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Latchman D.S. Ч Transcription Factors: A practical Approach
Latchman D.S. Ч Transcription Factors: A practical Approach

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Ќазвание: Transcription Factors: A practical Approach

јвтор: Latchman D.S.

јннотаци€:

Univ. College of London, UK. Provides a comprehensive guide to the methods currently available to characterize the function and activity of an individual transcription factor. A new chapter covers the use of in vitro transcription assays. For researchers. Previous edition: c1993. Hardcover, softcover is also available.


язык: en

–убрика: Ѕиологи€/

—татус предметного указател€: √отов указатель с номерами страниц

ed2k: ed2k stats

√од издани€: 1999

 оличество страниц: 303

ƒобавлена в каталог: 01.12.2006

ќперации: ѕоложить на полку | —копировать ссылку дл€ форума | —копировать ID
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ѕредметный указатель
$\beta$-galactosidase, assay      200Ч201
'Supershift' gel mobility shift analysis, non-DNA-binding transcription factors      90Ч91
ABCD (avidin-biotin complex on DNA) assay, protein-protein interactions      209Ч211
Adenovirus major-late promoter, and in vitro transcription      222 224Ч225
Affinity chromatography, method      110Ч111
Alkylation of DNA with dimethyl sulphate (DMS), method      40Ч41
Amino acids, degeneracy of codons      149Ч150
Amplification of DNA from bacterial colonies, method      156Ч157
Antibodies, characterization of DNA-binding proteins      19Ч21
Antibodies, detection of DNA-transcription factor complexes      171
Antibodies, for screening bacteriophage expression libraries      134Ч136
Antibodies, method for binding      21
Antibodies, method for production      135
Antibodies, phosphorylation-site-specific      283
Antibodies, specificity      20Ч21
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      116Ч117
Blunt-end ligation, cloning of PCR products      155Ч156
Bradford assay for protein concentration, method      13
Brain in vitro transcription assay      215Ч217 222Ч226
Brain, nuclear extracts from      215Ч216 217Ч222
Bromodeoxyuridine-substituted DNA, cross-linking with ultraviolet light      77Ч80
c-Myc, protein modification      286
Calcium phosphate-mediated transfection      198Ч200
Cations, requirement for binding of transcription factors      21
CDNA and genomic libraries, method for low-stringency hybridization      147Ч148
CDNA expression libraries, cloning by complementation      138Ч139
CDNA expression libraries, cloning transcription factors      123Ч126
CDNA expression libraries, expression in eukaryotic cells      137Ч138
CDNA expression libraries, library selection      124
CDNA expression libraries, plaque purification      126
CDNA expression libraries, plating      125Ч126
CDNA expression libraries, screening methods      126Ч139
CDNA expression libraries, use in polymerase chain reaction (PCR)      153
CDNA isolation, design of oligonucleotides      118Ч121
Cell cycle control      261Ч263
Cell membranes, permeabilization      49
Chloramphenicol acetyl transferase (CAT), assay      201Ч202
Chromatin, structure      229Ч230
Chromatin, transcription from      217 229Ч259
Cloning, cDNA expression libraries      123Ч126 138Ч139
Cloning, methods for PCR products      155Ч156
Cloning, target genes for transcription factors      174Ч177
Cloning, transcription factors      145Ч164
CNBr, cleavage of proteins to peptides      114Ч115
CNBr-activated Sepharose 4B, for DNA affinity chromatography      104Ч105 108Ч109
Co-immunoprecipitation, analysis of interactions between transcription factors      92Ч94
Codons, degeneracy      149Ч150
Cofactors, DNA-binding proteins      21
Cooperative binding, analysis      86Ч87
COUP-TF, interaction with non-DNA-binding transcription factor S300-II      88Ч89
CpG islands, enrichment in genes      169
CpG islands, genomic binding-site cloning      173Ч174
Cross-linking of transcription factors      85Ч86 94
Cross-linking, transcription factors to DNA      78Ч80 81Ч82
CTCF factor, purification      98 105Ч108 112
Dephosphorylation of proteins, method      269Ч270
Dimerization, transcription factors      84Ч86
Dimethyl sulphate (DMS), interference assay      42Ч43
Dimethyl sulphate (DMS), modification of DNA      39 40Ч41 48Ч51 53
Dimethylpimelidate (DMP), cross-linking agent      86
Dithiobis(succinimylpropionate) (DSP), protein cross-linker      93Ч94
DNA affinity chromatography, purification of DNA-binding proteins      104Ч111
DNA fragments, nitrocellulose binding assay      176
DNA in vitro modification of DNA with DMS      53
DNA labelling with DNA polymerase      8Ч10
DNA labelling, end labelling      28Ч29 32Ч34
DNA labelling, single strand      29Ч30
DNA mobility shift assay for DNA-binding proteins      1Ч25 202 204Ч206
DNA mobility shift assay, analysis of tertiary structure      84Ч85
DNA mobility shift assay, applications      2Ч6
DNA mobility shift assay, binding of transcription factors to nucleosomes      255
DNA mobility shift assay, binding reaction      12Ч13
DNA mobility shift assay, identification of transcription factors      4Ч6
DNA mobility shift assay, limitations      6
DNA mobility shift assay, measurement of transcription factor levels      4Ч5
DNA mobility shift assay, preparation of labelled oligonucleotide probes      7Ч8
DNA mobility shift assay, principle      2Ч4
DNA mobility shift assay, selection of DNA probe      6Ч7
DNA mobility shift assay, sequence specificity      3Ч5 18Ч20 128 135Ч137 138 141
DNA modification in vivo      48Ч51
DNA modification, dimethyl sulphate (DMS)      39 40Ч41 48Ч51
DNA modification, ethylnitrosourea (ENU)      40
DNA probes, selection for DNA mobility shift assay      6Ч7
DNA, cross-linking to transcription factors      77Ч82
DNA, dephosphorylation methods      8
DNA, end labelling methods      7Ч8 33Ч34 120 246Ч247
DNA, packing into chromatin      229Ч230
DNA, piperidine cleavage      53Ч55
DNA, purification      51Ч53
DNA, supercoiling and promoter activity      226Ч227
DNA-binding activity, mobility shift assay      1Ч25 202 204Ч206
DNA-binding assays, preparation of $3^2P$-labelled oligonucleotides      204Ч205
DNA-binding proteins, characterization      19Ч23
DNA-binding proteins, cloning      123Ч143
DNA-binding proteins, cofactors      21
DNA-binding proteins, concentration with biotinylated oligonucleotides      108 111
DNA-binding proteins, detection      2Ч14
DNA-binding proteins, DNA mobility shift assay      1Ч25
DNA-binding proteins, DNA sequence specificity      3Ч5
DNA-binding proteins, guanidinium chloride denaturation and renaturation      132Ч134
DNA-binding proteins, identification      4 19Ч23 111
DNA-binding proteins, interactions with other proteins      23Ч24
DNA-binding proteins, molecular weight determination      2Ч3 17 98
DNA-binding proteins, production of peptides from      114Ч117
DNA-binding proteins, proteolytic clipping band-shift assay      21Ч23
DNA-binding proteins, purification      17 97Ч114
DNA-binding proteins, requirement for cations      21 see
DNA-binding specificity, transcription factors      17Ч19
DNA-binding specificity, use of competitor DNA      3Ч5 18Ч20
DNA-cellulose chromatography, purification of DNA-binding proteins      103Ч104
DNA-protein complexes footprint analysis      27Ч62 see
DNA-protein interactions, determination of affinity      205Ч206
DNAase I footprinting      37Ч38 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      261Ч262 264Ч265
Electro-mobility shift assay (EMSA)      see DNA mobility shift assay
Electroporation of COS-1 cells, method      194
Electroporation, for transfection of transcription factors      198Ч199
Enhancer activity, genomic DNA fragments      176Ч177
Enzymes, introduction into cells      49
Enzymes, production of peptides from DNA-binding proteins      115
Ethylnitrosourea (ENU), DNA modification      40
Expression vectors, organization      192Ч193
Far-Western approach, screening cDNA expression libraries      137
Ferrous EDTA, use in footprint analysis      38Ч39
Footprint analysis in vitro      29Ч47
Footprint analysis in vivo      47Ч61
Footprint analysis of binding sites on closed circular plasmids      31 43Ч47
Footprint analysis of binding sites on end-labelled fragments      29Ч43
Footprint analysis, choice of linear DNA molecules      30Ч34
Footprint analysis, DNA-protein complexes      27Ч62
Footprint analysis, interference assays      27Ч29 39Ч43 84
Footprint analysis, ligation-mediated PCR (LMPCR)      32Ч33 34Ч35 47Ч49
Footprint analysis, method      45Ч47 59Ч61
Footprint analysis, protection analysis      27Ч29 37Ч39
Footprint analysis, protection from DNase I digestion      37Ч38 84
Footprint analysis, protein sources for binding      34Ч37
Fragment probes, labelling of      8Ч10
G-free cassette assay, for transcription      64Ч66 68
GATA1 factor, purification      98 101 103 105Ч106
GATA1 factor, quantity in cells      97
Gel filtration chromatography, molecular weight determination      69Ч72
Gel filtration chromatography, properties of matrices      70Ч71
Gel mobility shift assay, analysis of protein-protein interactions      209 210
Gel mobility shift assay, non-DNA-binding transcription factors      88 90Ч91
Gel retardation assay      see DNA mobility shift assay; gel mobility shift assay
Gene promoters, TAATGARAT sequence      1Ч2
Genes, enrichment in CpG islands      169
Genome sequences, databases      160 162
Genomic binding-site, cloning cloning procedure      172Ч173
Genomic binding-site, concentration of DNA-protein complex      170Ч171
Genomic binding-site, identification of target genes      165Ч179
Genomic binding-site, preparation of transcription factor protein      167Ч169
Genomic binding-site, principle      165Ч167
Genomic binding-site, source of DNA      169Ч170
Genomic binding-site, use of CpG islands      169 173Ч174
Glycerol gradient centrifugation, molecular weight determination      73Ч74
Glycosylation, transcription factors      285Ч290
GST pull-down assay, analysis of protein-protein interactions      206Ч207
GST-fusion proteins, method for expression      190Ч191
GST-fusion proteins, purification      191
Guanidinium chloride, denaturation and renaturation of DNA-binding proteins      132Ч134
HeLa cells, preparation of nuclear extracts      66Ч67
Helix-loop-helix proteins, properties      161
Herpes simplex virus 1 (HSV-1)      1Ч2 23Ч24
Histone acetylation, effects on transcription      257 262
Histones, and transcription      230 257 262
Histones, packing of DNA into chromatin      229Ч230
Histones, preparation      236Ч242
Homeobox proteins, properties      161
Hydroxyapatite, purification of histones      236 238Ч239 241
Immunoprecipitation, analysis of protein-protein interactions      208Ч209
Immunoprecipitation, detection of DNA-transcription factor complexes      171
in vitro transcription and adenovirus major-late promoter      222 224Ч225
in vitro transcription and neurofilament (NF) promoter      222 224Ч225 227
in vitro transcription and promoter templates      226Ч227
in vitro transcription and translation, method      188
in vitro transcription, method      68 223Ч224
Insect cells, overexpression of cloned transcription factors      194
Lectins, analysis of protein glycosylation      286Ч288
Library plating and replica lifts, method      125Ч126
Ligation-mediated polymerase chain reaction (LMPCR), for in vivo footprinting      32Ч33 34Ч35 47Ч49
Ligation-mediated polymerase chain reaction (LMPCR), method      56Ч59
Ligation-mediated polymerase chain reaction (LMPCR), preparation of DNA for      53Ч55
Ligation-mediated polymerase chain reaction (LMPCR), preparation of linkers      55Ч56
Ligation-mediated polymerase chain reaction (LMPCR), resolution      56Ч61
Linear DNA, method for protection from DNase I      37Ч38
Lipofection, for transfection of transcription factors      198Ч199
Luciferase, assay      200Ч201
Lysogen, generation from purified phage stock      139Ч140
Mammalian cells, expression of transcription factors      15Ч16 192Ч194 195
Mass spectrometry, analysis of protein phosphorylation      284Ч285
Mass spectrometry, identification of protein sequences      97
Mass spectrometry, measurement of mass of peptides      115
Mass spectrometry, method for preparing proteins      119Ч120
Methidium-propyl EDTA, use in footprint analysis      38
Microbore reverse-phase chromatography, separation of peptides      114
Micrococcal nuclease, analysis of reconstituted nucleosomes      253Ч255
Minichromosomes, preparation of nucleosome arrays      234
Molecular weight determination, calibration      69Ч70 73Ч74
Molecular weight determination, denatured transcription factors      76Ч83
Molecular weight determination, DNA-binding proteins      2Ч3 98
Molecular weight determination, methods      3 17 69Ч77
Molecular weight determination, transcription factors      69Ч76 98
Mononucleosome templates, analysis of transcription elongation      231
Mononucleosome templates, analysis of transcription initiation      231
Mononucleosome templates, binding of transcription factors      255Ч257
Mononucleosome templates, position of transcription factor binding site      243Ч244
Mononucleosome templates, preparation      232Ч233 234Ч236 243Ч255
Mononucleosome templates, transcription      230Ч232
Myelin, effect on isolation of nuclei      219Ч220
Neurofilament (NF) promoter, and in vitro transcription      222 224Ч225 227
Non-denaturing gradient electrophoresis, molecular weight determination      75Ч76
Non-DNA-binding transcription factors, 'supershift' gel mobility shift analysis      90Ч91
Non-DNA-binding transcription factors, DNAase footprinting      88
Non-DNA-binding transcription factors, gel mobility shift analysis      88 90Ч91
Non-DNA-binding transcription factors, restoration of activity      89
Non-DNA-binding transcription factors, S300-II      88Ч89
Northern blot analysis, transcription factor binding sites      175
Nuclear extracts, Drosophila embryo      233
Nuclear extracts, preparation      66Ч67 99Ч103 215Ч216 217Ч222
Nuclear extracts, Xenopus      233
Nuclear proteins, extraction from rat brain      220Ч222
Nuclear proteins, methods of preparation      11 36 67 101Ч103
Nuclease P1, use in footprint analysis      38
Nuclei, effect of myelin on isolation from brain      219Ч220
Nuclei, isolation from rat brain      217Ч220
Nuclei, preparation from whole tissue      102Ч103
Nucleoplasmin, reconstitution of nucleosomes      235Ч236
Nucleosome arrays      see nucleosome templates
Nucleosome core particles, preparation method      250Ч252
Nucleosome templates, analysis of transcription elongation      232
Nucleosome templates, analysis of transcription initiation      231
Nucleosome templates, binding of transcription factors      255Ч257
Nucleosome templates, essential components      234
Nucleosome templates, preparation      232Ч234
Nucleosomes and transcription      230
Nucleosomes, characterization of reconstituted      252Ч255
Nucleosomes, packing of DN A into chromatin      229Ч230
Nucleosomes, reconstitution      247Ч249
Octamer family, transcription factors      1Ч2 20 23Ч24 261Ч263 266 268Ч269 273
Oestrogen receptor      165 177Ч178 181Ч182 208Ч209
Oestrogen receptor binding site, nucleotide sequence      202 204
Oestrogen receptor in vitro transcription and translation      187Ч189
Oestrogen receptor, DNA-binding domain      167Ч168 170 172
Oestrogen receptor, interaction with steroid receptor coactivator protein SRC1a      207
Oestrogen receptor, ligand-binding domain      189Ч190
Oestrogen receptor, transcriptional activation by      196Ч197
Oestrogen receptor, zinc fingers      167Ч168
Oestrogen response element, binding site      197
Oestrogen-responsive genes, isolation      165 172 177Ч178
Oligonucleotides for DNA mobility shift assay      7Ч8
Oligonucleotides for screening libraries      114 130Ч131
Oligonucleotides, design for cDNA isolation      118Ч121
Oligonucleotides, method for hybridization to library filters      120Ч121
Orthologous genes, isolation from phylogenetically diverse organisms      145
P53 tumour suppressor, glycosylation      286
PCR products, cloning      155Ч156
PCR products, method for direct sequencing      157Ч158
PCR, see polymerase chain reaction (PCR) PCR deletion analysis, method      184
Peptide mapping for phosphorylation sites, method      277Ч278
Peptide tags, for purification of proteins      185
Peptides, measurement of mass by mass spectroscopy      115
Peptides, preparation methods      114Ч117
Phenanthroline-copper, use in footprint analysis      38Ч39
Phosphatases, use in analysis of protein phosphorylation      267Ч270
Phosphoamino acid analysis, method      280
Phosphorylation, retinoblastoma (pRb) protein      261Ч262
Phosphorylation, synthetic peptides      282Ч283
Phosphorylation, transcription factors      261Ч285
Piperidine, cleavage of modified DNA      48 53Ч55
Plasmids, footprint analysis      43Ч47
Polymerase chain reaction (PCR) and cloning transcription factors      148Ч160
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      158Ч160
Polymerase chain reaction (PCR), choice of template      151 153Ч155
Polymerase chain reaction (PCR), cloning of products      155Ч156
Polymerase chain reaction (PCR), methods for screening libraries      154Ч155
Polymerase chain reaction (PCR), preparation of deletion mutants of transcription factors      182Ч185
Polymerase chain reaction (PCR), preparation of point mutations of transcription factors      185Ч187
Polymerase chain reaction (PCR), reaction conditions      151
Polymerase chain reaction (PCR), selection of primers      148Ч149 150 152 182Ч183 185
Polymerase chain reaction (PCR), sequencing of products      155Ч158
Polymerase chain reaction (PCR), standard method      153Ч154
Polymerase chain reaction (PCR), whole genome PCR method      171
POU-domain proteins, properties      161
Progesterone receptors, assay      64Ч66
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      226Ч227
Promoter templates and supercoiling of DNA      226Ч227
Promoters for transcription assays      64
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