Compositions and methods for gene editing are provided. In some embodiments, provided is a polynucleotide encoding an RNA-guided DNA binding agent such as N. meningitidis Cas9 that can provide one or more of improved editing efficiency, reduced immunogenicity, or other benefits.

The invention of the disclosure features compositions and methods for treating spinal muscular atrophy (SMA) by introducing alterations to a survival of motor neuron 2 (SMN2) polynucleotide(s) in a cell. In particular embodiments, the invention provides a base editor system (e.g., a fusion protein or complex comprising a programmable DNA binding protein, a nucleobase editor, and gRNA) for modifying an SMN2 polynucleotide(s), where the alteration is associated with increased expression of the SMN2 polypeptide(s) encoded by the polynucleotide(s).

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 invention features compositions and methods for introducing mutations into the hepatitis B virus (HBV) genome.

Provided are a composition for inducing DNA single strand breaks in DNA, the composition comprising a cytidine deaminase, an inactivated target-specific endonuclease, and a guide RNA, a method for inducing a single-strand break in DNA, using the same, a method for analyzing a nucleic acid sequence of a base-editing-introduced DNA, and a method for identifying (or measuring or detecting) a base-editing site, base-editing efficiency at an on-target site, an off-target site, and/or target specificity.

Disclosed are adenosine deaminases, base editors comprising the adenosine deaminases and complexes comprising the base editors. The adenosine deaminases and the base editors exhibited superior adenine editing effects and achieved A.Math.T base pair to G.Math.C base pair transformation at DNA level.

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.

Materials and methods for using modified Cas9-APOBEC fusion polypeptides for targeted modification of specific DNA sequences are provided herein.

The invention of the disclosure features compositions and methods for treating hereditary angioedema by introducing one or more alterations to a kallikrein B1 (KLKB1) polynucleotide in a cell. In particular embodiments, the invention provides a base editor system (e.g., a fusion protein or complex comprising a programmable DNA binding protein, a nucleobase editor, and gRNA) for modifying a KLKB1 polynucleotide, where the modification is associated with reduced expression and/or reduced activity of the KLKB1 polypeptide encoded by the polynucleotide.

The present invention provides a complex containing a nucleic acid sequence-recognizing module and a proteolysis tag, wherein the module is linked to the proteolysis tag, the module specifically binds to a target nucleotide sequence in a double stranded DNA, and the tag consists of (i) a peptide containing 3 hydrophobic amino acid residues at the C-terminal, or (ii) a peptide containing 3 amino acid residues at the C-terminal wherein at least a part of the amino acid residues is substituted by serine.