Abstract: The presently disclosed subject matter provides for expression cassettes that allow for expression of a globin gene or a functional portion thereof, vectors comprising thereof, and cells transduced with such expression cassettes and vectors. The presently disclosed subject matter further provides methods for treating a hemoglobinopathy in a subject comprising administering an effective amount of such transduced cells to the subject.

Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.

Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.

Abstract: Provided herein are methods for identifying high potency genomic insulator elements that can be used in a vector composition e.g., that are useful for preventing unwanted expression of neighboring genes, such as proto-oncogenes, when administered to a subject in need thereof. Also provided herein are methods for treating disease and methods for administering a nucleic acid to a subject using such vectors.

Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.

Abstract: DNA cleaving enzymes are disclosed. The DNA cleaving enzymes are fused to a heterologous DNA binding domain that is designed to bind to a target nucleic acid sequence. Nucleic acids and expression cassettes encoding the DNA cleaving enzymes are also provided. Methods for genome editing using the DNA cleaving enzymes, fusion proteins, and compositions thereof are disclosed herein.

Abstract: The presently disclosed subject matter provides for expression cassettes that allow for expression of a globin gene or a functional portion thereof, vectors comprising thereof, and cells transduced with such expression cassettes and vectors. The presently disclosed subject matter further provides methods for treating a hemoglobinopathy in a subject comprising administering an effective amount of such transduced cells to the subject.

Abstract: The present disclosure provides methods and compositions for modulating expression of a target gene in a cell by reducing binding of an endogenous transcription factor to a regulatory sequence of the target gene. The method includes introducing into the cell a DNA binding polypeptide (DBF) that binds a sequence in regulatory region of a target gene bound by a transcription factor (TF), thereby displacing the TF and modulating expression of the target gene. The DBF may be designed to bind a sequence comprising the binding site for the TF and additional nucleotides present on one or both sides of the sequence. Accordingly, the DBF specifically binds to binding site for the TF in the target gene but not in other genes that are also regulated by binding of the TF but do not include the nucleotides present on one or both sides of the sequence.

Abstract: 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.

Abstract: Provided herein are expression cassettes comprising at least one copy of an enhancer element, wherein the enhancer element comprises or consists essentially of a nucleotide sequence at least 50% identical to any one of SEQ ID NOs: 1-10 and vectors comprising the expression cassettes. Also provided herein are cells transduced with the expression cassettes or the vectors. Further described herein are pharmaceutical compositions comprising an effective amount of one or more of: the cell, the expression cassette, or the vector of this disclosure. Also disclosed herein are methods of treating a hemoglobinopathy in a subject, comprising administering an effective amount of the pharmacological compositions described herein.

Abstract: Disclosed herein are methods of detecting a target nucleic acid sequence, determining the localization of the target nucleic acid sequence, and/or quantifying the number of target nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH.

Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.

Abstract: Disclosed herein are methods of utilizing machine learning methods to analyze microscope images of populations of cells.

Abstract: Provided herein are polypeptides, compositions comprising the polypeptides and methods for genome editing and gene regulation (e.g., activation and/or repression) using the polypeptides or the compositions comprising the polypeptides, such as, DNA binding domains derived from the genus of Ralstonia. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a TALE protein, such as, a Xanthomonas TALE protein. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a DNA binding protein derived from bacteria of the genus Ralstonia.

Abstract: The present disclosure provides polypeptides, compositions thereof, and methods for suppressing expression of a target gene such as PDCD1, CTLA4, LAG3, or TIM-3. The polypeptides disclosed herein include a DNA binding domain (DBD) that binds to a sequence of the target gene and a transcriptional repressor domain that suppresses expression of the target gene. The transcriptional repressor domain may be a known transcriptional repressor or may be a novel transcriptional repressor disclosed herein. Also disclosed herein are novel transcriptional repressors that are conjugated to a heterologous DNA binding domain and mediate suppression of expression of a target gene bound by the DNA binding domain.

Abstract: The present disclosure provides genome engineering proteins, e.g., nucleic acid binding domains and/or functional domains that have a net positive charge and are cell permeable and can be introduced into the cells without the use of a carrier such as micelles, vesicles, liposomes, and the like.

Abstract: Disclosed herein are methods of detecting a target nucleic acid sequence, determining the localization of the target nucleic acid sequence, and/or quantifying the number of target nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH.

Abstract: Provided herein are methods and compositions for use in detecting on-target and/or off-target cleavage of genomic DNA in a cell by a nuclease. The on-target and off-target cleavage is detected by using oligonucleotides that bind to the single-stranded 3?-overhang created at the cleavage site. The nuclease may be an engineered nuclease comprising a nucleic acid binding domain that binds to a target nucleic acid of interest.

Abstract: Provided herein are DNA binding domains comprising a plurality of repeat units, wherein each repeat unit is expanded or contracted in length. Also provided herein are DNA binding domains comprising a plurality of repeat units, wherein each repeat unit is separated from a neighboring repeat unit by a linker. In certain aspects, the linker includes a recognition site. Also disclosed are DNA binding proteins that include a fragment of N-cap sequence of a TALE protein. The TALE protein may be a Xanthomonas TALE protein.

Abstract: Disclosed herein are methods of detecting a target viral nucleic acid sequence, determining the localization of the target viral nucleic acid sequence, and/or quantifying the number of target viral nucleic acid sequences in a cell. This method may be used on small target nucleic acid sequences, and may be referred to as Nano-FISH or viral Nano-FISH.