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Nucleus and gene expression
Nucleus and gene expression The interplay of transcriptional and post-transcriptional mechanisms that regulate gene expression Editorial overview Elisa Izaurralde and David L Spector Current Opinion in Cell Biology 2004, 16:219–222 0955-0674/$ – see front matter ß 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.ceb.2004.04.005
Elisa Izaurralde European Molecular Biology Laboratory, Gene Expression Program, Meyerhofstrasse 1. D-69117 Heidelberg, Germany
Elisa Izaurralde is a Research Group leader at the European Molecular Biology Laboratory. Her laboratory studies mechanisms of posttranscriptional regulation of gene expression with particular emphasis on the nuclear export of messenger RNAs to the cytoplasm and mRNA turnover. David L Spector Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
David L Spector is a Professor at Cold Spring Harbor Laboratory. His laboratory studies nuclear organization and the dynamics of gene expression in living cells.
www.sciencedirect.com
Abbreviations EJC exon–exon junction complex mRNP messenger ribonucleoprotein particle NPC nuclear pore complex RNAi RNA interference RNAP RNA polymerase
During the past years post-transcriptional mechanisms have emerged as central pathways in the regulation of gene expression. In particular, the discovery of RNA-mediated gene silencing processes (RNA interference or RNAi) has revolutionized the field of gene expression both conceptually and experimentally. RNAi silences gene expression in a sequence-specific manner in response to the presence of double-stranded RNA. The identification of the key molecular players in this process has been followed by an increased appreciation that they function as part of large protein assemblies that act at the interface of transcriptional and post-transcriptional regulatory circuits (see the review by Murchison and Hannon). Indeed, RNAi and related processes have been shown to regulate heterochromatin formation resulting in transcriptional silencing or to act at the post-transcriptional level, either by targeting mRNAs for degradation or by inhibiting translation. Consequently, the gene silencing apparatus intersects the chromatin remodeling machineries in the nucleus, and the translation and mRNA turnover machineries in the cytoplasm. The first review in this issue by Murchison and Hannon covers recent progress on RNAi, as this topic has ramifications in all steps of gene expression. This is followed by four reviews, which examine the following topics: the regulation of heterochromatin by histone modifications and RNAi, the maintenance of chromatin states by the polycomb group of proteins, the inactivation of one X chromosome in female mammals (a specialized epigenetic mechanism regulating the expression of an entire chromosome), and how spatial localization in the nucleus can influence gene expression. The next reviews cover events in mRNA biogenesis. Starting from the regulation of transcription, we move into aspects related to the cotranscriptional assembly and processing of messenger ribonucleoprotein particles (mRNPs) and their export to the cytoplasm through nuclear pore complexes. The next group of three reviews focuses on cytoplasmic mRNP metabolism including mRNA turnover, the transport of mRNPs to specific cytoplasmic locations, and localized translation. The next two reviews focus on the dynamics of the nuclear pore complex during the cell cycle and how defects in nuclear lamin A are correlated with hereditary human diseases. The issue concludes with a review on the cellular response to DNA damage and the maintenance of genome stability, and a commentary on the Current Opinion in Cell Biology 2004, 16:219–222
220 Nucleus and gene expression
controversy surrounding the links between transcription and translation: does protein synthesis occur in the nucleus? Although the field of gene silencing was for a long time a rather quiet area of research, recent advances have turned it into one of the most exciting areas of current biology. Grewal and Rice discuss recent advances in the initiation and maintenance of heterochromatin. While methylation of histone H3 has been shown to be associated with inactive chromatin, Grewal and Rice discuss recent reports that indicate that different degrees of methylation (mono-, di-, and tri-) are correlated with different degrees of gene regulation. For example, while H3 Lys9 trimethylation is associated with constitutive heterochromatin, H3 Lys9 mono- and dimethylation were recently found to be enriched within transcriptionally silent regions of chromatin, suggesting an association with facultative heterochromatin. An additional interesting example of how chromatin modifications can function in vivo comes from the silencing of transposons and repetitive sequences by the formation of repressive heterochromatin structures, a mechanism thought to neutralize the invasion of transposable elements and viruses. Finally, the role of an RNAi effector complex, RITS, which links siRNAs to heterochromatin in S. pombe is discussed in relation to a step-wise model of epigenetic gene silencing. Lund and van Lohuizen continue on the theme of silencing by discussing emerging mechanisms underlying silencing by polycomb group proteins. Of particular interest in this regard has been the finding that E(z)/EZH2 is a histone H3 methyltransferase with specificity for lysines 9 and 27. The K27 methylation mark appears to facilitate the recruitment of other members of a polycomb complex to target regions of chromatin. Several models are discussed with regard to how transcriptional repression is maintained by polycomb complexes. The field of X chromosome inactivation represents an interesting paradigm to study how gene silencing of nearly an entire chromosome is established and heritably maintained. Edith Heard discusses recent data regarding the ‘counting’ and ‘choice’ functions of the X-inactivation center (Xic). Of particular interest here is the role of a 20 kb bipartite domain lying 30 to Xist, which is required for counting, and the antisense transcript Tsix, which is a potential regulator of choice. While Xist RNA is a mark of the inactive X chromosome(s), a recent study is discussed that has shown that the chromosomal association and silencing abilities of Xist RNA are functionally separable. The finding that the BRCA1 protein may be required for XIST RNA coating of the inactive X chromosome in somatic cells provides a very provocative result in light of BRCA1 mutations that are associated with breast and ovarian cancer. Continuing on the theme of histone modifications, recent findings are discussed that have Current Opinion in Cell Biology 2004, 16:219–222
indicated that the polycomb group proteins Eed (ESC) and Enx1 (EZ) may be implicated in both imprinted and random X-inactivation. In addition, the involvement of the histone variant H2AX in male meiotic sex chromosome inactivation, which is Xist-independent, is also discussed. Above the level of nucleosomes and histone modifications, important insight into gene expression can be gleaned from studies on the organization of chromatin within the cell nucleus. Chambeyron and Bickmore discuss two new approaches that have revealed the b-globin locus to be organized into a looped domain mediated through flanking hypersensitive sites forming an active chromatin hub. They then go on to discuss three models that have addressed how this looped structure may be formed and maintained. Finally, the interplay between nuclear domains and chromatin that may facilitate activation/repression of gene expression is discussed. Sims, Mandal and Reinberg discuss the assembly and dynamics of the RNA polymerase (RNAP) II transcription machinery. Of particular interest here is the continually expanding interplay between the transcription and RNA processing machineries. They discuss recent studies that have identified U1 snRNA as a component of the TFIIH complex and the role of introns and promoterproximal splicing sites in influencing transcription rates. In addition, the role of the FACT complex in destabilizing nucleosomes to allow for RNAP II passage as well as its recently identified chaperone activity, suggesting that it also plays a role in re-establishing chromatin structure after RNAP II traverses a nucleosome, are discussed. Although histone methylation is thought to be an extremely stable modification, recent studies have indicated that methylation patterns can be dynamic. This activity is discussed with regard to the recent identification of chromatin remodeling complexes that are involved in histone exchange. Of particular interest, specific histone H3 variant chaperone complexes were recently identified that mediate the incorporation of the histone variants H3.1 and H3.3 in a DNA-replication-dependent and -independent manner, respectively. It has become increasingly clear that the fidelity and efficiency of gene expression relies on the interconnection of transcription and post-transcriptional processes. As briefly discussed above, proteins acting at different steps of gene expression are often part of multimeric complexes that may not necessarily play a role in a single step, but may influence directly or indirectly upstream or downstream events. Several reviews in this issue deal with this central paradigm in gene expression. As discussed in the reviews by Reinberg, Proudfoot, Moore, Stutz, Parker and Davis and their co-authors, we understand a great deal about the interplay between transcription, mRNP assembly, mRNA processing and cytoplasmic mRNA www.sciencedirect.com
Editorial overview Izaurralde and Spector 221
metabolism. It is known that mRNAs are assembled into ribonucleoprotein particles co-transcriptionally and that the assembly process itself impacts on transcription elongation and post-transcriptional steps of gene expression. Indeed, some of the proteins that associate with nascent transcripts accompany the mRNA to the cytoplasm and influence their translation, cytoplasmic localization and eventually their degradation. Moreover, the protein composition of the mRNP particle changes as the nucleic acid progresses through pre-mRNA processing, nuclear export, translation and decay. This might be best exemplified by the assembly and dynamics of the components of the exon–exon junction complex (EJC). As reviewed by Moore et al., the EJC is a multimeric protein complex deposited at exon–exon boundaries by the spliceosome and some of its components are exported to the cytoplasm together with the mRNA. Although the EJC was thought to link splicing and export, recent studies have shown that the EJC does not play a major role in this process. The review by Tange, Nott and Moore summarizes the fastmoving advances in this area, where components of this complex have been shown to play a role in nonsensemediated mRNA decay in mammals and in cytoplasmic mRNA localization in Drosophila. The review by Vinciguerra and Stutz clearly articulates the inter-relationships between transcription, mRNP biogenesis and nuclear mRNP export, as well as recent advances in deciphering the mechanisms involved in linking these processes. Much of the evidence for these links comes from the detection of protein–protein interactions between specific components of the transcription, RNA-processing and export machineries. Although these observations have been interpreted as evidence for molecular coupling of multiple processes, future studies will need to establish whether a functional coupling between these processes exists, and how it contributes to gene expression at the genomic level. The review by Baker and Parker focuses on mRNA turnover and more specifically on the nonsense-mediated mRNA decay pathway, a surveillance mechanism that degrades mRNAs with premature translation termination codons. This area of research has rapidly established links between mRNA decay and processing. In mammals, it has now been shown that EJC components play an essential role in this process, providing a rationale for the longstanding observation that premature stop codons are defined relative to their distance to exon–exon boundaries. A major development in the past two years has been the unexpected observation of the compartmentalization of mRNA decay factors in cytoplasmic domains or bodies enriched in distinct subsets of mRNA degradation factors. Progress in identifying and characterizing the factors involved in mRNA localization in the cytoplasm and the varied mechanisms by which mRNAs are targeted www.sciencedirect.com
to their specific locations is described in detail in the review by Van de Bor and Davis. This review is nicely complemented by the review by Huang and Richter describing the fascinating details of how localized mRNAs are maintained in a translational silent state until they reach their final destination. An emerging concept in this field is the remarkable complexity of the RNA sequences (the so-called zip codes) that specify the final destination of the mRNA. These sequences include several motifs, some of which may specify a sub-destination in the cell or may be required to anchor the mRNA once it reaches its destination. Moreover, as mRNA localization is tightly coupled with translational control, some of these sequences are required to recruit translational repressor proteins, which are bound to mRNAs undergoing transport. Emerging evidence indicates that mRNAs are transported as part of huge complexes containing more than a single mRNP and even ribosomes. How these complexes are assembled remains to be established but it is clear that this process begins cotranscriptionally. For instance, as mentioned above, the components of the EJC have been recently shown to be required for the localization of a specific mRNA to the posterior pole of Drosophila oocytes. Another general theme that is becoming increasingly clear is that the trans-acting factors that interpret the cis-acting RNA sequences may change during the life of an mRNA. Understanding the complexity of this process will require new experimental approaches and in particular, as reviewed by Van de Bor and Davis, new microscopic methods that allow the direct visualization of mRNPs undergoing transport. In order for gene expression to be carried out, extensive communication must occur between the nuclear and cytoplasmic compartments. Rabut, Le´ na´ rt and Ellenberg review recent studies on the dynamics of the nuclear pore complex (NPC) during the cell cycle. While several nucleoporins have been shown to be stably associated with NPCs during interphase, others are highly dynamic with exchange rates of just a few minutes. In cells with a closed mitosis, the core scaffold of the NPC remains unchanged while the peripheral structures seem to undergo molecular rearrangements that allow a limited mixing of the cytoplasm and nucleus, which may be essential for cell cycle progression. In contrast, in cells that undergo an open mitosis, complete disruption of the nuclear envelope and dispersal of even the core nucleoporins has been observed. In addition, studies are discussed that have used RNAi and immunodepletion to examine the role of various nucleoporins in NPC structure and function. The nuclear lamins reside within the nucleus, primarily just inside the nuclear envelope. Over the past four years an increasing number of missense mutations in the lamin A gene have been identified resulting in at least eight different clinically definable diseases referred to as Current Opinion in Cell Biology 2004, 16:219–222
222 Nucleus and gene expression
laminopathies. Mounkes and Stewart focus on the most recently identified disease connection, Hutchinson Gilford Progeria Syndrome (HGPS) or premature aging. Various models are discussed regarding how a mutation in such a basic nuclear protein can result in this disease and how cell biological studies are providing clues to how progeria develops and progresses. Upon DNA damage, repair proteins come together into foci to allow the repair process to be carried out. In the last review, Lisby and Rothstein describe the composition and dynamics of DNA repair foci. Interestingly, live cell analysis has shown that these foci can assemble and disassemble within minutes and multiple DNA breaks can be repaired at a single focus. Recent studies are discussed that have provided evidence defining four stages in the assembly/disassembly process of repair foci. Finally, one example in which the molecular coupling between two steps of gene expression has raised controversy and stimulated intensive research is the possible
Current Opinion in Cell Biology 2004, 16:219–222
link between the transcription and translation machineries. In their commentary Dahlberg and Lund review the experiments that have lead to the proposal that translation can occur in the nucleus and the experiments that argue against it. They conclude that although nuclear translation is an attractive hypothesis, in the absence of additional evidence, translation is unlikely to occur within the nuclear compartment. The field of nuclear organization and gene expression covers a huge array of approaches and disciplines. A major challenge in the future will be to integrate the information obtained at all levels of investigation to generate a complete picture of regulatory circuits leading to cell- or tissue-specific patterns of gene expression. We will also need to integrate information provided by structural studies at atomic resolution with the information gathered from functional and dymamic studies of nuclear and cytoplasmic components in order to understand ultimately how their spatial distribution influences gene expression.
www.sciencedirect.com
Elisa Izaurralde European Molecular Biology Laboratory, Gene Expression Program, Meyerhofstrasse 1. D-69117 Heidelberg, Germany
Elisa Izaurralde is a Research Group leader at the European Molecular Biology Laboratory. Her laboratory studies mechanisms of posttranscriptional regulation of gene expression with particular emphasis on the nuclear export of messenger RNAs to the cytoplasm and mRNA turnover. David L Spector Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724 USA
David L Spector is a Professor at Cold Spring Harbor Laboratory. His laboratory studies nuclear organization and the dynamics of gene expression in living cells.
www.sciencedirect.com
Abbreviations EJC exon–exon junction complex mRNP messenger ribonucleoprotein particle NPC nuclear pore complex RNAi RNA interference RNAP RNA polymerase
During the past years post-transcriptional mechanisms have emerged as central pathways in the regulation of gene expression. In particular, the discovery of RNA-mediated gene silencing processes (RNA interference or RNAi) has revolutionized the field of gene expression both conceptually and experimentally. RNAi silences gene expression in a sequence-specific manner in response to the presence of double-stranded RNA. The identification of the key molecular players in this process has been followed by an increased appreciation that they function as part of large protein assemblies that act at the interface of transcriptional and post-transcriptional regulatory circuits (see the review by Murchison and Hannon). Indeed, RNAi and related processes have been shown to regulate heterochromatin formation resulting in transcriptional silencing or to act at the post-transcriptional level, either by targeting mRNAs for degradation or by inhibiting translation. Consequently, the gene silencing apparatus intersects the chromatin remodeling machineries in the nucleus, and the translation and mRNA turnover machineries in the cytoplasm. The first review in this issue by Murchison and Hannon covers recent progress on RNAi, as this topic has ramifications in all steps of gene expression. This is followed by four reviews, which examine the following topics: the regulation of heterochromatin by histone modifications and RNAi, the maintenance of chromatin states by the polycomb group of proteins, the inactivation of one X chromosome in female mammals (a specialized epigenetic mechanism regulating the expression of an entire chromosome), and how spatial localization in the nucleus can influence gene expression. The next reviews cover events in mRNA biogenesis. Starting from the regulation of transcription, we move into aspects related to the cotranscriptional assembly and processing of messenger ribonucleoprotein particles (mRNPs) and their export to the cytoplasm through nuclear pore complexes. The next group of three reviews focuses on cytoplasmic mRNP metabolism including mRNA turnover, the transport of mRNPs to specific cytoplasmic locations, and localized translation. The next two reviews focus on the dynamics of the nuclear pore complex during the cell cycle and how defects in nuclear lamin A are correlated with hereditary human diseases. The issue concludes with a review on the cellular response to DNA damage and the maintenance of genome stability, and a commentary on the Current Opinion in Cell Biology 2004, 16:219–222
220 Nucleus and gene expression
controversy surrounding the links between transcription and translation: does protein synthesis occur in the nucleus? Although the field of gene silencing was for a long time a rather quiet area of research, recent advances have turned it into one of the most exciting areas of current biology. Grewal and Rice discuss recent advances in the initiation and maintenance of heterochromatin. While methylation of histone H3 has been shown to be associated with inactive chromatin, Grewal and Rice discuss recent reports that indicate that different degrees of methylation (mono-, di-, and tri-) are correlated with different degrees of gene regulation. For example, while H3 Lys9 trimethylation is associated with constitutive heterochromatin, H3 Lys9 mono- and dimethylation were recently found to be enriched within transcriptionally silent regions of chromatin, suggesting an association with facultative heterochromatin. An additional interesting example of how chromatin modifications can function in vivo comes from the silencing of transposons and repetitive sequences by the formation of repressive heterochromatin structures, a mechanism thought to neutralize the invasion of transposable elements and viruses. Finally, the role of an RNAi effector complex, RITS, which links siRNAs to heterochromatin in S. pombe is discussed in relation to a step-wise model of epigenetic gene silencing. Lund and van Lohuizen continue on the theme of silencing by discussing emerging mechanisms underlying silencing by polycomb group proteins. Of particular interest in this regard has been the finding that E(z)/EZH2 is a histone H3 methyltransferase with specificity for lysines 9 and 27. The K27 methylation mark appears to facilitate the recruitment of other members of a polycomb complex to target regions of chromatin. Several models are discussed with regard to how transcriptional repression is maintained by polycomb complexes. The field of X chromosome inactivation represents an interesting paradigm to study how gene silencing of nearly an entire chromosome is established and heritably maintained. Edith Heard discusses recent data regarding the ‘counting’ and ‘choice’ functions of the X-inactivation center (Xic). Of particular interest here is the role of a 20 kb bipartite domain lying 30 to Xist, which is required for counting, and the antisense transcript Tsix, which is a potential regulator of choice. While Xist RNA is a mark of the inactive X chromosome(s), a recent study is discussed that has shown that the chromosomal association and silencing abilities of Xist RNA are functionally separable. The finding that the BRCA1 protein may be required for XIST RNA coating of the inactive X chromosome in somatic cells provides a very provocative result in light of BRCA1 mutations that are associated with breast and ovarian cancer. Continuing on the theme of histone modifications, recent findings are discussed that have Current Opinion in Cell Biology 2004, 16:219–222
indicated that the polycomb group proteins Eed (ESC) and Enx1 (EZ) may be implicated in both imprinted and random X-inactivation. In addition, the involvement of the histone variant H2AX in male meiotic sex chromosome inactivation, which is Xist-independent, is also discussed. Above the level of nucleosomes and histone modifications, important insight into gene expression can be gleaned from studies on the organization of chromatin within the cell nucleus. Chambeyron and Bickmore discuss two new approaches that have revealed the b-globin locus to be organized into a looped domain mediated through flanking hypersensitive sites forming an active chromatin hub. They then go on to discuss three models that have addressed how this looped structure may be formed and maintained. Finally, the interplay between nuclear domains and chromatin that may facilitate activation/repression of gene expression is discussed. Sims, Mandal and Reinberg discuss the assembly and dynamics of the RNA polymerase (RNAP) II transcription machinery. Of particular interest here is the continually expanding interplay between the transcription and RNA processing machineries. They discuss recent studies that have identified U1 snRNA as a component of the TFIIH complex and the role of introns and promoterproximal splicing sites in influencing transcription rates. In addition, the role of the FACT complex in destabilizing nucleosomes to allow for RNAP II passage as well as its recently identified chaperone activity, suggesting that it also plays a role in re-establishing chromatin structure after RNAP II traverses a nucleosome, are discussed. Although histone methylation is thought to be an extremely stable modification, recent studies have indicated that methylation patterns can be dynamic. This activity is discussed with regard to the recent identification of chromatin remodeling complexes that are involved in histone exchange. Of particular interest, specific histone H3 variant chaperone complexes were recently identified that mediate the incorporation of the histone variants H3.1 and H3.3 in a DNA-replication-dependent and -independent manner, respectively. It has become increasingly clear that the fidelity and efficiency of gene expression relies on the interconnection of transcription and post-transcriptional processes. As briefly discussed above, proteins acting at different steps of gene expression are often part of multimeric complexes that may not necessarily play a role in a single step, but may influence directly or indirectly upstream or downstream events. Several reviews in this issue deal with this central paradigm in gene expression. As discussed in the reviews by Reinberg, Proudfoot, Moore, Stutz, Parker and Davis and their co-authors, we understand a great deal about the interplay between transcription, mRNP assembly, mRNA processing and cytoplasmic mRNA www.sciencedirect.com
Editorial overview Izaurralde and Spector 221
metabolism. It is known that mRNAs are assembled into ribonucleoprotein particles co-transcriptionally and that the assembly process itself impacts on transcription elongation and post-transcriptional steps of gene expression. Indeed, some of the proteins that associate with nascent transcripts accompany the mRNA to the cytoplasm and influence their translation, cytoplasmic localization and eventually their degradation. Moreover, the protein composition of the mRNP particle changes as the nucleic acid progresses through pre-mRNA processing, nuclear export, translation and decay. This might be best exemplified by the assembly and dynamics of the components of the exon–exon junction complex (EJC). As reviewed by Moore et al., the EJC is a multimeric protein complex deposited at exon–exon boundaries by the spliceosome and some of its components are exported to the cytoplasm together with the mRNA. Although the EJC was thought to link splicing and export, recent studies have shown that the EJC does not play a major role in this process. The review by Tange, Nott and Moore summarizes the fastmoving advances in this area, where components of this complex have been shown to play a role in nonsensemediated mRNA decay in mammals and in cytoplasmic mRNA localization in Drosophila. The review by Vinciguerra and Stutz clearly articulates the inter-relationships between transcription, mRNP biogenesis and nuclear mRNP export, as well as recent advances in deciphering the mechanisms involved in linking these processes. Much of the evidence for these links comes from the detection of protein–protein interactions between specific components of the transcription, RNA-processing and export machineries. Although these observations have been interpreted as evidence for molecular coupling of multiple processes, future studies will need to establish whether a functional coupling between these processes exists, and how it contributes to gene expression at the genomic level. The review by Baker and Parker focuses on mRNA turnover and more specifically on the nonsense-mediated mRNA decay pathway, a surveillance mechanism that degrades mRNAs with premature translation termination codons. This area of research has rapidly established links between mRNA decay and processing. In mammals, it has now been shown that EJC components play an essential role in this process, providing a rationale for the longstanding observation that premature stop codons are defined relative to their distance to exon–exon boundaries. A major development in the past two years has been the unexpected observation of the compartmentalization of mRNA decay factors in cytoplasmic domains or bodies enriched in distinct subsets of mRNA degradation factors. Progress in identifying and characterizing the factors involved in mRNA localization in the cytoplasm and the varied mechanisms by which mRNAs are targeted www.sciencedirect.com
to their specific locations is described in detail in the review by Van de Bor and Davis. This review is nicely complemented by the review by Huang and Richter describing the fascinating details of how localized mRNAs are maintained in a translational silent state until they reach their final destination. An emerging concept in this field is the remarkable complexity of the RNA sequences (the so-called zip codes) that specify the final destination of the mRNA. These sequences include several motifs, some of which may specify a sub-destination in the cell or may be required to anchor the mRNA once it reaches its destination. Moreover, as mRNA localization is tightly coupled with translational control, some of these sequences are required to recruit translational repressor proteins, which are bound to mRNAs undergoing transport. Emerging evidence indicates that mRNAs are transported as part of huge complexes containing more than a single mRNP and even ribosomes. How these complexes are assembled remains to be established but it is clear that this process begins cotranscriptionally. For instance, as mentioned above, the components of the EJC have been recently shown to be required for the localization of a specific mRNA to the posterior pole of Drosophila oocytes. Another general theme that is becoming increasingly clear is that the trans-acting factors that interpret the cis-acting RNA sequences may change during the life of an mRNA. Understanding the complexity of this process will require new experimental approaches and in particular, as reviewed by Van de Bor and Davis, new microscopic methods that allow the direct visualization of mRNPs undergoing transport. In order for gene expression to be carried out, extensive communication must occur between the nuclear and cytoplasmic compartments. Rabut, Le´ na´ rt and Ellenberg review recent studies on the dynamics of the nuclear pore complex (NPC) during the cell cycle. While several nucleoporins have been shown to be stably associated with NPCs during interphase, others are highly dynamic with exchange rates of just a few minutes. In cells with a closed mitosis, the core scaffold of the NPC remains unchanged while the peripheral structures seem to undergo molecular rearrangements that allow a limited mixing of the cytoplasm and nucleus, which may be essential for cell cycle progression. In contrast, in cells that undergo an open mitosis, complete disruption of the nuclear envelope and dispersal of even the core nucleoporins has been observed. In addition, studies are discussed that have used RNAi and immunodepletion to examine the role of various nucleoporins in NPC structure and function. The nuclear lamins reside within the nucleus, primarily just inside the nuclear envelope. Over the past four years an increasing number of missense mutations in the lamin A gene have been identified resulting in at least eight different clinically definable diseases referred to as Current Opinion in Cell Biology 2004, 16:219–222
222 Nucleus and gene expression
laminopathies. Mounkes and Stewart focus on the most recently identified disease connection, Hutchinson Gilford Progeria Syndrome (HGPS) or premature aging. Various models are discussed regarding how a mutation in such a basic nuclear protein can result in this disease and how cell biological studies are providing clues to how progeria develops and progresses. Upon DNA damage, repair proteins come together into foci to allow the repair process to be carried out. In the last review, Lisby and Rothstein describe the composition and dynamics of DNA repair foci. Interestingly, live cell analysis has shown that these foci can assemble and disassemble within minutes and multiple DNA breaks can be repaired at a single focus. Recent studies are discussed that have provided evidence defining four stages in the assembly/disassembly process of repair foci. Finally, one example in which the molecular coupling between two steps of gene expression has raised controversy and stimulated intensive research is the possible
Current Opinion in Cell Biology 2004, 16:219–222
link between the transcription and translation machineries. In their commentary Dahlberg and Lund review the experiments that have lead to the proposal that translation can occur in the nucleus and the experiments that argue against it. They conclude that although nuclear translation is an attractive hypothesis, in the absence of additional evidence, translation is unlikely to occur within the nuclear compartment. The field of nuclear organization and gene expression covers a huge array of approaches and disciplines. A major challenge in the future will be to integrate the information obtained at all levels of investigation to generate a complete picture of regulatory circuits leading to cell- or tissue-specific patterns of gene expression. We will also need to integrate information provided by structural studies at atomic resolution with the information gathered from functional and dymamic studies of nuclear and cytoplasmic components in order to understand ultimately how their spatial distribution influences gene expression.
www.sciencedirect.com