The year 2010 marked the 300th anniversary of Antony van Leeuwenhoeck's description of amphibian and avian nuclei. The field is now poised to enter a new realm of inquiry and discovery. Most objects in the nucleus have been described by light and electron microscopy, but we are now beginning a new era to study the dynamics of the nuclear components and further elucidate their molecular functions. These topics have been the focus of lively meetings: the EMBO conference on Nuclear Structure and Dynamics and the Cold Spring Harbor Laboratory meeting on Nuclear Organization and Function which was highlighted at last summer's symposium. A book entitled The Nucleus edited by David Spector and Tom Misteli has just been published and provides a scholarly review of this emerging field. This book is a “must read” for anyone working on nuclear dynamics, serving as general background in a cover-to-cover reading or as a reference with citations of the pertinent literature for a given subject. This book is a nice sequel to the Cold Spring Harbor Symposium volume on the same subject. Typically the symposium chapters primarily review the research from the author's laboratory, whereas this new book gives a more comprehensive overview of each subfield.
The publication of this book has coincided with the launching of the new journal, Nucleus, and will be of major interest to the readers of this journal. The book editors are leaders in this field and as members of the editorial board of Nucleus, they have a broad overview of this field which has helped them to craft this new book. The tone of the book is well set by an excellent introductory chapter by Thoru Pederson who relates the history of various ways that the nucleus has been studied, spanning the era of isolation to mobility of nuclear components to single molecule studies. The historical background is echoed in most of the chapters; after review of the subfield in each chapter and sometimes mention of links to human disease, the chapters conclude with tracks for future investigations.
This book is divided into several sections. Working from the outside inwards, the first section describes the nuclear periphery: the nuclear envelope, nuclear lamins, lamin-binding proteins, the nuclear pore complex and nuclear transport. A main focus of the nuclear envelope chapter is nuclear envelope breakdown and reformation in the cell cycle. The chapter on lamins describes their structure which sets the framework for elucidation of functions, including regulation of nuclear shape, roles in and after mitosis, binding PCNA to exert a role in DNA replication, association with certain transcription factors, regulation of chromatin organization and involvement in epigenetic regulation. Many of the functions of lamins are mediated by lamin-associated proteins that are reviewed in the third chapter. These proteins help to tether chromatin to other nuclear structures, and the LINC complex links the nuclear interior to the cytoplasm, assisting in signaling between these cellular compartments. The section on the nuclear periphery concludes with an excellent chapter on structure and function of nuclear pore complexes.
The second section of this book explores the topic of chromosomes and chromatin starting off with a discussion of chromosome territories (CTs). Although the concept arose more than a century ago with Rabl (1885) and the term was used by Boveri in his experiments with Ascaris, the subject fell out of favor and only recently has been revived. The question centers on how chromosomes are arranged in three dimensional space in the nucleus as well as the dynamic nature of chromosome positions. For example, long range interactions of “gene kissing”, as revealed by 3C (chromosome conformation capture) or 4C (chromosome conformation capture-on-chip) techniques, might underlie mechanisms of gene activation or repression. This chapter does an excellent job in reviewing various models of nuclear architecture and the methods to test the models. Some of the concepts and methods in this chapter are elaborated upon further in the subsequent chapter on gene positioning. For example, the ChIA-PET method (chromatin interaction analysis by pairedend tag sequencing) enriches 3C products associated with a specific protein. This fascinating chapter ends with an interesting summary of altered gene positioning in disease. The important topic of higher order structure of chromatin is reviewed in another chapter and the field now awaits new conceptual advances. The field of dosage compensation is expertly reviewed in the next chapter that compares mechanisms used in worms, flies and mammals. The bottom line is that different mechanisms are used by different organisms. This chapter provides a change of perspective in model systems, as much of the rest of this book focuses on mammalian cells in culture. The subject of various model organisms is expanded upon in the subsequent outstanding chapter on the nucleus in budding yeast. The awesome power of yeast genetics holds the potential to allow the identification and mutation of proteins and sequences that control nuclear structural organization. Despite the power of yeast genetics, it may not be a suitable model to elucidate certain aspects of nuclear organization in higher eukaryotes, since yeast lack a nuclear lamina, exhibit a closed mitosis (no nuclear envelope breakdown) and have only a few nuclear bodies. Nonetheless, a lot of important information has emerged from studies on yeast. For example, nucleolar tethering of tRNA genes leads to tgm (tRNA gene-mediated gene silencing). Silencing also occurs at telomere foci at the nuclear periphery; the telomeric protein Est1 interacts with the nuclear membrane protein Mps3 to anchor chromosomes to the nuclear envelope. However, unlike telomeric heterochromatin, not all DNA at the nuclear periphery is silent. The nuclear pore components associate with actively transcribed genes, perhaps to facilitate Blobel's hypothesized “gene gating” (1985). Many puzzles still remain to be solved, such as the seeming contradiction that DNA double strand breaks accumulate at Rad52 foci in the nuclear interior, yet some nuclear pore components appear to be involved in DNA repair. This section concludes with a thought provoking chapter on nuclear actin, which may help RNA polymerase to slide along the DNA and also may mediate chromatin remodeling. Whether an actin motor is used for movement in the nucleus remains unclear.
The third section of this book has an amazing amount of information on the diverse number of nuclear bodies. The most prominent and first described nuclear body is the nucleolus known for its role in ribosome biogenesis. However, many lines of recent evidence have conspired to suggest that the nucleolus is plurifunctional. Microscopy has demonstrated that it is a site for SRP (signal recognition particle) assembly, a site housing some micro RNAs, and may have some links with the cell cycle. This may just be the tip of the iceberg, as many other proteins have been discovered in the nucleolus by proteomic analysis. Since the main focus of this chapter is on other functions of the nucleolus, only brief mention is made of the established role in ribosome biogenesis, and the topic of traffic of molecules into the nucleolus is not included. The next chapter deals with nuclear speckles that are sites for storage/assembly/modification of splicing factors but not the site of splicing itself. It has been hypothesized that speckles organize active genes on their periphery. Other functions for speckles may be forthcoming, as proteomic analysis revealed that speckles also contain other proteins related to RNA polymerase II transcription. An excellent chapter on Cajal bodies traces them from their description as accessory bodies by Cajal (1903) through the present. Cajal bodies function as the site of modification of snRNAs, guided by scaRNAs. Also, Cajal bodies are the site of U4/U6.U5 tri-snRNP formation. Despite these and other possible functions, Cajal bodies do not seem to be essential for viability, nor is the Cajal body component coilin essential. In fact, coilin has not yet been found in yeast or in C. elegans. Moreover, snRNA modification still occurs normally in flies that lack coilin (and thus also lack Cajal bodies that are organized by coilin). So, why bother to have Cajal bodies if the cell can function without them? The picture becomes even more complex with the recent observation that as oogenesis proceeds in Drosophila, the Cajal bodies break down in the nurse cells and histone locus bodies (that also contain coilin) accumulate. The relationship between Cajal bodies and histone locus bodies is just beginning to be clarified, and raises the question of whether the Cajal bodies studied extensively in Xenopus might really be histone locus bodies.
We are just at the frontier to discover the functions of numerous other bodies of the nucleus, which are described in several chapters of this book. Most PML protein is diffuse in the nucleus, but it can localize to discrete PML bodies. There is a correlation with stress, and PML may regulate some aspect of homologous recombination. There is an undefined relationship of PML with the nucleolus. The association of PML with a variety of proteins sets the stage for future studies to sort out the functions of PML. The perinucleolar compartment (PNC) contains several, but not all RNA polymerase III transcripts (it lacks U6 snRNA and tRNA), and the PNC structure requires RNA polymerase III transcription. Many mysteries remain, however. Why does the PNC contain some proteins that bind to mRNA and are needed for its processing (e.g., PTB), but not contain mRNA itself? Is there chromosomal DNA associated with the PNC? Why is the PNC correlated with metastasis of solid tumor cancer cells? This observation may prove to be of great clinical significance. Paraspeckles were discovered in 2002, less than a decade ago, and are the youngest of the nuclear bodies. They contain long non-coding RNAs, one of which (NEAT1) is needed for paraspeckle formation. Paraspeckles control the retention of A to I edited mRNA. An intriguing relationship may exist with the nucleolus, as the paraspeckle protein PSPC1 cycles to the nucleolus. Nuclear stress bodies seem to be human specific (do we have more stress than other organisms?!); they form after heat shock and contain hsf1 and satellite III transcripts. Finally, there are yet other orphan nuclear bodies, which vary with cell type. This section of the book concludes with an excellent chapter on the biogenesis of nuclear bodies, exemplifying the principle of self-organization. For example, in a recent landmark paper it was shown that when Cajal body components (e.g., coilin or SMN) are tethered to a chromosomal site, a Cajal body can form de novo at that site. There are several cases known where a nuclear body forms at the site of transcription, such as the nucleolus and ribosomal DNA transcription, the histone locus body and histone mRNA synthesis, nuclear stress granules and satellite III transcription. Many but not all nuclear bodies disappear during mitosis and reform after its completion.
The next section of this book focuses on functional aspects of the nucleus, not dealing with molecular biology mechanisms per se, but rather with their relationship to nuclear structure. Thus, in the chapter on RNA transcription, foci forming transcription factories are described. The issue is skirted of whether transcription factories are associated with a nuclear matrix, as originally proposed. In fact, the introductory chapter debunks the concept of the nuclear matrix. The chapter on DNA replication focuses on timing of DNA synthesis at replicons that synthesize DNA early or late in S phase, reviewing applications of new methodologies such as DNA combing or DNA microarrays to address this experimental question. The defined focus of this chapter precludes discussion of other topics at the forefront of the DNA replication field. Yet other chapters in this section review the topics of DNA damage and RNA processing and export. The work covered in this section shows the powerful potential of current studies employing modern methods of genomics/proteomics, 3D architecture of the nucleus by microscopy and by 3C methods, and single nucleotide studies such as DNA combing.
The last section of this book reviews nuclear architecture in differentiation and disease. There are chapters on diseases related to the nuclear envelope and lamins, nuclear ataxis, and RNA splicing. A masterful chapter summarizes the diverse information on higher order genome organization and disease. Mutations in the insulator CTCF lead to genomic instability and trinucleotide repeat expansion. Cohesins are located near the CTCF sites, and there may be non-mitotic roles of cohesins. Another protein described in this chapter is the oncogene c-myc that regulates chromatin structure, helping to keep it open; one of the targets of c-myc is the histone acetyl transferase (HAT) GCN5. In yet another example described in this chapter, increased cancer cell invasion occurs after depletion of the protein HP1 that is needed to promote heterochromatin formation.
There are a few negatives of this book. First, in some places it would have been useful to have included a cross-reference to other relevant chapters, such as mention in the nuclear envelope chapter that nuclear pores and traffic are ignored because they are covered in a subsequent chapter. Little is mentioned about the link of lamins with various diseases such as that of premature aging (progeria), and the reader does not discover this until the end of the book in the concluding section on diseases. Second, the accompanying figures are variable, and some chapters would have benefitted from more figures of original data or from summary cartoons. Third, in some chapters the coverage and references are somewhat incomplete. For example, the DNA replication chapter does not include some important recent papers (from David Gilbert, Carl Schildkraut and others) on timing of DNA synthesis. Fourth, the reprinted tables of compositional and quantitative nuclear parameters from a 1976 handbook at the end of the book may be less useful than envisioned by the editors. Instead, an updated table of David Spector's “Snapshot” article in Cell in 2006 would have been a nice addition. Despite these somewhat minor issues, the positives far outweigh the negatives and this book is highly recommended as worth having on one's bookshelf. It is a valuable resource.