Gene Control

Description

COVER......Page 1 PREFACE......Page 8 ACKNOWLEDGMENTS......Page 9 CONTENTS IN BRIEF......Page 10 CONTENTS IN DETAIL......Page 11 Specific methods can be used to study the expression of individual proteins in tissues and cells......Page 18 General methods can be used for studying the overall protein composition of tissues and cells......Page 19 Specific methods can be used to study the expression of individual mRNAs in different tissues and cells......Page 23 General methods can be used to study the overall population of mRNAs expressed in different tissues and cells......Page 24 1.3 THE DNA CONTENT OF DIFFERENT CELL TYPES IS GENERALLY THE SAME......Page 26 General methods can be used to study the total DNA in different tissues and cells......Page 27 Exceptional cases do exist in which changes to the DNA occur in specific tissues or cell types......Page 30 1.4 TRANSCRIPTIONAL OR POST-TRANSCRIPTIONAL CONTROL?......Page 32 Studies of nuclear RNA suggest that gene transcription is regulated......Page 33 Pulse labeling studies directly demonstrate transcriptional control......Page 35 Nuclear run-on assays allow transcriptional control to be demonstrated for a wide range of genes......Page 36 Polytene chromosomes provide further evidence for transcriptional control......Page 38 Transcriptional control can operate at the level of chromatin structure and at the level of production of the primary RNA transcript......Page 39 1.5 SMALL RNAs AND THE REGULATION OF GENE EXPRESSION......Page 40 miRNAs are processed from a single-stranded precursor which folds to form a double-stranded hairpin loop......Page 41 Many siRNAs are processed from a double-stranded precursor......Page 42 KEY CONCEPTS......Page 44 FURTHER READING......Page 45 Regulation of transcription in eukaryotes is much more complex than in prokaryotes......Page 46 Cells can remain committed to a particular differentiated state even in the absence of its phenotypic characteristics......Page 47 Cells can become committed to a particular differentiated state prior to actual phenotypic differentiation......Page 48 The nucleosome is the basic unit of chromatin structure......Page 50 Nucleosome structure or position can be altered by chromatin-remodeling processes......Page 53 Histones are subject to a variety of post-translational modifications......Page 54 Histone variants are encoded by distinct genes to those encoding the standard histone isoforms......Page 60 The 30 nm fiber represents a further compaction of the beads-on-a-string structure......Page 61 Histone H1 and post-translational modifications of the other histones are involved in the formation of the 30 nm fiber......Page 62 The 30 nm fiber is further compacted by looping......Page 64 Locus-control regions regulate the chromatin structure of a large region of DNA......Page 65 Insulators block the inappropriate spread of particular chromatin structures......Page 67 Heterochromatin is a very tightly packed form of chromatin......Page 68 CONCLUSIONS......Page 69 KEY CONCEPTS......Page 70 FURTHER READING......Page 71 INTRODUCTION......Page 72 Active DNA is organized in a nucleosomal structure......Page 73 Active or potentially active chromatin shows enhanced sensitivity to DNaseI digestion......Page 74 Decreased DNA methylation is associated with active or potentially active genes......Page 76 DNA methylation patterns can be propagated stably through cell divisions......Page 79 DNA methylation recruits inhibitory proteins that produce a tightly packed chromatin structure......Page 81 Acetylation......Page 83 Methylation......Page 85 Ubiquitination and sumoylation......Page 89 Phosphorylation......Page 90 The different histone modifications interact functionally with one another......Page 91 Histone modifications interact with DNA methylation to regulate chromatin structure......Page 92 RNAi can induce alterations in chromatin structure......Page 93 DNaseI-hypersensitive sites can be identified in active or potentially active genes......Page 95 DNaseI-hypersensitive sites frequently correspond to regulatory DNA sequences......Page 97 DNaseI-hypersensitive sites represent areas which are either nucleosome-free or have an altered nucleosomal structure......Page 98 Chromatin remodeling can be produced by proteins capable of displacing nucleosomes or altering their structure......Page 99 The SWI–SNF and NURF chromatin-remodeling complexes are recruited to the DNA by a variety of different mechanisms......Page 101 3.6 OTHER SITUATIONS IN WHICH CHROMATIN STRUCTURE IS REGULATED......Page 102 The active and inactive X chromosomes have a different chromatin structure......Page 103 The XIST regulatory RNA is specifically transcribed on the inactive X chromosome......Page 104 Genomic imprinting involves the specific inactivation of either the maternally or paternally inherited copy of specific genes......Page 105 Imprinting involves changes in chromatin structure......Page 107 CONCLUSIONS......Page 109 FURTHER READING......Page 110 4.1 TRANSCRIPTION BY RNA POLYMERASES......Page 112 Transcription by RNA polymerase III is more complex than for RNA polymerase I......Page 113 Transcription by RNA polymerase II is much more complex than transcription by RNA polymerases I and III......Page 116 Transcription by the three different polymerases has a number of common features......Page 118 Transcription takes place in defined regions of the nucleus......Page 122 Transcriptional elongation requires further phosphorylation of RNA polymerase II......Page 124 Termination of transcription occurs downstream of the polyadenylation signal......Page 126 4.3 THE GENE PROMOTER......Page 127 The 70 kDa heat-shock protein gene contains a typical promoter for RNA polymerase II......Page 128 The heat-shock element is found only in heat-inducible genes......Page 129 Other response elements are found in the promoters of genes with different patterns of expression......Page 131 The proteins binding to short DNA sequence elements can be characterized by a variety of techniques......Page 133 Promoter regulatory elements act by binding factors which either affect chromatin structure and/or influence transcription directly......Page 137 Enhancers are regulatory sequences that act at a distance to increase gene expression......Page 138 Many enhancers have cell-type- or tissue-specific activity......Page 140 Proteins bound at enhancers can interact with promoter-bound factors and/or alter chromatin structure......Page 142 Silencers can act at a distance to inhibit gene expression......Page 145 CONCLUSIONS......Page 147 KEY CONCEPTS......Page 148 FURTHER READING......Page 149 INTRODUCTION......Page 150 5.1 DNA BINDING BY TRANSCRIPTION FACTORS......Page 152 The helix-turn-helix motif is found in a number of transcription factors which regulate gene expression during embryonic development......Page 153 The helix-turn-helix domain found in homeodomain proteins is a DNA-binding domain......Page 154 In the POU domain transcription factors, the homeodomain forms part of a larger DNA-binding motif......Page 156 The two-cysteine–two-histidine (Cys2His2) zinc finger is found in multiple copies in many transcription factors......Page 158 The nuclear receptors contain two copies of a multi-cysteine zinc finger distinct from the Cys2His2 zinc finger......Page 160 The leucine zipper is a dimerization domain which allows DNA binding by the adjacent basic domain......Page 164 In some transcription factors, the basic DNA-binding domain is found associated with a helix-loop-helix dimerization domain......Page 165 Dimerization between factors provides an additional level of regulation......Page 166 Other domains can also mediate DNA binding......Page 167 Activation domains can be identified by “domain-swap” experiments......Page 169 Several different classes of activation domain exist......Page 171 How is transcription activated?......Page 172 Activators can interact with TFIID......Page 173 Activators can interact with the mediator and SAGA complexes......Page 174 Activators can interact with co-activators......Page 175 Activators can interact with modulators of chromatin structure......Page 177 Activators have a multitude of targets......Page 178 Repressors can act indirectly by inhibiting the positive effect of activators......Page 179 Repressors can act directly by inhibiting the assembly or activity of the basal transcriptional complex......Page 181 Regulation of transcription can occur at the elongation stage, as well as at initiation......Page 183 Factors which regulate transcriptional elongation target the C-terminal domain of RNA polymerase II......Page 185 5.5 REGULATION OF TRANSCRIPTION BY RNA POLYMERASES I AND III......Page 186 Transcription by RNA polymerases I and III can be regulated by altering the expression or activity of components of the basal transcriptional complex......Page 187 Regulation of transcription by RNA polymerase III can involve specific transcription factors binding to RNA as well as to DNA......Page 188 KEY CONCEPTS......Page 189 FURTHER READING......Page 190 The capping process modifies the 5' end of the RNA transcript......Page 192 The cap enhances translation of the mRNA by the ribosome......Page 193 Polyadenylation enhances the stability of the mRNA......Page 195 Specific RNAs and proteins catalyze the process of RNA splicing......Page 197 Transcriptional initiation and elongation are coupled to post-transcriptional processes......Page 202 Post-transcriptional processes can interact with one another......Page 203 RNA transport is coupled to other post-transcriptional processes......Page 204 Translation of the mRNA takes place on cytoplasmic ribosomes......Page 206 Translational initiation involves initiation factors binding to the cap......Page 207 Translational elongation involves base-pairing of triplet codons in the mRNA with tRNA anticodons......Page 208 Translational termination occurs at specific stop codons......Page 211 RNA degradation occurs in both the nucleus and the cytoplasm......Page 212 RNA degradation in the cytoplasm involves prior de-adenylation and decapping of the mRNA......Page 213 KEY CONCEPTS......Page 215 FURTHER READING......Page 216 INTRODUCTION......Page 218 Alternative splicing represents a major regulatory process which supplements transcriptional control......Page 219 Alternative RNA splicing involves specific splicing factors that promote or inhibit the use of specific splice sites......Page 226 Factors regulating alternative splicing have been identified by genetic and biochemical methods......Page 227 The processes of transcription and alternative splicing interact with one another......Page 231 Alternative RNA splicing is a very widely used method of supplementing transcriptional control......Page 232 Other cases of RNA editing involve a change from an A to an I residue......Page 234 Specific proteins can regulate the transport of individual mRNAs from nucleus to cytoplasm......Page 236 RNA transport processes can also regulate the location of individual mRNAs within the cytoplasm......Page 238 Specific sequences in the mRNA are involved in the regulation of its stability......Page 240 RNA stability changes supplement transcriptional control in cases where a rapid response is required......Page 242 Translational control can involve either modifications in the cellular translational apparatus or specific proteins which recognize sequences in the target RNA......Page 243 Translational control can be produced by modifications in the cellular translation apparatus......Page 244 Translational control can be produced by proteins binding to specific sequences in the RNA itself......Page 247 Small RNAs can inhibit gene expression post-transcriptionally......Page 252 Small RNAs can induce mRNA degradation......Page 253 Small RNAs can repress mRNA translation......Page 254 miRNAs regulate gene expression at multiple levels......Page 257 KEY CONCEPTS......Page 258 FURTHER READING......Page 259 Transcription factors can be regulated by controlling their synthesis or by controlling their activity......Page 260 Multiple mechanisms regulate transcription factor activity......Page 262 Members of the nuclear receptor family of transcription factors are activated by binding of the appropriate ligand......Page 263 Following ligand-mediated activation, the glucocorticoid receptor can repress as well as activate gene transcription......Page 266 The HSF is activated by stressful stimuli and induces the transcription of genes encoding protective proteins......Page 268 Transcription factors can be phosphorylated by kinases activated by specific intracellular second messengers such as cyclic AMP......Page 269 Transcription factors can be phosphorylated by signaling cascades consisting of several protein kinases......Page 271 Transcription factor activity can be regulated by phosphorylation of an inhibitory protein: the NFκB/IκB system......Page 272 Acetylation......Page 274 Methylation......Page 275 Ubiquitination and sumoylation......Page 276 Transcription factors can be activated by cleavage of a membrane-bound precursor......Page 277 Cleavage of a lipid link can be used to activate a transcription factor......Page 279 The PI3-kinase/Akt system plays a key role in regulating gene expression in response to growth factors or insulin......Page 280 Akt regulates mRNA translation via the TOR kinase, which phosphorylates proteins involved in translation......Page 281 Akt/TOR can also stimulate mRNA translation by enhancing the transcription of genes encoding RNAs and proteins involved in protein synthesis......Page 282 A variety of kinases inhibit translation by phosphorylating eIF2......Page 283 Individual kinases can produce multi-level regulation of gene expression......Page 284 CONCLUSIONS......Page 285 KEY CONCEPTS......Page 288 FURTHER READING......Page 289 Regulation of mRNA translation occurs following fertilization......Page 290 Transcriptional control processes activate the embryonic genome......Page 291 The Oct4 and Cdx2 transcription factors regulate the differentiation of ICM and trophectoderm cells......Page 293 ES cells can differentiate into a wide variety of cell types......Page 294 ES-cell-specific transcription factors can activate or repress the expression of their target genes......Page 296 ES-cell-specific transcription factors regulate genes encoding chromatin-modifying enzymes and miRNAs......Page 298 ES cells have an unusual pattern of histone methylation......Page 299 The polycomb complex regulates histone methylation in ES cells......Page 301 Chromatin structure in ES cells is regulated by multiple effects on histones......Page 303 A gradient in expression of the Bicoid transcription factor defines the anterior–posterior axis in the early Drosophila embryo......Page 305 Bicoid activates a cascade of genes encoding other transcription factors, producing a segmented pattern of Eve gene expression......Page 306 The Bicoid system involves both transcriptional and post-transcriptional regulation......Page 307 Homeodomain transcription factors specify segment identity in the Drosophila embryo......Page 308 Homeodomain transcription factors are also found in mammals......Page 309 Mammalian Hox genes are expressed in specific regions of the developing embryo......Page 310 Transcription of individual Hox genes is regulated by gene-specific regulatory regions......Page 311 Hox gene transcription is also dependent on the position of the gene in the Hox gene cluster......Page 312 Differential regulation of different Hox genes by Sonic Hedgehog controls the differentiation of cells in the neural tube......Page 313 Regulation of Hox gene expression by Sonic Hedgehog is also involved in limb formation......Page 315 CONCLUSIONS......Page 316 KEY CONCEPTS......Page 317 FURTHER READING......Page 318 INTRODUCTION......Page 320 The MyoD protein can induce muscle cell differentiation......Page 322 MyoD is a basic helix-loop-helix transcription factor which is able to regulate gene expression......Page 323 MyoD is regulated by controlling both its synthesis and its activity......Page 324 Other muscle-specific transcription factors can induce muscle cell differentiation......Page 325 MEF2 is a downstream regulator of muscle-cell specific gene transcription......Page 327 Basic helix-loop-helix transcription factors are also involved in neuronal differentiation......Page 330 The REST transcription factor represses the expression of neuronal genes......Page 332 Neuronal cells express specific alternative splicing factors......Page 334 Translational control plays a key role in synaptic plasticity in neuronal cells......Page 336 miRNAs play a key role in the regulation of neuronal gene expression......Page 337 Yeast cells can be a or α in mating type......Page 339 The SBF transcription factor activates HO transcription only in the G1 phase of the cell cycle......Page 340 The a and α gene products are homeodomain-containing transcription factors......Page 341 The α1 and α2 proteins interact with the MCM1 transcription factor to respectively activate α-specific genes and repress a-specific genes......Page 342 The a1 factor plays a key role in repressing haploid-specific genes in diploid cells......Page 343 The yeast mating-type system offers insights of relevance to multicellular organisms......Page 344 CONCLUSIONS......Page 346 KEY CONCEPTS......Page 347 FURTHER READING......Page 348 Oncogenes were originally identified in cancer-causing viruses......Page 350 Cellular proto-oncogenes are present in the genome of normal cells......Page 351 Cellular proto-oncogenes can cause cancer when they are over-expressed or mutated......Page 353 Viruses can induce elevated expression of oncogenes......Page 354 A variety of cellular mechanisms mediate enhanced expression of proto-oncogenes in different cancers......Page 355 The Fos and Jun oncogene proteins are cellular transcription factors which can cause cancer when over-expressed......Page 357 The v-erbA oncogene protein is a mutant form of the cellular thyroid hormone receptor......Page 359 Other transcription factor-related oncogenes are over-expressed due to chromosomal translocations......Page 361 Chromosomal translocations can also produce novel oncogenic fusion proteins involving transcription factors......Page 362 Anti-oncogenes encode proteins which restrain cellular growth......Page 365 The p53 protein is a DNA-binding transcription factor......Page 366 The retinoblastoma protein interacts with other proteins to regulate transcription......Page 369 Other anti-oncogene proteins also regulate transcription......Page 371 Oncogenes and anti-oncogenes interact to regulate the expression of genes encoding proteins which control cellular growth......Page 373 Oncogenes and anti-oncogenes interact to regulate the expression of RNAs and proteins involved in mRNA translation......Page 375 Oncogenes and anti-oncogenes interact to regulate the expression of microRNAs......Page 376 CONCLUSIONS......Page 377 KEY CONCEPTS......Page 378 FURTHER READING......Page 379 DNA-binding transcription factors......Page 380 DNA-binding sites for specific transcription factors......Page 381 Transcriptional co-activators......Page 383 DNA methylation......Page 384 Histone-modifying enzymes......Page 385 Chromatin-remodeling complexes......Page 386 RNA splicing......Page 387 12.4 INFECTIOUS DISEASES AND CELLULAR GENE EXPRESSION......Page 390 Therapy could be achieved by altering the expression of transcription factors......Page 392 Therapy could be achieved by altering the activity of transcription factors......Page 393 Therapy could be achieved using designer zinc fingers to alter gene transcription......Page 395 Therapy could be achieved by modulating RNA splicing......Page 396 KEY CONCEPTS......Page 398 FURTHER READING......Page 399 Transcription factors interact with one another to regulate transcription......Page 400 DNA-binding transcription factors interact with co-activators/co-repressors and with regulators of chromatin structure......Page 401 Histone modifications play a central role in the regulation of chromatin structure......Page 402 Gene regulation is highly complex and involves both transcriptional and post-transcriptional regulation......Page 403 RNA molecules play a central role in regulating gene expression......Page 404 Regulatory networks control gene expression......Page 405 FURTHER READING......Page 407 GLOSSARY......Page 408 INDEX......Page 426