Integrated system for programmable dna methylation

An engineered DNA methylation system comprising:

• a. a reporter module comprising a nucleic acid sequence encoding one or more DNA binding domain target sites, one or more GATC nucleic acid sequences, a promoter nucleic acid sequence, and a nucleic acid sequence encoding an output protein molecule;
• b. a writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a writer fusion protein comprising:
• a DNA binding protein or domain thereof and a mutant DNA adenine methyltransferase, wherein the writer module binds the one or more DNA binding domain target sites and methylate adenines (A) of the one or more GATC nucleic acid sequences of the synthetic reporter module, thereby initiating adenine methylation;
• c. a reader-effector module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-effector fusion protein comprising:
• a methyl-adenine DNA binding domain of DpnI endonuclease and one or more transcriptional effector domains, wherein the reader-effector module recognizes methylated adenines and can recruit one or more regulatory factors to the synthetic reporter module;
• and
• d. a reader-writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-writer fusion protein comprising:
• a mutant DNA adenine methyltransferase and a methyl-adenine DNA binding domain of DpnI endonuclease, wherein the reader-writer fusion protein propagates the adenine methylation initiated by the writer fusion protein module.

A cell comprising an engineered DNA methylation system comprising:

• a. a reporter module comprising a nucleic acid sequence encoding one or more DNA binding domain target sites, one or more GATC nucleic acid sequences, a promoter nucleic acid sequence, and a nucleic acid sequence encoding an output protein molecule;
• b. a writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a writer fusion protein comprising:
• a DNA binding protein or domain thereof and a mutant DNA adenine methyltransferase;
• c. a reader-effector module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-effector fusion protein comprising:
• of a methyl-adenine DNA binding domain of DpnI endonuclease and one or more transcriptional effector domains;
• and
• d. a reader-writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-writer fusion protein comprising:
• a mutant DNA adenine methyltransferase and a methyl-adenine DNA binding domain of DpnI endonuclease.

A method of modulating adenine methylation status of a target sequence comprising introducing an engineered DNA methylation system comprising:

• a. a reporter module comprising a nucleic acid sequence encoding one or more DNA binding domain target sites, one or more GATC nucleic acid sequences, a promoter nucleic acid sequence, and a nucleic acid sequence encoding an output protein molecule;
• b. a writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a writer fusion protein comprising:
• a DNA binding protein or domain thereof and a mutant DNA adenine methyltransferase;
• c. a reader-effector module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-effector fusion protein comprising:
• of a methyl-adenine DNA binding domain of DpnI endonuclease and one or more transcriptional effector domains;
• and
• d. a reader-writer module comprising a promoter sequence operably linked to a nucleic acid sequence encoding a reader-writer fusion protein comprising:
• a mutant DNA adenine methyltransferase and a methyl-adenine DNA binding domain of DpnI endonuclease;
• into a cell or artificial cell.