The invention relates to a nucleic acid comprising at least one methylation-protectable restriction element, the methylation-protectable restriction element comprising: (i) a type IIS restriction enzyme recognition sequence, or a partial type IIS restriction enzyme recognition sequence, that is recognised by a type IIS restriction enzyme that cleaves outside of the recognition sequence; (ii) a DNA methylase recognition sequence that is recognised and methylated by a DNA methylase, wherein the DNA methylase recognition sequence is identical to, or is encompassed within, the type IIS restriction recognition sequence, such that methylation of the nucleic acid by the DNA methylase methylates the type IIS restriction enzyme recognition sequence and protects the nucleic acid from cleavage by the type IIS restriction enzyme; and (iii) a recognition sequence for a sequence-specific DNA-binding protein, wherein the recognition sequence is positioned such that the binding of the sequence-specific DNA-binding protein overlaps with the DNA methylase recognition sequence such that binding of the sequence-specific DNA-binding protein is capable of preventing methylation of the type IIS restriction enzyme recognition sequence by the DNA methylase such that it is not protected from cleavage by the type IIS restriction enzyme. The invention further relates to associated methods of nucleic acid assembly.

Disclosed herein are artificially synthesized nucleic acid constructs to guide an epigenetic modification for at least partially silencing or activating a target gene in an organism such as a plant or seed, and formulations thereof. Also disclosed are methods of applying such nucleic acid constructs to the plant or to the seed. Also disclosed are engineered seeds and plants obtained by the epigenetic modification.

In alternative embodiments, provided are products of manufacture and kits, and methods, for treating or ameliorating a Mycobacterium tuberculosis (TB) or a Mycobacterium africanum infection. In alternative embodiments, provided are products of manufacture and kits, and methods, that comprise or comprise use of DNA methylation inhibitory molecules for treating or ameliorating a Mycobacterium tuberculosis (TB) infection. In alternative embodiments, provided are methods and device for classifying drug-resistance phenotype, or diagnosing Multi-drug resistant Tuberculosis (MDR-TB), eXtensively Drug Resistant phenotype (XDR) tuberculosis, or for clinical decision support. In alternative embodiments, provided are kits for or treating or diagnosing drug resistance of, prognosing, or assisting in clinical decision making for a Mycobacterium tuberculosis (TB) or the Mycobacterium africanum infection.

Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.

Cofactor analogues for methyltransferases are disclosed. The compounds are represented by formula (I) wherein R1 is COOH or COO—; X is an organic or inorganic anion carrying one or more negative charges; Y and Y′ are H, or an alkyl; R2 is NH.sub.2, NHBoc, or H; and Z is S or Se. R comprises a carbon-carbon double bond, carbon-oxygen double bond, carbon-sulfur double bond, carbon-nitrogen double bond, a carbon-carbon triple bond, carbon-nitrogen triple bond, an aromatic carbocyclic or heterocyclic system in β-position to the sulfonium center, unsaturated c-c bond, or c-heteroatom bond where the heteroatom is O, N, S.

Methods for using seeds comprising an epigenetic trait for reproducibly producing seed lots for sale with similar agronomic performance over multiple years and production cycles are provided.

The present disclosure provides for base editors which satisfy a need in the art for installation of targeted transversions of thymine (T) to adenine (A), or correspondingly, trans versions of adenine (A) to thymine (T). The nucleobase editor domains include a nucleic acid programmable DNA binding protein and an adenosine methyltransferase domain. The base editors may be engineered through the use of continuous or non-continuous evolution systems, such as phage-assisted continuous evolution (PACE). In particular, the present disclosure provides for evolved adenine-to-thymine (or thymine-to-adenine) base editor variants that overcome deficiencies in the art for base editors that can install single-base A:T to T:A transversion mutations. In some embodiments, methods for targeted nucleic acid editing are provided. In some embodiments, pharmaceutical compositions comprising, and vectors and kits for the generation of, targeted base editors are provided. In some embodiments, cells containing such vectors are provided. In some embodiments, methods of treatment comprising administering the base editors are provided.

Disclosed herein are artificially synthesized nucleic acid constructs to guide an epigenetic modification for at least partially silencing or activating a target gene in an organism such as a plant or seed, and formulations thereof. Also disclosed are methods of applying such nucleic acid constructs to the plant or to the seed. Also disclosed are engineered seeds and plants obtained by the epigenetic modification.

The invention provides methods of transforming photosynthetic organisms, such as green algae. The methods involve methylating one or more DNA fragments of a DNA construct and transforming the one or more fragments into the photosynthetic organism. The DNA fragments can be the product of a DNA amplification procedure, such as PCR or a PCR-like procedure. In one embodiment the one or more fragments of DNA that comprise a DNA construct are dam methylated prior to being transformed into the photosynthetic organism.

Provided herein are, inter alia, compositions and methods for manipulation of genomes of living organisms.