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Gene splicing

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https://www.readbyqxmd.com/read/28214988/an-alternative-splice-variant-of-human-%C3%AE-a-crystallin-modulates-the-oligomer-ensemble-and-the-chaperone-activity-of-%C3%AE-crystallins
#1
Waldemar Preis, Annika Bestehorn, Johannes Buchner, Martin Haslbeck
In humans, ten genes encode small heat shock proteins with lens αA-crystallin and αB-crystallin representing two of the most prominent members. The canonical isoforms of αA-crystallin and αB-crystallin collaborate in the eye lens to prevent irreversible protein aggregation and preserve visual acuity. α-Crystallins form large polydisperse homo-oligomers and hetero-oligomers and as part of the proteostasis system bind substrate proteins in non-native conformations, thereby stabilizing them. Here, we analyzed a previously uncharacterized, alternative splice variant (isoform 2) of human αA-crystallin with an exchanged N-terminal sequence...
February 18, 2017: Cell Stress & Chaperones
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
#2
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/28212797/ca-2-calmodulin-dependent-protein-kinase-ii-in-vascular-smooth-muscle
#3
F Z Saddouk, R Ginnan, H A Singer
Ca(2+)-dependent signaling pathways are central regulators of differentiated vascular smooth muscle (VSM) contractile function. In addition, Ca(2+) signals regulate VSM gene transcription, proliferation, and migration of dedifferentiated or "synthetic" phenotype VSM cells. Synthetic phenotype VSM growth and hyperplasia are hallmarks of pervasive vascular diseases including hypertension, atherosclerosis, postangioplasty/in-stent restenosis, and vein graft failure. The serine/threonine protein kinase Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) is a ubiquitous mediator of intracellular Ca(2+) signals...
2017: Advances in Pharmacology
https://www.readbyqxmd.com/read/28212793/mir-634-is-a-pol-iii-dependent-intronic-microrna-regulating-alternative-polyadenylated-isoforms-of-its-host-gene-prkca
#4
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/28211989/timothy-syndrome-1-genotype-without-syndactyly-and-major-extracardiac-manifestations
#5
Róbert Sepp, Lidia Hategan, Attila Bácsi, Judit Cseklye, László Környei, János Borbás, Márta Széll, Tamás Forster, István Nagy, Zoltán Hegedűs
Timothy syndrome 1 (TS1) is a rare genetic disorder characterized by multisystem abnormalities including QT prolongation, congenital heart defects, facial dysmorphism, episodic hypoglycemia, and neurological symptoms. A morphological hallmark of TS1 is syndactyly, present in all cases. TS1 is caused by the canonical p.Gly406Arg mutation in the alternatively spliced exon 8A in the CACNA1C gene, encoding for the main cardiac L-type calcium channel. A variant case of TS1 is reported. The proband had intermittent fetal bradycardia with heart rate of 72 bpm...
March 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/28211799/increased-expression-of-long-non-coding-rna-glidr-in-prostate-cancer
#6
Yingyi Zhang, Zhe Kong, Yalong Zhang, Wenhua Huang, Hai Wu, Xuechao Wan, Yao Li
Prostate cancer (PCa) was one of the most common cancers in males in China. Long non-coding RNAs (lncRNA), a class of non-coding RNAs with more than 200 nucleotides, played key roles in the progression of prostate cancer. GLIDR, a novel long intergenic ncRNA, was found to be upregulated in tumors compared to normal tissues by using publically databases. In the clinical validation cohort, our results showed GLIDR was significantly up-regulated in prostate cancer samples and cell lines. To explore the potential functions of the GLIDR, we constructed gene co-expression networks and applied GO analysis...
February 3, 2017: Cancer Biomarkers: Section A of Disease Markers
https://www.readbyqxmd.com/read/28211484/regulation-of-mrna-splicing-by-mecp2-via-epigenetic-modifications-in-the-brain
#7
Tian-Lin Cheng, Jingqi Chen, Huida Wan, Bin Tang, Weidong Tian, Lujian Liao, Zilong Qiu
Mutations of X-linked gene Methyl CpG binding protein 2 (MECP2) are the major causes of Rett syndrome (RTT), a severe neurodevelopmental disorder. Duplications of MECP2-containing genomic segments lead to severe autistic symptoms in human. MECP2-coding protein methyl-CpG-binding protein 2 (MeCP2) is involved in transcription regulation, microRNA processing and mRNA splicing. However, molecular mechanisms underlying the involvement of MeCP2 in mRNA splicing in neurons remain largely elusive. In this work we found that the majority of MeCP2-associated proteins are involved in mRNA splicing using mass spectrometry analysis with multiple samples from Mecp2-null rat brain, mouse primary neuron and human cell lines...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28210711/intergenically-spliced-chimeric-rnas-in-cancer
#8
Yuemeng Jia, Zhongqiu Xie, Hui Li
Gene fusions and their encoded products (fusion RNAs and proteins) are viewed as one of the hallmarks of cancer. Traditionally, they were thought to be generated solely by chromosomal rearrangements. However, recent discoveries of trans-splicing and cis-splicing events between neighboring genes, suggest that there are other mechanisms to generate chimeric fusion RNAs without corresponding changes in DNA. In addition, chimeric RNAs have been detected in normal physiology, complicating the use of fusions in cancer detection and therapy...
September 2016: Trends in Cancer
https://www.readbyqxmd.com/read/28209301/iswi-atp-dependent-remodeling-of-nucleoplasmic-%C3%AF-speckles-in-the-brain-of-drosophila-melanogaster
#9
Luca Lo Piccolo, Andrea Attardi, Rosa Bonaccorso, Lorenzo Li Greci, Giorgio Giurato, Antonia Maria Rita Ingrassia, Maria Cristina Onorati
Heterogeneous nuclear ribonucleoproteins (hnRNPs) belong to the RNA-binding proteins family. They are involved in processing heterogeneous nuclear RNAs (hnRNAs) into mature mRNAs. These proteins participate in every step of mRNA cycle, such as mRNA export, localization, translation, stability and alternative splicing. At least 14 major hnRNPs, which have structural and functional homologues in mammals, are expressed in Drosophila melanogaster. Until now, six of these hnRNPs are known to be nucleus-localized and associated with the long non-coding RNA (lncRNA) heat shock responsive ω (hsrω) in the omega speckle compartments (ω-speckles)...
December 22, 2016: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28208770/splicing-and-polyadenylation-of-human-papillomavirus-type-16-mrnas
#10
REVIEW
Chengjun Wu, Naoko Kajitani, Stefan Schwartz
The human papillomavirus type 16 (HPV16) life cycle can be divided into an early stage in which the HPV16 genomic DNA is replicated, and a late stage in which the HPV16 structural proteins are synthesized and virions are produced. A strong coupling between the viral life cycle and the differentiation state of the infected cell is highly characteristic of all HPVs. The switch from the HPV16 early gene expression program to the late requires a promoter switch, a polyadenylation signal switch and a shift in alternative splicing...
February 9, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28208661/differential-binding-of-three-major-human-adar-isoforms-to-coding-and-long-non-coding-transcripts
#11
Josephine Galipon, Rintaro Ishii, Yutaka Suzuki, Masaru Tomita, Kumiko Ui-Tei
RNA editing by deamination of adenosine to inosine is an evolutionarily conserved process involved in many cellular pathways, from alternative splicing to miRNA targeting. In humans, it is carried out by no less than three major adenosine deaminases acting on RNA (ADARs): ADAR1-p150, ADAR1-p110, and ADAR2. However, the first two derive from alternative splicing, so that it is currently impossible to delete ADAR1-p110 without also knocking out ADAR1-p150 expression. Furthermore, the expression levels of ADARs varies wildly among cell types, and no study has systematically explored the effect of each of these isoforms on the cell transcriptome...
February 11, 2017: Genes
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
#12
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/28205582/aurora-a-regulates-expression-of-ar-v7-in-models-of-castrate-resistant-prostate-cancer
#13
Dominic Jones, Martin Noble, Steve R Wedge, Craig N Robson, Luke Gaughan
Androgen receptor variants (AR-Vs) provide a mechanism of therapy evasion in castrate-resistant prostate cancer (CRPC), yet mechanisms of regulation remain largely unknown. Here we investigate the role of Aurora A kinase on AR-Vs in models of CRPC and show depletion of Aurora A reduces AR-V target gene expression. Importantly, knockdown of Aurora A reconfigures splicing of AR pre-mRNA to discriminately down-regulate synthesis of AR-V transcripts, including AR-V7, without effecting full-length AR mRNA; and as a consequence, AR-V-driven proliferation and survival of CRPC cells is markedly reduced...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205568/luman-contributes-to-brefeldin-a-induced-prion-protein-gene-expression-by-interacting-with-the-erse26-element
#14
Marc-André Déry, Andréa C LeBlanc
The cellular prion protein (PrP) is essential for transmissible prion diseases, but its exact physiological function remains unclear. Better understanding the regulation of the human prion protein gene (PRNP) expression can provide insight into this elusive function. Spliced XBP1 (sXBP1) was recently shown to mediate endoplasmic reticulum (ER) stress-induced PRNP expression. In this manuscript, we identify Luman, a ubiquitous, non-canonical unfolded protein response (UPR), as a novel regulator of ER stress-induced PRNP expression...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28203606/dna-methylation-in-oligodendroglial-cells-during-developmental-myelination-and-in-disease
#15
Sarah Moyon, Patrizia Casaccia
Oligodendrocyte progenitor cells (OPC) are the myelinating cells of the central nervous system (CNS). During development, they differentiate into mature oligodendrocytes (OL) and ensheath axons, providing trophic and functional support to the neurons. This process is regulated by the dynamic expression of specific transcription factors, which, in turn, is controlled by epigenetic marks such as DNA methylation. Here we discuss recent findings showing that DNA methylation levels are differentially regulated in the oligodendrocyte lineage during developmental myelination, affecting both genes expression and alternative splicing events...
2017: Neurogenesis (Austin, Tex.)
https://www.readbyqxmd.com/read/28203567/identification-of-three-novel-splicing-variants-and-expression-analysis-of-chicken-gpr1-gene
#16
Xueyou Zhang, Qihai Xiao, Kai Tian, Yan Wang, Xiaoling Zhao, Huadong Yin, Diyan Li, Qing Zhu
GPR1 is a G protein-coupled receptor that plays critical roles in eukaryotic cells: typically, response to glucose stimulation, lipid accumulation, and transmitting nutrition signals to cAMP pathway. However, the alternative splicing of the GPR1 gene and its expression pattern in chicken tissues and ovarian follicles were unknown. In our current study, we used RACE-PCR to identify three GPR1 variants, including the full-length variant (GPR1-va1) and two alternatively spliced variants (GPR1-va2, GPR1-vb). Quantitative real-time PCR examined the expression pattern of GPR1 mRNA in chicken tissues and ovarian follicles...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28202468/the-crumbs_c-isoform-of-drosophila-shows-tissue-and-stage-specific-expression-and-prevents-light-dependent-retinal-degeneration
#17
Stephanie Spannl, Alexandra Kumichel, Sarita Hebbar, Katja Kapp, Marcos Gonzalez-Gaitan, Sylke Winkler, Rosana Blawid, Gregor Jessberger, Elisabeth Knust
Drosophila Crumbs (Crb) is a key regulator of epithelial polarity and fulfils a plethora of other functions, such as growth regulation, morphogenesis of photoreceptor cells and prevention of retinal degeneration. This raises the question how a single gene regulates such diverse functions, which in mammals are controlled by three different paralogs. Here, we show that in Drosophila different Crb protein isoforms are differentially expressed as a result of alternative splicing. All isoforms are transmembrane proteins that differ by just one EGF-like repeat in their extracellular portion...
February 15, 2017: Biology Open
https://www.readbyqxmd.com/read/28199965/whole-exome-sequencing-identified-a-homozygous-brdt-mutation-in-a-patient-with-acephalic-spermatozoa
#18
Lin Li, Yanwei Sha, Xi Wang, Ping Li, Jing Wang, Kehkooi Kee, Binbin Wang
Acephalic spermatozoa is a very rare disorder of male infertility. Here, in a patient from from a consanguineous family, we have identified, by whole-exome sequencing, a homozygous mutation (c.G2783A, p.G928D) in the BRDT gene. The gene product, BRDT, is a testis-specific protein that is considered an important drug target for male contraception. The G928D mutation is in the P-TEFb binding domain, which mediates the interaction with transcription elongation factor and might affect the transcriptional activities of downstream genes...
February 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28198676/global-transcriptome-analysis-reveals-extensive-gene-remodeling-alternative-splicing-and-differential-transcription-profiles-in-non-seed-vascular-plant-selaginella-moellendorffii
#19
Yan Zhu, Longxian Chen, Chengjun Zhang, Pei Hao, Xinyun Jing, Xuan Li
BACKGROUND: Selaginella moellendorffii, a lycophyte, is a model plant to study the early evolution and development of vascular plants. As the first and only sequenced lycophyte to date, the genome of S. moellendorffii revealed many conserved genes and pathways, as well as specialized genes different from flowering plants. Despite the progress made, little is known about long noncoding RNAs (lncRNA) and the alternative splicing (AS) of coding genes in S. moellendorffii. Its coding gene models have not been fully validated with transcriptome data...
January 25, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28198669/ulfasqtl-an-ultra-fast-method-of-composite-splicing-qtl-analysis
#20
Qian Yang, Yue Hu, Jun Li, Xuegong Zhang
BACKGROUND: Alternative splicing plays important roles in many regulatory processes and diseases in human. Many genetic variants contribute to phenotypic differences in gene expression and splicing that determine variations in human traits. Detecting genetic variants that affect splicing phenotypes is essential for understanding the functional impact of genetic variations on alternative splicing. For many situations, the key phenotype is the relative splicing ratios of alternative isoforms rather than the expression values of individual isoforms...
January 25, 2017: BMC Genomics
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