CHROMATIN PROTOCOLS

By E. DAKAD

1 EXPRESSION AND PURIFICATION OF RECOMBINANT HISTONES AND NUCLEOSOME RECONSTITUTION 2 PREPARATION AND ANALYSIS OF POSITIONED NUCLEOSOMES 3 SITE-DIRECTED CHEMICAL PROBING OF HISTONE–DNA INTERACTIONS 4 BASE-PAIR RESOLUTION MAPPING OF NUCLEOSOMES IN VITRO 5 EQUILIBRIUM AND DYNAMIC NUCLEOSOME STABILITY 6 NUCLEOSOME STRUCTURE AND DYNAMICS 7 ANALYSIS OF LINKER HISTONE BINDING TO MONO- AND DINUCLEOSOMES 8 QUANTITATIVE ANALYSIS OF CHROMATIN HIGHER-ORDER ORGANIZATION USING AGAROSE GEL ELECTROPHORESIS 9 ANALYTICAL ULTRACENTRIFUGATION OF CHROMATIN 10 ANALYSIS OF CHROMATIN BY SCANNING FORCE MICROSCOPY 11 IN VIVO MAPPING OF NUCLEOSOMES USING PSORALEN-DNA CROSSLINKING AND PRIMER EXTENSION 12 PREPARATION OF CHROMATIN ASSEMBLY EXTRACTS FROM XENOPUS OOCYTES 13 PREPARATION OF CHROMATIN ASSEMBLY EXTRACTS FROM PREBLASTODERM DROSOPHILA EMBRYOS 14 A SOLID-PHASE APPROACH FOR THE ANALYSIS OF RECONSTITUTED CHROMATIN CONTENTS 15 RECONSTITUTION AND ANALYSIS OF HYPERACETYLATED CHROMATIN 16 ASSEMBLY OF MITOTIC CHROMOSOMES IN XENOPUS EGG EXTRACT 17 NUCLEOTIDE EXCISION REPAIR COUPLED TO CHROMATIN ASSEMBLY 18 PHOTOLYASE 19 TRANSCRIPTIONAL AND STRUCTURAL ANALYSES OF ISOLATED SV40 CHROMATIN 20 IN VITRO REPLICATION OF CHROMATIN TEMPLATES 21 ANALYSIS OF HMG-14/-17-CONTAINING CHROMATIN 22 IDENTIFICATION AND ANALYSIS OF NATIVE NUCLEOSOMAL HISTONE ACETYLTRANSFERASE COMPLEXES 23 ANALYSIS OF NUCLEOSOME DISRUPTION BY ATP-DRIVEN CHROMATIN REMODELING COMPLEXES 24 NUCLEOSOME REMODELING FACTOR NURF AND IN VITRO TRANSCRIPTION OF CHROMATIN 25 AN SDS-PAGE-BASED ENZYME ACTIVITY ASSAY FOR THE DETECTION AND IDENTIFICATION OF HISTONE ACETYLTRANSFERASES 26 ANALYSIS OF DNASEI HYPERSENSITIVE SITES IN CHROMATIN BY CLEAVAGE IN PERMEABILIZED CELLS 27 MAPPING OF NUCLEOSOME POSITIONS IN YEAST 28 ANALYSIS OF DNA TOPOLOGY IN YEAST CHROMATIN 29 DNA METHYLTRANSFERASES AS PROBES FOR CHROMATIN STRUCTURE IN YEAST 30 RESTRICTION NUCLEASES AS PROBES FOR CHROMATIN STRUCTURE 31 GENOMIC FOOTPRINTING USING NUCLEASES 32 IN SITU ANALYSIS OF CHROMATIN PROTEINSDURING DEVELOPMENT AND CELL DIFFERENTIATION USING FLOW CYTOMETRY 33 MAPPING DNA TARGET SITES OF CHROMATIN PROTEINS IN VIVO BY FORMALDEHYDE CROSSLINKING 34 MAPPING DNA INTERACTION SITES OF CHROMOSOMAL PROTEINS 35 UV LASER FOOTPRINTING AND PROTEIN–DNA CROSSLINKING 36 AN IN VIVO UV CROSSLINKING ASSAY THAT DETECTS DNA BINDING BY SEQUENCE-SPECIFIC TRANSCRIPTION FACTORS