Provided herein is a cell-free biosensor lateral flow device kit for detection of analytes of interest and methods of using thereof. The device comprises a substrate and a first end, wherein the first end comprises a sample loading portion. The device additionally may comprise a sensor module, wherein the sensor module comprises an allosteric transcription factor regulated in vitro transcription reaction, and a transduction module, wherein the transduction module comprises Bait and Prey nucleic acids which sense the output of the sensor element and a reporter conjugate which accumulates at a test zone when an analyte the sensor element senses is present in the sample.

Provided herein is a cell-free biosensor lateral flow device kit for detection of analytes of interest and methods of using thereof. The device comprises a substrate and a first end, wherein the first end comprises a sample loading portion. The device additionally may comprise a sensor module, wherein the sensor module comprises an allosteric transcription factor regulated in vitro transcription reaction, and a transduction module, wherein the transduction module comprises Bait and Prey nucleic acids which sense the output of the sensor element and a reporter conjugate which accumulates at a test zone when an analyte the sensor element senses is present in the sample.

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.

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 methods of identifying RNA targets of RNA binding proteins. In aspects, the disclosure relates to a method of identifying RNA molecules bound by RNA binding proteins. Some embodiments of the present disclosure relate to a method that can definitively identify direct RNA-target interactions with targeted proteins without the requirement for immunoprecipitation or gel extraction. In some embodiments, the method may include combining multiple antibodies in the same sample.

The present disclosure relates to methods of identifying RNA targets of RNA binding proteins. In aspects, the disclosure relates to a method of identifying RNA molecules bound by RNA binding proteins. Some embodiments of the present disclosure relate to a method that can definitively identify direct RNA-target interactions with targeted proteins without the requirement for immunoprecipitation or gel extraction. In some embodiments, the method may include combining multiple antibodies in the same sample.

A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, including: contacting a permeabilized cell or nucleus with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease that is inactive or an activatable transposome; activating the nuclease or transposase, thereby excising the sequence of chromatin DNA bound to the chromatin-associated factor of interest; isolating the excised DNA; and determining the sequence of the excised DNA, thereby detecting binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in the cell.

A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, including: contacting a permeabilized cell or nucleus with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease that is inactive or an activatable transposome; activating the nuclease or transposase, thereby excising the sequence of chromatin DNA bound to the chromatin-associated factor of interest; isolating the excised DNA; and determining the sequence of the excised DNA, thereby detecting binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in the cell.

A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, including: contacting a permeabilized cell or nucleus with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease that is inactive or an activatable transposome; activating the nuclease or transposase, thereby excising the sequence of chromatin DNA bound to the chromatin-associated factor of interest; isolating the excised DNA; and determining the sequence of the excised DNA, thereby detecting binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in the cell.

A method for detecting the binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in a cell, including: contacting a permeabilized cell or nucleus with a specific binding agent that specifically recognizes the chromatin-associated factor of interest, wherein the specific binding agent is linked to a nuclease that is inactive or an activatable transposome; activating the nuclease or transposase, thereby excising the sequence of chromatin DNA bound to the chromatin-associated factor of interest; isolating the excised DNA; and determining the sequence of the excised DNA, thereby detecting binding of a chromatin-associated factor of interest to a sequence of chromatin DNA in the cell.