Methods, compositions, kits, and systems are provided for identifying regions of genomic DNA bound to a protein. The methods may include contacting genomic DNA with an adenine methyltransferase (A-MTase), where the A-MTase causes methylation of adenine residues in regions of the genomic DNA not bound to a protein; and conducting single molecule long read sequencing of the contacted genomic DNA to detect locations in the genomic DNA lacking methylated adenine residues to identify regions of genomic DNA bound to a protein. The bound regions may be nucleosome positions and the methods may determinenucleosome positions in genomic DNA. Also provided are methods for visualization of regions of chromatin not bound to a protein and spatially available as a substrate for an adenine methyltransferase (A-MTase) in a cell by visualizing location of methylated adenines after contacting the cells with the A-MTase.

The present disclosure relates to site-specific disrupting agents for modulating, e.g., decreasing, expression of a target plurality of genes in a cell. In some embodiments, the target plurality of genes comprises pro-inflammatory genes, e.g., CXCL1, CXCL2, CXCL3, CXCL4, CXCL5, CXCL6, CXCL7, and IL-8. In some embodiments, the method comprises using a first site-specific disrupting agent that targets a first anchor sequence and a second site-specific disrupting agents that disrupts a second anchor sequence.

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

The present disclosure provides, inter alia, methods for treating a disease characterized by an abnormal level of m6dA in a subject, such as cancer, methods of modifying a nucleic acid from a cell, methods for identifying protein binding sites on DNA, methods of mediating DNA N6-adenine methylation, methods of modulating nucleosome organization and/or transcription in a cell, using MTA1c or any components thereof. The present disclosure also provides methods of generating a synthetic chromosome and synthetic chromosomes made by such methods. Pharmaceutical compositions comprising MTA1c or any components thereof and kits containing such compositions or for carrying out such processes are further provided. Eukaryotic cells, vectors and transgenic organisms comprising MTA1c or any components thereof are also provided. Synthetic chromosomes and methods of making same are also provided.

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

The inventive technology may include novel systems for regulation of the expression of bacterial genes through the introduction of antisense RNA (asRNA) that may disrupt expression of targeted pathogenic genes and/or their products (mRNA, proteins). In some embodiments, the inventive technology may include novel genetically engineered donor bacterial strains that are configured to efficiently and continuously deliver asRNA polynucleotides to a recipient pathogen and downregulate expression or one or more essential genes.

Methods for delivering non-mitochondrial proteins to mitochondria are provided. Also provided are nucleic acid constructs comprising a coding sequence encoding a DNA-binding polypeptide, fused to a mitochondrial targeting sequence (MTS) and a nuclear export signal (NES), and the encoded proteins. The construct successfully delivers DNA binding proteins to the mitochondrion. A chimeric methylase based on the above construct is successfully delivered to mitochondria, resulting in modification of mtDNA.

Provided herein are gene repressor systems comprising fusion proteins, such as fusion proteins comprising a DNA binding domain such as a TALE, zinc finger or catalytically-dead CRISPR protein and guide nucleic acid (gRNA), which are useful in the repression of a proprotein convertase subtilisin kexin Type 9 (PCSK9) gene. Also provided are methods of using such systems to repress transcription of PCSK9.

Provided herein are gene repressor systems comprising fusion proteins, such as fusion proteins comprising a DNA binding domain such as a TALE, zinc finger or catalytically-dead CRISPR protein and guide nucleic acid (gRNA), which are useful in the repression of a proprotein convertase subtilisin/kexin Type 9 (PCSK9) gene. Also provided are methods of using such systems to repress transcription of PCSK9.

Cofactor analogs 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 -position to the sulfonium center, unsaturated c-c bond, or c-heteroatom bond where the heteroatom is O, N, S.