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https://www.readbyqxmd.com/read/28807725/the-rnf146-e3-ubiquitin-ligase-is-required-for-the-control-of-wnt-signaling-and-body-pattern-formation-in-xenopus
#1
Xuechen Zhu, Rui Xing, Renbo Tan, Rongyang Dai, Qinghua Tao
The RING finger protein Rnf146 encodes an E3 ubiquitin ligase capable of targeting poly-ADP-ribosylated substrates for proteasomal degradation. Rnf146 has been identified as a critical regulator of Axin1 and thus of Wnt/β-catenin signaling. However its physiological significance in vertebrate embryonic development remains to be demonstrated. In this study, we take advantages of early Xenopus embryos to demonstrate that Rnf146 is essential for embryonic pattern formation. Depletion of zygotic Rnf146 using a translation blocking morpholino oligo (MO) results in anteriorized development and increased expression the anterior marker gene Otx2, consistent the notion that Rnf146 is a positive regulator of Wnt/β-catenin signaling through negatively regulating Axin1 expression...
August 11, 2017: Mechanisms of Development
https://www.readbyqxmd.com/read/28765332/n1-src-kinase-is-required-for-primary-neurogenesis-in-xenopus-tropicalis
#2
Philip A Lewis, Isobel C Bradley, Alastair R Pizzey, Harry V Isaacs, Gareth J O Evans
The presence of the neuronal-specific N1-Src splice variant of the C-Src tyrosine kinase is conserved through vertebrate evolution, suggesting an important role in complex nervous systems. Alternative splicing involving an N1-Src-specific microexon leads to a 5 or 6 aa insertion into the SH3 domain of Src. A prevailing model suggests that N1-Src regulates neuronal differentiation via cytoskeletal dynamics in the growth cone. Here we investigated the role of n1-src in the early development of the amphibian Xenopus tropicalis, and found that n1-src expression is regulated in embryogenesis, with highest levels detected during the phases of primary and secondary neurogenesis...
August 30, 2017: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/28704609/hydrophilic-and-cell-penetrable-pyrrolidinyl-peptide-nucleic-acid-via-post-synthetic-modification-with-hydrophilic-side-chains
#3
Haruthai Pansuwan, Boonsong Ditmangklo, Chotima Vilaivan, Banphot Jiangchareon, Porntip Pan-In, Supason Wanichwecharungruang, Tanapat Palaga, Thanesuan Nuanyai, Chaturong Suparpprom, Tirayut Vilaivan
Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose-phosphate was replaced by a peptide-like backbone. The absence of negative charge in the PNA backbone leads to several unique behaviors including a stronger binding and salt independency of the PNA-DNA duplex stability. However, PNA possesses poor aqueous solubility and cannot directly penetrate cell membranes. These are major obstacles that limit in vivo applications of PNA. In previous strategies, the PNA can be conjugated to macromolecular carriers or modified with positively charged side chains such as guanidinium groups to improve the aqueous solubility and cell permeability...
August 11, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28655711/long-noncoding-rna-foxd3-as1-regulates-oxidative-stress-induced-apoptosis-via-sponging-microrna-150
#4
Duo Zhang, Heedoo Lee, Jeffrey A Haspel, Yang Jin
The function of most human long noncoding RNAs (lncRNAs) remains unclear. Our studies identified a highly up-regulated mammalian lncRNA, FOXD3-AS1, known as linc1623 in mouse, in the setting of hyperoxia/reactive oxygen species (ROS)-induced lung injury. We found that ROS induced a robust expression of FOXD3-AS1 in mouse lung tissue. Functionally, FOXD3-AS1 promoted oxidative stress-induced lung epithelial cell death. In human lung epithelial cells, the microRNA-150 (miR-150) was identified to interact with FOXD3-AS1; this finding was confirmed using the luciferase reporter assays...
June 27, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28628208/carbocyclic-c-c-bond-formation-intramolecular-radical-ring-closure-to-yield-diastereomerically-pure-7-s-me-or-7-r-me-carba-lna-nucleotide-analogs
#5
Oleksandr Plashkevych, Ram Shankar Upadhayaya, Jyoti Chattopadhyaya
In light of the impressive gene-silencing properties of carba-LNA modified oligo DNA and RNA, both in antisense RNA and siRNA approaches, which have been confirmed as proof-of-concept for biochemical applications in post-transcriptional gene silencing, we envision the true potential of carba-LNA modifications to be revealed soon. Herein we provide detailed protocols for synthesis of carba-LNA-A, -G, -(5-Me) C, and -T nucleosides on a medium/large scale (gram scale), as well as important guidelines for incorporation of these modified carba-LNAs into DNA or RNA oligonucleotides...
June 19, 2017: Current Protocols in Nucleic Acid Chemistry
https://www.readbyqxmd.com/read/28524599/modulation-of-nuclear-rest-by-alternative-splicing-a-potential-therapeutic-target-for-huntington-s-disease
#6
Guo-Lin Chen, Qi Ma, Dharmendra Goswami, Jianyu Shang, Gregory M Miller
Huntington's disease (HD) is caused by a genetically mutated huntingtin (mHtt) protein with expanded polyQ stretch, which impairs cytosolic sequestration of the repressor element-1 silencing transcription factor (REST), resulting in excessive nuclear REST and subsequent repression of neuronal genes. We recently demonstrated that REST undergoes extensive, context-dependent alternative splicing, of which exon-3 skipping (∆E3 )-a common event in human and nonhuman primates-causes loss of a motif critical for REST nuclear targeting...
May 19, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28366767/fda-approved-oligonucleotide-therapies-in-2017
#7
REVIEW
Cy A Stein, Daniela Castanotto
Oligonucleotides (oligos) have been under clinical development for approximately the past 30 years, beginning with antisense oligonucleotides (ASOs) and apatmers and followed about 15 years ago by siRNAs. During that lengthy period of time, numerous clinical trials have been performed and thousands of trial participants accrued onto studies. Of all the molecules evaluated as of January 2017, the regulatory authorities assessed that six provided clear clinical benefit in rigorously controlled trials. The story of these six is given in this review...
May 3, 2017: Molecular Therapy: the Journal of the American Society of Gene Therapy
https://www.readbyqxmd.com/read/28364229/invention-and-early-history-of-morpholinos-from-pipe-dream-to-practical-products
#8
James E Summerton
Beginning with my concept in 1969 to treat disease at the nucleic acid level using antisense nucleic acids, antisense has evolved to the current Morpholino oligos. Morpholinos have been the dominant gene knockdown system in developmental biology. Lack of delivery technologies has limited their use in adult animals (including humans), though alteration in muscles in Duchenne muscular dystrophy (DMD) allows delivery into adult muscle. Morpholinos are currently in Phase 3 clinical trials for DMD and a Morpholino oligo for skipping dystrophin exon 51 has been approved by the US FDA...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28125734/identification-of-mir-21-5p-as-a-functional-regulator-of-mesothelin-expression-using-microrna-capture-affinity-coupled-with-next-generation-sequencing
#9
Chiara De Santi, Sebastian Vencken, Jonathon Blake, Bettina Haase, Vladimir Benes, Federica Gemignani, Stefano Landi, Catherine M Greene
MicroRNAs (miRNAs) are small non-coding RNAs that regulate mRNA expression mainly by silencing target transcripts via binding to miRNA recognition elements (MREs) in the 3'untranslated region (3'UTR). The identification of bona fide targets is challenging for researchers working on the functional aspect of miRNAs. Recently, we developed a method (miR-CATCH) based on biotinylated DNA antisense oligonucleotides that capture the mRNA of interest and facilitates the characterisation of miRNAs::mRNA interactions in a physiological cellular context...
2017: PloS One
https://www.readbyqxmd.com/read/27860312/cytochrome-p450-26a1-modulates-natural-killer-cells-in-mouse-early-pregnancy
#10
Chao-Yang Meng, Zhong-Yin Li, Wen-Ning Fang, Zhi-Hui Song, Dan-Dan Yang, Dan-Dan Li, Ying Yang, Jing-Pian Peng
Cytochrome P450 26A1 (CYP26A1) has a spatiotemporal expression pattern in the uterus, with a significant increase in mRNA and protein levels during peri-implantation. Inhibiting the function or expression of CYP26A1 can cause pregnancy failure, suggesting an important regulatory role of CYP26A1 in the maintenance of pregnancy. However, little is known about the exact mechanism involved. In this study, using a pCR3.1-cyp26a1 plasmid immunization mouse model and a Cyp26a1-MO (Cyp26a1-specific antisense oligos) knockdown mouse model, we report that the number of Dolichos biflorus agglutinin (DBA) lectin-positive uterine natural killer (uNK) cells was reduced in pCR3...
April 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/27830347/mito-porter-for-mitochondrial-delivery-and-mitochondrial-functional-analysis
#11
Yuma Yamada, Hideyoshi Harashima
Mitochondria are attractive organelles that have the potential to contribute greatly to medical therapy, the maintenance of beauty and health, and the development of the life sciences. Therefore, it would be expected that the further development of mitochondrial drug delivery systems (DDSs) would exert a significant impact on the medical and life sciences. To achieve such an innovative objective, it will be necessary to deliver various cargoes to mitochondria in living cells. However, only a limited number of approaches are available for accomplishing this...
November 10, 2016: Handbook of Experimental Pharmacology
https://www.readbyqxmd.com/read/27797146/innovative-technologies-in-nanomedicines-from-passive-targeting-to-active-targeting-from-controlled-pharmacokinetics-to-controlled-intracellular-pharmacokinetics
#12
Yusuke Sato, Yu Sakurai, Kazuaki Kajimoto, Takashi Nakamura, Yuma Yamada, Hidetaka Akita, Hideyoshi Harashima
Nanomedicines promise to extend drug therapy from small molecular compounds to proteins/nucleic acids/genes. Multifunctional envelope-type nanodevices (MENDs) have been developed for delivering such molecules to the site of action. The YSK-MEND contains new types of pH-responsive cationic lipids to efficiently deliver siRNA to hepatocytes via receptor-mediated endocytosis and use in treating hepatitis C and B in model mice. The RGD ligand is introduced to target tumor endothelial cells (TEC) and RGD-MEND is able to send siRNA to TEC to regulate the function of tumor microenvironments...
January 2017: Macromolecular Bioscience
https://www.readbyqxmd.com/read/27792754/characterization-of-zebrafish-models-of-marinesco-sj%C3%A3-gren-syndrome
#13
Genri Kawahara, Yukiko K Hayashi
SIL1 is a nucleotide exchange factor for the endoplasmic reticulum chaperone, BiP. Mutations in the SIL1 gene cause Marinesco-Sjögren syndrome (MSS), an autosomal recessive disease characterized by cerebellar ataxia, mental retardation, congenital cataracts, and myopathy. To create novel zebrafish models of MSS for therapeutic drug screening, we analyzed phenotypes in sil1 knock down fish by two different antisense oligo morpholinos. Both sil1 morphants had abnormal formation of muscle fibers and irregularity of the myosepta...
2016: PloS One
https://www.readbyqxmd.com/read/27746303/a-versatile-tandem-rna-isolation-procedure-to-capture-in-vivo-formed-mrna-protein-complexes
#14
Ana M Matia-González, Valentina Iadevaia, André P Gerber
We describe a tandem RNA isolation procedure (TRIP) that enables purification of in vivo formed messenger ribonucleoprotein (mRNP) complexes. The procedure relies on the purification of polyadenylated mRNAs with oligo(dT) beads from cellular extracts, followed by the capture of specific mRNAs with 3'-biotinylated 2'-O-methylated antisense RNA oligonucleotides, which are recovered with streptavidin beads. TRIP was applied to isolate in vivo crosslinked mRNP complexes from yeast, nematodes and human cells for subsequent analysis of RNAs and bound proteins...
April 15, 2017: Methods: a Companion to Methods in Enzymology
https://www.readbyqxmd.com/read/27694625/challenges-of-crispr-cas9-applications-for-long-non-coding-rna-genes
#15
Ashish Goyal, Ksenia Myacheva, Matthias Groß, Marcel Klingenberg, Berta Duran Arqué, Sven Diederichs
The CRISPR/Cas9 system provides a revolutionary genome editing tool for all areas of molecular biology. In long non-coding RNA (lncRNA) research, the Cas9 nuclease can delete lncRNA genes or introduce RNA-destabilizing elements into their locus. The nuclease-deficient dCas9 mutant retains its RNA-dependent DNA-binding activity and can modulate gene expression when fused to transcriptional repressor or activator domains. Here, we systematically analyze whether CRISPR approaches are suitable to target lncRNAs...
September 30, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27659977/capture-hybridization-analysis-of-dna-targets
#16
Alec N Sexton, Martin Machyna, Matthew D Simon
There are numerous recent cases where chromatin modifying complexes associate with long noncoding RNA (lncRNA), stoking interest in lncRNA genomic localization and associated proteins. Capture Hybridization Analysis of RNA Targets (CHART) uses complementary oligonucleotides to purify an RNA with its associated genomic DNA or proteins from formaldehyde cross-linked chromatin. Deep sequencing of the purified DNA fragments gives a comprehensive profile of the potential lncRNA biological targets in vivo. The combined identification of the genomic localization of RNA and its protein partners can directly inform hypotheses about RNA function, including recruitment of chromatin modifying complexes...
2016: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27381842/knockdown-of-gene-expression-by-antisense-morpholino-oligos-in-preimplantation-mouse-embryos-cultured-in%C3%A2-vitro
#17
Yuki Sato, Shiori Sato, Takahiro Kikuchi, Asumi Nonaka, Yuki Kumagai, Akira Sasaki, Masayuki Kobayashi
Knockdown of gene expression by antisense morpholino oligos (MOs) is a simple and effective method for analyzing the roles of genes in mammalian cells. Here, we demonstrate the efficient delivery of MOs by Endo-Porter (EP), a special transfection reagent for MOs, into preimplantation mouse embryos cultured in vitro. A fluorescein-labeled control MO was applied for monitoring the incorporation of MOs into developing 2-cell embryos in the presence of varying amounts of EP and bovine serum albumin. In optimized conditions, fluorescence was detected in 2-cell embryos within a 3-h incubation period...
September 15, 2016: Analytical Biochemistry
https://www.readbyqxmd.com/read/27328644/dazl-is-a-critical-player-for-primordial-germ-cell-formation-in-medaka
#18
Mingyou Li, Feng Zhu, Zhendong Li, Ni Hong, Yunhan Hong
The DAZ family genes boule, daz and dazl have conserved functions in primordial germ cell (PGC) migration, germ stem cell proliferation, differentiation and meiosis progression. It has remained unknown whether this family is required for PGC formation in developing embryos. Our recent study in the fish medaka (Oryzias latipes) has defined dnd as the critical PGC specifier and predicted the presence of additional factors essential for PGC formation. Here we report that dazl is a second key player for medaka PGC formation...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27285612/multi-exon-skipping-using-cocktail-antisense-oligonucleotides-in-the-canine-x-linked-muscular-dystrophy
#19
Bailey Miskew Nichols, Yoshitsugu Aoki, Mutsuki Kuraoka, Joshua J A Lee, Shin'ichi Takeda, Toshifumi Yokota
Duchenne muscular dystrophy (DMD) is one of the most common lethal genetic diseases worldwide, caused by mutations in the dystrophin (DMD) gene. Exon skipping employs short DNA/RNA-like molecules called antisense oligonucleotides (AONs) that restore the reading frame and produce shorter but functional proteins. However, exon skipping therapy faces two major hurdles: limited applicability (up to only 13% of patients can be treated with a single AON drug), and uncertain function of truncated proteins. These issues were addressed with a cocktail AON approach...
May 24, 2016: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/27197559/cyp2aa9-regulates-haematopoietic-stem-cell-development-in-zebrafish
#20
Jingying Chen, Jianbo He, Li Li, Deqin Yang, Lingfei Luo
Definitive haematopoiesis occurs during the lifetime of an individual, which continuously replenishes all blood and immune cells. During embryonic development, haematopoietic stem cell (HSC) formation is tightly controlled by growth factors, signalling molecules and transcription factors. But little is known about roles of the cytochrome P450 (CYP) 2 family member in the haematopoiesis. Here we report characterization and functional studies of Cyp2aa9, a novel zebrafish Cyp2 family member. And demonstrate that the cyp2aa9 is required for the HSC formation and homeostasis...
2016: Scientific Reports
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