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https://www.readbyqxmd.com/read/29237052/multimode-drug-inducible-crispr-cas9-devices-for-transcriptional-activation-and-genome-editing
#1
Jia Lu, Chen Zhao, Yingze Zhao, Jingfang Zhang, Yue Zhang, Li Chen, Qiyuan Han, Yue Ying, Shuai Peng, Runna Ai, Yu Wang
Precise investigation and manipulation of dynamic biological processes often requires molecular modulation in a controlled inducible manner. The clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) has emerged as a versatile tool for targeted gene editing and transcriptional programming. Here, we designed and vigorously optimized a series of Hybrid drug Inducible CRISPR/Cas9 Technologies (HIT) for transcriptional activation by grafting a mutated human estrogen receptor (ERT2) to multiple CRISPR/Cas9 systems, which renders them 4-hydroxytamoxifen (4-OHT) inducible for the access of genome...
December 9, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29236091/noncoding-copy-number-variations-are-associated-with-congenital-limb-malformation
#2
Ricarda Flöttmann, Bjørt K Kragesteen, Sinje Geuer, Magdalena Socha, Lila Allou, Anna Sowińska-Seidler, Laure Bosquillon de Jarcy, Johannes Wagner, Aleksander Jamsheer, Barbara Oehl-Jaschkowitz, Lars Wittler, Deepthi de Silva, Ingo Kurth, Idit Maya, Fernando Santos-Simarro, Wiebke Hülsemann, Eva Klopocki, Roger Mountford, Alan Fryer, Guntram Borck, Denise Horn, Pablo Lapunzina, Meredith Wilson, Bénédicte Mascrez, Denis Duboule, Stefan Mundlos, Malte Spielmann
PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing...
October 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29235467/in-situ-functional-dissection-of-rna-cis-regulatory-elements-by-multiplex-crispr-cas9-genome-engineering
#3
Qianxin Wu, Quentin R V Ferry, Toni A Baeumler, Yale S Michaels, Dimitrios M Vitsios, Omer Habib, Roland Arnold, Xiaowei Jiang, Stefano Maio, Bruno R Steinkraus, Marta Tapia, Paolo Piazza, Ni Xu, Georg A Holländer, Thomas A Milne, Jin-Soo Kim, Anton J Enright, Andrew R Bassett, Tudor A Fulga
RNA regulatory elements (RREs) are an important yet relatively under-explored facet of gene regulation. Deciphering the prevalence and functional impact of this post-transcriptional control layer requires technologies for disrupting RREs without perturbing cellular homeostasis. Here we describe genome-engineering based evaluation of RNA regulatory element activity (GenERA), a clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 platform for in situ high-content functional analysis of RREs...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233900/systematic-crispr-cas9-mediated-modifications-of-plasmodium-yoelii-apiap2-genes-reveal-functional-insights-into-parasite-development
#4
Cui Zhang, Zhenkui Li, Huiting Cui, Yuanyuan Jiang, Zhenke Yang, Xu Wang, Han Gao, Cong Liu, Shujia Zhang, Xin-Zhuan Su, Jing Yuan
Malaria parasites have a complex life cycle with multiple developmental stages in mosquito and vertebrate hosts, and different developmental stages express unique sets of genes. Unexpectedly, many transcription factors (TFs) commonly found in eukaryotic organisms are absent in malaria parasites; instead, a family of genes encoding proteins similar to the plant Apetala2 (ApiAP2) transcription factors is expanded in the parasites. Several malaria ApiAP2 genes have been shown to play a critical role in parasite development; however, the functions of the majority of the ApiAP2 genes remain to be elucidated...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29233895/disabling-a-type-i-e-crispr-cas-nuclease-with-a-bacteriophage-encoded-anti-crispr-protein
#5
April Pawluk, Megha Shah, Marios Mejdani, Charles Calmettes, Trevor F Moraes, Alan R Davidson, Karen L Maxwell
CRISPR (clustered regularly interspaced short palindromic repeat)-Cas adaptive immune systems are prevalent defense mechanisms in bacteria and archaea. They provide sequence-specific detection and neutralization of foreign nucleic acids such as bacteriophages and plasmids. One mechanism by which phages and other mobile genetic elements are able to overcome the CRISPR-Cas system is through the expression of anti-CRISPR proteins. Over 20 different families of anti-CRISPR proteins have been described, each of which inhibits a particular type of CRISPR-Cas system...
December 12, 2017: MBio
https://www.readbyqxmd.com/read/29232857/mir-34a-regulates-sperm-motility-in-zebrafish
#6
Wenjie Guo, Binyue Xie, Shuting Xiong, Xufang Liang, Jian-Fang Gui, Jie Mei
Increasing attention has been focused on the role of microRNAs in post-transcription regulation during spermatogenesis. Recently, the miR-34 family has been shown to be involved in the spermatogenesis, but the clear function of the miR-34 family in spermatogenesis is still obscure. Here we analyzed the function of miR-34a, a member of the miR-34 family, during spermatogenesis using miR-34a knockout zebrafish generated by the clustered regularly interspaced short palindromic repeats/associated protein 9 (CRISPR/Cas9) system...
December 10, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29230929/application-of-protoplast-technology-to-crispr-cas9-mutagenesis-from-single-cell-mutation-detection-to-mutant-plant-regeneration
#7
Choun-Sea Lin, Chen-Tran Hsu, Ling-Hung Yang, Lan-Ying Lee, Jin-Yuan Fu, Qiao-Wei Cheng, Fu-Hui Wu, Han Chen-Wei Hsiao, Yesheng Zhang, Ru Zhang, Wan-Jung Chang, Chen-Ting Yu, Wen Wang, Li-Jen Liao, Stanton B Gelvin, Ming-Che Shih
Plant protoplasts are useful for assessing the efficiency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR Associated Protein 9 (Cas9) mutagenesis. We improved the process of protoplast isolation and transfection of several plant species. We also developed a method to isolate and regenerate single mutagenized Nicotianna tabacum protoplasts into mature plants. Following transfection of protoplasts with constructs encoding Cas9 and sgRNAs, target gene DNA could be amplified for further analysis to determine mutagenesis efficiency...
December 12, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/29229728/cas9-enhances-bacterial-virulence-by-repressing-the-regr-transcriptional-regulator-in-streptococcus-agalactiae
#8
Ke Ma, Qing Cao, Su Luo, Zhaofei Wang, Guangjin Liu, Chengping Lu, Yongjie Liu
Clustered regularly interspaced palindromic repeats (CRISPR) and its associated cas genes have been demonstrated to regulate self-genes and virulence in many pathogens. In this study, we found that inactivation of cas9 caused reduced adhesion and intracellular survival of the piscine Streptococcus agalactiae strain GD201008-001 and significantly decreased the virulence of this strain in zebrafish and mice. Further investigation indicated that the regR transcriptional regulator was upregulated in the Δcas9 mutant...
December 11, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/29229685/the-essential-role-of-phospho-t38-cpi-17-in-the-maintenance-of-physiological-blood-pressure-using-genetically-modified-mice
#9
Qunhui Yang, Wataru Fujii, Noriyuki Kaji, Shigeru Kakuta, Kodai Kada, Masayoshi Kuwahara, Hirokazu Tsubone, Hiroshi Ozaki, Masatoshi Hori
PKC-potentiated phosphorylation-dependent inhibitory protein of protein phosphatase 1 (CPI-17), an endogenous myosin phosphatase inhibitory protein, is considered a key molecule for Ca2+ sensitization of the contractile apparatus. Here, we have used clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 to generate CPI-17-deficient [knockout (KO)] and threonine 38 (T38)-phospho-resistant mice [Threonine mutant into Alanine (TA)], and then effects of CPI-17 on vascular contractility in vitro and mean blood pressure (MBP) in vivo were investigated...
December 11, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/29228730/wisp2-disruption-represses-cxcr4-expression-and-inhibits-bmscs-homing-to-injured-liver
#10
Dan Qin, Yi Yan, Bian Hu, Wanpo Zhang, Hanmin Li, Xiaodong Li, Shenghui Liu, Depeng Dai, Xiongji Hu, Xingxu Huang, Lisheng Zhang
Liver regeneration/repair is a compensatory regrowth following acute liver failure, and bone marrow-derived mesenchyme stem cell (BMSC) transplantation is an effective therapy that promotes liver regeneration/repair. Wnt1 inducible signaling pathway protein 2 (Wisp2) is highly expressed in BMSCs, however, its function remains unclear. In this work, we used clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein -9 nuclease (CRISPR/Cas9) genome editing technology to knockdown Wisp2 in BMSCs, and these modified cells were then transplanted into rats which were induced by the 2-AAF/PH...
November 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29224076/next-generation-sequencing-of-genome-wide-crispr-screens
#11
Edwin H Yau, Tariq M Rana
Genome-wide functional genomic screens utilizing the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 system have proven to be a powerful tool for systematic genomic perturbation in mammalian cells and provide an alternative to previous screens utilizing RNA interference technology. The wide availability of these libraries through public plasmid repositories as well as the decreasing cost and speed in quantifying these screens using high-throughput next-generation sequencing (NGS) allows for the adoption of the technology in a variety of laboratories interested in diverse biologic questions...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29221716/crispr-based-gene-drives-for-pest-control
#12
Gus R McFarlane, C Bruce A Whitelaw, Simon G Lillico
Clustered regularly interspaced short palindromic repeats (CRISPR)-based gene drives (GDs) could be used to spread desirable genetic elements through wild populations. With the imminent development of this technology in vertebrates, we believe that it is timely to highlight two forms of sex-ratio distorting GDs that show potential as pest management tools.
November 9, 2017: Trends in Biotechnology
https://www.readbyqxmd.com/read/29221602/what-can-palindromic-rheumatism-tell-us
#13
REVIEW
Kulveer Mankia, Paul Emery
Palindromic rheumatism (PR) is a syndrome characterised by recurrent, self-resolving inflammatory attacks in and around the joints. An association between PR and rheumatoid arthritis (RA) has long been postulated; a significant proportion of PR patients eventually develop RA and the majority also have anti-CCP antibodies. Therefore, PR is often considered a prodrome of RA. However, the clinical and imaging phenotype of PR has several important distinctions from RA. This suggests that despite the similarities, distinct disease mechanisms are at play...
February 2017: Best Practice & Research. Clinical Rheumatology
https://www.readbyqxmd.com/read/29221599/symptoms-in-individuals-at-risk-of-rheumatoid-arthritis
#14
REVIEW
Gurpreet Singh Jutley, Zahira P Latif, Karim Raza
An increasing interest in treating individuals at risk of rheumatoid arthritis (RA) to prevent the development of this chronic condition has focussed attention on the identification of risk factors of this disease. Most patients who develop RA progress through a preceding symptomatic phase that may take the form of arthralgia, palindromic rheumatism or unclassified arthritis before a disease currently classifiable as RA is established. An understanding of symptoms that identify individuals as being at risk of RA is a critical issue...
February 2017: Best Practice & Research. Clinical Rheumatology
https://www.readbyqxmd.com/read/29218031/crispr-cas-systems-in-bacteroides-fragilis-an-important-pathobiont-in-the-human-gut-microbiome
#15
Mehrdad Tajkarimi, Hannah M Wexler
Background: While CRISPR-Cas systems have been identified in bacteria from a wide variety of ecological niches, there are no studies to describe CRISPR-Cas elements in Bacteroides species, the most prevalent anaerobic bacteria in the lower intestinal tract. Microbes of the genus Bacteroides make up ~25% of the total gut microbiome. Bacteroides fragilis comprises only 2% of the total Bacteroides in the gut, yet causes of >70% of Bacteroides infections. The factors causing it to transition from benign resident of the gut microbiome to virulent pathogen are not well understood, but a combination of horizontal gene transfer (HGT) of virulence genes and differential transcription of endogenous genes are clearly involved...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29215041/crispr-cas9-delivery-with-one-single-adenoviral-vector-devoid-of-all-viral-genes
#16
Eric Ehrke-Schulz, Maren Schiwon, Theo Leitner, Stephan Dávid, Thorsten Bergmann, Jing Liu, Anja Ehrhardt
The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system revolutionized the field of gene editing but viral delivery of the CRISPR/Cas9 system has not been fully explored. Here we adapted clinically relevant high-capacity adenoviral vectors (HCAdV) devoid of all viral genes for the delivery of the CRISPR/Cas9 machinery using a single viral vector. We present a platform enabling fast transfer of the Cas9 gene and gRNA expression units into the HCAdV genome including the option to choose between constitutive or inducible Cas9 expression and gRNA multiplexing...
December 7, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29212218/optimized-guide-rna-structure-for-genome-editing-via-cas9
#17
Jianyong Xu, Wei Lian, Yuning Jia, Lingyun Li, Zhong Huang
The genome editing tool Cas9-gRNA (guide RNA) has been successfully applied in different cell types and organisms with high efficiency. However, more efforts need to be made to enhance both efficiency and specificity. In the current study, we optimized the guide RNA structure of Streptococcus pyogenes CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas (CRISPR-associated) system to improve its genome editing efficiency. Comparing with the original functional structure of guide RNA, which is composed of crRNA and tracrRNA, the widely used chimeric gRNA has shorter crRNA and tracrRNA sequence...
November 7, 2017: Oncotarget
https://www.readbyqxmd.com/read/29212058/genetic-analysis-and-crispr-typing-of-salmonella-enterica-serovar-enteritidis-from-different-sources-revealed-potential-transmission-from-poultry-and-pig-to-human
#18
Qiuchun Li, Xin Wang, Kequan Yin, Yachen Hu, Haiyan Xu, Xiaolei Xie, Lijuan Xu, Xiao Fei, Xiang Chen, Xinan Jiao
Salmonella enterica serovar Enteritidis (S. Enteritidis) is one of the most prevalent serotypes in Salmonella isolated from poultry and the most commonly reported cause of human salmonellosis. In this study, we aimed to assess the genetic diversity of 329 S. Enteritidis strains isolated from different sources from 2009 to 2016 in China. Clustered regularly interspaced short palindromic repeat (CRISPR) typing was used to characterize these 262 chicken clinical isolates, 38 human isolates, 18 pig isolates, six duck isolates, three goose isolates and two isolates of unknown source...
November 28, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/29208713/sbcc-sbcd-and-exoi-process-convergent-forks-to-complete-chromosome-replication
#19
Brian M Wendel, Jessica M Cole, Charmain T Courcelle, Justin Courcelle
SbcC-SbcD are the bacterial orthologs of Mre11-Rad50, a nuclease complex essential for genome stability, normal development, and viability in mammals. In vitro, these enzymes degrade long DNA palindromic structures. When inactivated along with ExoI in Escherichia coli, or Sae2 in eukaryotes, palindromic amplifications arise and propagate in cells. However, long DNA palindromes are not normally found in bacterial or human genomes, leaving the cellular substrates and function of these enzymes unknown. Here, we show that during the completion of DNA replication, convergent replication forks form a palindrome-like structural intermediate that requires nucleolytic processing by SbcC-SbcD and ExoI before chromosome replication can be completed...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29208606/emerging-role-of-crispr-cas9-technology-for-micrornas-editing-in-cancer-research
#20
REVIEW
Guillermo Aquino-Jarquin
MicroRNAs (miRNA) are small, noncoding RNA molecules with a master role in the regulation of important tasks in different critical processes of cancer pathogenesis. Because there are different miRNAs implicated in all the stages of cancer, for example, functioning as oncogenes, this makes these small molecules suitable targets for cancer diagnosis and therapy. RNA-mediated interference has been one major approach for sequence-specific regulation of gene expression in eukaryotic organisms. Recently, the CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 system, first identified in bacteria and archaea as an adaptive immune response to invading genetic material, has been explored as a sequence-specific molecular tool for editing genomic sequences for basic research in life sciences and for therapeutic purposes...
December 5, 2017: Cancer Research
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