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https://www.readbyqxmd.com/read/29452418/phf20-collaborates-with-parp1-to-promote-stemness-and-aggressiveness-of-neuroblastoma-cells-through-activation-of-sox2-and-oct4
#1
Wenyong Long, Wei Zhao, Bo Ning, Jing Huang, Junjun Chu, Linfeng Li, Qianquan Ma, Changsheng Xing, Helen Y Wang, Qing Liu, Rong-Fu Wang
The differentiation status of neuroblastoma (NB) strongly correlates with its clinical outcomes; however, the molecular mechanisms driving maintenance of stemness and differentiation remain poorly understood. Here, we show that plant homeodomain finger-containing protein 20 (PHF20) functions as a critical epigenetic regulator in sustaining stem cell-like phenotype of NB by using CRISPR/Cas9-based targeted knockout (KO) for high-throughput screening of gene function in NB cell differentiation. Expression of PHF20 in NB was significantly associated with high aggressiveness of the tumor and poor outcomes for NB patients...
February 14, 2018: Journal of Molecular Cell Biology
https://www.readbyqxmd.com/read/29452156/establishment-of-a-prkag2-cardiac-syndrome-disease-model-and-mechanism-study-using-human-induced-pluripotent-stem-cells
#2
Yongkun Zhan, Xiaolei Sun, Bin Li, Huanhuan Cai, Chen Xu, Qianqian Liang, Chao Lu, Ruizhe Qian, Sifeng Chen, Lianhua Yin, Wei Sheng, Guoying Huang, Aijun Sun, Junbo Ge, Ning Sun
PRKAG2 cardiac syndrome is a distinct form of human cardiomyopathy characterized by cardiac hypertrophy, ventricular pre-excitation and progressive cardiac conduction disorder. However, it remains unclear how mutations in the PRKAG2 gene give rise to such a complicated disease. To investigate the underlying molecular mechanisms, we generated disease-specific hiPSC-derived cardiomyocytes from two brothers both carrying a heterozygous missense mutation c.905G>A (R302Q) in the PRKAG2 gene and further corrected the R302Q mutation with CRISPR-Cas9 mediated genome editing...
February 13, 2018: Journal of Molecular and Cellular Cardiology
https://www.readbyqxmd.com/read/29451908/cas9-mediated-excision-of-proximal-dnasei-h3k4me3-signatures-confers-robust-silencing-of-microrna-and-long-non-coding-rna-genes
#3
Harshavardhan Janga, Marina Aznaourova, Fabian Boldt, Katrin Damm, Arnold Grünweller, Leon N Schulte
CRISPR/Cas9-based approaches have greatly facilitated targeted genomic deletions. Contrary to coding genes however, which can be functionally knocked out by frame-shift mutagenesis, non-coding RNA (ncRNA) gene knockouts have remained challenging. Here we present a universal ncRNA knockout approach guided by epigenetic hallmarks, which enables robust gene silencing even in provisionally annotated gene loci. We build on previous work reporting the presence of overlapping histone H3 lysine 4 tri-methylation (H3K4me3) and DNaseI hypersensitivity sites around the transcriptional start sites of most genes...
2018: PloS One
https://www.readbyqxmd.com/read/29451876/comparative-genomic-analysis-of-the-multispecies-probiotic-marketed-product-vsl-3
#4
François P Douillard, Diego Mora, Robyn T Eijlander, Michiel Wels, Willem M de Vos
Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials...
2018: PloS One
https://www.readbyqxmd.com/read/29450543/mutation-in-the-zebrafish-cct2-gene-leads-to-abnormalities-of-cell-cycle-and-cell-death-in-the-retina-a-model-of-cct2-related-leber-congenital-amaurosis
#5
Yuriko Minegishi, Naoki Nakaya, Stanislav I Tomarev
Purpose: The compound heterozygous mutations in the β subunit of chaperonin containing TCP-1 (CCT), encoded by CCT2, lead to the Leber congenital amaurosis (LCA). In this study, a cct2 mutant line of zebrafish was established to investigate the role of CCT2 mutations in LCA in vertebrates. Methods: A cct2 mutant zebrafish line was produced using the CRISPR-Cas9 system. Changes in the eyes of developing wild-type and mutant larvae were monitored using microscopy, immunostaining, TUNEL, and EdU assays...
February 1, 2018: Investigative Ophthalmology & Visual Science
https://www.readbyqxmd.com/read/29450416/a-g-quadruplex-motif-at-the-3-end-of-sgrnas-improves-crispr-cas9-based-genome-editing-efficiency
#6
Smita Nahar, Paras Sehgal, Mohd Azhar, Manish Rai, Amrita Singh, Sridhar Sivasubbu, Debojyoti Chakraborty, Souvik Maiti
Originating as a component of prokaryotic adaptive immunity, the type II CRISPR/Cas9 system has been repurposed for targeted genome editing in various organisms. Although Cas9 can bind and cleave DNA efficiently under in vitro conditions, its activity inside a cell can vary dramatically between targets owing to the differences between genomic loci and the availability of enough Cas9/sgRNA (single guide RNA) complex molecules for cleavage. Most methods have so far relied on Cas9 protein engineering or base modifications in the sgRNA sequence to improve CRISPR/Cas9 activity...
February 16, 2018: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/29449584/crispr-whole-genome-screening-identifies-new-necroptosis-regulators-and-ripk1-alternative-splicing
#7
Marinella G Callow, Colin Watanabe, Katherine E Wickliffe, Russell Bainer, Sarah Kummerfield, Julie Weng, Trinna Cuellar, Vasantharajan Janakiraman, Honglin Chen, Ben Chih, Yuxin Liang, Benjamin Haley, Kim Newton, Michael R Costa
The necroptotic cell death pathway is a key component of human pathogen defense that can become aberrantly derepressed during tissue homeostasis to contribute to multiple types of tissue damage and disease. While formation of the necrosome kinase signaling complex containing RIPK1, RIPK3, and MLKL has been extensively characterized, additional mechanisms of its regulation and effector functions likely remain to be discovered. We screened 19,883 mouse protein-coding genes by CRISPR/Cas9-mediated gene knockout for resistance to cytokine-induced necroptosis and identified 112 regulators and mediators of necroptosis, including 59 new candidate pathway components with minimal or no effect on cell growth in the absence of necroptosis induction...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449560/knockout-of-zebrafish-interleukin-7-receptor-il7r-by-the-crispr-cas9-system-delays-retinal-neurodevelopment
#8
Shijiao Cai, Yang Chen, Yue Shang, Jianlin Cui, Zongjin Li, Yuhao Li
Interleukin 7 receptor (il7r), a transmembrane receptor, belongs to the type I cytokine receptor family. Il7r is involved in the pathogenesis of neurodegenerative disorders, such as multiple sclerosis. Targeted knockdown of il7r leads to delayed myelination, highlighting the potential role of il7r in the development of the nervous system. Zebrafish is an ideal model for the study of neurogenesis; moreover, the il7r gene is highly conserved between zebrafish and human. The aim of the present study was to investigate the novel function of il7r in neurogenesis...
February 15, 2018: Cell Death & Disease
https://www.readbyqxmd.com/read/29449551/mutations-in-cfap43-and-cfap44-cause-male-infertility-and-flagellum-defects-in-trypanosoma-and-human
#9
Charles Coutton, Alexandra S Vargas, Amir Amiri-Yekta, Zine-Eddine Kherraf, Selima Fourati Ben Mustapha, Pauline Le Tanno, Clémentine Wambergue-Legrand, Thomas Karaouzène, Guillaume Martinez, Serge Crouzy, Abbas Daneshipour, Seyedeh Hanieh Hosseini, Valérie Mitchell, Lazhar Halouani, Ouafi Marrakchi, Mounir Makni, Habib Latrous, Mahmoud Kharouf, Jean-François Deleuze, Anne Boland, Sylviane Hennebicq, Véronique Satre, Pierre-Simon Jouk, Nicolas Thierry-Mieg, Beatrice Conne, Denis Dacheux, Nicolas Landrein, Alain Schmitt, Laurence Stouvenel, Patrick Lorès, Elma El Khouri, Serge P Bottari, Julien Fauré, Jean-Philippe Wolf, Karin Pernet-Gallay, Jessica Escoffier, Hamid Gourabi, Derrick R Robinson, Serge Nef, Emmanuel Dulioust, Raoudha Zouari, Mélanie Bonhivers, Aminata Touré, Christophe Arnoult, Pierre F Ray
Spermatogenesis defects concern millions of men worldwide, yet the vast majority remains undiagnosed. Here we report men with primary infertility due to multiple morphological abnormalities of the sperm flagella with severe disorganization of the sperm axoneme, a microtubule-based structure highly conserved throughout evolution. Whole-exome sequencing was performed on 78 patients allowing the identification of 22 men with bi-allelic mutations in DNAH1 (n = 6), CFAP43 (n = 10), and CFAP44 (n = 6). CRISPR/Cas9 created homozygous CFAP43/44 male mice that were infertile and presented severe flagellar defects confirming the human genetic results...
February 15, 2018: Nature Communications
https://www.readbyqxmd.com/read/29449511/crispr-cas12a-target-binding-unleashes-indiscriminate-single-stranded-dnase-activity
#10
Janice S Chen, Enbo Ma, Lucas B Harrington, Maria Da Costa, Xinran Tian, Joel M Palefsky, Jennifer A Doudna
CRISPR-Cas12a (Cpf1) proteins are RNA-guided enzymes that bind and cut DNA as components of bacterial adaptive immune systems. Like CRISPR-Cas9, Cas12a has been harnessed for genome editing based on its ability to generate targeted, double-stranded DNA (dsDNA) breaks. Here we show that RNA-guided DNA binding unleashes indiscriminate single-stranded DNA (ssDNA) cleavage activity by Cas12a that completely degrades ssDNA molecules. We find that target-activated, non-specific ssDNase cleavage is also a property of other type V CRISPR-Cas12 enzymes...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449508/multiplexed-and-portable-nucleic-acid-detection-platform-with-cas13-cas12a-and-csm6
#11
Jonathan S Gootenberg, Omar O Abudayyeh, Max J Kellner, Julia Joung, James J Collins, Feng Zhang
Rapid detection of nucleic acids is integral for clinical diagnostics and biotechnological applications. We recently developed a platform termed SHERLOCK (<u>S</u>pecific<u>H</u>igh Sensitivity<u>E</u>nzymatic<u>R</u>eporter Un<u>LOCK</u>ing) that combines isothermal pre-amplification with Cas13 to detect single molecules of RNA or DNA. Through characterization of CRISPR enzymology and application development, we report here four advances integrated into SHERLOCKv2: 1) 4-channel single reaction multiplexing using orthogonal CRISPR enzymes; 2) quantitative measurement of input down to 2 aM; 3) 3...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449507/rewritable-multi-event-analog-recording-in-bacterial-and-mammalian-cells
#12
Weixin Tang, David R Liu
We present two CRISPR-mediated analog multi-event recording apparatus (CAMERA) systems that use base editors and Cas9 nucleases to record cellular events in bacteria and mammalian cells. The devices record signal amplitude or duration as changes in the ratio of mutually exclusive DNA sequences (CAMERA 1), or as single-base modifications (CAMERA 2). We achieved recording of multiple stimuli in bacteria or mammalian cells, including exposure to antibiotics, nutrients, viruses, light, and changes in Wnt signaling...
February 15, 2018: Science
https://www.readbyqxmd.com/read/29449471/-camera-records-cell-action-with-new-crispr-tricks
#13
Jon Cohen
No abstract text is available yet for this article.
February 16, 2018: Science
https://www.readbyqxmd.com/read/29449428/a-novel-piperidine-identified-by-stem-cell-based-screening-attenuates-pulmonary-arterial-hypertension-via-regulating-bmp2-and-ptgs2-levels
#14
Yanjiang Xing, Shuang Zhao, Qingxia Wei, Shiqiang Gong, Xin Zhao, Fang Zhou, Rafia Ai-Lamki, Daniel Ortmann, Mingxia Du, Roger Pedersen, Guangdong Shang, Shuyi Si, Nicholas W Morrell, Jun Yang
Genetic defects in bone morphogenetic protein type-II receptor (BMPRII) signalling and inflammation contribute to the pathogenesis of pulmonary arterial hypertension (PAH). The receptor is activated by BMP ligands, which also enhance BMPR2 transcription. A small molecule BMP upregulator with selectivity on vascular endothelium would represent a desirable therapeutic intervention for PAH.We assayed compounds identified in the screening of BMP2 upregulators for their ability to increase expression of Inhibitor of DNA binding 1 (Id1), using a dual reporter driven specifically in human embryonic stem cell (hESC)-derived endothelial cells (ECs)...
February 15, 2018: European Respiratory Journal: Official Journal of the European Society for Clinical Respiratory Physiology
https://www.readbyqxmd.com/read/29449377/haploid-embryonic-stem-cells-can-be-enriched-and-maintained-by-simple-filtration
#15
Chao Qu, Meng Yan, Suming Yang, Lingbo Wang, Qi Yin, Yuan Liu, Yeguang Chen, Jinsong Li
Haploid mammalian embryonic stem cells (haESCs) serve as a powerful tool for genetic analyses at both cellular and organismal levels. However, spontaneous diploidization of haESCs limits their use in these analyses. Addition of small molecules to culture medium to control the cell cycle can slow down diploidization, but cell-sorting methods such as FACS are still required to enrich haploid cells for long-term maintenance in vitro. Here, acting on our observation that haploid and diploidized cells differ in diameter, we developed a simplified filtration method to enrich haploid cells from cultured haESCs...
February 15, 2018: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/29448764/frontiers-in-crispr
#16
Alyson G Weidmann
CRISPR-based approaches to genetic engineering are progressing at a rapid pace and present exciting new avenues for science, medicine, and technology. Many of the most cutting-edge advances in genome engineering are encompassed in the Research Articles, Reviews, and Perspectives in this special issue, often with an eye toward future directions for the field. Yet, many questions remain at this new frontier. We asked over 100 CRISPR researchers, including our contributing authors, for their perspectives on some of the most pressing questions surrounding the future of genome engineering and the CRISPR-Cas platform, the challenges that lie ahead, and opportunities for chemists and chemical biologists to drive creative molecular solutions...
February 16, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29448763/special-issue-on-the-chemical-biology-of-crispr
#17
Alyson G Weidmann, Amit Choudhary
No abstract text is available yet for this article.
February 16, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29448761/spotlight-a-conversation-with-laura-kiessling-and-jennifer-doudna
#18
Laura L Kiessling, Jennifer A Doudna
ACS Chemical Biology recorded a special podcast, in which Editor-in-Chief Laura Kiessling (Massachusetts Institute of Technology) interviews CRISPR investigator and former Associate Editor Jennifer Doudna (University of California, Berkeley). Listen to the podcast here . A transcript of the interview, which has been lightly edited, is published here as part of our Special Issue on the Chemical Biology of CRISPR.
February 16, 2018: ACS Chemical Biology
https://www.readbyqxmd.com/read/29448634/comparison-of-the-off-target-effects-among-one-base-to-three-base-mismatched-targets-of-grna-using-a-blue-to-white-assay
#19
Qian Wang, Li Xiao, Lin Zhou, Wanping Sun, Chungen Xing, Kai Li, Nongyue He
The present study was designed to test a new strategy for comparing the off-target effects of CRISPR/cas9 employing a blue/white colony based assay. Eight types of AmpR plasmids with matched, one base mismatched, two bases mismatched and three bases mismatched targets were constructed. The wild typed alpha peptide of the beta-glactosidase gene and some with mutations, chosen as the targets, were successfully subcloned into the plasmids in an inframe pattern. The relevant gRNA and cas9 were subcloned into the ChloR plasmid...
March 1, 2018: Journal of Nanoscience and Nanotechnology
https://www.readbyqxmd.com/read/29447858/intrathecal-injection-of-scaav9-higf1-prolongs-the-survival-of-als-model-mice-by-inhibiting-the-nf-kb-pathway
#20
HaoJie Hu, HuiQian Lin, WeiSong Duan, Can Cui, ZhongYao Li, YaKun Liu, Wan Wang, Di Wen, Ying Wang, ChunYan Li
Amyotrophic lateral sclerosis (ALS) is a chronic, fatal neurodegenerative disorder characterized by the progressive loss of upper and lower motor neurons. Currently, there is no effective drug for ALS. Recent studies in ALS model mice have shown that insulin-like growth factor-1 (IGF1) may be a promising therapeutic drug. We demonstrate that self-complementary adeno-associated virus serum type 9 encoding the human IGF1 (scAAV9-hIGF1) could significantly postpone the onset and slow down the progression of the disease owning to inhibiting the NF-κB signalling pathway...
February 12, 2018: Neuroscience
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