Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Abil, 2015, Engineering reprogrammable RNA-binding proteins for study and manipulation of the transcriptome, Mol. Biosyst., 11, 2658, 10.1039/C5MB00289C

Abudayyeh, 2016, C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector, Science, 353, aaf5573, 10.1126/science.aaf5573

Anantharaman, 2013, Comprehensive analysis of the HEPN superfamily: identification of novel roles in intra-genomic conflicts, defense, pathogenesis and RNA processing, Biol. Direct, 8, 15, 10.1186/1745-6150-8-15

Baba, 2006, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol. Syst. Biol., 2, 10.1038/msb4100050

Bernhart, 2006, Local RNA base pairing probabilities in large sequences, Bioinformatics, 22, 614, 10.1093/bioinformatics/btk014

Biswas, 2013, CRISPRTarget: bioinformatic prediction and analysis of crRNA targets, RNA Biol., 10, 817, 10.4161/rna.24046

Camacho, 2009, BLAST+: architecture and applications, BMC Bioinformatics, 10, 421, 10.1186/1471-2105-10-421

Cong, 2013, Multiplex genome engineering using CRISPR/Cas systems, Science, 339, 819, 10.1126/science.1231143

Crooks, 2004, WebLogo: a sequence logo generator, Genome Res., 14, 1188, 10.1101/gr.849004

East-Seletsky, 2016, Two distinct RNase activities of CRISPR-C2c2 enable guide-RNA processing and RNA detection, Nature, 538, 270, 10.1038/nature19802

Edgar, 2007, PILER-CR: fast and accurate identification of CRISPR repeats, BMC Bioinformatics, 8, 18, 10.1186/1471-2105-8-18

Filipovska, 2011, Designer RNA-binding proteins: new tools for manipulating the transcriptome, RNA Biol., 8, 978, 10.4161/rna.8.6.17907

Gerdes, 2003, Experimental determination and system level analysis of essential genes in Escherichia coli MG1655, J. Bacteriol., 185, 5673, 10.1128/JB.185.19.5673-5684.2003

Hale, 2009, RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex, Cell, 139, 945, 10.1016/j.cell.2009.07.040

Heidrich, 2015, Investigating CRISPR RNA biogenesis and function using RNA-seq, Methods Mol. Biol., 1311, 1, 10.1007/978-1-4939-2687-9_1

Henikoff, 1992, Amino acid substitution matrices from protein blocks, Proc. Natl. Acad. Sci. USA, 89, 10915, 10.1073/pnas.89.22.10915

Hildebrand, 2009, Fast and accurate automatic structure prediction with HHpred, Proteins, 77, 128, 10.1002/prot.22499

Jiang, 2016, Degradation of phage transcripts by CRISPR-associated rnases enables type III CRISPR-Cas immunity, Cell, 164, 710, 10.1016/j.cell.2015.12.053

Kim, 2013, Crystal structure and nucleic acid-binding activity of the CRISPR-associated protein Csx1 of Pyrococcus furiosus, Proteins, 81, 261, 10.1002/prot.24183

Konermann, 2015, Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex, Nature, 517, 583, 10.1038/nature14136

Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324

Lorenz, 2011, ViennaRNA Package 2.0, Algorithms Mol. Biol., 6, 26, 10.1186/1748-7188-6-26

Mackay, 2011, The prospects for designer single-stranded RNA-binding proteins, Nat. Struct. Mol. Biol., 18, 256, 10.1038/nsmb.2005

Makarova, 2015, An updated evolutionary classification of CRISPR-Cas systems, Nat. Rev. Microbiol., 13, 722, 10.1038/nrmicro3569

Mali, 2013, RNA-guided human genome engineering via Cas9, Science, 339, 823, 10.1126/science.1232033

Marraffini, 2015, CRISPR-Cas immunity in prokaryotes, Nature, 526, 55, 10.1038/nature15386

Mohanraju, 2016, Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems, Science, 353, aad5147, 10.1126/science.aad5147

Möller, 2001, Evaluation of methods for the prediction of membrane spanning regions, Bioinformatics, 17, 646, 10.1093/bioinformatics/17.7.646

Ran, 2015, In vivo genome editing using Staphylococcus aureus Cas9, Nature, 520, 186, 10.1038/nature14299

Remmert, 2011, HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment, Nat. Methods, 9, 173, 10.1038/nmeth.1818

Sheppard, 2016, The CRISPR-associated Csx1 protein of Pyrococcus furiosus is an adenosine-specific endoribonuclease, RNA, 22, 216, 10.1261/rna.039842.113

Shmakov, 2015, Discovery and functional characterization of diverse class 2 CRISPR-Cas systems, Mol. Cell, 60, 385, 10.1016/j.molcel.2015.10.008

Shmakov, 2017, Diversity and evolution of class 2 CRISPR–Cas systems, Nat. Rev. Microbiol, 10.1038/nrmicro.2016.184

Staals, 2013, Structure and activity of the RNA-targeting type III-B CRISPR-Cas complex of Thermus thermophilus, Mol. Cell, 52, 135, 10.1016/j.molcel.2013.09.013

Staals, 2014, RNA targeting by the type III-A CRISPR-Cas Csm complex of Thermus thermophilus, Mol. Cell, 56, 518, 10.1016/j.molcel.2014.10.005

Tafer, 2008, The impact of target site accessibility on the design of effective siRNAs, Nat. Biotechnol., 26, 578, 10.1038/nbt1404

Tamulaitis, 2014, Programmable RNA shredding by the type III-A CRISPR-Cas system of Streptococcus thermophilus, Mol. Cell, 56, 506, 10.1016/j.molcel.2014.09.027

Wright, 2016, Biology and applications of CRISPR systems: harnessing nature’s toolbox for genome engineering, Cell, 164, 29, 10.1016/j.cell.2015.12.035

Yates, 2016, Ensembl 2016, Nucleic Acids Res., 44, D710, 10.1093/nar/gkv1157

Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system, Cell, 163, 759, 10.1016/j.cell.2015.09.038