المؤلفون: Wu, Xuebing, Scott, David A, Kriz, Andrea J, Chiu, Anthony C, Hsu, Patrick D, Dadon, Daniel B, Cheng, Albert W, Trevino, Alexandro E, Konermann, Silvana, Chen, Sidi, Jaenisch, Rudolf, Zhang, Feng, Sharp, Phillip A

المصدر: Nature Biotechnology. 32(7)

مصطلحات موضوعية: Animals, Base Sequence, Binding Sites, CRISPR-Cas Systems, Cells, Cultured, DNA-Binding Proteins, Deoxyribonuclease I, Embryonic Stem Cells, Genome, Mice, Models, Genetic, Molecular Sequence Data, Protein Binding

الوصف: Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped genome-wide binding sites of a catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with single guide RNAs (sgRNAs) in mouse embryonic stem cells (mESCs). Each of the four sgRNAs we tested targets dCas9 to between tens and thousands of genomic sites, frequently characterized by a 5-nucleotide seed region in the sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin inaccessibility decreases dCas9 binding to other sites with matching seed sequences; thus 70% of off-target sites are associated with genes. Targeted sequencing of 295 dCas9 binding sites in mESCs transfected with catalytically active Cas9 identified only one site mutated above background levels. We propose a two-state model for Cas9 binding and cleavage, in which a seed match triggers binding but extensive pairing with target DNA is required for cleavage.

وصف الملف: application/pdf

الوصول الحر: https://escholarship.org/uc/item/5zp6v5jfTest

المؤلفون: Konermann, Silvana¹, Brigham, Mark D.², Trevino, Alexandro E.³, Hsu, Patrick D.⁴, Heidenreich, Matthias³, Le Cong⁵, Platt, Randall J.³, Scott, David A.³, Church, George M.⁶, Zhang, Feng³

المصدر: Nature. 8/22/2013, Vol. 500 Issue 7463, p472-476. 5p. 14 Graphs.

مصطلحات موضوعية: *GENETIC transcription, *ANIMAL epigenetics, *GENE expression, *HOMEOSTASIS, *DNA-binding proteins, *CRYPTOCHROMES

مستخلص: The dynamic nature of gene expression enables cellular programming, homeostasis and environmental adaptation in living systems. Dissection of causal gene functions in cellular and organismal processes therefore necessitates approaches that enable spatially and temporally precise modulation of gene expression. Recently, a variety of microbial and plant-derived light-sensitive proteins have been engineered as optogenetic actuators, enabling high-precision spatiotemporal control of many cellular functions. However, versatile and robust technologies that enable optical modulation of transcription in the mammalian endogenous genome remain elusive. Here we describe the development of light-inducible transcriptional effectors (LITEs), an optogenetic two-hybrid system integrating the customizable TALE DNA-binding domain with the light-sensitive cryptochrome 2 protein and its interacting partner CIB1 from Arabidopsis thaliana. LITEs do not require additional exogenous chemical cofactors, are easily customized to target many endogenous genomic loci, and can be activated within minutes with reversibility. LITEs can be packaged into viral vectors and genetically targeted to probe specific cell populations. We have applied this system in primary mouse neurons, as well as in the brain of freely behaving mice in vivo to mediate reversible modulation of mammalian endogenous gene expression as well as targeted epigenetic chromatin modifications. The LITE system establishes a novel mode of optogenetic control of endogenous cellular processes and enables direct testing of the causal roles of genetic and epigenetic regulation in normal biological processes and disease states. [ABSTRACT FROM AUTHOR]

المؤلفون: Alexandro E. Trevino, Anthony C. Chiu, Patrick D. Hsu, David A. Scott, Sidi Chen, Albert W. Cheng, Andrea J. Kriz, Phillip A. Sharp, Silvana Konermann, Feng Zhang, Daniel B. Dadon, Rudolf Jaenisch, Xuebing Wu

المساهمون: Massachusetts Institute of Technology. Department of Biology, McGovern Institute for Brain Research at MIT, Whitehead Institute for Biomedical Research, Koch Institute for Integrative Cancer Research at MIT, Wu, Xuebing, Chiu, Anthony Chun-yin, Chen, Sidi, Sharp, Phillip A., Scott, David Arthur, Hsu, Patrick, Trevino, Alexandro E., Konermann, Silvana M., Zhang, Feng, Kriz, Andrea J., Dadon, Daniel Benjamin, Jaenisch, Rudolf

المصدر: Nature biotechnology, vol 32, iss 7
PMC

مصطلحات موضوعية: Cells, Molecular Sequence Data, Biomedical Engineering, Bioengineering, Biology, Applied Microbiology and Biotechnology, Article, Mice, Genetic, Models, CRISPR, Animals, Deoxyribonuclease I, Guide RNA, Binding site, Gene, Cells, Cultured, Embryonic Stem Cells, Genetics, Cultured, Binding Sites, Genome, Base Sequence, Models, Genetic, Cas9, Chromatin, DNA-Binding Proteins, Protospacer adjacent motif, Molecular Medicine, CRISPR-Cas Systems, Biotechnology, Protein Binding

الوصف: Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped genome-wide binding sites of a catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with single guide RNAs (sgRNAs) in mouse embryonic stem cells (mESCs). Each of the four sgRNAs we tested targets dCas9 to between tens and thousands of genomic sites, frequently characterized by a 5-nucleotide seed region in the sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin inaccessibility decreases dCas9 binding to other sites with matching seed sequences; thus 70% of off-target sites are associated with genes. Targeted sequencing of 295 dCas9 binding sites in mESCs transfected with catalytically active Cas9 identified only one site mutated above background levels. We propose a two-state model for Cas9 binding and cleavage, in which a seed match triggers binding but extensive pairing with target DNA is required for cleavage.
National Institutes of Health (U.S.) (Grant RO1-GM34277)
National Institutes of Health (U.S.) (Grant R01-CA133404)
National Cancer Institute (U.S.) (Grant PO1-CA42063)
National Cancer Institute (U.S.) (Cancer Center Support (Core) Grant P30-CA14051)
National Institutes of Health (U.S.) (Director's Pioneer Award 1DP1-MH100706)
Damon Runyon Cancer Research Foundation
Kinship Foundation. Searle Scholars Program
Simons Foundation

وصف الملف: application/pdf

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d93a41c1c755061d128c6bddf0d92a93Test
https://europepmc.org/articles/PMC4145672Test/

المساهمون: Wu, Xuebing, Scott, David A., Kriz, Andrea J., Chiu, Anthony C., Hsu, Patrick D., Dadon, Daniel B., Cheng, Albert W., Trevino, Alexandro E., Konermann, Silvana, Chen, Sidi, Jaenisch, Rudolf, Zhang, Feng, Sharp, Phillip A.

المصدر: Nat Biotechnol. 32(7):670-676.

مصطلحات موضوعية: Article, Animals, Base Sequence, Binding Sites, CRISPR-Cas Systems, Cells, Cultured, DNA-Binding Proteins, Deoxyribonuclease I, Embryonic Stem Cells, Genome, Mice, Models, Genetic, Molecular Sequence Data, Protein Binding

الوصف: Bacterial type II CRISPR-Cas9 systems have been widely adapted for RNA-guided genome editing and transcription regulation in eukaryotic cells, yet their in vivo target specificity is poorly understood. Here we mapped genome-wide binding sites of a catalytically inactive Cas9 (dCas9) from Streptococcus pyogenes loaded with single guide RNAs (sgRNAs) in mouse embryonic stem cells (mESCs). Each of the four sgRNAs we tested targets dCas9 to between tens and thousands of genomic sites, frequently characterized by a 5-nucleotide seed region in the sgRNA and an NGG protospacer adjacent motif (PAM). Chromatin inaccessibility decreases dCas9 binding to other sites with matching seed sequences; thus 70% of off-target sites are associated with genes. Targeted sequencing of 295 dCas9 binding sites in mESCs transfected with catalytically active Cas9 identified only one site mutated above background levels. We propose a two-state model for Cas9 binding and cleavage, in which a seed match triggers binding but extensive pairing with target DNA is required for cleavage. ; 1DP1-MH100706/DP/NCCDPHP CDC HHS/United States ; P01 CA042063/CA/NCI NIH HHS/United States ; P01-CA42063/CA/NCI NIH HHS/United States ; P30 CA014051/CA/NCI NIH HHS/United States ; P30-CA14051/CA/NCI NIH HHS/United States ; R01 CA133404/CA/NCI NIH HHS/United States ; R01 GM034277/GM/NIGMS NIH HHS/United States ; R01-CA133404/CA/NCI NIH HHS/United States ; R01-GM34277/GM/NIGMS NIH HHS/United States ; R37 GM034277/GM/NIGMS NIH HHS/United States ; R37 HD045022/HD/NICHD NIH HHS/United States ; Howard Hughes Medical Institute/United States ; 2015-01-01T00:00:00Z ; 24752079 ; PMC4145672

العلاقة: http://stacks.cdc.gov/view/cdc/30092Test/

الإتاحة: http://stacks.cdc.gov/view/cdc/30092Test/