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Nature Biotechnology

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https://www.readbyqxmd.com/read/28398345/genome-wide-target-specificities-of-crispr-rna-guided-programmable-deaminases
#1
Daesik Kim, Kayeong Lim, Sang-Tae Kim, Sun-Heui Yoon, Kyoungmi Kim, Seuk-Min Ryu, Jin-Soo Kim
Cas9-linked deaminases, also called base editors, enable targeted mutation of single nucleotides in eukaryotic genomes. However, their off-target activity is largely unknown. Here we modify digested-genome sequencing (Digenome-seq) to assess the specificity of a programmable deaminase composed of a Cas9 nickase (nCas9) and the deaminase APOBEC1 in the human genome. Genomic DNA is treated with the base editor and a mixture of DNA-modifying enzymes in vitro to produce DNA double-strand breaks (DSBs) at uracil-containing sites...
April 10, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398344/induction-of-functional-dopamine-neurons-from-human-astrocytes-in-vitro-and-mouse-astrocytes-in-a-parkinson-s-disease-model
#2
Pia Rivetti di Val Cervo, Roman A Romanov, Giada Spigolon, Débora Masini, Elisa Martín-Montañez, Enrique M Toledo, Gioele La Manno, Michael Feyder, Christian Pifl, Yi-Han Ng, Sara Padrell Sánchez, Sten Linnarsson, Marius Wernig, Tibor Harkany, Gilberto Fisone, Ernest Arenas
Cell replacement therapies for neurodegenerative disease have focused on transplantation of the cell types affected by the pathological process. Here we describe an alternative strategy for Parkinson's disease in which dopamine neurons are generated by direct conversion of astrocytes. Using three transcription factors, NEUROD1, ASCL1 and LMX1A, and the microRNA miR218, collectively designated NeAL218, we reprogram human astrocytes in vitro, and mouse astrocytes in vivo, into induced dopamine neurons (iDANs)...
April 10, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28369033/crispr-cas9-epigenome-editing-enables-high-throughput-screening-for-functional-regulatory-elements-in-the-human-genome
#3
Tyler S Klann, Joshua B Black, Malathi Chellappan, Alexias Safi, Lingyun Song, Isaac B Hilton, Gregory E Crawford, Timothy E Reddy, Charles A Gersbach
Large genome-mapping consortia and thousands of genome-wide association studies have identified non-protein-coding elements in the genome as having a central role in various biological processes. However, decoding the functions of the millions of putative regulatory elements discovered in these studies remains challenging. CRISPR-Cas9-based epigenome editing technologies have enabled precise perturbation of the activity of specific regulatory elements. Here we describe CRISPR-Cas9-based epigenomic regulatory element screening (CERES) for improved high-throughput screening of regulatory element activity in the native genomic context...
April 3, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28346402/large-scale-design-of-robust-genetic-circuits-with-multiple-inputs-and-outputs-for-mammalian-cells
#4
Benjamin H Weinberg, N T Hang Pham, Leidy D Caraballo, Thomas Lozanoski, Adrien Engel, Swapnil Bhatia, Wilson W Wong
Engineered genetic circuits for mammalian cells often require extensive fine-tuning to perform as intended. We present a robust, general, scalable system, called 'Boolean logic and arithmetic through DNA excision' (BLADE), to engineer genetic circuits with multiple inputs and outputs in mammalian cells with minimal optimization. The reliability of BLADE arises from its reliance on recombinases under the control of a single promoter, which integrates circuit signals on a single transcriptional layer. We used BLADE to build 113 circuits in human embryonic kidney and Jurkat T cells and devised a quantitative, vector-proximity metric to evaluate their performance...
March 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28346401/targeted-base-editing-in-rice-and-tomato-using-a-crispr-cas9-cytidine-deaminase-fusion
#5
Zenpei Shimatani, Sachiko Kashojiya, Mariko Takayama, Rie Terada, Takayuki Arazoe, Hisaki Ishii, Hiroshi Teramura, Tsuyoshi Yamamoto, Hiroki Komatsu, Kenji Miura, Hiroshi Ezura, Keiji Nishida, Tohru Ariizumi, Akihiko Kondo
We applied a fusion of CRISPR-Cas9 and activation-induced cytidine deaminase (Target-AID) for point mutagenesis at genomic regions specified by single guide RNAs (sgRNAs) in two crop plants. In rice, we induced multiple herbicide-resistance point mutations by multiplexed editing using herbicide selection, while in tomato we generated marker-free plants with homozygous heritable DNA substitutions, demonstrating the feasibility of base editing for crop improvement.
March 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28319085/synergistic-drug-combinations-for-cancer-identified-in-a-crispr-screen-for-pairwise-genetic-interactions
#6
Kyuho Han, Edwin E Jeng, Gaelen T Hess, David W Morgens, Amy Li, Michael C Bassik
Identification of effective combination therapies is critical to address the emergence of drug-resistant cancers, but direct screening of all possible drug combinations is infeasible. Here we introduce a CRISPR-based double knockout (CDKO) system that improves the efficiency of combinatorial genetic screening using an effective strategy for cloning and sequencing paired single guide RNA (sgRNA) libraries and a robust statistical scoring method for calculating genetic interactions (GIs) from CRISPR-deleted gene pairs...
March 20, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28244995/highly-efficient-rna-guided-base-editing-in-mouse-embryos
#7
Kyoungmi Kim, Seuk-Min Ryu, Sang-Tae Kim, Gayoung Baek, Daesik Kim, Kayeong Lim, Eugene Chung, Sunghyun Kim, Jin-Soo Kim
Base editors (BEs) composed of a cytidine deaminase fused to CRISPR-Cas9 convert cytidine to uridine, leading to single-base-pair substitutions in eukaryotic cells. We delivered BE mRNA or ribonucleoproteins targeting the Dmd or Tyr gene via electroporation or microinjection into mouse zygotes. F0 mice showed nonsense mutations with an efficiency of 44-57% and allelic frequencies of up to 100%, demonstrating an efficient method to generate mice with targeted point mutations.
February 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28244994/precise-base-editing-in-rice-wheat-and-maize-with-a-cas9-cytidine-deaminase-fusion
#8
Yuan Zong, Yanpeng Wang, Chao Li, Rui Zhang, Kunling Chen, Yidong Ran, Jin-Long Qiu, Daowen Wang, Caixia Gao
Targeted base editing in plants without the need for a foreign DNA donor or double-stranded DNA cleavage would accelerate genome modification and breeding in a wide array of crops. We used a CRISPR-Cas9 nickase-cytidine deaminase fusion to achieve targeted conversion of cytosine to thymine from position 3 to 9 within the protospacer in both protoplasts and regenerated rice, wheat and maize plants at frequencies of up to 43.48%.
February 27, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28191903/efficient-genome-editing-in-the-mouse-brain-by-local-delivery-of-engineered-cas9-ribonucleoprotein-complexes
#9
Brett T Staahl, Madhurima Benekareddy, Claire Coulon-Bainier, Ashwin A Banfal, Stephen N Floor, Jennifer K Sabo, Cole Urnes, Gabriela Acevedo Munares, Anirvan Ghosh, Jennifer A Doudna
We demonstrate editing of post-mitotic neurons in the adult mouse brain following injection of Cas9 ribonucleoprotein (RNP) complexes in the hippocampus, striatum and cortex. Engineered variants of Cas9 with multiple SV40 nuclear localization sequences enabled a tenfold increase in the efficiency of neuronal editing in vivo. These advances indicate the potential of genome editing in the brain to correct or inactivate the underlying genetic causes of neurological diseases.
February 13, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398333/top-heart-failure-contender-serelaxin-flops
#10
(no author information available yet)
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398332/drugmakers-accused-of-exploiting-orphan-drug-incentives-fueling-price-problem
#11
Brady Huggett
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398331/with-all-due-respect-to-maholo-lab-automation-isn-t-anthropomorphic
#12
David W McClymont, Paul S Freemont
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398330/remote-detection-of-buried-landmines-using-a-bacterial-sensor
#13
Shimshon Belkin, Sharon Yagur-Kroll, Yossef Kabessa, Victor Korouma, Tali Septon, Yonatan Anati, Cheinat Zohar-Perez, Zahi Rabinovitz, Amos Nussinovitch, Aharon J Agranat
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398329/robotic-crowd-biology-with-maholo-labdroids
#14
Nozomu Yachie, Tohru Natsume
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398328/around-the-world-in-a-month
#15
(no author information available yet)
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398327/recent-patents-in-epigenetic-targeting
#16
(no author information available yet)
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398325/single-minded-crispr-screening
#17
Bryan R Lanning, Christopher R Vakoc
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398324/national-academies-report-has-broad-support
#18
Paul Vincelli, Douglas Jackson-Smith, Michael Holsapple, Michael A Grusak, Matthew Harsh, Theodore Klein, James Lambert, B Markus Lange, David M Lodge, Jill McCluskey, Angus Murphy, Marian L Neuhouser, Carl Pray, Susan Weller
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398323/nature-biotechnology-s-academic-spinouts-of-2016
#19
Aaron Bouchie, Laura DeFrancesco, Cormac Sheridan, Sarah Webb
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
https://www.readbyqxmd.com/read/28398322/the-best-spot-to-park-a-car
#20
Katarzyna Marcinkiewicz
No abstract text is available yet for this article.
April 11, 2017: Nature Biotechnology
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