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https://www.readbyqxmd.com/read/29036676/anti-crisprdb-a-comprehensive-online-resource-for-anti-crispr-proteins
#1
Chuan Dong, Ge-Fei Hao, Hong-Li Hua, Shuo Liu, Abraham Alemayehu Labena, Guoshi Chai, Jian Huang, Nini Rao, Feng-Biao Guo
CRISPR-Cas is a tool that is widely used for gene editing. However, unexpected off-target effects may occur as a result of long-term nuclease activity. Anti-CRISPR proteins, which are powerful molecules that inhibit the CRISPR-Cas system, may have the potential to promote better utilization of the CRISPR-Cas system in gene editing, especially for gene therapy. Additionally, more in-depth research on these proteins would help researchers to better understand the co-evolution of bacteria and phages. Therefore, it is necessary to collect and integrate data on various types of anti-CRISPRs...
September 25, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036619/the-effects-of-dna-supercoiling-on-g-quadruplex-formation
#2
Doreen A T Sekibo, Keith R Fox
Guanine-rich DNAs can fold into four-stranded structures that contain stacks of G-quartets. Bioinformatics studies have revealed that G-rich sequences with the potential to adopt these structures are unevenly distributed throughout genomes, and are especially found in gene promoter regions. With the exception of the single-stranded telomeric DNA, all genomic G-rich sequences will always be present along with their C-rich complements, and quadruplex formation will be in competition with the corresponding Watson-Crick duplex...
September 28, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29036477/a-single-active-site-in-the-mariner-transposase-cleaves-dna-strands-of-opposite-polarity
#3
Corentin Claeys Bouuaert, Ronald Chalmers
The RNase H structural fold defines a large family of nucleic acid metabolizing enzymes that catalyze phosphoryl transfer reactions using two divalent metal ions in the active site. Almost all of these reactions involve only one strand of the nucleic acid substrates. In contrast, cut-and-paste transposases cleave two DNA strands of opposite polarity, which is usually achieved via an elegant hairpin mechanism. In the mariner transposons, the hairpin intermediate is absent and key aspects of the mechanism by which the transposon ends are cleaved remained unknown...
September 19, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29035510/crispri-and-crispra-screens-in-mammalian-cells-for-precision-biology-and-medicine
#4
Martin Kampmann
Next-generation DNA sequencing technologies have led to a massive accumulation of genomic and transcriptomic data from patients and healthy individuals. The major challenge ahead is to understand the functional significance of the elements of the human genome and transcriptome, and implications for diagnosis and treatment. Genetic screens in mammalian cells are a powerful approach to systematically elucidate gene function in health and disease states. In particular, recently developed CRISPR/Cas9-based screening approaches have enormous potential to uncover mechanisms and therapeutic strategies for human diseases...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29035497/conformational-dynamics-of-dna-binding-and-cas3-recruitment-by-the-crispr-rna-guide-cascade-complex
#5
Paul B G van Erp, Angela Patterson, Ravi Kant, Luke Berry, Sarah M Golden, Brittney L Forsman, Joshua Carter, Ryan N Jackson, Brian Bothner, Blake Wiedenheft
Bacteria and archaea rely on CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided adaptive immune systems for sequence specific elimination of foreign nucleic acids. In Escherichia coli, short CRISPR-derived RNAs (crRNAs) assemble with Cas (CRISPR-associated) proteins into a 405-kilodalton multi-subunit surveillance complex called Cascade (CRISPR-associated complex for antiviral defense). Cascade binds foreign DNA complementary to the crRNA guide and recruits Cas3, a trans-acting nuclease-helicase required for target degradation...
October 16, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29035360/ezh2-promotes-degradation-of-stalled-replication-forks-by-recruiting-mus81-through-histone-h3-trimethylation
#6
Beatrice Rondinelli, Ewa Gogola, Hatice Yücel, Alexandra A Duarte, Marieke van de Ven, Roxanne van der Sluijs, Panagiotis A Konstantinopoulos, Jos Jonkers, Raphaël Ceccaldi, Sven Rottenberg, Alan D D'Andrea
The emergence of resistance to poly-ADP-ribose polymerase inhibitors (PARPi) poses a threat to the treatment of BRCA1 and BRCA2 (BRCA1/2)-deficient tumours. Stabilization of stalled DNA replication forks is a recently identified PARPi-resistance mechanism that promotes genomic stability in BRCA1/2-deficient cancers. Dissecting the molecular pathways controlling genomic stability at stalled forks is critical. Here we show that EZH2 localizes at stalled forks where it methylates Lys27 on histone 3 (H3K27me3), mediating recruitment of the MUS81 nuclease...
October 16, 2017: Nature Cell Biology
https://www.readbyqxmd.com/read/29034641/-establishment-of-l-periaxin-gene-knock-out-rsc96-cell-line
#7
Min Liang, Tingting Peng, Yawei Shi
Periaxin, a protein of noncompact myelin, is specifically expressed in the peripheral nervous system (PNS). There are two protein isoform L-periaxin and S-Periaxin by alternative splicing of periaxin gene, playing an important role in the initiation of myelin formation. So far, 18 different mutation sites in L-periaxin gene have been found to induce the peripheral demyelinating neurological charcot-marie-tooth diseases subtype 4F (CMT4F). The technique of activation of transcription activator-like effector nucleases (TALENS) was used to knock out the L-periaxin gene in RSC 96 cell line of Rattus...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29034633/-comparison-of-effects-of-staphylococcal-nuclease-a-fused-with-different-exogenous-dna-fragments
#8
Lixia Fu, Dejun Ji, Xubin Lu, Xian'gan Han, Wenzhi Wei
Staphylococcal nuclease A (SNA) may be used to produce bacterial ghosts for further inactivation of host bacteria and elimination of residual genetic materials. It is still controversial if SNA without signal peptide can be secreted to extracellular matrix and if fusion with other peptide is required for its function in the cytoplasm of host bacteria. To clarify this dispute, a series of temperature-inducible plasmids carrying SNA alone or SNA fused with partial sequences of λ phage cro gene (cSNA) or Mycobacterium tuberculosis urease gene (uSNA) were constructed and evaluated in Escherichia coli...
December 25, 2016: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29032444/modulating-signaling-networks-by-crispr-cas9-mediated-transposable-element-insertion
#9
REVIEW
Luis María Vaschetto
In a recent past, transposable elements (TEs) were referred to as selfish genetic components only capable of copying themselves with the aim of increasing the odds of being inherited. Nonetheless, TEs have been initially proposed as positive control elements acting in synergy with the host. Nowadays, it is well known that TE movement into host genome comprises an important evolutionary mechanism capable of increasing the adaptive fitness. As insights into TE functioning are increasing day to day, the manipulation of transposition has raised an interesting possibility of setting the host functions, although the lack of appropriate genome engineering tools has unpaved it...
October 14, 2017: Current Genetics
https://www.readbyqxmd.com/read/29032264/building-a-safer-and-faster-car-seatbelts-airbags-and-crispr
#10
REVIEW
Miguel-Angel Perales, Partow Kebriaei, Leslie S Kean, Michel Sadelain
Therapeutic T cell engineering has recently garnered widespread interest owing to the success of CD19 (Chimeric Antigen Receptor) CAR therapy. CARs are synthetic receptors for antigen that redirect the specificity and reprogram the function of the T cells in which they are genetically introduced. CARs targeting CD19, a cell surface molecule found in most leukemias and lymphomas, have yielded high remission rates in patients with chemorefractory, relapsed disease, including acute lymphoblastic leukemia, chronic lymphocytic leukemia and non-Hodgkin lymphoma...
October 12, 2017: Biology of Blood and Marrow Transplantation
https://www.readbyqxmd.com/read/29031850/nucleic-acid-loading-and-fluorescent-labeling-of-isolated-extracellular-vesicles-requires-adequate-purification
#11
Stephan Stremersch, Toon Brans, Kevin Braeckmans, Stefaan De Smedt, Koen Raemdonck
Extracellular vesicles (EVs) are nanosized vesicular structures released by cells to communicate with one another. The growing interest in the (patho)physiological function and potential pharmaceutical application of these vesicles is accompanied by a vast number of new research groups entering this research field and a plethora of different protocols to separate EVs from non-vesicular components. This lack of uniformity often generates conflicting or difficult-to-compare results. Here we provide a comparative analysis of different EV isolation strategies, discussing the purity of the final isolate and highlighting the importance of purity on downstream experimental readouts...
October 11, 2017: International Journal of Pharmaceutics
https://www.readbyqxmd.com/read/29028415/crispr-cas9-mediated-noncoding-rna-editing-in-human-cancers
#12
Jie Yang, Xiaodan Meng, Jinchang Pan, Nan Jiang, Chengwei Zhou, Zhenhua Wu, Zhaohui Gong
Cancer is characterized by multiple genetic and epigenetic alterations, including a higher prevalence of mutations of oncogenes and/or tumor suppressors. Mounting evidences have shown that noncoding RNAs (ncRNAs) are involved in the epigenetic regulation of cancer genes and their associated pathways. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease 9 (CRISPR/Cas9) system, a revolutionary genome-editing technology, has shed light on ncRNA-based cancer therapy. Here, we briefly introduce the classifications and mechanisms of CRISPR/Cas9 system...
October 13, 2017: RNA Biology
https://www.readbyqxmd.com/read/29027965/enhancing-the-therapeutic-delivery-of-oligonucleotides-by-chemical-modification-and-nanoparticle-encapsulation
#13
REVIEW
Yating Sun, Yarong Zhao, Xiuting Zhao, Robert J Lee, Lesheng Teng, Chenguang Zhou
Oligonucleotide (ON) drugs, including small interfering RNA (siRNA), microRNA (miRNA) and antisense oligonucleotides, are promising therapeutic agents. However, their low membrane permeability and sensitivity to nucleases present challenges to in vivo delivery. Chemical modifications of the ON offer a potential solution to improve the stability and efficacy of ON drugs. Combined with nanoparticle encapsulation, delivery at the site of action and gene silencing activity of chemically modified ON drugs can be further enhanced...
October 13, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/29027167/characterization-of-the-nucleosome-landscape-by-micrococcal-nuclease-sequencing-mnase-seq
#14
Wieteke Anna Maria Hoeijmakers, Richárd Bártfai
MNase-seq allows the genome-wide examination of the nucleosome landscape by determination of nucleosome positioning and occupancy. Typically, native or formaldehyde fixed chromatin is subjected to digestion by micrococcal nuclease (MNase), which degrades linker DNA and yields mainly mono-nucleosomes. The resulting material can be processed directly or can be subjected to an optional chromatin immunoprecipitation step (MNase-ChIP-seq). De-crosslinked and purified DNA is then subjected to next-generation sequencing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29027166/dna-accessibility-by-mnase-digestions
#15
Ann-Kristin Östlund Farrants
Micrococcal nuclease (MNase) digestion of chromatin cuts linker DNA between neighboring nucleosomes and in this way generates mononucleosomes. The protected fragments can then be analyzed by genome-wide sequencing techniques or by quantitative PCR to obtain information about the positions of nucleosomes in the chromatin. Nucleosomes are differentially sensitive to MNase digestion, which means that titrations of MNase should be performed to obtain a comprehensive map of the nucleosome positions of a chromatin region or genome...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29023106/noncoding-rna-surveillance-the-ends-justify-the-means
#16
Cedric Belair, Soyeong Sim, Sandra L Wolin
Numerous surveillance pathways sculpt eukaryotic transcriptomes by degrading unneeded, defective, and potentially harmful noncoding RNAs (ncRNAs). Because aberrant and excess ncRNAs are largely degraded by exoribonucleases, a key characteristic of these RNAs is an accessible, protein-free 5' or 3' end. Most exoribonucleases function with cofactors that recognize ncRNAs with accessible 5' or 3' ends and/or increase the availability of these ends. Noncoding RNA surveillance pathways were first described in budding yeast, and there are now high-resolution structures of many components of the yeast pathways and significant mechanistic understanding as to how they function...
October 12, 2017: Chemical Reviews
https://www.readbyqxmd.com/read/29022923/gadd45a-opens-up-the-promoter-regions-of-mir-295-facilitating-pluripotency-induction
#17
Linpeng Li, Keshi Chen, Yi Wu, Qi Long, Danyun Zhao, Bochao Ma, Duanqing Pei, Xingguo Liu
MicroRNAs (miRNAs) play crucial roles in the establishment of pluripotent state by controlling pluripotent network. However, the molecular mechanisms controlling miRNAs during somatic cell reprogramming remain obscure. In this study, we show Gadd45a (growth arrest and DNA-damage-inducible protein 45a) enhances reprogramming by activating miR-295. Furthermore, we show that Gadd45a binds the promoter regions of miR-295. Nuclease accessibility assay indicates that Gadd45a opens the promoter regions of miR-295...
October 12, 2017: Cell Death & Disease
https://www.readbyqxmd.com/read/29021890/zebrafish-knockout-of-down-syndrome-gene-dyrk1a-shows-social-impairments-relevant-to-autism
#18
Oc-Hee Kim, Hyun-Ju Cho, Enna Han, Ted Inpyo Hong, Krishan Ariyasiri, Jung-Hwa Choi, Kyu-Seok Hwang, Yun-Mi Jeong, Se-Yeol Yang, Kweon Yu, Doo-Sang Park, Hyun-Woo Oh, Erica E Davis, Charles E Schwartz, Jeong-Soo Lee, Hyung-Goo Kim, Cheol-Hee Kim
BACKGROUND: DYRK1A maps to the Down syndrome critical region at 21q22. Mutations in this kinase-encoding gene have been reported to cause microcephaly associated with either intellectual disability or autism in humans. Intellectual disability accompanied by microcephaly was recapitulated in a murine model by overexpressing Dyrk1a which mimicked Down syndrome phenotypes. However, given embryonic lethality in homozygous knockout (KO) mice, no murine model studies could present sufficient evidence to link Dyrk1a dysfunction with autism...
2017: Molecular Autism
https://www.readbyqxmd.com/read/29021165/preclinical-modeling-highlights-the-therapeutic-potential-of-hematopoietic-stem-cell-gene-editing-for-correction-of-scid-x1
#19
Giulia Schiroli, Samuele Ferrari, Anthony Conway, Aurelien Jacob, Valentina Capo, Luisa Albano, Tiziana Plati, Maria C Castiello, Francesca Sanvito, Andrew R Gennery, Chiara Bovolenta, Rahul Palchaudhuri, David T Scadden, Michael C Holmes, Anna Villa, Giovanni Sitia, Angelo Lombardo, Pietro Genovese, Luigi Naldini
Targeted genome editing in hematopoietic stem/progenitor cells (HSPCs) is an attractive strategy for treating immunohematological diseases. However, the limited efficiency of homology-directed editing in primitive HSPCs constrains the yield of corrected cells and might affect the feasibility and safety of clinical translation. These concerns need to be addressed in stringent preclinical models and overcome by developing more efficient editing methods. We generated a humanized X-linked severe combined immunodeficiency (SCID-X1) mouse model and evaluated the efficacy and safety of hematopoietic reconstitution from limited input of functional HSPCs, establishing thresholds for full correction upon different types of conditioning...
October 11, 2017: Science Translational Medicine
https://www.readbyqxmd.com/read/29020979/perfectly-matched-20-nucleotide-guide-rna-sequences-enable-robust-genome-editing-using-high-fidelity-spcas9-nucleases
#20
Dingbo Zhang, Huawei Zhang, Tingdong Li, Kunling Chen, Jin-Long Qiu, Caixia Gao
High-fidelity SpCas9 variants (eSpCas9 and SpCas9-HF1) have been engineered to reduce off-target effects. We found that changes in guide RNA length induced significant reductions in the editing activities of SpCas9 variants in plant cells. Single guide RNAs harboring precise, perfectly matched 20-nucleotide guide sequences are necessary for high on-target editing activities of eSpCas9 and SpCas9-HF1. Precise 20-nucleotide guide sequences derived from tRNA-sgRNA precursors enable robust on-target editing by these variants with enhanced specificity...
October 11, 2017: Genome Biology
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