Mechanisms in transcriptional regulation:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Malden, MA [u.a.]
Blackwell
2008
|
| Ausgabe: | 1. publ. |
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XIII, 231 S. Ill., graph. Darst. |
| ISBN: | 1405103701 9781405103701 |
Internformat
MARC
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| 100 | 1 | |a Courey, Albert J. |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Mechanisms in transcriptional regulation |c Albert J. Courey |
| 250 | |a 1. publ. | ||
| 264 | 1 | |a Malden, MA [u.a.] |b Blackwell |c 2008 | |
| 300 | |a XIII, 231 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Bacteria |x genetics | |
| 650 | 4 | |a Eukaryotic Cells |x physiology | |
| 650 | 4 | |a Genetic transcription |x Regulation | |
| 650 | 4 | |a Transcription factors | |
| 650 | 4 | |a Transcription, Genetic | |
| 650 | 0 | 7 | |a Eukaryoten |0 (DE-588)4070991-7 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Regulation |0 (DE-588)4049075-0 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Transkription |g Genetik |0 (DE-588)4185906-6 |2 gnd |9 rswk-swf |
| 650 | 0 | 7 | |a Genregulation |0 (DE-588)4122166-7 |2 gnd |9 rswk-swf |
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| 856 | 4 | 2 | |m Digitalisierung UB Regensburg |q application/pdf |u http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015713897&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |3 Inhaltsverzeichnis |
| 999 | |a oai:aleph.bib-bvb.de:BVB01-015713897 | ||
Datensatz im Suchindex
| _version_ | 1804136608102875136 |
|---|---|
| adam_text | Full contents
List of boxes
xi
Preface
xii
Acknowledgments
xiv
1
The vocabulary of transcription
1
1.1
Introduction
1
1.2
The vocabulary of transcription
2
1.2.1
RNA
biogenesis
2
1.2.2
The transcriptional machinery
4
1.2.3
Cis-elements
7
1.3
Evolutionarily conserved mechanisms of transcription
8
1.3.1
Conservation across the three domains of life
8
1.3.2
Model eukaryotic organisms (and a plug for genetics)
9
1.4
What s coming up
10
Problems
14
Further reading
14
2
RNA polymerases
and the transcription cycle
16
2.1
Introduction
17
2.2
Core
RNA
polymerases
17
2.2.1
Bacterial core polymerases
19
2.2.2
Eukaryotic and archaeal core polymerases
19
2.3
Transcriptional elongation
23
2.3.1
Phosphoester linkage formation
23
2.3.2
Features of the ternary elongation complex
29
2.3.3
RNA polymerase
as a motor
32
2.3.4
Elongation factors and backtracking
33
2.4
Transcriptional initiation
36
2.4.1
Distinct mechanisms for promoter recognition in bacteria
and eukaryotes
36
2.4.2
Bacterial
σ
factors and promoter specificity
37
2.5
Transcriptional termination
42
2.5.1
Why terminate?
42
2.5.2
Termination in bacteria
42
2.5.3
Termination in eukaryotes
43
V/H
CONTENTS
2.6
Summary
45
Problems
46
Further reading
47
The eukaryotic basal machinery
49
3.1
Introduction
50
3.2
The class II core promoter
50
3.3
The catalog of factors
52
3.4
Pathway to the preinitiation complex
52
3.5
Promoter recognition and nucleation of the PIC by TFIID
58
3.5.1
TATA box recognition by TBP
58
3.5.2
TBP-associated factors and their function in TFIID
59
3.6
TFIIB: a functional analog of bacterial
σ
factors
61
3.6.1
TFIIB as a bridge between the promoter and polymerase
61
3.6.2
BRF, a TFIIB paralog in the class III machinery,
and promoter melting
62
3.6.3
Functional similarity between TFIIB family proteins and
σ
64
3.7
TFIIH in promoter opening and promoter clearance
65
3.7.1
A unique
DNA helicase
requirement for class II promoter
opening
65
3.7.2
A connection between
DNA
repair and transcription
66
3.7.3
TFIIH and
RNA
polymerase II phosphorylation
67
3.8
Summary
69
Problems
69
Further reading
70
Mechanisms of transcriptional activation
72
4.1
Introduction
73
4.2
Paradigms from
E. coli
73
4.2.1
CRP: a sensor of the nutritional environment
73
4.2.2
ÀcI:
regulator of the lysis/lysogeny switch
75
4.2.3
Sequence-specific
DNA
recognition: the helix-turn-helix motif
76
4.2.4
Dimerization
77
4.2.5
Multiple targets for activators in the transcriptional machinery
77
4.2.6
How do activator-RNA polymerase contacts activate
promoters?
78
4.3
Eukaryotic activators and their targets
86
4.3.1
The modular nature of eukaryotic activators
86
4.3.2
The Mediator: a special activator target in the eukaryotic
transcriptional machinery
90
4.3.3
Release of Pol II from a paused state as a mechanism of
activation
95
4.4
Summary
97
Problems
98
Further reading
99
CONTENTS
IX
5 Transcriptional
control
through the modification of chromatin structure
101
5.1
Introduction
102
5.2
Chromatin structure
103
5.2.1
The nucleosome
103
5.2.2
Higher order chromatin structure
104
5.2.3
Euchromatin and heterochromatin
105
5.3
Histone modification
107
5.3.1
Lysine acetylation:
diverse roles in gene activation
109
5.3.2
Lysine
methylation: a chemically stable histone mark
117
5.3.3
Cross talk between histone marks
118
5.4
ATP-dependent chromatin remodeling enzymes
119
5.4.1
A diverse family of chromatin remodeling complexes
119
5.4.2
ATP-fueled motors for increasing
DNA
accessibility
121
5.4.3
Targeting of chromatin remodeling complexes
124
5.5
Protein motifs that recognize modified histones
124
5.5.1
Chromodomains
125
5.5.2
Bromodomains
125
5.6
Coordination of activator-coactivator interactions
126
5.7
Summary
127
Problems
129
Further reading
130
6
Epigenetic control of transcription
133
6.1
Introduction
134
6.1.1
Common themes in epigenetics: a central role for
histone methylation
137
6.2
Heterochromatic silencing
137
6.2.1
Chromosomal inheritance of the silent state
138
6.2.2
Histone methylation and maintenance of the silent state
142
6.2.3
Initiation of heterochromatic silencing
144
6.2.4
Evolutionary conservation of mechanisms for
heterochromatic silencing
146
6.2.5 DNA
methylation and heterochromatin
148
6.2.6
A distinct mechanism for heterochromatic silencing in
budding yeast
149
6.3
Epigenetic control by Polycomb and Trithorax group proteins
150
6.3.1
Combinatorial control of segment identity
150
6.3.2
Establishment and maintenance phases of homeotic
gene expression
152
6.3.3
Parallels between heterochromatic and PcG silencing
154
6.3.4
Maintenance of the active state by TrxG
155
6.3.5
A model for the epigenetic regulation of homeotic
gene activity
158
6.4
X chromosome inactivation: parallels to heterochromatic and
Polycomb group silencing
159
CONTENTS
6.4.1
Random inactivation of the X
chromosome
159
6.4.2
Cis-acting
RNA
in X inactivation
160
6.4.3
Histone modifications characteristic of both heterochromatic
and PcG silencing on
Xi 162
6.5
Summary
162
Problems
164
Further reading
164
7
Combinatorial control in development and signal transduction
167
7.1
Introduction
168
7.2
Synergy and antagonism
169
7.2.1
Integration of regulatory inputs by cis-regulatory modules
169
7.2.2
The AND and NOT operators
169
7.3
Synergy and the enhanceosome
172
7.3.1
Enhanceosome assembly and architectural factors
172
7.3.2
Cooperative recruitment of coactivators by enhanceosomes
174
7.3.3
Sequential coactivator recruitment
176
7.4
Antagonism and stripe formation
176
7.4.1
Developmental regulatory networks
178
7.4.2
Short-range repression and stripe formation
178
7.5
Antagonism and the signal-mediated switch
183
7.5.1
Nuclear receptors: antagonism between coregulators
185
7.5.2
Receptor tyrosine kinase pathways: competition for
a common
DNA
element
188
7.6
Summary
189
Problems
192
Further reading
192
Answers to problems
194
Glossary
199
Index
220
Color plate section between pp.
82
and
83
|
| adam_txt |
Full contents
List of boxes
xi
Preface
xii
Acknowledgments
xiv
1
The vocabulary of transcription
1
1.1
Introduction
1
1.2
The vocabulary of transcription
2
1.2.1
RNA
biogenesis
2
1.2.2
The transcriptional machinery
4
1.2.3
Cis-elements
7
1.3
Evolutionarily conserved mechanisms of transcription
8
1.3.1
Conservation across the three domains of life
8
1.3.2
Model eukaryotic organisms (and a plug for genetics)
9
1.4
What's coming up
10
Problems
14
Further reading
14
2
RNA polymerases
and the transcription cycle
16
2.1
Introduction
17
2.2
Core
RNA
polymerases
17
2.2.1
Bacterial core polymerases
19
2.2.2
Eukaryotic and archaeal core polymerases
19
2.3
Transcriptional elongation
23
2.3.1
Phosphoester linkage formation
23
2.3.2
Features of the ternary elongation complex
29
2.3.3
RNA polymerase
as a motor
32
2.3.4
Elongation factors and backtracking
33
2.4
Transcriptional initiation
36
2.4.1
Distinct mechanisms for promoter recognition in bacteria
and eukaryotes
36
2.4.2
Bacterial
σ
factors and promoter specificity
37
2.5
Transcriptional termination
42
2.5.1
Why terminate?
42
2.5.2
Termination in bacteria
42
2.5.3
Termination in eukaryotes
43
V/H
CONTENTS
2.6
Summary
45
Problems
46
Further reading
47
The eukaryotic basal machinery
49
3.1
Introduction
50
3.2
The class II core promoter
50
3.3
The catalog of factors
52
3.4
Pathway to the preinitiation complex
52
3.5
Promoter recognition and nucleation of the PIC by TFIID
58
3.5.1
TATA box recognition by TBP
58
3.5.2
TBP-associated factors and their function in TFIID
59
3.6
TFIIB: a functional analog of bacterial
σ
factors
61
3.6.1
TFIIB as a bridge between the promoter and polymerase
61
3.6.2
BRF, a TFIIB paralog in the class III machinery,
and promoter melting
62
3.6.3
Functional similarity between TFIIB family proteins and
σ
64
3.7
TFIIH in promoter opening and promoter clearance
65
3.7.1
A unique
DNA helicase
requirement for class II promoter
opening
65
3.7.2
A connection between
DNA
repair and transcription
66
3.7.3
TFIIH and
RNA
polymerase II phosphorylation
67
3.8
Summary
69
Problems
69
Further reading
70
Mechanisms of transcriptional activation
72
4.1
Introduction
73
4.2
Paradigms from
E. coli
73
4.2.1
CRP: a sensor of the nutritional environment
73
4.2.2
ÀcI:
regulator of the lysis/lysogeny switch
75
4.2.3
Sequence-specific
DNA
recognition: the helix-turn-helix motif
76
4.2.4
Dimerization
77
4.2.5
Multiple targets for activators in the transcriptional machinery
77
4.2.6
How do activator-RNA polymerase contacts activate
promoters?
78
4.3
Eukaryotic activators and their targets
86
4.3.1
The modular nature of eukaryotic activators
86
4.3.2
The Mediator: a special activator target in the eukaryotic
transcriptional machinery
90
4.3.3
Release of Pol II from a paused state as a mechanism of
activation
95
4.4
Summary
97
Problems
98
Further reading
99
CONTENTS
IX
5 Transcriptional
control
through the modification of chromatin structure
101
5.1
Introduction
102
5.2
Chromatin structure
103
5.2.1
The nucleosome
103
5.2.2
Higher order chromatin structure
104
5.2.3
Euchromatin and heterochromatin
105
5.3
Histone modification
107
5.3.1
Lysine acetylation:
diverse roles in gene activation
109
5.3.2
Lysine
methylation: a chemically stable histone mark
117
5.3.3
Cross talk between histone marks
118
5.4
ATP-dependent chromatin remodeling enzymes
119
5.4.1
A diverse family of chromatin remodeling complexes
119
5.4.2
ATP-fueled motors for increasing
DNA
accessibility
121
5.4.3
Targeting of chromatin remodeling complexes
124
5.5
Protein motifs that recognize modified histones
124
5.5.1
Chromodomains
125
5.5.2
Bromodomains
125
5.6
Coordination of activator-coactivator interactions
126
5.7
Summary
127
Problems
129
Further reading
130
6
Epigenetic control of transcription
133
6.1
Introduction
134
6.1.1
Common themes in epigenetics: a central role for
histone methylation
137
6.2
Heterochromatic silencing
137
6.2.1
Chromosomal inheritance of the silent state
138
6.2.2
Histone methylation and maintenance of the silent state
142
6.2.3
Initiation of heterochromatic silencing
144
6.2.4
Evolutionary conservation of mechanisms for
heterochromatic silencing
146
6.2.5 DNA
methylation and heterochromatin
148
6.2.6
A distinct mechanism for heterochromatic silencing in
budding yeast
149
6.3
Epigenetic control by Polycomb and Trithorax group proteins
150
6.3.1
Combinatorial control of segment identity
150
6.3.2
Establishment and maintenance phases of homeotic
gene expression
152
6.3.3
Parallels between heterochromatic and PcG silencing
154
6.3.4
Maintenance of the active state by TrxG
155
6.3.5
A model for the epigenetic regulation of homeotic
gene activity
158
6.4
X chromosome inactivation: parallels to heterochromatic and
Polycomb group silencing
159
CONTENTS
6.4.1
Random inactivation of the X
chromosome
159
6.4.2
Cis-acting
RNA
in X inactivation
160
6.4.3
Histone modifications characteristic of both heterochromatic
and PcG silencing on
Xi 162
6.5
Summary
162
Problems
164
Further reading
164
7
Combinatorial control in development and signal transduction
167
7.1
Introduction
168
7.2
Synergy and antagonism
169
7.2.1
Integration of regulatory inputs by cis-regulatory modules
169
7.2.2
The "AND" and "NOT" operators
169
7.3
Synergy and the enhanceosome
172
7.3.1
Enhanceosome assembly and architectural factors
172
7.3.2
Cooperative recruitment of coactivators by enhanceosomes
174
7.3.3
Sequential coactivator recruitment
176
7.4
Antagonism and stripe formation
176
7.4.1
Developmental regulatory networks
178
7.4.2
Short-range repression and stripe formation
178
7.5
Antagonism and the signal-mediated switch
183
7.5.1
Nuclear receptors: antagonism between coregulators
185
7.5.2
Receptor tyrosine kinase pathways: competition for
a common
DNA
element
188
7.6
Summary
189
Problems
192
Further reading
192
Answers to problems
194
Glossary
199
Index
220
Color plate section between pp.
82
and
83 |
| any_adam_object | 1 |
| any_adam_object_boolean | 1 |
| author | Courey, Albert J. |
| author_facet | Courey, Albert J. |
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| author_sort | Courey, Albert J. |
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| id | DE-604.BV022506921 |
| illustrated | Illustrated |
| index_date | 2024-07-02T17:57:51Z |
| indexdate | 2024-07-09T20:59:06Z |
| institution | BVB |
| isbn | 1405103701 9781405103701 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-015713897 |
| oclc_num | 173367793 |
| open_access_boolean | |
| owner | DE-703 DE-M49 DE-BY-TUM DE-29T DE-355 DE-BY-UBR DE-11 |
| owner_facet | DE-703 DE-M49 DE-BY-TUM DE-29T DE-355 DE-BY-UBR DE-11 |
| physical | XIII, 231 S. Ill., graph. Darst. |
| publishDate | 2008 |
| publishDateSearch | 2008 |
| publishDateSort | 2008 |
| publisher | Blackwell |
| record_format | marc |
| spelling | Courey, Albert J. Verfasser aut Mechanisms in transcriptional regulation Albert J. Courey 1. publ. Malden, MA [u.a.] Blackwell 2008 XIII, 231 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Bacteria genetics Eukaryotic Cells physiology Genetic transcription Regulation Transcription factors Transcription, Genetic Eukaryoten (DE-588)4070991-7 gnd rswk-swf Regulation (DE-588)4049075-0 gnd rswk-swf Transkription Genetik (DE-588)4185906-6 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf Transkription Genetik (DE-588)4185906-6 s Regulation (DE-588)4049075-0 s Eukaryoten (DE-588)4070991-7 s DE-604 Genregulation (DE-588)4122166-7 s b DE-604 Digitalisierung UB Regensburg application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015713897&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Courey, Albert J. Mechanisms in transcriptional regulation Bacteria genetics Eukaryotic Cells physiology Genetic transcription Regulation Transcription factors Transcription, Genetic Eukaryoten (DE-588)4070991-7 gnd Regulation (DE-588)4049075-0 gnd Transkription Genetik (DE-588)4185906-6 gnd Genregulation (DE-588)4122166-7 gnd |
| subject_GND | (DE-588)4070991-7 (DE-588)4049075-0 (DE-588)4185906-6 (DE-588)4122166-7 |
| title | Mechanisms in transcriptional regulation |
| title_auth | Mechanisms in transcriptional regulation |
| title_exact_search | Mechanisms in transcriptional regulation |
| title_exact_search_txtP | Mechanisms in transcriptional regulation |
| title_full | Mechanisms in transcriptional regulation Albert J. Courey |
| title_fullStr | Mechanisms in transcriptional regulation Albert J. Courey |
| title_full_unstemmed | Mechanisms in transcriptional regulation Albert J. Courey |
| title_short | Mechanisms in transcriptional regulation |
| title_sort | mechanisms in transcriptional regulation |
| topic | Bacteria genetics Eukaryotic Cells physiology Genetic transcription Regulation Transcription factors Transcription, Genetic Eukaryoten (DE-588)4070991-7 gnd Regulation (DE-588)4049075-0 gnd Transkription Genetik (DE-588)4185906-6 gnd Genregulation (DE-588)4122166-7 gnd |
| topic_facet | Bacteria genetics Eukaryotic Cells physiology Genetic transcription Regulation Transcription factors Transcription, Genetic Eukaryoten Regulation Transkription Genetik Genregulation |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=015713897&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT coureyalbertj mechanismsintranscriptionalregulation |