understood how the β and γ isoforms are regulated following splicing. Using gene targeting and RNAi, we showed that depletion of the nonsense-mediated mRNA decay (NMD) factor SMG7 or UPF1 significantly induced p53β but had minimal effect on p53γ...
December 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29235382/exploiting-differential-rna-splicing-patterns-a-potential-new-group-of-therapeutic-targets-in-cancer
#19
Nidhi Jyotsana, Michael Heuser
Mutations in genes associated with splicing have been found in hematologic malignancies, but also in solid cancers. Aberrant cancer specific RNA splicing either results from mutations or misexpression of the spliceosome genes directly, or from mutations in splice sites of oncogenes or tumor suppressors. Areas covered: In this review, we present molecular targets of aberrant splicing in various malignancies, information on existing and emerging therapeutics against such targets, and strategies for future drug development...
December 13, 2017: Expert Opinion on Therapeutic Targets
https://www.readbyqxmd.com/read/29234324/long-non-coding-rnas-emerging-and-versatile-regulators-in-host-virus-interactions
#20
REVIEW
Xing-Yu Meng, Yuzi Luo, Muhammad Naveed Anwar, Yuan Sun, Yao Gao, Huawei Zhang, Muhammad Munir, Hua-Ji Qiu
Long non-coding RNAs (lncRNAs) are a class of non-protein-coding RNA molecules, which are involved in various biological processes, including chromatin modification, cell differentiation, pre-mRNA transcription and splicing, protein translation, etc. During the last decade, increasing evidence has suggested the involvement of lncRNAs in both immune and antiviral responses as positive or negative regulators. The immunity-associated lncRNAs modulate diverse and multilayered immune checkpoints, including activation or repression of innate immune signaling components, such as interleukin (IL)-8, IL-10, retinoic acid inducible gene I, toll-like receptors 1, 3, and 8, and interferon (IFN) regulatory factor 7, transcriptional regulation of various IFN-stimulated genes, and initiation of the cell apoptosis pathways...
2017: Frontiers in Immunology
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