Some aspects of this disclosure provide strategies, systems, reagents, methods, and kits that are useful for enginerring Cas9 and Cas9 variants that have increased activity on target sequences that do not contain the canonical PAM sequence. In some embodiments, fusion proteins comprising such Cas9 variants and nucleic acid editing domains, e.g., deaminase domains, are provided.

The invention provides a method of modifying a targeted site of gram-positive bacterium of a double stranded DNA. The method includes contacting the double-stranded DNA with a complex of a nucleic acid sequence-recognizing module that specifically binds to a target nucleotide sequence in a given double stranded DNA and a nucleic acid base converting enzyme to convert, delete, or insert one or more nucleotides in the targeted site without cleaving at least one strand of the double stranded DNA in the targeted site, by introducing the nucleic acid encoding the complex into the gram-positive bacterium. The invention also provide a nucleic acid-modifying enzyme complex of a nucleic acid sequence-recognizing module that specifically binds to a target nucleotide sequence in a double stranded DNA of a gram-positive bacterium and a nucleic acid base converting enzyme bonded to each other, which complex is used for the method.

Methods and compositions are provided for identifying any of the presence, location and phasing of methylated and/or hydroxymethylated cytosines in nucleic acids including long stretches of DNA. In some embodiments, the method may comprise reacting a first portion (aliquot) of a nucleic acid sample with a dioxygenase and optionally a glucosyltransferase in a reaction mixture containing the nucleic acid followed by a reaction with a cytidine deaminase to detect and optionally map .sup.5mC in a DNA. Optionally, a second portion can be reacted with glucosyltransferase followed by reaction with a cytidine deaminase to detect and optionally map .sup.5hmC in a DNA

Some aspects of this disclosure relate to strategies, systems, methods, compositions, and kits that are useful for production (e.g., evolution) of cytidine deaminase protein variants that are characterized by increased soluble expression and/or stability relative to the wild-type cytidine deaminase protein from which they are evolved. In some embodiments, evolved cytidine deaminase variants described by the disclosure are useful for incorporation into targeted nucleic acid editing proteins, for example in fusion proteins with a Cas9 domain or variant thereof.

The disclosure provides systems, compositions, kits, and methods useful for the targeted site-specific modifications of RNA molecules. Generally, the systems, compositions, kits, and methods described herein comprise a polypeptide or a nucleic acid encoding the polypeptide. The polypeptide comprises a first domain comprising a catalytic domain of an RNA modifying enzyme and a second domain comprising a MID domain of an Argonaute (Ago) protein. The systems, compositions, kits, and methods can also comprise an oligonucleotide for targeting the polypeptide to a target RNA. A method for modifying a target RNA, comprises contacting the target RNA with a polypeptide or a nucleic acid encoding the polypeptide and with an oligonucleotide described herein. Some exemplary modifications of the target RNA include, but are not limited to, site-specific deamination of an adenosine, deamination of a cytidine, methylation (e.g., methylation at position 6) of an adenosine, and demethylation of m6-adenosine in the target RNA.

The present disclosure provides systems and methods for m.sup.6A-dependent delivery and m.sup.6A-dependent delivery targeted of a polypeptide to a cell. In certain embodiments, compositions, systems, and methods are provided that provide for m.sup.6A-dependent delivery of effector proteins, for example, effector proteins, such as a tumor suppression proteins and m6a regulation systems, mediated by CRISPRi in embodiments.

Methods and compositions for performing highly sensitive in vitro assays to define substrate preferences and off-target sites of nucleic-acid binding, modifying, and cleaving agents.

This disclosure provides systems, methods, and compositions for RNA-guided RNA-targeting CRISPR effectors for the treatment of diseases as well as diagnostics. In some embodiments, nucleotide deaminase functionalized CRISPR systems for RNA editing RNA knockdown, viral resistance, splicing modulation, RNA tracking, translation modulation, and epi-transcriptomic modifications are disclosed.

The present disclosure generally relates to compositions (e.g., nucleic acid constructs, vectors, plasmids, engineered cells, etc.) and methods using the same for selecting and/or making an antigen-binding molecule of interest (e.g., an immune receptor, an antibody or functional fragment thereof) with improved affinity to a target antigen.

Provided are gene therapy technologies, including specifically designed and tested guide RNA sequences for improved base editors, useful for increasing the expression of the gamma-globin gene. The guide RNA sequences may target the BCL11A erythroid enhancer or the gamma-globin promoter, or both at the same time. The base editors can include nucleobase deaminase inhibitor that inhibits the editing activity of the base editors until they are bound to the target sites. These gene therapy technologies are useful for treating diseases including beta-thalassemia and sickle cell anemia, among others.