Abstract: This present invention relates to methods for improved assays to quantify the level of chromatin targets from biological samples. These assays can be used for the detection of global levels of epigenetic modifications (e.g., histone and DNA modifications), chromatin associated proteins, or chromatin associated ribonucleic acids (RNA). The invention further relates to assay kits that include the reagents needed to prepare biological samples and perform said improved chromatin assays.

Abstract: The invention relates generally to methods for preparing recombinant nucleosomes. In particular, the invention relates to methods for ligating a histone peptide onto a fully assembled recombinant nucleosome. The invention further relates to modified core histone proteins, histone peptides to be ligated to the modified core histone proteins, and fully assembled recombinant nucleosomes and libraries of recombinant nucleosomes prepared by the methods of the invention.

Abstract: The present invention relates to DNA-barcoded recombinant nucleosomes and polynucleosomes that have been engineered for use as spike-in controls for the quantitative mapping of chromatin associated proteins using Chromatin ImmunoPrecipitation (ChIP) assays, tethered enzyme-based mapping assays, and other chromatin mapping assays. The invention further relates to methods of using the engineered DNA-barcoded recombinant nucleosomes in ChIP assays, tethered enzyme-based mapping assays, and other chromatin mapping assays.

Abstract: This present invention relates to methods for carrying out chromatin mapping assays that use enzymes to incorporate barcoded DNA at targeted genomic regions followed by long-read sequencing (e.g., Third Generation Sequencing (TGS)). This approach enables the mapping of chromatin targets using TGS and can be used for a wide range of elements or features, including histone post-translational modifications, chromatin associated proteins, nucleosome positioning, and chromatin accessibility. The invention further relates to kits and reagents for carrying out the methods on chromatin samples that include one or more cells.

Abstract: The present invention relates to DNA-barcoded recombinant nucleosomes and polynucleosomes that have been engineered for use as spike-in controls for chromatin accessibility assays, chromatin mapping assays, e.g., using tethered enzymes, as well as other chromatin assays. The invention further relates to methods of using the engineered DNA-barcoded recombinant nucleosomes in chromatin accessibility assays, chromatin mapping assays, as well as other chromatin assays.

Abstract: The invention relates generally to methods for preparing recombinant nucleosomes. In particular, the invention relates to methods for ligating a histone peptide onto a fully assembled recombinant nucleosome.

Abstract: The invention relates to the use of recombinant/semi-synthetic nucleosomes carrying histone and/or DNA modifications as a reference standard for quantification of covalently modified (on the histone proteins or wrapping DNA), variant, or mutant nucleosomes (collectively “modified nucleosomes” or “nucleosome modifications”) from a biological sample. The invention further relates to methods of using the assay to accurately quantify single or combinatorial nucleosome modifications as biomarkers of disease.

Abstract: The invention relates to the use of recombinant/semi-synthetic nucleosomes carrying histone and/or DNA modifications as a reference standard for quantification of covalently modified (on the histone proteins or wrapping DNA), variant, or mutant nucleosomes (collectively “modified nucleosomes” or “nucleosome modifications”) from a biological sample. The invention further relates to methods of using the assay to accurately quantify single or combinatorial nucleosome modifications as biomarkers of disease.

Abstract: The invention relates to the use of recombinant/semi-synthetic nucleosomes carrying histone and/or DNA modifications as a reference standard for quantification of covalently modified (on the histone proteins or wrapping DNA), variant, or mutant nucleosomes (collectively “modified nucleosomes” or “nucleosome modifications”) from a biological sample. The invention further relates to methods of using the assay to accurately quantify single or combinatorial nucleosome modifications as biomarkers of disease.