University of California

University of Vienna

Other

Emmanuelle Charpentier

Caribou Biosciences, Inc.

Yale University

Pfizer Corporation

National Technology & Engineering Solutions of Sandia, LLC

The J. David Gladstone Institute, a Testamentary Trust Established Under the Will of J. David Gladstone

Jennifer A Doudna

Martin Jinek

Krzysztof Chylinski

Jillian F Banfield

Lucas Benjamin Harrington

Rachel E Haurwitz

David Burstein

Janice S Chen

Spencer Charles Knight

Basem Al-Shayeb

Andrew Paul May

Paul Daniel Donohoue

Matthew Merrill Carter

Mitchell R O'Connell

David Paez-Espino

James M Berger

Patrick Pausch

Enbo Ma

Samuel H Sternberg

James Harrison Doudna Cate

Alexandra East-Seletsky

Benjamin L Oakes

Blake Wiedenheft

Robert T Batey

Louise J Lucast

Steven C Strutt

Chun-Hao Huang

Nami Saghaei

Christof Fellmann

David Frank Savage

Haridha Shivram

Emine Kaya

Kyle E Watters

Kaihong Zhou

Brett T Staahl

Spiros Liras

Lei S Qi

Benjamin A Thuma

Vincent Mascitti

Melanie Ott

Oscar Negrete

Adam P Arkin

Steven Lin

James K Nunez

Nikos C Kyrpides

Mitchell Ray O′Connell

Abraham I Flamholz

Junjie Liu

Parinaz Fozouni

Natalia Orlova

Ian J MacRae

David W Taylor, Jr

Fuguo Jiang

Kilian R Knoll

Romain Rouet

Dana Nadler

Anirvan Ghosh

Rayka Yokoo

Addison V Wright

Paul Donohoue

The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA. The present disclosure provides methods of modulating transcription of a target nucleic acid.

CRISPR-Cas effector polypeptides and methods of use thereof

Provided are compositions and methods for detecting a target DNA (double stranded or single stranded) in a sample. In some embodiments, a subject method includes: (a) contacting the sample with: (i) a type V CRISPR/Cas effector protein (e.g., a Cas12 protein such as Cas12a, Cas12b, Cas12c, Cas12d, Cas12e); (ii) a guide RNA (comprising a region that binds to the type V CRISPR/Cas effector protein, and a guide sequence that hybridizes with the target DNA); and (iii) a detector DNA that is single stranded (i.e., a 'single stranded detector DNA') and does not hybridize with the guide sequence of the guide RNA; and (b) measuring a detectable signal produced by cleavage (by the type V CRISPR/Cas effector protein) of the single stranded detector DNA. Also provided are compositions and methods for cleaving single stranded DNAs (e.g., non-target ssDNAs), e.g., inside of a cell.

Type V CRISPR/Cas effector proteins for cleaving ssDNAs and detecting target DNAs

The present disclosure provides RNA-guided CRISPR-Cas effector proteins, nucleic acids encoding same, and compositions comprising same. The present disclosure provides ribonucleoprotein complexes comprising: an RNA-guided CRISPR-Cas effector protein of the present disclosure; and a guide RNA. The present disclosure provides methods of modifying a target nucleic acid, using an RNA-guided CRISPR-Cas effector protein of the present disclosure and a guide RNA.

In one aspect, the present disclosure provides a method for identifying treatment targets relating to tumors. In another aspect, the present disclosure provides a method for identifying biomarkers and molecular features of normal and cancer cells.

Methods and kits for identifying cancer treatment targets

Genetically engineered cells

The present disclosure provides variant type V CRISPR/Cas effector polypeptides, fusion polypeptides comprising the variant type V CRISPR/Cas effector polypeptides, and nucleic acids comprising nucleotide sequences encoding the variant polypeptides and fusion polypeptides. The present disclosure provides methods of binding, or binding and nicking, a target nucleic acid, using a variant type V CRISPR/Cas effector polypeptide of the present disclosure. The present disclosure provides methods of detecting a single-stranded DNA, using a variant type V CRISPR/Cas effector polypeptide of the present disclosure.

Variant type V CRISPR/Cas effector polypeptides and methods of use thereof

Provided are compositions and methods that include one or more of: (1) a 'CasZ' protein (also referred to as a CasZ polypeptide), a nucleic acid encoding the CasZ protein, and/or a modified host cell comprising the CasZ protein (and/or a nucleic acid encoding the same); (2) a CasZ guide RNA that binds to and provides sequence specificity to the CasZ protein, a nucleic acid encoding the CasZ guide RNA, and/or a modified host cell comprising the CasZ guide RNA (and/or a nucleic acid encoding the same); and (3) a CasZ transactivating noncoding RNA (trancRNA) (referred to herein as a “CasZ trancRNA”), a nucleic acid encoding the CasZ trancRNA, and/or a modified host cell comprising the CasZ trancRNA (and/or a nucleic acid encoding the same).

CasZ compositions and methods of use

The present disclosure provides CasY proteins, nucleic acids encoding the CasY proteins, and modified host cells comprising the CasY proteins and/or nucleic acids encoding same. CasY proteins are useful in a variety of applications, which are provided. The present disclosure provides CasY guide RNAs that bind to and provide sequence specificity to the CasY proteins, nucleic acids encoding the CasY guide RNAs, and modified host cells comprising the CasY guide RNAs and/or nucleic acids encoding same. CasY guide RNAs are useful in a variety of applications, which are provided. The present disclosure provides methods of identifying a CRISPR RNA-guided endonuclease.

RNA-guided nucleic acid modifying enzymes and methods of use thereof

Provided are compositions and methods that include a CasY transactivating noncoding RNA (trancRNA) (referred to herein as a 'CasY trancRNA'), nucleic acids encoding the CasY trancRNA, and/or a modified host cell comprising the CasY trancRNA (and/or a nucleic acid encoding the same). Subject compositions and methods can also include one or more of: (a) a “CasY” protein (also referred to as a CasY polypeptide, a Cas12d protein, and a Cas12d polypeptide), a nucleic acid encoding the CasY protein, and/or a modified host cell comprising the CasY protein (and/or a nucleic acid encoding the same); and (b) a CasY guide RNA (also referred to herein as a “Cas12d guide RNA”) that binds to and provides sequence specificity to the CasY protein, a nucleic acid encoding the CasY guide RNA, and/or a modified host cell comprising the CasY guide RNA (and/or a nucleic acid encoding the same).

CasY compositions and methods of use

The present disclosure provides AcrIIA7 polypeptides, nucleic acids encoding the AcrIIA7 polypeptides, and kits comprising the AcrIIA7 polypeptides and/or nucleic acids encoding the ACRIIA7 polypeptides. The present disclosure provides methods of inhibiting an activity of a Cas9 polypeptide.

Modulators of CAS9 polypeptides and methods of use thereof

The present disclosure relates to methods using CRISPR-Cas13a enzyme, complexed with HIV or HCV crRNAs to specifically and sensitively detect and quantify the presence of HIV or HCV RNA in a sample. These methods can be used to diagnose HIV or HCV infection, quantify the concentration of HIV or HCV RNA present in a sample, identify the presence of different HIV or HCV splice variants, subtypes, or mutations, and to monitor reactivation of HIV or HCV transcription.

HIV or HCV detection with CRISPR-CAS13A

The present disclosure provides a DNA-targeting RNA that comprises a targeting sequence and, together with a modifying polypeptide, provides for site-specific modification of a target DNA and/or a polypeptide associated with the target DNA. The present disclosure further provides site-specific modifying polypeptides. The present disclosure further provides methods of site-specific modification of a target DNA and/or a polypeptide associated with the target DNA The present disclosure provides methods of modulating transcription of a target nucleic acid in a target cell, generally involving contacting the target nucleic acid with an enzymatically inactive Cas9 polypeptide and a DNA-targeting RNA. Kits and compositions for carrying out the methods are also provided. The present disclosure provides genetically modified cells that produce Cas9; and Cas9 transgenic non-human multicellular organisms.

Methods and compositions for RNA-directed target DNA modification and for RNA-directed modulation of transcription

Growing community of inventors

Berkeley, CA, United States of America

Jennifer A Doudna