(12) United States Patent (10) Patent No.: US 9,506,915 B2 Tackett Et Al

(12) United States Patent (10) Patent No.: US 9,506,915 B2 Tackett Et Al

USOO9506915B2 (12) United States Patent (10) Patent No.: US 9,506,915 B2 Tackett et al. (45) Date of Patent: *Nov. 29, 2016 (54) METHODS AND KITS FOR ISOLATION AND 2012fO270273 A1 10/2012 Zhang et al. ANALYSIS OF A CHROMATIN REGION 2015,0111788 A1* 4/2015 Fernandez ......... C12N 15, 1093 506/26 (71) Applicants: Alan J. Tackett, Little Rock, AR (US); Stephanie Byrum, Little Rock, AR OTHER PUBLICATIONS (US); Sean Taverna, Little Rock, AR Agelopoulos et al., “Developmental regulation of chromatin con (US); Kevin Raney, Little Rock, AR formation by Hox proteins in Drosophila'. Cell Rep., 2012, pp. (US); Zachary Waldrip, Little Rock, 350-359, vol. 1, No. 4. AR (US) Akiyoshi et al., “Quantitative proteomic analysis of purified yeast kinetochores identifies a PP1 regulatory subunit”. Genes & Devel (72) Inventors: Alan J. Tackett, Little Rock, AR (US); opment, 2009, pp. 2887-2899, vol. 23. Stephanie Byrum, Little Rock, AR Barski et al., “High-Resolution Profiling of Histone Methylations in the Human Genome”, Cell, 2007, pp. 823-837, vol. 129. (US); Sean Taverna, Little Rock, AR Bock et al., “Detailed specificity analysis of antibodies binding to (US); Kevin Raney, Little Rock, AR modified histone tails with peptide arrays'. Epigenetics, 2011, pp. (US); Zachary Waldrip, Little Rock, 256-263, vol. 6, No. 2. AR (US) Boffa et al., “Isolation of active genes containing CAG repeats by DNA strand invasion by a peptide nucleic acid”. Proc. Natl. Acad. (73) Assignee: BOARD OF TRUSTEES OF THE Sci. USA, 1995, pp. 1901-1905, vol. 92. UNIVERSITY OF ARKANSAS, Little Byrum et al., “Quantitative analysis of histone exchange for tran Scriptionally active chromatin”. Journal of Clinical Bioinformatics, Rock, AR (US) 2011, 5 pgs... vol. 1. Byrum et al., “Analysis of Histone Exchange during Chromatin (*) Notice: Subject to any disclaimer, the term of this Purification”. J Integr Omics, 2011, pp. 61-65, vol. 1, No. 1. patent is extended or adjusted under 35 Byrum et al., “A Quantitative Proteomic Analysis of FFPE Mela U.S.C. 154(b) by 0 days. noma'. J. Culan. Pathol., 2011, pp. 933-936, vol. 38, No. 11. Byrum et al., “Analysis of Stable and Transient Protein-Protein This patent is Subject to a terminal dis Interactions'. Methods Mol. Biol., 2012, pp. 143-152, vol. 833. claimer. Byrum et al., “ChaP-MS: A Method for Identification of Proteins and Histone Posttranslational Modifications at a Single Genomic (21) Appl. No.: 14/744,844 Locus”. Cell Rep., 2012, pp. 198-205, vol. 2, No. 1. Byrum et al., “Purification of a specific native genomic locus for proteomic analysis'. Nucleic Acids Research, 2013, e195, pp. 1-6, (22) Filed: Jun. 19, 2015 vol. 41, No. 20. Byrum et al., “Quantitative Proteomics Identifies Activation of (65) Prior Publication Data Hallmark Pathways of Cancer in Patient Melanoma, U Proteomics Bioinform., 2013, pp. 043-050, vol. 6, No. 3. US 2015/0338398 A1 Nov. 26, 2015 Cermak et al., “Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting”. Nucleic Acids Research, 2011. e82, 11 pgs... vol. 39, No. 12. Related U.S. Application Data Chait, “Mass spectrometry in the Postgenomic Era', Annu. Rev. (63) Continuation-in-part of application No. 14/081,812, Biochem., 2011, pp. 239-246, vol. 80. filed on Nov. 15, 2013. Chi et al., "Covalent histone modifications—miswritten, misinter preted, and miserased in human cancers', Nat. Rev. Cancer, 2010, (60) Provisional application No. 62/014,428, filed on Jun. pp. 457-469, vol. 10, No. 7. 19, 2014, provisional application No. 61/726,936, Dai et al., “Global Epiproteomic Signatures Distinguish Embryonic Stem Cells from Differentiated Cells”, Stem Cells, 2007, pp. 2567 filed on Nov. 15, 2012, provisional application No. 2574, vol. 25. 61/875,969, filed on Sep. 10, 2013. Dedon et al., “Formaldehyde Cross-Linking and Immunoprecipita tion Demonstrate Developmental Changes in H1 Association with (51) Int. Cl. Transcriptionally Active Genes', Molecular and Cellular Biology, GOIN 33/53 (2006.01) 1991, pp. 1729-1733, vol. 11, No. 3. GOIN 33/68 (2006.01) DéJardin et al., “Purification of Proteins Associated with Specific Genomic Loci, Cell, 2009, pp. 175-186, vol. 136, No. 1. (52) U.S. Cl. DiCarlo et al., “Genome engineering in Saccharomyces cerevisiae CPC ...... G0IN 33/5308 (2013.01); G0IN 33/6875 using CRISPR-Cas systems'. Nucleic Acids Research, 2013, pp. (2013.01); G0IN 2440/00 (2013.01); G0IN 4336-4343, vol. 41, No. 7. 2570/00 (2013.01) Doyle et al., “TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: (58) Field of Classification Search tools for TAL effector design and target prediction'. Nucleic Acids None Research, 2012, pp. W 117-W 122, vol. 40. See application file for complete search history. (Continued) (56) References Cited Primary Examiner — Jacob Cheu (74) Attorney, Agent, or Firm — Polsinelli PC U.S. PATENT DOCUMENTS (57) ABSTRACT 6,453,242 B1 9/2002 Eisenberg et al. The present invention encompasses methods of identifying 6,534,261 B1 3/2003 Cox, III et al. proteins and protein modifications of proteins specifically 2011 O239315 A1 9/2011 Bonas et al. associated with a chromatin. 2011 O262908 A1 10/2011 Kingston et al. 2012/0040857 A1 2/2012 Kingston et al. 16 Claims, 22 Drawing Sheets 2012/0110685 A1 5/2012 Bonas et al. (12 of 22 Drawing Sheet(s) Filed in Color) US 9,506,915 B2 Page 2 (56) References Cited Platt et al., “The yeast galactose genetic Switch is mediated by the formation of a Gal4p-Ga180p-Gal3p complex”. The EMBO Jour nal, 1998, pp. 4086-4091, vol. 17, No. 14. OTHER PUBLICATIONS Pokholok et al., “Genome-wide Map of Nucleosome Acetylation Fu et al., “High frequency off-target mutagenesis induced by and Methylation in Yeast”. Cell, 2005, pp. 517-527, vol. 122. Ren et al., “Genome-Wide Location and Function of DNA Binding CRISPR-Cas nucleases in human cells', Nat Biotechnol., 2013, pp. Proteins”. Science, 2000, pp. 2306-2309, vol. 290. 822-826, vol. 31, No. 9. Robertson et al., “Genome-wide profiles of STAT1 DNA association Fujita et al., “Efficient isolation of specific genomic regions and using chromatin immunoprecipitation and massively parallel identification of associated proteins by engineered DNA-binding sequencing', Nature Methods, 2007, pp. 651-657, vol. 4, No. 8. molecule-mediated chromatin immunoprecipitation (enChIP) using Rossant, “StemCells and Early Lineage Development,” Cell, 2008, CRISPR, Biochemical and Biophysical Research Communica pp. 527-531, vol. 132. tions, 2013, pp. 132-136, vol. 439. Scholze et al., “TAL effector-DNA specificity,”, Virulence, 2010, Gei?ler et al., “Transcriptional Activators of Human Genes with vol. 1, No. 5, pp. 428-432. Scholze et al., “TAL effectors are remote controls for gene activa Programmable DNA-Specificity”. PLoS One, 2011, e19509, vol. 6, tion.” Current Opinion in Microbiology, 2011, vol. 14, pp. 47-53. No. 5. Shukla et al., “SAGA-associated Sgf73p facilitates formation of the Griesenbeck et al., “Affinity Purification of Specific Chromatin preinitiation complex assembly at the promoters wither in a HAT Segments from Chromosomal Loci in Yeast'. Molecular and Cel dependent or independent manner in vivo”. Nucleic Acids Research, lular Biology, 2003, pp. 9275-9282, vol. 23, No. 24. 2006, vol. 34, No. 21, pp. 5225-6232. Hamperl et al., “Compositional and structural analysis of selected Smart et al., “Mapping the local protein interactome of the NuA3 chromosomal domains from Saccharomyces cerevisiae', Nucleic histone acetyltransferase,” Protein Science, 2009, vol. 18, pp. Acids Research, 2014, e2, 20 pgs... vol. 42, No. 1. 1987-1997. Ho et al., “Chromatin remodelling during development”. Nature, Tackett et al., “I-DIRT. A General Method for Distinguishing 2010, pp. 474-484, vol. 463. between Specific and Nonspecific Protein Interactions,” Journal of Hoshino et al., “Insertional chromatin immunoprecipitation: A Proteome Research, 2005, vol. 4, pp. 1752-1756. method for isolating specific genomic regions'. Journal of Biosci Tackett et al., “Proteomic and genomic characterization of chroma ence and Bioengineering, 2009, pp. 446-449, vol. 108, No. 5. tin complexes at the boundary.” J. Cell Biol., 2005, vol. 169, No. 1, Houseley et al., “AncRNA Modulates Histone Modification and pp. 36-47. mRNA Induction in the Yeast GAL Gene Cluster'. Molecular Cell, Taverna et al., “YnglPHD Finger Binding to H3 Trimethylated at 2008, pp. 685-695, vol. 32. K4 Promotes NuA3 HAT Activity at K14 of H3 and Transcription Jiang et al., “CRISPR—assisted editing of bacterial genomes”. Nat at a Subset of Targeted ORFs'. Molecular Cell, 2006, vol. 24, pp. Biotechnol., 2013, pp. 233-239, vol. 31, No. 3. 785-796. Johnson et al., “Genome-Wide Mapping of In Vivo Protein-DNA Taverna et al., “Long-distance combinatorial linkage between Interactions”, Science, 2007, pp. 1497-1502, vol. 316. methylation and acetylation on histone-H3N termini’. Pro. Natl. Jones et al., “The Epigenomics of Cancer', Cell, 2007, pp. 683-692, Acad. Sci. USA, 2007, vol. 104, No. 7, pp. 2086-2091. vol. 128, No. 4. Unnikrishnan et al., “Dynamic changes in histone acetylation regu Kouzarides, “Chromatin Modifications and Their Function'. Cell, late origins of DNA replication.” Nat. Struct. Mol. Biol., 2010, vol. 2007, pp. 693-705, vol. 128. 17, No. 4, pp. 430-437. Mali et al., "Cas9 as a versatile tool for engineering biology”. Nat Zybailov et al., “Statistical Analysis of Membrane Proteome Methods, 2013, pp. 957-963, vol. 10, No. 10. Expression Changes in Saccharomyces cerevisiae,” Journal of Martin, “Isolation of a pluripotent cell line from early mouse Proteome Research, 2006, vol. 5, No. 9, pp. 2339-2347. embryos cultured in medium conditioned by bratocarcinoma stem Notice of Allowance and Fees Due related to U.S. Appl. No. cells”. Proc. Natl. Acad. Sci. USA, 1981, pp. 7634-7638, vol. 78, 14/081,812 dated Oct.

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