|
|
 |
| Àâòîðèçàöèÿ |
|
|
|
| Ïîèñê ïî óêàçàòåëÿì |
|
|
|
|
|
|
|
 |
|
|
|
| Latchman D.S. — Transcription Factors: A practical Approach |
|
|
|
| Ïðåäìåòíûé óêàçàòåëü |
 -galactosidase, assay 200—201
'Supershift' gel mobility shift analysis, non-DNA-binding transcription factors 90—91
ABCD (avidin-biotin complex on DNA) assay, protein-protein interactions 209—211
Adenovirus major-late promoter, and in vitro transcription 222 224—225
Affinity chromatography, method 110—111
Alkylation of DNA with dimethyl sulphate (DMS), method 40—41
Amino acids, degeneracy of codons 149—150
Amplification of DNA from bacterial colonies, method 156—157
Antibodies, characterization of DNA-binding proteins 19—21
Antibodies, detection of DNA-transcription factor complexes 171
Antibodies, for screening bacteriophage expression libraries 134—136
Antibodies, method for binding 21
Antibodies, method for production 135
Antibodies, phosphorylation-site-specific 283
Antibodies, specificity 20—21
Bacteriophage expression libraries see cDNA expression libraries
Baculovirus, expression of cloned transcription factors 17 194 195
Biotinylated oligonucleotides, concentration of DNA-binding proteins 108 111
Blotting peptides to PVDF membranes, method 116—117
Blunt-end ligation, cloning of PCR products 155—156
Bradford assay for protein concentration, method 13
Brain in vitro transcription assay 215—217 222—226
Brain, nuclear extracts from 215—216 217—222
Bromodeoxyuridine-substituted DNA, cross-linking with ultraviolet light 77—80
c-Myc, protein modification 286
Calcium phosphate-mediated transfection 198—200
Cations, requirement for binding of transcription factors 21
CDNA and genomic libraries, method for low-stringency hybridization 147—148
CDNA expression libraries, cloning by complementation 138—139
CDNA expression libraries, cloning transcription factors 123—126
CDNA expression libraries, expression in eukaryotic cells 137—138
CDNA expression libraries, library selection 124
CDNA expression libraries, plaque purification 126
CDNA expression libraries, plating 125—126
CDNA expression libraries, screening methods 126—139
CDNA expression libraries, use in polymerase chain reaction (PCR) 153
CDNA isolation, design of oligonucleotides 118—121
Cell cycle control 261—263
Cell membranes, permeabilization 49
Chloramphenicol acetyl transferase (CAT), assay 201—202
Chromatin, structure 229—230
Chromatin, transcription from 217 229—259
Cloning, cDNA expression libraries 123—126 138—139
Cloning, methods for PCR products 155—156
Cloning, target genes for transcription factors 174—177
Cloning, transcription factors 145—164
CNBr, cleavage of proteins to peptides 114—115
CNBr-activated Sepharose 4B, for DNA affinity chromatography 104—105 108—109
Co-immunoprecipitation, analysis of interactions between transcription factors 92—94
Codons, degeneracy 149—150
Cofactors, DNA-binding proteins 21
Cooperative binding, analysis 86—87
COUP-TF, interaction with non-DNA-binding transcription factor S300-II 88—89
CpG islands, enrichment in genes 169
CpG islands, genomic binding-site cloning 173—174
Cross-linking of transcription factors 85—86 94
Cross-linking, transcription factors to DNA 78—80 81—82
CTCF factor, purification 98 105—108 112
Dephosphorylation of proteins, method 269—270
Dimerization, transcription factors 84—86
Dimethyl sulphate (DMS), interference assay 42—43
Dimethyl sulphate (DMS), modification of DNA 39 40—41 48—51 53
Dimethylpimelidate (DMP), cross-linking agent 86
Dithiobis(succinimylpropionate) (DSP), protein cross-linker 93—94
DNA affinity chromatography, purification of DNA-binding proteins 104—111
DNA fragments, nitrocellulose binding assay 176
DNA in vitro modification of DNA with DMS 53
DNA labelling with DNA polymerase 8—10
DNA labelling, end labelling 28—29 32—34
DNA labelling, single strand 29—30
DNA mobility shift assay for DNA-binding proteins 1—25 202 204—206
DNA mobility shift assay, analysis of tertiary structure 84—85
DNA mobility shift assay, applications 2—6
DNA mobility shift assay, binding of transcription factors to nucleosomes 255
DNA mobility shift assay, binding reaction 12—13
DNA mobility shift assay, identification of transcription factors 4—6
DNA mobility shift assay, limitations 6
DNA mobility shift assay, measurement of transcription factor levels 4—5
DNA mobility shift assay, preparation of labelled oligonucleotide probes 7—8
DNA mobility shift assay, principle 2—4
DNA mobility shift assay, selection of DNA probe 6—7
DNA mobility shift assay, sequence specificity 3—5 18—20 128 135—137 138 141
DNA modification in vivo 48—51
DNA modification, dimethyl sulphate (DMS) 39 40—41 48—51
DNA modification, ethylnitrosourea (ENU) 40
DNA probes, selection for DNA mobility shift assay 6—7
DNA, cross-linking to transcription factors 77—82
DNA, dephosphorylation methods 8
DNA, end labelling methods 7—8 33—34 120 246—247
DNA, packing into chromatin 229—230
DNA, piperidine cleavage 53—55
DNA, purification 51—53
DNA, supercoiling and promoter activity 226—227
DNA-binding activity, mobility shift assay 1—25 202 204—206
DNA-binding assays, preparation of  -labelled oligonucleotides 204—205
DNA-binding proteins, characterization 19—23
DNA-binding proteins, cloning 123—143
DNA-binding proteins, cofactors 21
DNA-binding proteins, concentration with biotinylated oligonucleotides 108 111
DNA-binding proteins, detection 2—14
DNA-binding proteins, DNA mobility shift assay 1—25
DNA-binding proteins, DNA sequence specificity 3—5
DNA-binding proteins, guanidinium chloride denaturation and renaturation 132—134
DNA-binding proteins, identification 4 19—23 111
DNA-binding proteins, interactions with other proteins 23—24
DNA-binding proteins, molecular weight determination 2—3 17 98
DNA-binding proteins, production of peptides from 114—117
DNA-binding proteins, proteolytic clipping band-shift assay 21—23
DNA-binding proteins, purification 17 97—114
DNA-binding proteins, requirement for cations 21 see
DNA-binding specificity, transcription factors 17—19
DNA-binding specificity, use of competitor DNA 3—5 18—20
DNA-cellulose chromatography, purification of DNA-binding proteins 103—104
DNA-protein complexes footprint analysis 27—62 see
DNA-protein interactions, determination of affinity 205—206
DNAase I footprinting 37—38 84
DNAase I footprinting, binding of transcription factors to nucleosomes 255
DNAase I footprinting, non-DNA-binding transcription factors 88 see
Drosophila embryo, nuclear extracts 233
E2F family, transcription factors 261—262 264—265
Electro-mobility shift assay (EMSA) see DNA mobility shift assay
Electroporation of COS-1 cells, method 194
Electroporation, for transfection of transcription factors 198—199
Enhancer activity, genomic DNA fragments 176—177
Enzymes, introduction into cells 49
Enzymes, production of peptides from DNA-binding proteins 115
Ethylnitrosourea (ENU), DNA modification 40
Expression vectors, organization 192—193
Far-Western approach, screening cDNA expression libraries 137
Ferrous EDTA, use in footprint analysis 38—39
Footprint analysis in vitro 29—47
Footprint analysis in vivo 47—61
Footprint analysis of binding sites on closed circular plasmids 31 43—47
Footprint analysis of binding sites on end-labelled fragments 29—43
Footprint analysis, choice of linear DNA molecules 30—34
Footprint analysis, DNA-protein complexes 27—62
Footprint analysis, interference assays 27—29 39—43 84
Footprint analysis, ligation-mediated PCR (LMPCR) 32—33 34—35 47—49
Footprint analysis, method 45—47 59—61
Footprint analysis, protection analysis 27—29 37—39
Footprint analysis, protection from DNase I digestion 37—38 84
Footprint analysis, protein sources for binding 34—37
Fragment probes, labelling of 8—10
G-free cassette assay, for transcription 64—66 68
GATA1 factor, purification 98 101 103 105—106
GATA1 factor, quantity in cells 97
Gel filtration chromatography, molecular weight determination 69—72
Gel filtration chromatography, properties of matrices 70—71
Gel mobility shift assay, analysis of protein-protein interactions 209 210
Gel mobility shift assay, non-DNA-binding transcription factors 88 90—91
| Gel retardation assay see DNA mobility shift assay; gel mobility shift assay
Gene promoters, TAATGARAT sequence 1—2
Genes, enrichment in CpG islands 169
Genome sequences, databases 160 162
Genomic binding-site, cloning cloning procedure 172—173
Genomic binding-site, concentration of DNA-protein complex 170—171
Genomic binding-site, identification of target genes 165—179
Genomic binding-site, preparation of transcription factor protein 167—169
Genomic binding-site, principle 165—167
Genomic binding-site, source of DNA 169—170
Genomic binding-site, use of CpG islands 169 173—174
Glycerol gradient centrifugation, molecular weight determination 73—74
Glycosylation, transcription factors 285—290
GST pull-down assay, analysis of protein-protein interactions 206—207
GST-fusion proteins, method for expression 190—191
GST-fusion proteins, purification 191
Guanidinium chloride, denaturation and renaturation of DNA-binding proteins 132—134
HeLa cells, preparation of nuclear extracts 66—67
Helix-loop-helix proteins, properties 161
Herpes simplex virus 1 (HSV-1) 1—2 23—24
Histone acetylation, effects on transcription 257 262
Histones, and transcription 230 257 262
Histones, packing of DNA into chromatin 229—230
Histones, preparation 236—242
Homeobox proteins, properties 161
Hydroxyapatite, purification of histones 236 238—239 241
Immunoprecipitation, analysis of protein-protein interactions 208—209
Immunoprecipitation, detection of DNA-transcription factor complexes 171
in vitro transcription and adenovirus major-late promoter 222 224—225
in vitro transcription and neurofilament (NF) promoter 222 224—225 227
in vitro transcription and promoter templates 226—227
in vitro transcription and translation, method 188
in vitro transcription, method 68 223—224
Insect cells, overexpression of cloned transcription factors 194
Lectins, analysis of protein glycosylation 286—288
Library plating and replica lifts, method 125—126
Ligation-mediated polymerase chain reaction (LMPCR), for in vivo footprinting 32—33 34—35 47—49
Ligation-mediated polymerase chain reaction (LMPCR), method 56—59
Ligation-mediated polymerase chain reaction (LMPCR), preparation of DNA for 53—55
Ligation-mediated polymerase chain reaction (LMPCR), preparation of linkers 55—56
Ligation-mediated polymerase chain reaction (LMPCR), resolution 56—61
Linear DNA, method for protection from DNase I 37—38
Lipofection, for transfection of transcription factors 198—199
Luciferase, assay 200—201
Lysogen, generation from purified phage stock 139—140
Mammalian cells, expression of transcription factors 15—16 192—194 195
Mass spectrometry, analysis of protein phosphorylation 284—285
Mass spectrometry, identification of protein sequences 97
Mass spectrometry, measurement of mass of peptides 115
Mass spectrometry, method for preparing proteins 119—120
Methidium-propyl EDTA, use in footprint analysis 38
Microbore reverse-phase chromatography, separation of peptides 114
Micrococcal nuclease, analysis of reconstituted nucleosomes 253—255
Minichromosomes, preparation of nucleosome arrays 234
Molecular weight determination, calibration 69—70 73—74
Molecular weight determination, denatured transcription factors 76—83
Molecular weight determination, DNA-binding proteins 2—3 98
Molecular weight determination, methods 3 17 69—77
Molecular weight determination, transcription factors 69—76 98
Mononucleosome templates, analysis of transcription elongation 231
Mononucleosome templates, analysis of transcription initiation 231
Mononucleosome templates, binding of transcription factors 255—257
Mononucleosome templates, position of transcription factor binding site 243—244
Mononucleosome templates, preparation 232—233 234—236 243—255
Mononucleosome templates, transcription 230—232
Myelin, effect on isolation of nuclei 219—220
Neurofilament (NF) promoter, and in vitro transcription 222 224—225 227
Non-denaturing gradient electrophoresis, molecular weight determination 75—76
Non-DNA-binding transcription factors, 'supershift' gel mobility shift analysis 90—91
Non-DNA-binding transcription factors, DNAase footprinting 88
Non-DNA-binding transcription factors, gel mobility shift analysis 88 90—91
Non-DNA-binding transcription factors, restoration of activity 89
Non-DNA-binding transcription factors, S300-II 88—89
Northern blot analysis, transcription factor binding sites 175
Nuclear extracts, Drosophila embryo 233
Nuclear extracts, preparation 66—67 99—103 215—216 217—222
Nuclear extracts, Xenopus 233
Nuclear proteins, extraction from rat brain 220—222
Nuclear proteins, methods of preparation 11 36 67 101—103
Nuclease P1, use in footprint analysis 38
Nuclei, effect of myelin on isolation from brain 219—220
Nuclei, isolation from rat brain 217—220
Nuclei, preparation from whole tissue 102—103
Nucleoplasmin, reconstitution of nucleosomes 235—236
Nucleosome arrays see nucleosome templates
Nucleosome core particles, preparation method 250—252
Nucleosome templates, analysis of transcription elongation 232
Nucleosome templates, analysis of transcription initiation 231
Nucleosome templates, binding of transcription factors 255—257
Nucleosome templates, essential components 234
Nucleosome templates, preparation 232—234
Nucleosomes and transcription 230
Nucleosomes, characterization of reconstituted 252—255
Nucleosomes, packing of DN A into chromatin 229—230
Nucleosomes, reconstitution 247—249
Octamer family, transcription factors 1—2 20 23—24 261—263 266 268—269 273
Oestrogen receptor 165 177—178 181—182 208—209
Oestrogen receptor binding site, nucleotide sequence 202 204
Oestrogen receptor in vitro transcription and translation 187—189
Oestrogen receptor, DNA-binding domain 167—168 170 172
Oestrogen receptor, interaction with steroid receptor coactivator protein SRC1a 207
Oestrogen receptor, ligand-binding domain 189—190
Oestrogen receptor, transcriptional activation by 196—197
Oestrogen receptor, zinc fingers 167—168
Oestrogen response element, binding site 197
Oestrogen-responsive genes, isolation 165 172 177—178
Oligonucleotides for DNA mobility shift assay 7—8
Oligonucleotides for screening libraries 114 130—131
Oligonucleotides, design for cDNA isolation 118—121
Oligonucleotides, method for hybridization to library filters 120—121
Orthologous genes, isolation from phylogenetically diverse organisms 145
P53 tumour suppressor, glycosylation 286
PCR products, cloning 155—156
PCR products, method for direct sequencing 157—158
PCR, see polymerase chain reaction (PCR) PCR deletion analysis, method 184
Peptide mapping for phosphorylation sites, method 277—278
Peptide tags, for purification of proteins 185
Peptides, measurement of mass by mass spectroscopy 115
Peptides, preparation methods 114—117
Phenanthroline-copper, use in footprint analysis 38—39
Phosphatases, use in analysis of protein phosphorylation 267—270
Phosphoamino acid analysis, method 280
Phosphorylation, retinoblastoma (pRb) protein 261—262
Phosphorylation, synthetic peptides 282—283
Phosphorylation, transcription factors 261—285
Piperidine, cleavage of modified DNA 48 53—55
Plasmids, footprint analysis 43—47
Polymerase chain reaction (PCR) and cloning transcription factors 148—160
Polymerase chain reaction (PCR), 'in-and-out'PCR 153
Polymerase chain reaction (PCR), 'touchdown PCR' 151
Polymerase chain reaction (PCR), annealing temperature 149 151
Polymerase chain reaction (PCR), artefacts 158—160
Polymerase chain reaction (PCR), choice of template 151 153—155
Polymerase chain reaction (PCR), cloning of products 155—156
Polymerase chain reaction (PCR), methods for screening libraries 154—155
Polymerase chain reaction (PCR), preparation of deletion mutants of transcription factors 182—185
Polymerase chain reaction (PCR), preparation of point mutations of transcription factors 185—187
Polymerase chain reaction (PCR), reaction conditions 151
Polymerase chain reaction (PCR), selection of primers 148—149 150 152 182—183 185
Polymerase chain reaction (PCR), sequencing of products 155—158
Polymerase chain reaction (PCR), standard method 153—154
Polymerase chain reaction (PCR), whole genome PCR method 171
POU-domain proteins, properties 161
Progesterone receptors, assay 64—66
Progesterone receptors, cooperative binding to progesterone-response elements (PREs) 87
Progesterone-response elements (PREs), cooperative binding of progesterone receptors 87
Progesterone-response elements (PREs), synergistic progesterone inducibility 87
Promoter templates and in vitro transcription 226—227
Promoter templates and supercoiling of DNA 226—227
Promoters for transcription assays 64
|
|
|
| Ðåêëàìà |
|
|
|
|
|
|
|
|
Î ïðîåêòå