Massachusetts Institute of Technology

The Broad Institute, Inc.

Harvard College

Leland Stanford Junior University

The University of Tokyo

University of Iowa Research Foundation

The Government of the United States of America As Represented by the Secretary of the Deptartment of Health and Human Services

Rutgers, the State University of New Jersey

Children's Medical Center Corporation

The Rockefeller University

The General Hospital Corporation

University of Pittsburgh

Dana-farber-cancer Institute Inc.

Tufts College

Massachusetts Eye and Ear Infirmary

Feng Zhang

Omar O Abudayyeh

Jonathan S Gootenberg

Karl A Deisseroth

Viviana Gradinaru

Le Cong

Bernd Zetsche

Fei Ran

Ian Slaymaker

Eric Lander

Patrick D Hsu

Silvana Konermann

David Benjamin Turitz Cox

Neville Espi Sanjana

James Joseph Collins

David Arthur Scott

Winston X Yan

Randall Jeffrey Platt

Edward Stuart Boyden

Beverly L Davidson

M Bret Schneider

Osamu Nureki

Hiroshi Nishimasu

Edgardo Rodriguez

Julia Joung

Chie-yu Lin

Aviv Regev

Eric S Lander

Mark Daniel Brigham

Aaron Smargon

Yuri I Wolf

Sergey Shmakov

Kira S Makarova

Han Altae-Tran

Matthias Heidenreich

Jordi Mata-Fink

Alexis Borisy

Deborah Palestrant

James E Dahlman

Linyi Gao

Konstantin Severinov

Alim Ladha

Ryuichiro Ishitani

Eugene Koonin

Yinqing Li

Ekaterina Semenova

Ophir Shalem

Lukasz Swiech

Neena Pyzocha

Leonid Minakhin

Guilhem Faure

Chie-Yu Lin

Sourav Choudhury

Soumya Kannan

Joshua Asher Weinstein

George M Church

Phillip A Sharp

Jaimie M Henderson

Stuart H Orkin

Pardis Sabeti

Sriram Kosuri

Daniel E Bauer

Cameron Myhrvold

Sidi Chen

Guoping Feng

Alexandro Trevino

Alexander Aravanis

Johnathan S Gootenberg

Catherine Amanda Freije

Yang Zhou

Sara Jones

Jonathan Strecker

Sangeeta N Bhatia

Henry Ignatius Smith

David Jacob Mishelevich

David A Weitz

Paul Blainey

David Bikard

Luciano Marraffini

Levi A Garraway

Jennifer Rubin Grandis

Deborah Hung

James Gregory Goodberlet

Jeffrey Todd Hastings

David Feldman

Anindita Basu

Roby Bhattacharyya

David Root

Vyas Ramanan

Jesse Engreitz

John G Doench

Naomi Habib

Jason Wright

Ella Nicole Biewener Hartenian

Mohammed Reza Mirzazadeh

Nicola Crosetto

Wenyan Jiang

Ann Marie Egloff

Nicholas Stransky

Disclosed here is a method of identifying novel CRISPR effectors, comprising: identifying sequences in a genomic or metagenomic database encoding a CRISPR array; identifying one or more Open Reading Frames (ORFs) in said selected sequences within 10 kb of the CRISPR array; discarding all loci encoding proteins which are assigned to known CRISPR-Cas subtypes and, optionally, all loci encoding a protein of less than 700 amino acids; and identifying putative novel CRISPR effectors, and optionally classifying them based on structure analysis.

Methods for identifying class 2 crispr-cas systems

The invention provides for systems, methods, and compositions for altering expression of target gene sequences and related gene products. Provided are structural information on the Cas protein of the CRISPR-Cas system, use of this information in generating modified components of the CRISPR complex, vectors and vector systems which encode one or more components or modified components of a CRISPR complex, as well as methods for the design and use of such vectors and components. Also provided are methods of directing CRISPR complex formation in eukaryotic cells and methods for utilizing the CRISPR-Cas system. In particular the present invention comprehends optimized functional CRISPR-Cas enzyme systems. In particular the present invention comprehends engineered new guide architectures to be used in optimized CRISPR-Cas enzyme systems.

Engineering of systems, methods and optimized guide compositions with new architectures for sequence manipulation

Embodiments of the disclosure include compositions and methods for treating diseases (e.g., brain diseases) using genetic engineered cells. In some cases, the cells are engineered hematopoietic stem cells (HSCs), which are capable of engrafting to a central nervous system and differentiating to progeny cells (e.g., microglial cells).

Microglial progenitors for regeneration of functional microglia in the central nervous system and therapeutics uses thereof

The present invention offers a new approach for highly multiplexed, programmable antiviral therapies that directly target viral RNA, and can be flexibly adapted to target novel viruses or emerging outbreak pathogens. Class 2, type VI CRISPR system-based therapies can be used in combination with existing antiviral compounds for viruses where such compounds exist, either by increasing their efficacy or by preventing the evolution of specific drug resistance mutations. Perhaps most excitingly, if a virus evolves resistance to a specific guide RNA sequence, it is easy to switch to a different guide RNA sequence, or to design a new guide sequence to target the new mutation. Such approaches should prevent the widespread development of resistance to Class 2, type VI CRISPR system-based therapies.

CRISPR system based antiviral therapy

The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Methods for making and using and uses of such systems, methods, and compositions and products from such methods and uses are also disclosed and claimed.

CRISPR enzymes and systems

The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA. Aspects of the invention in particular relate to Cpf1 mutants having altered PAM specificity.

CRISPR enzymes and systems with modified pam specificity

The invention provides for delivery, engineering and optimization of systems, methods, and compositions for manipulation of sequences and/or activities of target sequences especially for use as to nucleotide repeat disorders. Provided are delivery systems and tissues or organ which are targeted as sites for delivery especially for use as to nucleotide repeat disorders. Also provided are vectors and vector systems some of which encode one or more components of a CRISPR complex or system especially for use as to nucleotide repeat disorders, as well as methods for the design and of such. Also provided are methods of directing CRISPR complex or system formation in eukaryotic cells especially for use as to nucleotide repeat disorders including with consideration of specificity for target recognition and avoidance of toxicity and editing or modifying a target site in a genomic locus of interest to alter or improve the status of a disease or a condition.

Compositions and methods of use of CRISPR-Cas systems in nucleotide repeat disorders

The present invention generally relates to plants comprising a CRISPR system or parts of a CRISPR system, compositions, containers, polynucleotide, vectors, delivery systems, parts of plants, methods for production, CRISPR systems, and components thereof. Further aspects of the invention include a method for identifying a CRISPR system which is functional in a plant cell and a method for improving a CRISPR system in a plant.

CRISPR-systems for modifying a trait of interest in a plant

The disclosure includes non-naturally occurring or engineered CRISPR systems and proteins, associated with a delivery system comprising a virus component and a lipid component. The disclosure includes CRISPR proteins associated with capsid proteins, e.g., AAV VP1VP2, and/or VP3, on the surface of or internal to the AAV, along with compositions, systems and complexes involving the AAV-CRISPR protein, nucleic acid molecules and vectors encoding the same, deliver}-systems, and uses therefor.

Delivery of large payloads

The invention provides for systems, methods, and compositions for targeting nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a novel DNA-targeting CRISPR effector protein and at least one targeting nucleic acid component like a guide RNA.

CPF1 complexes with reduced indel activity

In one aspect, embodiments disclosed herein are directed to engineered CRISPRCas effector proteins that comprise at least one modification compared to an unmodified CRISPR-Cas effector protein that enhances binding of the of the CRISPR complex to the binding site and/or alters editing preference as compared to wild type. In certain example embodiments, the CRISPR-Cas effector protein is a Type II effector protein. In certain other example embodiments, the Type V effector protein is Cas9 or an orthologs or engineered variant thereof. Example Cas9 proteins suitable for use in the embodiments disclosed herein are discussed in further detail below.

The invention provides for systems, methods, and compositions for targeting and editing nucleic acids. In particular, the invention provides non-naturally occurring or engineered DNA-targeting systems comprising a DNA-targeting Cpf1 protein, at least one guide molecule, and at least one cytidine deaminase protein or catalytic domain thereof.

Systems, methods, and compositions for targeted nucleic acid editing

The invention provides a cell library for use in detecting protein expression comprising a plurality of cells, wherein each cell comprises a polynucleotide sequence encoding a detectable marker integrated into the genome of the cell in frame with a protein coding gene selected from a set of target genes, wherein the library comprises more than one cell tagged at each target gene, as well as a cell library for use in detecting protein interactions between a protein of interest and a set of target proteins and a cell library for use in detecting protein modifications. The invention also provides methods of constructing a cell library for use in proteomics, as well as methods for sequencing integration sites of a donor sequence inserted into the genome of a cell. Also provided are systems for analysis of proteins in a cell and kits comprising vectors for tagging a population of cells and for performing proteomics studies.

Sequencing-based proteomics

Growing community of inventors

Cambridge, MA, United States of America

Feng Zhang