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Translator Translate texts with the world's best machine translation technology, developed by the creators of Linguee. Linguee Look up words and phrases in comprehensive, reliable bilingual dictionaries and search through billions of online translations. Blog Press Information Linguee Apps. The eukaryotic cells may be those of or derived from a particular organism, such as a plant or a mammal, including but not limited to human, or non-human eukaryote or animal or mammal as herein discussed, e.


In general, codon optimization refers to a process of modifying a nucleic acid sequence for enhanced expression in the host cells of interest by replacing at least one codon e. Various species exhibit particular bias for certain codons of a particular amino acid. Codon bias differences in codon usage between organisms often correlates with the efficiency of translation of messenger RNA mRNA , which is in turn believed to be dependent on, among other things, the properties of the codons being translated and the availability of particular transfer RNA tRNA molecules.


The predominance of selected tRNAs in a cell is generally a reflection of the codons used most frequently in peptide synthesis.


Accordingly, genes can be tailored for optimal gene expression in a given organism based on codon optimization. See Nakamura, Y. Acids Res. Computer algorithms for codon optimizing a particular sequence for expression in a particular host cell are also available, such as Gene Forge Aptagen; Jacobus, Pa.


In some embodiments, one or more codons e. As to codon usage in yeast, reference is made to the online Yeast Genome database available at worldwideweb. As to codon usage in plants including algae, reference is made to Codon usage in higher plants, green algae, and cyanobacteria , Campbell and Gowri, Plant Physiol. In some embodiments, the RNA-targeting effector protein comprises about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the amino-terminus, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more NLSs at or near the carboxy-terminus, or a combination of these e.


In some embodiments, an NLS is considered near the N- or C-terminus when the nearest amino acid of the NLS is within about 1, 2, 3, 4, 5, 10, 15, 20, 25, 30, 40, 50, or more amino acids along the polypeptide chain from the N- or C-terminus. In general, strength of nuclear localization activity may derive from the number of NLSs in the nucleic acid-targeting effector protein, the particular NLS s used, or a combination of these factors. Detection of accumulation in the nucleus may be performed by any suitable technique.


For example, a detectable marker may be fused to the nucleic acid-targeting protein, such that location within a cell may be visualized, such as in combination with a means for detecting the location of the nucleus e.


Cell nuclei may also be isolated from cells, the contents of which may then be analyzed by any suitable process for detecting protein, such as immunohistochemistry, Western blot, or enzyme activity assay. Accumulation in the nucleus may also be determined indirectly, such as by an assay for the effect of nucleic acid-targeting complex formation e. In preferred embodiments of the herein described Cpf1 effector protein complexes and systems the codon optimized Cpf1 effector proteins comprise an NLS attached to the C-terminal of the protein.


In certain embodiments, other localization tags may be fused to the Cas protein, such as without limitation for localizing the Cas to particular sites in a cell, such as organells, such mitochondria, plastids, chloroplast, vesicles, golgi, nuclear or cellular membranes, ribosomes, nucleoluse, ER, cytoskeleton, vacuoles, centrosome, nucleosome, granules, centrioles, etc.


In some embodiments, one or more vectors driving expression of one or more elements of a nucleic acid-targeting system are introduced into a host cell such that expression of the elements of the nucleic acid-targeting system direct formation of a nucleic acid-targeting complex at one or more target sites.


For example, a nucleic acid-targeting effector enzyme and a nucleic acid-targeting guide RNA could each be operably linked to separate regulatory elements on separate vectors.


RNA s of the nucleic acid-targeting system can be delivered to a transgenic nucleic acid-targeting effector protein animal or mammal, e. Alternatively, two or more of the elements expressed from the same or different regulatory elements, may be combined in a single vector, with one or more additional vectors providing any components of the nucleic acid-targeting system not included in the first vector.


The coding sequence of one element may be located on the same or opposite strand of the coding sequence of a second element, and oriented in the same or opposite direction. In some embodiments, a single promoter drives expression of a transcript encoding a nucleic acid-targeting effector protein and the nucleic acid-targeting guide RNA, embedded within one or more intron sequences e.


In some embodiments, the nucleic acid-targeting effector protein and the nucleic acid-targeting guide RNA may be operably linked to and expressed from the same promoter. In some embodiments, one or more insertion sites e. When multiple different guide sequences are used, a single expression construct may be used to target nucleic acid-targeting activity to multiple different, corresponding target sequences within a cell.


For example, a single vector may comprise about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 15, 20, or more guide sequences. In some embodiments, about or more than about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more such guide-sequence-containing vectors may be provided, and optionally delivered to a cell.


In some embodiments, a vector comprises a regulatory element operably linked to an enzyme-coding sequence encoding a a nucleic acid-targeting effector protein.


Nucleic acid-targeting effector protein or nucleic acid-targeting guide RNA or RNA s can be delivered separately; and advantageously at least one of these is delivered via a particle complex.


Nucleic acid-targeting effector protein mRNA might be administered hours preferably around hours prior to the administration of nucleic acid-targeting guide RNA. Alternatively, nucleic acid-targeting effector protein mRNA and nucleic acid-targeting guide RNA can be administered together.


In one aspect, the invention provides methods for using one or more elements of a nucleic acid-targeting system. The nucleic acid-targeting complex of the invention provides an effective means for modifying a target DNA or RNA single or double stranded, linear or super-coiled.


The nucleic acid-targeting complex of the invention has a wide variety of utility including modifying e. As such the nucleic acid-targeting complex of the invention has a broad spectrum of applications in, e. An exemplary nucleic acid-targeting complex comprises a DNA or RNA-targeting effector protein complexed with a guide RNA hybridized to a target sequence within the target locus of interest.


In one embodiment, this invention provides a method of cleaving a target RNA. In an embodiment, the nucleic acid-targeting complex of the invention, when introduced into a cell, may create a break e.


For example, the method can be used to cleave a disease RNA in a cell. For example, an exogenous RNA template comprising a sequence to be integrated flanked by an upstream sequence and a downstream sequence may be introduced into a cell.


The upstream and downstream sequences share sequence similarity with either side of the site of integration in the RNA. The exogenous RNA template comprises a sequence to be integrated e. The sequence for integration may be a sequence endogenous or exogenous to the cell.


Thus, the sequence for integration may be operably linked to an appropriate control sequence or sequences. Alternatively, the sequence to be integrated may provide a regulatory function. The upstream sequence is a RNA sequence that shares sequence similarity with the RNA sequence upstream of the targeted site for integration.


Similarly, the downstream sequence is a RNA sequence that shares sequence similarity with the RNA sequence downstream of the targeted site of integration. An upstream or downstream sequence may comprise from about 20 bp to about bp, for example, about 50, , , , , , , , , , , , , , , , , , , , , , , , , or bp.


In some methods, the exemplary upstream or downstream sequence have about bp to about bp, about bp to about bp, or more particularly about bp to about bp. In some methods, the exogenous RNA template may further comprise a marker.


Such a marker may make it easy to screen for targeted integrations. Examples of suitable markers include restriction sites, fluorescent proteins, or selectable markers. The exogenous RNA template of the invention can be constructed using recombinant techniques see, for example, Sambrook et al. The presence of a double-stranded break facilitates integration of the template. In other embodiments, this invention provides a method of modifying expression of a RNA in a eukaryotic cell.


The method comprises increasing or decreasing expression of a target polynucleotide by using a nucleic acid-targeting complex that binds to the DNA or RNA e. In some methods, a target RNA can be inactivated to effect the modification of the expression in a cell. For example, upon the binding of a RNA-targeting complex to a target sequence in a cell, the target RNA is inactivated such that the sequence is not translated, the coded protein is not produced, or the sequence does not function as the wild-type sequence does.


The target RNA can be a sequence e. Examples of target RNA include a sequence associated with a signaling biochemical pathway, e. A disease-associated RNA also refers to a RNA transcribed from a gene possessing mutation s or genetic variation that is directly responsible or is in linkage disequilibrium with a gene s that is responsible for the etiology of a disease. The translated products may be known or unknown, and may be at a normal or abnormal level. In some embodiments, the method comprises allowing a nucleic acid-targeting complex to bind to the DNA or RNA such that said binding results in increased or decreased expression of said DNA or RNA; wherein the nucleic acid-targeting complex comprises a nucleic acid-targeting effector protein complexed with a guide RNA.


In fact, these sampling, culturing and re-introduction options apply across the aspects of the present invention. In one aspect, the invention provides for methods of modifying a target DNA or RNA in a eukaryotic cell, which may be in vivo, ex vivo or in vitro.


In some embodiments, the method comprises sampling a cell or population of cells from a human or non-human animal, and modifying the cell or cells. Culturing may occur at any stage ex vivo. The cell or cells may even be re-introduced into the non-human animal or plant.


For re-introduced cells it is particularly preferred that the cells are stem cells. Indeed, in any aspect of the invention, the nucleic acid-targeting complex may comprise a nucleic acid-targeting effector protein complexed with a guide RNA hybridized to a target sequence. The invention relates to the engineering and optimization of systems, methods and compositions used for the control of gene expression involving DNA or RNA sequence targeting, that relate to the nucleic acid-targeting system and components thereof.


An advantage of the present methods is that the CRISPR system minimizes or avoids off-target binding and its resulting side effects. In certain embodiments, the crRNA sequence is between 42 and 44 nucleotides in length, and the nucleic acid-targeting Cas protein is Cpf1 of Francisella tularensis subsp. In certain embodiments, the crRNA comprises, consists essentially of, or consists of 19 nucleotides of a direct repeat and between 23 and 25 nucleotides of spacer sequence, and the nucleic acid-targeting Cas protein is Cpf1 of Francisella tularensis subsp.


The use of two different aptamers each associated with a distinct nucleic acid-targeting guide RNAs allows an activator-adaptor protein fusion and a repressor-adaptor protein fusion to be used, with different nucleic acid-targeting guide RNAs, to activate expression of one DNA or RNA, whilst repressing another. They, along with their different guide RNAs can be administered together, or substantially together, in a multiplexed approach.


A large number of such modified nucleic acid-targeting guide RNAs can be used all at the same time, for example 10 or 20 or 30 and so forth, whilst only one or at least a minimal number of effector protein molecules need to be delivered, as a comparatively small number of effector protein molecules can be used with a large number modified guides.


The adaptor protein may be associated preferably linked or fused to one or more activators or one or more repressors. For example, the adaptor protein may be associated with a first activator and a second activator. The first and second activators may be the same, but they are preferably different activators. Three or more or even four or more activators or repressors may be used, but package size may limit the number being higher than 5 different functional domains.


Linkers are preferably used, over a direct fusion to the adaptor protein, where two or more functional domains are associated with the adaptor protein. Suitable linkers might include the GlySer linker. It is also envisaged that the nucleic acid-targeting effector protein-guide RNA complex as a whole may be associated with two or more functional domains.


For example, there may be two or more functional domains associated with the nucleic acid-targeting effector protein, or there may be two or more functional domains associated with the guide RNA via one or more adaptor proteins , or there may be one or more functional domains associated with the nucleic acid-targeting effector protein and one or more functional domains associated with the guide RNA via one or more adaptor proteins.


The fusion between the adaptor protein and the activator or repressor may include a linker. Linkers can be used between the guide RNAs and the functional domain activator or repressor , or between the nucleic acid-targeting Cas protein Cas and the functional domain activator or repressor. In one aspect, the invention provides a method of generating a model eukaryotic cell comprising a mutated disease gene.


In some embodiments, a disease gene is any gene associated an increase in the risk of having or developing a disease. In some embodiments, the method comprises a introducing one or more vectors into a eukaryotic cell, wherein the one or more vectors drive expression of one or more of: a Cpf1 enzyme and a protected guide RNA comprising a guide sequence linked to a direct repeat sequence; and b allowing a CRISPR complex to bind to a target polynucleotide to effect cleavage of the target polynucleotide within said disease gene, wherein the CRISPR complex comprises the Cpf1 enzyme complexed with the guide RNA comprising the sequence that is hybridized to the target sequence within the target polynucleotide, thereby generating a model eukaryotic cell comprising a mutated disease gene.


In some embodiments, said cleavage comprises cleaving one or two strands at the location of the target sequence by said Cpf1 enzyme. In some embodiments, said cleavage results in decreased transcription of a target gene. In some embodiments, the method further comprises repairing said cleaved target polynucleotide by non-homologous end joining NHEJ -based gene insertion mechanisms with an exogenous template polynucleotide, wherein said repair results in a mutation comprising an insertion, deletion, or substitution of one or more nucleotides of said target polynucleotide.


In some embodiments, said mutation results in one or more amino acid changes in a protein expression from a gene comprising the target sequence. In an aspect the invention provides methods as herein discussed wherein the host is a eukaryotic cell. In an aspect the invention provides a method as herein discussed wherein the host is a mammalian cell. In an aspect the invention provides a method as herein discussed, wherein the host is a non-human eukaryote cell.


In an aspect the invention provides a method as herein discussed, wherein the non-human eukaryote cell is a non-human mammal cell. In an aspect the invention provides a method as herein discussed, wherein the non-human mammal cell may be including, but not limited to, primate bovine, ovine, procine, canine, rodent, Leporidae such as monkey, cow, sheep, pig, dog, rabbit, rat or mouse cell.


In an aspect the invention provides a method as herein discussed, the cell may be a a non-mammalian eukaryotic cell such as poultry bird e. In an aspect the invention provides a method as herein discussed, the non-human eukaryote cell is a plant cell. In one aspect, the invention provides a method for developing a biologically active agent that modulates a cell signaling event associated with a disease gene.


In some embodiments, the method comprises a contacting a test compound with a model cell of any one of the above-described embodiments; and b detecting a change in a readout that is indicative of a reduction or an augmentation of a cell signaling event associated with said mutation in said disease gene, thereby developing said biologically active agent that modulates said cell signaling event associated with said disease gene. In another preferred embodiment of the invention the cell to be selected may be a eukaryotic cell.


Aspects of the invention allow for selection of specific cells without requiring a selection marker or a two-step process that may include a counter-selection system. In particular embodiments, the model eukaryotic cell is comprised within a model eukaryotic organism. In one aspect, the invention provides a recombinant polynucleotide comprising a guide sequence downstream of a direct repeat sequence, wherein the guide sequence when expressed directs sequence-specific binding of a Cpf1 CRISPR-Cas complex to a corresponding target sequence present in a eukaryotic cell.


In some embodiments, the target sequence is a viral sequence present in a eukaryotic cell. In some embodiments, the target sequence is a proto-oncogene or an oncogene. In some embodiments, the host cell comprises components a and b. In some embodiments, component a , component b , or components a and b are stably integrated into a genome of the host eukaryotic cell.


In some embodiments, component a further comprises two or more guide sequences operably linked to the first regulatory element, wherein when expressed, each of the two or more guide sequences direct sequence specific binding of a Cpf1 CRISPR-Cas complex to a different target sequence in a eukaryotic cell. In some embodiments, the Cpf1 enzyme is derived from Francisella tularensis 1 , Francisella tularensis subsp.


BV3L6 , Lachnospiraceae bacterium MA , Candidatus Methanoplasma termitum, Eubacterium eligens, Moraxella bovoculi , Leptospira inadai, Lachnospiraceae bacterium ND , Porphyromonas crevioricanis 3 , Prevotella disiens , or Porphyromonas macacae Cpf1, including any of the modified enzymes as described herein, and may include further alteration or mutation of the Cpf1, and can be a chimeric Cpf1.


In some embodiments, the Cpf1 lacks DNA strand cleavage activity e. In some embodiments, the first regulatory element is a polymerase III promoter.


In some embodiments, the second regulatory element is a polymerase II promoter. In some embodiments, the direct repeat has a minimum length of 16 nts and a single stem loop. In further embodiments the direct repeat has a length longer than 16 nts, preferably more than 17 nts, and has more than one stem loop or optimized secondary structures. In some embodiments, the guide sequence is at least 16, 17, 18, 19, 20, 25 nucleotides, or between , or between , or between nucleotides in length.


In one aspect, the invention provides a kit comprising one or more of the components described herein. In some embodiments, the kit comprises a vector system or host cell as described herein and instructions for using the kit.


Computational analysis of the primary structure of Cpf1 nucleases reveals three distinct regions FIG. Several small stretches of unstructured regions are predicted within the Cpf1 primary structure. Unstructured regions, which are exposed to the solvent and not conserved within different Cpf1 orthologs, are preferred sides for splits and insertions of small protein sequences FIGS.


In addition, these sides can be used to generate chimeric proteins between Cpf1 orthologs. Based on the above information, mutants can be generated which lead to inactivation of the enzyme or which modify the double strand nuclease to nickase activity. In alternative embodiments, this information is used to develop enzymes with reduced off-target effects described elsewhere herein. In certain of the above-described Cpf1 enzymes, the enzyme is modified by mutation of one or more residues including but not limited to positions D, E, E, D, DA, N, according to FnCpf1 protein or any corresponding ortholog.


Where the Cpf1 protein has nuclease activity, the Cpf1 protein may be modified to have diminished nuclease activity e. This is possible by introducing mutations into the nuclease domains of the Cpf1 and orthologs thereof. More particularly, the inactivated Cpf1 enzymes include enzymes mutated in amino acid positions As, As, As of AsCpf1 or corresponding positions in Cpf1 orthologs. Additionally, the inactivated Cpf1 enzymes include enzymes mutated in amino acid position Lb, , or of LbCpf1 or corresponding positions in Cpf1 orthologs.


In the event that Fok1 is provided, it is advantageous that multiple Fok1 functional domains are provided to allow for a functional dimer and that gRNAs are designed to provide proper spacing for functional use Fok1 as specifically described in Tsai et al. Nature Biotechnology, Vol. The adaptor protein may utilize known linkers to attach such functional domains.


In some cases it is advantageous that additionally at least one NLS is provided. Downloader Link Twitter E-Mail. External Reports. Risk Assessment. Network Behavior Contacts 1 domain and 1 host. View all details. Not all malicious and suspicious indicators are displayed. Please see the Emerging Threats section for more information.


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