Mitotic chromosome scaffold structure: new approaches to an old controversy

Genome-wide maps of nucleolus interactions reveal distinct layers of repressive chromatin domains

Eukaryotic chromosomes are folded into hierarchical domains, forming functional compartments. Nuclear periphery and nucleolus are two nuclear landmarks contributing to repressive chromosome architecture. However, while the role of nuclear lamina (NL) in genome organization has been well documented, the function of the nucleolus remains under-investigated due to the lack of methods for the identification of nucleolar associated domains (NADs). Here we have established DamID- and HiC-based methodologies to generate accurate genome-wide maps of NADs in embryonic stem cells (ESCs) and neural progenitor cells (NPCs), revealing layers of genome compartmentalization with distinct, repressive chromatin states based on the interaction with the nucleolus, NL, or both. NADs show higher H3K9me2 and lower H3K27me3 content than regions exclusively interacting with NL. Upon ESC differentiation into NPCs, chromosomes around the nucleolus acquire a more compact, rigid architecture with neural genes moving away from nucleoli and becoming unlocked for later activation. Further, histone modifications and the interaction strength within A and B compartments of NADs and LADs in ESCs set the choice to associate with NL or nucleoli upon dissociation from their respective compartments during differentiation. The methodologies here developed will make possible to include the nucleolar contribution in nuclear space and genome function in diverse biological systems.

The three-dimensional organization of the genome in cellular senescence and age-associated diseases

Recent advances in genomics and imaging technologies have increased our ability to interrogate the 3D conformation of chromosomes and to better understand principles of organization and dynamics, as well as how their alteration can lead to disease. In this review we describe how these technologies have shed new light into the role of the 3D organization of the genome in defining cellular states in aging and age-associated diseases. We compare the genomic organization in cellular senescence and cancer, discuss the role of the lamina in maintaining the structural and functional integrity of the genome, and we highlight the recent findings on how this organization breaks down in disease states.

A Topology-Centric View on Mitotic Chromosome Architecture

Mitotic chromosomes are long-known structures, but their internal organization and the exact process by which they are assembled are still a great mystery in biology. Topoisomerase II is crucial for various aspects of mitotic chromosome organization. The unique ability of this enzyme to untangle topologically intertwined DNA molecules (catenations) is of utmost importance for the resolution of sister chromatid intertwines. Although still controversial, topoisomerase II has also been proposed to directly contribute to chromosome compaction, possibly by promoting chromosome self-entanglements. These two functions raise a strong directionality issue towards topoisomerase II reactions that are able to disentangle sister DNA molecules (in trans) while compacting the same DNA molecule (in cis). Here, we review the current knowledge on topoisomerase II role specifically during mitosis, and the mechanisms that directly or indirectly regulate its activity to ensure faithful chromosome segregation. In particular, we discuss how the activity or directionality of this enzyme could be regulated by the SMC (structural maintenance of chromosomes) complexes, predominantly cohesin and condensin, throughout mitosis.

3D-CLEM Reveals that a Major Portion of Mitotic Chromosomes Is Not Chromatin

Recent studies have revealed the importance of Ki-67 and the chromosome periphery in chromosome structure and segregation, but little is known about this elusive chromosome compartment. Here we used correlative light and serial block-face scanning electron microscopy, which we term 3D-CLEM, to model the entire mitotic chromosome complement at ultra-structural resolution. Prophase chromosomes exhibit a highly irregular surface appearance with a volume smaller than metaphase chromosomes. This may be because of the absence of the periphery, which associates with chromosomes only after nucleolar disassembly later in prophase. Indeed, the nucleolar volume almost entirely accounts for the extra volume found in metaphase chromosomes. Analysis of wild-type and Ki-67-depleted chromosomes reveals that the periphery comprises 30%–47% of the entire chromosome volume and more than 33% of the protein mass of isolated mitotic chromosomes determined by quantitative proteomics. Thus, chromatin makes up a surprisingly small percentage of the total mass of metaphase chromosomes.

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3D-CLEM combines light and serial block-face scanning electron microscopy

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The complete architecture of all 46 human chromosomes has been defined

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A large portion of mitotic chromosomes is not composed of chromatin

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Chromosome volumes determined by light and electron microscopy differ dramatically

Condensin-Based Chromosome Organization from Bacteria to Vertebrates

Condensins are large protein complexes that play a central role in chromosome organization and segregation in the three domains of life. They display highly characteristic, rod-shaped structures with SMC (structural maintenance of chromosomes) ATPases as their core subunits and organize large-scale chromosome structure through active mechanisms. Most eukaryotic species have two distinct condensin complexes whose balanced usage is adapted flexibly to different organisms and cell types. Studies of bacterial condensins provide deep insights into the fundamental mechanisms of chromosome segregation. This Review surveys both conserved features and rich variations of condensin-based chromosome organization and discusses their evolutionary implications.

ATP-Dependent Chromatin Remodeling

In the eukaryotic nucleus, processes of DNA metabolism such as transcription, DNA replication, and repair occur in the context of DNA packaged into nucleosomes and higher order chromatin structures. In order to overcome the barrier presented by chromatin structures to the protein machinery carrying out these processes, the cell relies on a class of enzymes called chromatin remodeling complexes which catalyze ATP-dependent restructuring and repositioning of nucleosomes. Chromatin remodelers are large multi-subunit complexes which all share a common SF2 helicase ATPase domain in their catalytic subunit, and are classified into four different families-SWI/SNF, ISWI, CHD, INO80-based on the arrangement of other domains in their catalytic subunit as well as their non-catalytic subunit composition. A large body of structural, biochemical, and biophysical evidence suggests chromatin remodelers operate as histone octamer-anchored directional DNA translocases in order to disrupt DNA-histone interactions and catalyze nucleosome sliding. Remodeling mechanisms are family-specific and depend on factors such as how the enzyme engages with nucleosomal and linker DNA, features of DNA loop intermediates, specificity for mono- or oligonucleosomal substrates, and ability to remove histones and exchange histone variants. Ultimately, the biological function of chromatin remodelers and their genomic targeting in vivo is regulated by each complex's subunit composition, association with chromatin modifiers and histone chaperones, and affinity for chromatin signals such as histone posttranslational modifications.

Loops determine the mechanical properties of mitotic chromosomes

We introduce a new polymer model for mitotic chromosomes. The key assumption of the model is the ability of the chromatin fibre to cross-link to itself due to binding proteins. These protein-chromatin interactions are included by a probabilistic and dynamic mechanism. The hypothesis is motivated by the observation of high repulsive forces between ring polymers. We performed computer simulations to validate our model. Our results show that the presence of loops leads to a tight compaction and contributes significantly to the bending rigidity of chromosomes. Moreover, our qualitative prediction of the force elongation behaviour is close to experimental findings. The Dynamic Loop Model presented here indicates that the internal structure of mitotic chromosomes is based on self-organization of the chromatin fibre rather than attachment of chromatin to a protein scaffold. It also shows that the number and size of loops have a strong influence on the mechanical properties. We suggest that changes in the mechanical characteristics of chromosomes in different stages of the cell cycle, for example, can be explained by an altered internal loop structure.

Building mitotic chromosomes

Mitotic chromosomes are the iconic structures into which the genome is packaged to ensure its accurate segregation during mitosis. Although they have appeared on countless journal cover illustrations, there remains no consensus on how the chromatin fiber is packaged during mitosis. In fact, work in recent years has both added to existing controversies and sparked new ones. By contrast, there has been very significant progress in determining the protein composition of isolated mitotic chromosomes. Here, we discuss recent studies of chromosome organization and provide an in depth description of the latest proteomics studies, which have at last provided us with a definitive proteome for vertebrate chromosomes.

Dynamic plasticity of large-scale chromatin structure revealed by self-assembly of engineered chromosome regions

Interphase chromatin compaction well above the 30-nm fiber is well documented, but the structural motifs underlying this level of chromatin folding remain unknown. Taking a reductionist approach, we analyzed in mouse embryonic stem (ES) cells and ES-derived fibroblasts and erythroblasts the folding of 10-160-megabase pair engineered chromosome regions consisting of tandem repeats of bacterial artificial chromosomes (BACs) containing approximately 200 kilobases of mammalian genomic DNA tagged with lac operator (LacO) arrays. Unexpectedly, linear mitotic and interphase chromatid regions formed from noncontiguously folded DNA topologies. Particularly, in ES cells, these model chromosome regions self-organized with distant sequences segregating into functionally distinct, compact domains. Transcriptionally active and histone H3K27me3-modified regions positioned toward the engineered chromosome subterritory exterior, with LacO repeats and the BAC vector backbone localizing within an H3K9me3, HP1-enriched core. Differential compaction of Dhfr and alpha- and beta-globin transgenes was superimposed on dramatic, lineage-specific reorganization of large-scale chromatin folding, demonstrating a surprising plasticity of large-scale chromatin organization.

SUMO modification of DNA topoisomerase II: trying to get a CENse of it all

DNA topoisomerase II (topo II) is an essential determinant of chromosome structure and function, acting to resolve topological problems inherent in recombining, transcribing, replicating and segregating DNA. In particular, the unique decatenating activity of topo II is required for sister chromatids to disjoin and separate in mitosis. Topo II exhibits a dynamic localization pattern on mitotic chromosomes, accumulating at centromeres and axial chromosome cores prior to anaphase. In organisms ranging from yeast to humans, a fraction of topo II is targeted for SUMO conjugation in mitotic cells, and here we review our current understanding of the significance of this modification. As we shall see, an emerging consensus is that in metazoans SUMO modification is required for topo II to accumulate at centromeres, and that in the absence of this regulation there is an elevated frequency of chromosome non-disjunction, segregation errors, and aneuploidy. The underlying molecular mechanisms for how SUMO controls topo II are as yet unclear. In closing, however, we will evaluate two possible interpretations: one in which SUMO promotes enzyme turnover, and a second in which SUMO acts as a localization tag for topo II chromosome trafficking.

Analyzing Top2 distribution on yeast chromosomes by chromatin immunoprecipitation

In vertebrate cells, DNA topoisomerase II (Topo II), named Top2 in yeast, localizes along chromosome axes early in mitosis and concentrates within centromeric chromatin during metaphase. The factors controlling these changes in enzyme distribution are largely unknown. Insight into Topo II dynamics could potentially be derived through genetic approaches in yeast. In practice, however, the small size and limited compaction of yeast chromosomes has precluded a detailed analysis of Top2 localization along mitotic chromosomes. As an alternative approach, we describe a method for examining Top2 distribution using chromatin immunoprecipitation (ChIP). By adding a detergent solubilization step, this method allows efficient recovery of DNA sequences associated with Top2 in the insoluble chromosome scaffold fraction.

High precision size measurement of centromere 8 and the 8q24/c-myc gene region in metaphase and interphase human fibroblasts indicate differential condensation

The hypothesis that distinct chromatin domains expand and are remodelled differently when they undergo transcription, replication or cell cycle processes is well accepted. The condensation changes by which chromosomes are transformed at the metaphase-interphase transition are especially interesting and therefore extensively studied by light microscopy; however, quantitative information of the size on specific small chromatin domains during the cell cycle is scarce. In this respect, a serious problem is the determination of structural features close to the resolution limit. In this report we use a novel approach to quantify the lateral extent of the 8q24/c-myc gene domain and the centromeric region of chromosome 8 in doubly labelled normal human foreskin fibroblasts using confocal laser scanning microscopy (CLSM). The domains were analysed in both metaphase spreads and interphase nuclei. These high precision measurements revealed a somewhat smaller (few 10s of nm) lateral extension of the centromere region in metaphase compared to interphase. Surprisingly, within the same cells the lateral extension of the 8q24/c-myc region was significantly smaller in interphase than in metaphase. For comparison the centromere size was more condensed in metaphase than in interphase. This implies a different folding behaviour for specific chromatin domains with opposite condensation behaviour.

The role of specialized transcription factories in chromosome pairing

Homologous chromosomes can pair in somatic and germ line cells, and many mechanisms have been proposed to explain how they do so. One popular class of models involves base-pairing between DNA strands catalyzed by recombination proteins, but pairing still occurs in mutants lacking the relevant functional proteins. We discuss an alternative based on two observations: transcription occurs in factories that specialize in transcribing specific gene sub-sets, and chromosomes only pair when transcribed. Each chromosome in the haploid set has a unique array of transcription units strung along its length; we suggest each is organized into clouds of loops tethered to specialized factories. Only homologs share similar strings of clouds and factories. Pairing begins when a promoter on one chromosome initiates in the homologous and specialized factory organized mainly by its homologous partner. This transiently ties the two homologs together, to increase the chances that adjacent promoters initiate in their homologous factories and that the two homologs will be zipped together. Then, interactions between promoters and RNA polymerases in the factories mediate pairing.

The Drosophila cytosine-5 methyltransferase Dnmt2 is associated with the nuclear matrix and can access DNA during mitosis

Cytosine-5 methyltransferases of the Dnmt2 family are highly conserved in evolution and their biological function is being studied in several organisms. Although all structural DNA methyltransferase motifs are present in Dnmt2, these enzymes show a strong tRNA methyltransferase activity. In line with an enzymatic activity towards substrates other than DNA, Dnmt2 has been described to localize to the cytoplasm. Using molecular and biochemical approaches we show here that Dnmt2 is both a cytoplasmic and a nuclear protein. Sub-cellular fractionation shows that a significant amount of Dnmt2 is bound to the nuclear matrix. Sub-cellular localization analysis reveals that Dnmt2 proteins are enriched in actively dividing cells. Dnmt2 localization is highly dynamic during the cell cycle. Using live imaging we observed that Dnmt2-EGFP enters prophase nuclei and shows a spindle-like localization pattern during mitotic divisions. Additional experiments suggest that this localization is microtubule dependent and that Dnmt2 can access DNA during mitotic cell divisions. Our results represent the first comprehensive characterization of Dnmt2 proteins on the cellular level and have important implications for our understanding of the molecular activities of Dnmt2.

Analysis of the role of Aurora B on the chromosomal targeting of condensin I

During mitosis, chromosome condensation takes place, which entails the conversion of interphase chromatin into compacted mitotic chromosomes. Condensin I is a five-subunit protein complex that plays a central role in this process. Condensin I is targeted to chromosomes in a mitosis-specific manner, which is regulated by phosphorylation by mitotic kinases. Phosphorylation of histone H3 at serine 10 (Ser10) occurs during mitosis and its physiological role is a longstanding question. We examined the function of Aurora B, a kinase that phosphorylates Ser10, in the chromosomal binding of condensin I and mitotic chromosome condensation, using an in vitro system derived from Xenopus egg extract. Aurora B depletion from a mitotic egg extract resulted in the loss of H3 phosphorylation, accompanied with a 50% reduction of chromosomal targeting of condensin I. Alternatively, a portion of condensin I was bound to sperm chromatin, and chromosome-like structures were assembled when okadaic acid (OA) was supplemented in an interphase extract that lacks Cdc2 activity. However, chromosomal targeting of condensin I was abolished when Aurora B was depleted from the OA-treated interphase extract. From these results, it is suggested that Aurora B-dependent and Cdc2-independent pathways of the chromosomal targeting of condensin I are present.

A comparative proteome analysis of human metaphase chromosomes isolated from two different cell lines reveals a set of conserved chromosome-associated proteins

A comparative proteome analysis of human metaphase chromosomes between a typical epithelial-like cell, HeLa S3, and a lymphoma-type cell, BALL-1, was performed. One-dimensional (1-D) SDS-PAGE and radical-free and highly reducing two-dimensional electrophoresis (RFHR 2-DE) detected more than 200 proteins from chromosomes isolated from HeLa S3 cells, among which 189 proteins were identified by mass spectrometry (MS). Consistent with our recent four-layer structural model of a metaphase chromosome, all the identified proteins were grouped into four distinct levels of abundance. Both HeLa S3 and BALL-1 chromosomes contained specific sets of abundant chromosome structural and peripheral proteins in addition to less abundant chromosome coating proteins (CCPs). Furthermore, titin array analysis and a proteome analysis of the ultra-high molecular mass region indicated an absence of titin with their molecular weight (MW) more than 1000 kDa. Consequently, the present proteome analyses together with previous information on chromosome proteins provide the comprehensive list of proteins essential for the metaphase chromosome architecture.

Dynamic Chromatin Loops and the Regulation of Gene Expression

Although we have a draft sequence of the human genome, little is known about how the chromatin fiber is packed in three-dimensional (3D) space, or how packing affects function (Jackson 2003). We know packing plays a major role; the rate of transcription of a typical gene can vary over eight orders of magnitude (Ivarie et al. 1983), but deleting local elements like promoters and enhancers reduces expression by less than 5000-fold in transient transfection assays where the 3D “context” is missing. Common sense suggests the fiber cannot be packed randomly, but elucidating what any underlying order might be has proved difficult. First, the foldings of the chromatin fiber have dimensions below the resolution (≈200 nm) of the light microscope (LM) and so can only be seen by electron microscopy (EM), but then the fixation required can distort structure. Second, DNA is so long and packed so tightly it breaks and/or aggregates easily on isolation. Third, chromatin is poised in a metastable state so small charge alterations trigger changes in structure and function, and replacing the natural environment with our buffers often promotes aggregation.

Mitotic chromosome structure and condensation

Mitotic chromosome structure has been the cell biology equivalent of a 'riddle, wrapped in a mystery, inside an enigma'. Observations that genetic knockout or knockdown of condensin subunits or topoisomerase II cause only minimal perturbation in overall chromosome condensation, together with analysis of early stages of chromosome condensation and effects produced by histone H1 depletion, suggest a need to reconsider textbook models of mitotic chromosome condensation and organization.

Common Pathway of Chromosome Condensation in Mammalian Cells

Chromatin folding in the interphase nucleus is not known. We compared the pattern of chromatin condensation in Indian muntjac, Chinese hamster ovary, murine pre B, and K562 human erythroleukemia cells during the cell cycle. Fluorescent microscopy showed that chromosome condensation follows a general pathway. Synchronized cells were reversibly permeabilized and used to isolate interphase chromatin structures. Based on their structures two major categories of intermediates were distinguished: (1) decondensed chromatin and (2) condensed chromosomal forms. (1) Chromatin forms were found between the G1 and mid-S phase involving veil-like, supercoiled, fibrous, ribboned structures; (2) condensing chromosomal forms appeared in the late-S, G2, and M phase, including strings, chromatin bodies, elongated pre-chromosomes, pre-condensed chromosomes, and metaphase chromosomes. Results demonstrate that interphase chromosomes are clustered in domains; condensing interphase chromosomes are linearly arranged. Our results raise questions related to telomer sequences and to the chemical nature of chromosome connectivity.

Entropy-driven genome organization

DNA and RNA polymerases active on bacterial and human genomes in the crowded environment of a cell are modeled as beads spaced along a string. Aggregation of the large polymerizing complexes increases the entropy of the system through an increase in entropy of the many small crowding molecules; this occurs despite the entropic costs of looping the intervening DNA. Results of a quantitative cost/benefit analysis are consistent with observations that active polymerases cluster into replication and transcription "factories" in both pro- and eukaryotes. We conclude that the second law of thermodynamics acts through nonspecific entropic forces between engaged polymerases to drive the self-organization of genomes into loops containing several thousands (and sometimes millions) of basepairs.

Protein composition of human metaphase chromosomes analyzed by two-dimensional electrophoreses

A large amount of metaphase chromosomes were isolated from synchronized human cell lines by a polyamine procedure. All the chromosomal proteins extracted by an acetic acid extraction method were fully dissolved into the sample solutions for isoelectric focusing (IEF) or radical free and highly reduced (RFHR) two-dimensional electrophoreses (2-DEs). As a result, well-separated and highly reproducible 2-DE patterns were obtained. This could not be attained by an ordinary acetone precipitation method. The 2-DE patterns visualized using Coomassie Brilliant Blue (CBB) staining indicated that more than one hundred proteins were involved in the isolated metaphase chromosomes, although the most abundant proteins, histones, occupied a greater part of the chromosomal proteins. It was also shown that colcemid treatment for cell cycle synchronization had little effect on the 2-DE pattern compared to that obtained without the treatment. Furthermore, no significant differences were observed in the 2-DE patterns among the chromosomal proteins prepared from two different human cell lines, BALL-1 and K562. However, 2-DE analysis of isolated metaphase chromosomes from HeLa cells apparently showed a smaller number of proteins than the BALL-1 and K562 cell lines at a neutral pI range. The present study paves the way for elucidating protein composition of human metaphase chromosomes.

Nongenic transcription, gene regulation and action at a distance

In eukaryotes, motifs such as silencers, enhancers and locus control regions act over thousands of base pairs to regulate adjacent genes; insulators limit such effects, and barriers confine repressive heterochromatin to particular chromosomal segments. Recent results show that many of these motifs are nongenic transcription units, and two of them directly contact their targets lying further down the chromosome to loop the intervening DNA: the barriers (scs and scs') flanking the 87A7 heat-shock locus in the fly contact each other, and a locus control region touches the β-globin gene in the mouse. I hypothesize that the act of transcription underlies the function of these regulators; active polymerizing complexes tend to cluster into `factories' and this facilitates molecular contact between the transcribed regulator and its distant (and transcribed) target.

Condensin is required for nonhistone protein assembly and structural integrity of vertebrate mitotic chromosomes

The dramatic condensation of chromosomes that occurs during mitosis is widely thought to be largely controlled by a protein complex termed condensin. Here, we describe a conditional knockout of the condensin subunit ScII/SMC2 in chicken DT40 cells. In cells lacking this condensin subunit, chromosome condensation is delayed, but ultimately reaches near-normal levels. However, these chromosomes are structurally compromised. Kinetochores appear normal, but the localization of nonhistone proteins such as topoisomerase II and INCENP is aberrant. Both proteins also fail to partition into the chromosome scaffold fraction, which appears to be largely missing in the absence of condensin. Furthermore, the chromosomes lack structural integrity, as defined by an assay that tests the stability of the chromosomal higher-order structure. Thus, a major function of condensin is to promote the correct association of nonhistone proteins with mitotic chromosomes, and this is essential for establishment of a robust chromosome structure.

Micromechanics of chromatin and chromosomes

The enzymes that transcribe, recombine, package, and duplicate the eukaryotic genome all are highly processive and capable of generating large forces. Understanding chromosome function therefore will require analysis of mechanics as well as biochemistry. Here we review development of new biophysical-biochemical techniques for studying the mechanical properties of isolated chromatin fibers and chromosomes. We also discuss microscopy-based experiments on cells that visualize chromosome structure and dynamics. Experiments on chromatin tell us about its flexibility and fluctuation, as well as quantifying the forces generated during chromatin assembly. Experiments on whole chromosomes provide insight into the higher-order organization of chromatin; for example, recent experiments have shown that the mitotic chromosome is held together by isolated chromatin-chromatin links and not a large, mechanically contiguous non-DNA "scaffold".