The transcriptional basis of chromosome pairing

Somatic chromosome pairing has a determinant impact on 3D chromatin organization

In the nucleus, chromatin is intricately structured into multiple layers of 3D organization important for genome activity. How distinct layers influence each other is not well understood. In particular, the contribution of chromosome pairing to 3D chromatin organization has been largely neglected. Here, we address this question in Drosophila, an organism that shows robust chromosome pairing in interphasic somatic cells. The extent of chromosome pairing depends on the balance between pairing and anti-pairing factors, with the anti-pairing activity of the CAP-H2 condensin II subunit being the best documented. Here, we identify the zinc-finger protein Z4 as a strong anti-pairer that interacts with and mediates the chromatin binding of CAP-H2. We also report that hyperosmotic cellular stress induces fast and reversible chromosome unpairing that depends on Z4/CAP-H2. And, most important, by combining Z4 depletion and osmostress, we show that chromosome pairing reinforces intrachromosomal 3D interactions. On the one hand, pairing facilitates RNAPII occupancy that correlates with enhanced intragenic gene-loop interactions. In addition, acting at a distance, pairing reinforces chromatin-loop interactions mediated by Polycomb (Pc). In contrast, chromosome pairing does not affect which genomic intervals segregate to active (A) and inactive (B) compartments, with only minimal effects on the strength of A-A compartmental interactions. Altogether, our results unveil the intimate interplay between inter-chromosomal and intra-chromosomal 3D interactions, unraveling the interwoven relationship between different layers of chromatin organization and the essential contribution of chromosome pairing.

C-DNA may facilitate homologous DNA pairing

Recombination-independent homologous pairing represents a prominent yet largely enigmatic feature of chromosome biology. As suggested by studies in the fungus Neurospora crassa, this process may be based on the direct pairing of homologous DNA molecules. Theoretical search for the DNA structures consistent with those genetic results has led to an all-atom model in which the B-DNA conformation of the paired double helices is strongly shifted toward C-DNA. Coincidentally, C-DNA also features a very shallow major groove that could permit initial homologous contacts without atom-atom clashes. The hereby conjectured role of C-DNA in homologous pairing should encourage the efforts to discover its biological functions and may also clarify the mechanism of recombination-independent recognition of DNA homology.

Homologous pairing in short double-stranded DNA-grafted colloidal microspheres

Homologous pairing (HP), i.e., the pairing of similar or identical double-stranded DNA, is an insufficiently understood fundamental biological process. HP is now understood to also occur without protein mediation, but crucial mechanistic details remain poorly established. Unfortunately, systematic studies of sequence dependence are not practical due to the enormous number of nucleotide permutations and multiple possible conformations involved in existing biophysical strategies even when using as few as 150 basepairs. Here, we show that HP can occur in DNA as short as 18 basepairs in a colloidal microparticle-based system. Exemplary systematic studies include resolving opposing reports of the impact of % AT composition, validating the impact of nucleotide order and triplet framework and revealing isotropic bendability to be crucial for HP. These studies are enabled by statistical analysis of crystal size and fraction within coexisting fluid-crystal phases of double-stranded DNA-grafted colloidal microspheres, where crystallization is predicated by HP.

Homologous chromosome associations in domains before meiosis could facilitate chromosome recognition and pairing in wheat

The increasing human population demands an increase in crop yields that must be implemented through breeding programmes to ensure a more efficient and sustainable production of agro-food products. In the framework of breeding, genetic crosses are developed between cultivated species such as wheat and their relative species that are used as genetic donors to transfer desirable agronomic traits into the crop. Unfortunately, interspecific associations between chromosomes from the donor species and the cultivar are rare during meiosis, the process to produce gametes in organisms with sexual reproduction, hampering the transfer of genetic variability into wheat. In addition, little is known about how homologous (equivalent) chromosomes initiate interaction and recognition within the cell nucleus to enter meiosis. In this context, we aim to get insight into wheat chromatin structure, particularly the distribution of homologous chromosomes within the cell nucleus and their putative interactions in premeiotic stages to facilitate chromosome associations and recombination at the beginning of meiosis. Cytogenetics allows the study of both the structure and the behaviour of chromosomes during meiosis and is key in plant breeding. In this study we visualized an extra pair of barley homologous chromosomes in a wheat genetic background to study the spatial distribution, arrangements and interactions occurring exclusively between this pair of homologous chromosomes during premeiosis using fluorescence in situ hybridization (FISH). Our results suggest that homologous chromosomes can initiate interactions in premeiotic stages that could facilitate the processes of specific chromosome recognition and association occurring at the onset of meiosis.

Recombination-independent recognition of DNA homology for meiotic silencing in Neurospora crassa

The pairing of homologous chromosomes represents a critical step of meiosis in nearly all sexually reproducing species. In many organisms, pairing involves chromosomes that remain apparently intact. The mechanistic nature of homology recognition at the basis of such pairing is unknown. Using "meiotic silencing by unpaired DNA" (MSUD) as a model process, we demonstrate the existence of a cardinally different approach to DNA homology recognition in meiosis. The main advantage of MSUD over other experimental systems lies in its ability to identify any relatively short DNA fragment lacking a homologous allelic partner. Here, we show that MSUD does not rely on the canonical mechanism of meiotic recombination, yet it is promoted by REC8, a conserved component of the meiotic cohesion complex. We also show that certain patterns of interspersed homology are recognized as pairable during MSUD. Such patterns need to be colinear and must contain short tracts of sequence identity spaced apart at 21 or 22 base pairs. By using these periodicity values as a guiding parameter in all-atom molecular modeling, we discover that homologous DNA molecules can pair by forming quadruplex-based contacts with an interval of 2.5 helical turns. This process requires right-handed plectonemic coiling and additional conformational changes in the intervening double-helical segments. Our results 1) reconcile genetic and biophysical evidence for the existence of direct homologous double-stranded DNA (dsDNA)-dsDNA pairing, 2) identify a role for this process in initiating RNA interference, and 3) suggest that chromosomes can be cross-matched by a precise mechanism that operates on intact dsDNA molecules.

Oligopaint DNA FISH reveals telomere-based meiotic pairing dynamics in the silkworm, Bombyx mori

Accurate chromosome segregation during meiosis is essential for reproductive success. Yet, many fundamental aspects of meiosis remain unclear, including the mechanisms regulating homolog pairing across species. This gap is partially due to our inability to visualize individual chromosomes during meiosis. Here, we employ Oligopaint FISH to investigate homolog pairing and compaction of meiotic chromosomes and resurrect a classical model system, the silkworm Bombyx mori. Our Oligopaint design combines multiplexed barcoding with secondary oligo labeling for high flexibility and low cost. These studies illustrate that Oligopaints are highly specific in whole-mount gonads and on meiotic squashes. We show that meiotic pairing is robust in both males and females and that pairing can occur through numerous partially paired intermediate structures. We also show that pairing in male meiosis occurs asynchronously and seemingly in a transcription-biased manner. Further, we reveal that meiotic bivalent formation in B. mori males is highly similar to bivalent formation in C. elegans, with both of these pathways ultimately resulting in the pairing of chromosome ends with non-paired ends facing the spindle pole. Additionally, microtubule recruitment in both C. elegans and B. mori is likely dependent on kinetochore proteins but independent of the centromere-specifying histone CENP-A. Finally, using super-resolution microscopy in the female germline, we show that homologous chromosomes remain associated at telomere domains in the absence of chiasma and after breakdown and modification to the synaptonemal complex in pachytene. These studies reveal novel insights into mechanisms of meiotic homolog pairing both with or without recombination.

RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture

Three-dimensional (3D) genome organization has emerged as an important layer of gene regulation in development and disease. The functional properties of chromatin folding within individual chromosomes (i.e., intra-chromosomal or in cis) have been studied extensively. On the other hand, interactions across different chromosomes (i.e., inter-chromosomal or in trans) have received less attention, being often regarded as background noise or technical artifacts. This viewpoint has been challenged by emerging evidence of functional relationships between specific trans chromatin interactions and epigenetic control, transcription, and splicing. Therefore, it is an intriguing possibility that the key processes involved in the biogenesis of RNAs may both shape and be in turn influenced by inter-chromosomal genome architecture. Here I present the rationale behind this hypothesis, and discuss a potential experimental framework aimed at its formal testing. I present a specific example in the cardiac myocyte, a well-studied post-mitotic cell whose development and response to stress are associated with marked rearrangements of chromatin topology both in cis and in trans. I argue that RNA polymerase II clusters (i.e., transcription factories) and foci of the cardiac-specific splicing regulator RBM20 (i.e., splicing factories) exemplify the existence of trans-interacting chromatin domains (TIDs) with important roles in cellular homeostasis. Overall, I propose that inter-molecular 3D proximity between co-regulated nucleic acids may be a pervasive functional mechanism in biology.

Telomeres and Subtelomeres Dynamics in the Context of Early Chromosome Interactions During Meiosis and Their Implications in Plant Breeding

Genomic architecture facilitates chromosome recognition, pairing, and recombination. Telomeres and subtelomeres play an important role at the beginning of meiosis in specific chromosome recognition and pairing, which are critical processes that allow chromosome recombination between homologs (equivalent chromosomes in the same genome) in later stages. In plant polyploids, these terminal regions are even more important in terms of homologous chromosome recognition, due to the presence of homoeologs (equivalent chromosomes from related genomes). Although telomeres interaction seems to assist homologous pairing and consequently, the progression of meiosis, other chromosome regions, such as subtelomeres, need to be considered, because the DNA sequence of telomeres is not chromosome-specific. In addition, recombination operates at subtelomeres and, as it happens in rye and wheat, homologous recognition and pairing is more often correlated with recombining regions than with crossover-poor regions. In a plant breeding context, the knowledge of how homologous chromosomes initiate pairing at the beginning of meiosis can contribute to chromosome manipulation in hybrids or interspecific genetic crosses. Thus, recombination in interspecific chromosome associations could be promoted with the aim of transferring desirable agronomic traits from related genetic donor species into crops. In this review, we summarize the importance of telomeres and subtelomeres on chromatin dynamics during early meiosis stages and their implications in recombination in a plant breeding framework.

The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos

Genome organization involves cis and trans chromosomal interactions, both implicated in gene regulation, development, and disease. Here, we focus on trans interactions in Drosophila, where homologous chromosomes are paired in somatic cells from embryogenesis through adulthood. We first address long-standing questions regarding the structure of embryonic homolog pairing and, to this end, develop a haplotype-resolved Hi-C approach to minimize homolog misassignment and thus robustly distinguish trans-homolog from cis contacts. This computational approach, which we call Ohm, reveals pairing to be surprisingly structured genome-wide, with trans-homolog domains, compartments, and interaction peaks, many coinciding with analogous cis features. We also find a significant genome-wide correlation between pairing, transcription during zygotic genome activation, and binding of the pioneer factor Zelda. Our findings reveal a complex, highly structured organization underlying homolog pairing, first discovered a century ago in Drosophila. Finally, we demonstrate the versatility of our haplotype-resolved approach by applying it to mammalian embryos.

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus

Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologs is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Further studies in wheat and other polyploid species will be required to reveal whether these observations are specific to wheat meiosis.

Partition of Repeat-Induced Point Mutations Reveals Structural Aspects of Homologous DNA-DNA Pairing

In some fungi, a premeiotic process known as repeat-induced point mutation (RIP) can accurately identify and mutate nearly all gene-sized DNA repeats present in the haploid germline nuclei. Studies in Neurospora crassa have suggested that RIP detects sequence homology directly between intact DNA double helices, without strand separation and without the participation of RecA-like proteins. Those studies used the aggregated number of RIP mutations as a simple quantitative measure of RIP activity. Additional structural information about homologous DNA-DNA pairing during RIP can be extracted by analyzing spatial distributions of RIP mutations converted into profiles of partitioned RIP propensity (PRP). Further analysis shows that PRP is strongly affected by the topological configuration and the relative positioning of the participating DNA segments. Most notably, pairs of closely positioned repeats produce very distinct PRP profiles depending on whether these repeats are present in the direct or the inverted orientation. Such an effect can be attributed to a topology-dependent redistribution of the supercoiling stress created by the predicted limited untwisting of the DNA segments during pairing. This and other results raise a possibility that such pairing-induced fluctuations in DNA supercoiling can modulate the overall structure and properties of repetitive DNA. Such effects can be particularly strong in the context of long tandem-repeat arrays that are typically present in the pericentromeric and centromeric regions of chromosomes in many species of plants, fungi, and animals, including humans.

Homoeologous chromosome pairing across the eukaryote phylogeny

During the past quarter century, molecular phylogenetic inferences have significantly resolved evolutionary relationships spanning the eukaryotic tree of life. With improved phylogenies in hand, the focus of systematics will continue to expand from estimating species relationships toward examining the evolution of specific, fundamental traits across the eukaryotic tree. Undoubtedly, this will expose knowledge gaps in the evolution of key traits, particularly with respect to non-model lineages. Here, we examine one such trait across eukaryotes-the regulation of homologous chromosome pairing during meiosis-as an illustrative example. Specifically, we present an overview of the breakdown of homologous chromosome pairing in model eukaryotes and provide a discussion of various meiotic aberrations that result in the failure of homolog recognition, with a particular focus on lineages with a history of hybridization and polyploidization, across major eukaryotic clades. We then explore what is known about these processes in natural and non-model eukaryotic taxa, thereby exposing disparities in our understanding of this key trait among non-model groups.

Recombination-independent recognition of DNA homology for repeat-induced point mutation

Numerous cytogenetic observations have shown that homologous chromosomes (or individual chromosomal loci) can engage in specific pairing interactions in the apparent absence of DNA breakage and recombination, suggesting that canonical recombination-mediated mechanisms may not be the only option for sensing DNA/DNA homology. One proposed mechanism for such recombination-independent homology recognition involves direct contacts between intact double-stranded DNA molecules. The strongest in vivo evidence for the existence of such a mechanism is provided by the phenomena of homology-directed DNA modifications in fungi, known as repeat-induced point mutation (RIP, discovered in Neurospora crassa) and methylation-induced premeiotically (MIP, discovered in Ascobolus immersus). In principle, Neurospora RIP can detect the presence of gene-sized DNA duplications irrespectively of their origin, underlying nucleotide sequence, coding capacity or relative, as well as absolute positions in the genome. Once detected, both sequence copies are altered by numerous cytosine-to-thymine (C-to-T) mutations that extend specifically over the duplicated region. We have recently shown that Neurospora RIP does not require MEI-3, the only RecA/Rad51 protein in this organism, consistent with a recombination-independent mechanism. Using an ultra-sensitive assay for RIP mutation, we have defined additional features of this process. We have shown that RIP can detect short islands of homology of only three base-pairs as long as many such islands are arrayed with a periodicity of 11 or 12 base-pairs along a pair of DNA molecules. While the presence of perfect homology is advantageous, it is not required: chromosomal segments with overall sequence identity of only 35-36 % can still be recognized by RIP. Importantly, in order for this process to work efficiently, participating DNA molecules must be able to co-align along their lengths. Based on these findings, we have proposed a model, in which sequence homology is detected by direct interactions between slightly-extended double-stranded DNAs. As a next step, it will be important to determine if the uncovered principles also apply to other processes that involve recombination-independent interactions between homologous chromosomal loci in vivo as well as to protein-free DNA/DNA interactions that were recently observed under biologically relevant conditions in vitro.

Investigating the Interplay between Sister Chromatid Cohesion and Homolog Pairing in Drosophila Nuclei

Following DNA replication, sister chromatids must stay connected for the remainder of the cell cycle in order to ensure accurate segregation in the subsequent cell division. This important function involves an evolutionarily conserved protein complex known as cohesin; any loss of cohesin causes premature sister chromatid separation in mitosis. Here, we examined the role of cohesin in sister chromatid cohesion prior to mitosis, using fluorescence in situ hybridization (FISH) to assay the alignment of sister chromatids in interphase Drosophila cells. Surprisingly, we found that sister chromatid cohesion can be maintained in G2 with little to no cohesin. This capacity to maintain cohesion is widespread in Drosophila, unlike in other systems where a reduced dependence on cohesin for sister chromatid segregation has been observed only at specific chromosomal regions, such as the rDNA locus in budding yeast. Additionally, we show that condensin II antagonizes the alignment of sister chromatids in interphase, supporting a model wherein cohesin and condensin II oppose each other’s functions in the alignment of sister chromatids. Finally, because the maternal and paternal homologs are paired in the somatic cells of Drosophila, and because condensin II has been shown to antagonize this pairing, we consider the possibility that condensin II-regulated mechanisms for aligning homologous chromosomes may also contribute to sister chromatid cohesion.

As cells grow, they replicate their DNA to give rise to two copies of each chromosome, known as sister chromatids, which separate from each other once the cell divides. To ensure that sister chromatids end up in different daughter cells, they are kept together from DNA replication until mitosis via a connection known as cohesion. A protein complex known as cohesin is essential for this process. Our work in Drosophila cells suggests that factors other than cohesin also contribute to sister chromatid cohesion in interphase. Additionally, we observed that the alignment of sister chromatids is regulated by condensin II, a protein complex involved in the compaction of chromosomes prior to division as well as the regulation of inter-chromosomal associations. These findings highlight that, in addition to their important individual functions, cohesin and condensin II proteins may interact to organize chromosomes over the course of the cell cycle. Finally, building on prior observations that condensin II is involved in the regulation of somatic homolog pairing in Drosophila, our work suggests that the mechanisms underlying homolog pairing may also contribute to sister chromatid cohesion.

Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes

During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated.

The role of chromosomal retention of noncoding RNA in meiosis

Meiosis is a process of fundamental importance for sexually reproducing eukaryotes. During meiosis, homologous chromosomes pair with each other and undergo homologous recombination, ultimately producing haploid sets of recombined chromosomes that will be inherited by the offspring. Compared with the extensive progress that has been made in understanding the molecular mechanisms underlying recombination, how homologous sequences pair with each other is still poorly understood. The diversity of the underlying mechanisms of pairing present in different organisms further increases the complexity of this problem. Involvement of meiosis-specific noncoding RNA in the pairing of homologous chromosomes has been found in the fission yeast Schizosaccharomyces pombe. Although different organisms may have developed other or additional systems that are involved in chromosome pairing, the findings in S. pombe will provide new insights into understanding the roles of noncoding RNA in meiosis.

Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging

Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins.

Nuclear location and the control of developmental progression

It is now well established that the mammalian genome is highly organized. Chromosomes are structured as territories that only sporadically intermingle. Chromosome territories themselves are segregated into distinct environments, that is, the transcriptionally inert/repressive (heterochromatic) and permissive (euchromatic) compartments. The transcriptionally permissive compartment is organized into domains (∼0.5-3 Mb) that consist of bundles of loops, are gene-rich and closely associated by activating epigenetic marks. During ontogeny and developmental progression chromatin states are highly dynamic. Recent studies have shown that loci and domains readily switch compartments. Switching nuclear neighborhoods is closely associated with changes in transcriptional activity and extensive chromatin reorganization. Here we discuss the implications of a dynamic genome and how it relates to the control of developmental progression.

Selective association between nucleosomes with identical DNA sequences

Self-assembly is the autonomous organization of constituents into higher order structures or assemblages and is a fundamental mechanism in biological systems. There has been an unfounded idea that self-assembly may be used in the sensing and pairing of homologous chromosomes or chromatin, including meiotic chromosome pairing, polytene chromosome formation in Diptera and transvection. Recent studies proved that double-stranded DNA molecules have a sequence-sensing property and can self-assemble, which may play a role in the above phenomena. However, to explain these processes in terms of self-assembly, it first must be proved that nucleosomes retain a DNA sequence-sensing property and can self-assemble. Here, using atomic force microscopy (AFM)-based analyses and a quantitative interaction assay, we show that nucleosomes with identical DNA sequences preferentially associate with each other in the presence of Mg(2+) ions. Using Xenopus borealis 5S rDNA nucleosome-positioning sequence and 601 and 603 sequences, homomeric or heteromeric octa- or tetranucleosomes were reconstituted in vitro and induced to form weak intracondensates by MgCl(2). AFM clearly showed that DNA sequence-based selective association occurs between nucleosomes with identical DNA sequences. Selective association was also detected between mononucleosomes. We propose that nucleosome self-assembly and DNA self-assembly constitute the mechanism underlying sensing and pairing of homologous chromosomes or chromatin.

Chromosomally-retained RNA mediates homologous pairing

Pairing and recombination of homologous chromosomes are essential for ensuring correct segregation of chromosomes in meiosis. In S. pombe, chromosomes are first bundled at the telomeres (forming a telomere bouquet) and then aligned by oscillatory movement of the elongated “horsetail” nucleus (Fig. 1).^1,2 Telomere clustering and subsequent chromosome alignment promote pairing of homologous chromosomes.^3-5 However, this telomere-bundled alignment of chromosomes cannot be responsible for the specificity of chromosome pairing. Thus, there must be some mechanism to facilitate recognition of homologous partners after telomere clustering. Recent studies in S. pombe have shown that RNA transcripts retained on the chromosome, or RNA bodies, may play a role in recognition of homologous chromosomes for pairing (Fig. 1).⁶ Acting as fiducial markers of homologous loci they would abrogate the need for direct DNA sequence homology searching.

Nuclear localization of reporter genes activated by curved DNA

Curved DNA structures with a left-handed superhelical conformation can activate eukaryotic transcription. Mechanistically, these structures favor binding to histone cores and can function as a docking site for sliding nucleosomes. Thus, promoters with this kind of curved DNA can adopt a more open structure, facilitating transcription initiation. However, whether the curved DNA segment can affect localization of a reporter gene is an open question. Localization of a gene in the nucleus often plays an important role in its expression and this phenomenon may also have a curved DNA-dependent mechanism. We examined this issue in transient and stable assay systems using a 180-bp synthetic curved DNA with a left-handed superhelical conformation. The results clearly showed that curved DNA of this kind does not have a property to deliver reporter constructs to nuclear positions that are preferable for transcription. We also identify the spatial location to which electroporation delivers a reporter plasmid in the nucleus.

Homologue pairing in flies and mammals: gene regulation when two are involved

Chromosome pairing is usually discussed in the context of meiosis. Association of homologues in germ cells enables chromosome segregation and is necessary for fertility. A few organisms, such as flies, also pair their entire genomes in somatic cells. Most others, including mammals, display little homologue pairing outside of the germline. Experimental evidence from both flies and mammals suggests that communication between homologues contributes to normal genome regulation. This paper will contrast the role of pairing in transmitting information between homologues in flies and mammals. In mammals, somatic homologue pairing is tightly regulated, occurring at specific loci and in a developmentally regulated fashion. Inappropriate pairing, or loss of normal pairing, is associated with gene misregulation in some disease states. While homologue pairing in flies is capable of influencing gene expression, the significance of this for normal expression remains unknown. The sex chromosomes pose a particularly interesting situation, as females are able to pair X chromosomes, but males cannot. The contribution of homologue pairing to the biology of the X chromosome will also be discussed.

From meiosis to postmeiotic events: alignment and recognition of homologous chromosomes in meiosis

Recombination of homologous chromosomes is essential for correct reductional segregation of homologous chromosomes, which characterizes meiosis. To accomplish homologous recombination, chromosomes must find their homologous partners and pair with them within the spatial constraints of the nucleus. Although various mechanisms have developed in different organisms, two major steps are involved in the process of pairing: first, alignment of homologous chromosomes to bring them close to each other for recognition; and second, recognition of the homologous partner of each chromosome so that they can form an intimate pair. Here, we discuss the various mechanisms used for alignment and recognition of homologous chromosomes in meiosis.

Effects of chromosomal rearrangements on transvection at the yellow gene of Drosophila melanogaster

Homologous chromosomes are paired in somatic cells of Drosophila melanogaster. This pairing can lead to transvection, which is a process by which the proximity of homologous genes can lead to a change in gene expression. At the yellow gene, transvection is the basis for several examples of intragenic complementation involving the enhancers of one allele acting in trans on the promoter of a paired second allele. Using complementation as our assay, we explored the chromosomal requirements for pairing and transvection at yellow. Following a protocol established by Ed Lewis, we generated and characterized chromosomal rearrangements to define a region in cis to yellow that must remain intact for complementation to occur. Our data indicate that homolog pairing at yellow is efficient, as complementation was disrupted only in the presence of chromosomal rearrangements that break Collapse

Key Words Collapse

MESH Headings

• Animals
• Chromosome Aberrations
• Chromosomes/genetics
• Drosophila Proteins/genetics
• Drosophila melanogaster/genetics
• Female
• Gene Duplication
• Gene Expression Regulation
• Genetic Complementation Test
• Male
• Models, Genetic
• Mutation
• Translocation, Genetic

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Grants

• R01 GM061936 NIGMS NIH HHS
• R01 GM085169 NIGMS NIH HHS
• GM61936 NIGMS NIH HHS
• GM085169 NIGMS NIH HHS

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Affiliation(s)

Sharon A Ou Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
Elaine Chang
Szexian Lee
Katherine So
C-ting Wu
James R Morris

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Transcription factories

There is increasing evidence that different transcription units are transcribed together in discrete nuclear structures known as transcription factories. Various new techniques enable us to detect and characterize these structures. We review the latest findings and discuss how they support a model for transcription and chromosome organization.

A genomewide survey argues that every zygotic gene product is dispensable for the initiation of somatic homolog pairing in Drosophila

Studies from diverse organisms show that distinct interchromosomal interactions are associated with many developmental events. Despite recent advances in uncovering such phenomena, our understanding of how interchromosomal interactions are initiated and regulated is incomplete. During the maternal-to-zygotic transition (MZT) of Drosophila embryogenesis, stable interchromosomal contacts form between maternal and paternal homologous chromosomes, a phenomenon known as somatic homolog pairing. To better understand the events that initiate pairing, we performed a genomewide assessment of the zygotic contribution to this process. Specifically, we took advantage of the segregational properties of compound chromosomes to generate embryos lacking entire chromosome arms and, thus, all zygotic gene products derived from those arms. Using DNA fluorescence in situ hybridization (FISH) to assess the initiation of pairing at five separate loci, this approach allowed us to survey the entire zygotic genome using just a handful of crosses. Remarkably, we found no defect in pairing in embryos lacking any chromosome arm, indicating that no zygotic gene product is essential for pairing to initiate. From these data, we conclude that the initiation of pairing can occur independently of zygotic control and may therefore be part of the developmental program encoded by the maternal genome.

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.

Similar active genes cluster in specialized transcription factories

How transcription affects the way specific genes are arranged within the nucleus remains to be fully understood. We examine here whether transcription occurs in discrete sites (factories) containing the required machinery and whether these sites specialize in transcribing different genes. We cotransfected plasmids encoding a common origin of replication but different transcription units into cells, where they are assembled into minichromosomes that the cellular machinery replicates and transcribes. In cells containing thousands of minichromosomes, we found (using fluorescence in situ hybridization) active templates concentrated in only a few factories that transcribe particular units depending on the promoter type and the presence of an intron. Close proximity between similar transcription units, whether on two different minichromosomes or on host chromosomes and minichromosomes, is confirmed using chromosome conformation capture. We conclude that factories specialize in producing a particular type of transcript depending on promoter type and whether or not the gene contains an intron.

Epigenetic control may explain large within-plant heterogeneity of meiotic behavior in telocentric trisomics of rye

In telocentric trisomics (telotrisomics) of organisms in which the chromosomes normally have two distinct arms, a single chromosome arm with a centromere is present in addition to a complete diploid set of chromosomes. It is the simplest form of polysomy and suitable for analyzing meiotic pairing and recombination patterns in situations where chromosomes compete for pairing. When no suitable meiotic chromosome markers are available, four metaphase I configurations can be distinguished. Their relative frequencies are indicative of the pairing and recombination patterns. In short arm (1RS) telotrisomics of chromosome 1R of rye (Secale cereale) we observed great differences in pairing and recombination patterns among spikes from different tillers and clones of the same plants. Anthers within spikes were only very rarely different. We analyzed a large number of genotypes, including inbreds as well as hybrids. The effects of genetic and environmental conditions on heterogeneity, if any, were limited. Considering that the reproductive tissue of a spike is derived from one primordial cell, it seems that at the start of sexual differentiation there was variation among cells in chromosomal control, which at meiosis determines pairing and crossing-over competence. We suggest that it is an epigenetic system that rigidly maintains this pattern through generative differentiation. In competitive situations the combination most competent for pairing will pair preferentially, forming specific meiotic configurations with different frequencies for different spikes of the same plant. This would explain the heterogeneity between spikes and the homogeneity within spikes. The epigenetic system could involve chromatin conformation or DNA methylation. There were no signs of heterochromatinization.

The depletion attraction: an underappreciated force driving cellular organization

Cellular structures are shaped by hydrogen and ionic bonds, plus van der Waals and hydrophobic forces. In cells crowded with macromolecules, a little-known and distinct force—the “depletion attraction”—also acts. We review evidence that this force assists in the assembly of a wide range of cellular structures, ranging from the cytoskeleton to chromatin loops and whole chromosomes.

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.

Enhancer-promoter communication at the yellow gene of Drosophila melanogaster: diverse promoters participate in and regulate trans interactions

The many reports of trans interactions between homologous as well as nonhomologous loci in a wide variety of organisms argue that such interactions play an important role in gene regulation. The yellow locus of Drosophila is especially useful for investigating the mechanisms of trans interactions due to its ability to support transvection and the relative ease with which it can be altered by targeted gene replacement. In this study, we exploit these aspects of yellow to further our understanding of cis as well as trans forms of enhancer-promoter communication. Through the analysis of yellow alleles whose promoters have been replaced with wild-type or altered promoters from other genes, we show that mutation of single core promoter elements of two of the three heterologous promoters tested can influence whether yellow enhancers act in cis or in trans. This finding parallels observations of the yellow promoter, suggesting that the manner in which trans interactions are controlled by core promoter elements describes a general mechanism. We further demonstrate that heterologous promoters themselves can be activated in trans as well as participate in pairing-mediated insulator bypass. These results highlight the potential of diverse promoters to partake in many forms of trans interactions.

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.

Chromosomal variation in mammalian neuronal cells: known facts and attractive hypotheses

Chromosomal mosaicism is still a genetic enigma. Although the mechanisms and consequences of this phenomenon have been studied for over 50 years, there are a number of gaps in our knowledge concerning causes, genetic mechanisms, and phenotypic manifestations of chromosomal mosaicism. Neuronal cell-specific chromosomal mosaicism is not an exception. Originally, neuronal cells of the mammalian brain were assumed to possess identical genomes. However, recent studies have shown chromosomal variations, manifested as chromosome abnormalities in cells of the developing and adult mammalian nervous system. Here, we review data obtained on the variation in chromosome complement in mammalian neuronal cells and hypothesize about the possible relevance of large-scale genomic (i.e., chromosomal) variations to brain development and functions as well as neurodevelopmental and neurodegenerative disorders. We propose to cover the term "molecular neurocytogenetics to cover all studies the aim of which is to reveal chromosome variations and organization in the mammalian brain.

Meiotic messenger RNA and noncoding RNA targets of the RNA-binding protein Translin (TSN) in mouse testis

In postmeiotic male germ cells, TSN, formerly known as testis brain-RNA binding protein, is found in the cytoplasm and functions as a posttranscriptional regulator of a group of genes transcribed by the transcription factor CREM-tau. In contrast, in pachytene spermatocytes, TSN is found predominantly in nuclei. Tsn-null males show a reduced sperm count and high levels of apoptosis in meiotic cells, suggesting a critical function for TSN during meiosis. To identify meiotic target RNAs that associate in vivo with TSN, we reversibly cross-linked TSN to RNA in testis extracts from 17-day-old and adult mice and immunoprecipitated the complexes with an affinity-purified TSN antibody. Extracts from Tsn-null mice were used as controls. Cloning and sequencing the immunoprecipitated RNAs, we identified four new TSN target mRNAs, encoding diazepam-binding inhibitor-like 5, arylsulfatase A, a tetratricopeptide repeat structure-containing protein, and ring finger protein 139. In contrast to the population of postmeiotic translationally delayed mRNAs that bind TSN, these four mRNAs are initially expressed in pachytene spermatocytes. In addition, anti-TSN also precipitated a nonprotein-coding RNA (ncRNA), which is abundant in nuclei of pachytene spermatocytes and has a putative polyadenylation signal, but no open reading frame. A second similar ncRNA is adjacent to a GGA repeat, a motif frequently associated with recombination hot spots. RNA gel-shift assays confirm that the four new target mRNAs and the ncRNA specifically bind to TSN in testis extracts. These studies have, for the first time, identified both mRNAs and a ncRNA as TSN targets expressed during meiosis.

Plant chromosome homology: hypotheses relating rendezvous, recognition and reciprocal exchange

Many higher eukaryotes have dispersed repetitive DNA and multiple instances of segmental duplications. As well, many plants and lower animals are polyploids. Thus restricting reciprocal genetic exchange to truly homologous chromosomes is likely a multi-step process. We propose the following sequence of events. First the ability to form a synaptonemal complex (SC) prematurely (i.e. before homology checking/recognition) is precluded by the organization of chromosomes during premeiotic S phase. Next rough alignment is accomplished regionally by having key allelic transcription units brought to the same transcription center. Once rough alignment is accomplished, close alignment can occur in conjunction with homology checking/recognition. Successful homology checking produces changes that now permit SC formation within the region of the check. Some organisms (with challenges to true homology such as dispersed repetitive DNA and segmental duplications) may require that, for a region to be competent to form an SC, successful homology checks must occur at both ends of the region. Successful early SC formation may provide an environment in which recombination intermediates can be earmarked for resolution into crossovers. Later in prophase I SC formation can occur nonhomologously, if two unsynapsed chromosomal axes meet.

Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis

The production of mature germ cells capable of generating totipotent zygotes is a highly specialized and sexually dimorphic process. The transition from diploid primordial germ cell to haploid spermatozoa requires genome-wide reprogramming of DNA methylation, stage- and testis-specific gene expression, mitotic and meiotic division, and the histone-protamine transition, all requiring unique epigenetic control. Dnmt3L, a DNA methyltransferase regulator, is expressed during gametogenesis, and its deletion results in sterility. We found that during spermatogenesis, Dnmt3L contributes to the acquisition of DNA methylation at paternally imprinted regions, unique nonpericentric heterochromatic sequences, and interspersed repeats, including autonomous transposable elements. We observed retrotransposition of an LTR-ERV1 element in the DNA from Dnmt3L-/- germ cells, presumably as a result of hypomethylation. Later in development, in Dnmt3L-/- meiotic spermatocytes, we detected abnormalities in the status of biochemical markers of heterochromatin, implying aberrant chromatin packaging. Coincidentally, homologous chromosomes fail to align and form synaptonemal complexes, spermatogenesis arrests, and spermatocytes are lost by apoptosis and sloughing. Because Dnmt3L expression is restricted to gonocytes, the presence of defects in later stages reveals a mechanism whereby early genome reprogramming is linked inextricably to changes in chromatin structure required for completion of spermatogenesis.

Properties of unpaired DNA required for efficient silencing in Neurospora crassa

The presence of unpaired copies of a gene during meiosis triggers silencing of all copies of the gene in the diploid ascus cell of Neurospora. This phenomenon is called meiotic silencing and on the basis of genetic studies appears to be a post-transcriptional gene silencing (PTGS) mechanism. Previously, meiotic silencing was defined to be induced by the presence of a DNA region lacking an identical segment in the homologous chromosome. However, the determinants of unpaired DNA remained a mystery. Using the Ascospore maturation-1 (Asm-1) gene, we defined what needs to be "unpaired" to silence a gene. For efficient silencing, an unpaired region of DNA needs to be of a sufficient size and contain homology to the reporter transcript. The greater the size of the loop and the larger the homology to the reporter transcript, the better the resulting meiotic silencing is. Conversely, regions not containing homology to the transcript, e.g., intergenic regions, did not silence the reporter. Surprisingly, unpaired fragments lacking a canonical promoter silenced the reporter. Additionally, we detected the unpairing-dependent loss of a transcript during meiotic silencing. Our observations further support a PTGS mechanism for meiotic silencing and offer insight into the evolutionary consequences resulting from this novel meiotic checkpoint.

Plants, pairing and phenotypes--two's company?

An RNA-based communication network appears to play a crucial role in regulating gene expression and in repressing viral and transposon sequences in plant genomes. In this article, we consider the evidence that gene expression might also be controlled epigenetically at a level other than non-coding RNA species-chromosome pairing. This epigenetic communication between sequences might be based--as it is in other organisms--on the physical pairing between homologues and the transfer of information between corresponding epigenetic landscapes. We suggest that paramutation might represent just one--albeit extreme and obvious--facet of a pairing-based gene expression regulation system in plants. Further exciting evidence for pairing occurring between homologues in plants is now mounting. An appreciation that pairing interactions might be important throughout plant development could assist in understanding phenomena such as endosperm imprinting, hybrid phenotypes and inbreeding depression.

Transcription of Drosophila troponin I gene is regulated by two conserved, functionally identical, synergistic elements

The Drosophila wings-up A gene encodes Troponin I. Two regions, located upstream of the transcription initiation site (upstream regulatory element) and in the first intron (intron regulatory element), regulate gene expression in specific developmental and muscle type domains. Based on LacZ reporter expression in transgenic lines, upstream regulatory element and intron regulatory element yield identical expression patterns. Both elements are required for full expression levels in vivo as indicated by quantitative reverse transcription-polymerase chain reaction assays. Three myocyte enhancer factor-2 binding sites have been functionally characterized in each regulatory element. Using exon specific probes, we show that transvection is based on transcriptional changes in the homologous chromosome and that Zeste and Suppressor of Zeste 3 gene products act as repressors for wings-up A. Critical regions for transvection and for Zeste effects are defined near the transcription initiation site. After in silico analysis in insects (Anopheles and Drosophila pseudoobscura) and vertebrates (Ratus and Coturnix), the regulatory organization of Drosophila seems to be conserved. Troponin I (TnI) is expressed before muscle progenitors begin to fuse, and sarcomere morphogenesis is affected by TnI depletion as Z discs fail to form, revealing a novel developmental role for the protein or its transcripts. Also, abnormal stoichiometry among TnI isoforms, rather than their absolute levels, seems to cause the functional muscle defects.

Inheritance of Polycomb-dependent chromosomal interactions in Drosophila

Maintenance of cell identity is a complex task that involves multiple layers of regulation, acting at all levels of chromatin packaging, from nucleosomes to folding of chromosomal domains in the cell nucleus. Polycomb-group (PcG) and trithorax-group (trxG) proteins maintain memory of chromatin states through binding at cis-regulatory elements named PcG response elements or cellular memory modules. Fab-7 is a well-defined cellular memory module involved in regulation of the homeotic gene Abdominal-B (Abd-B). In addition to its action in cis, we show here by three-dimensional FISH that the Fab-7 element leads to association of transgenes with each other or with the endogenous Fab-7, even when inserted in different chromosomes. These long-distance interactions enhance PcG-mediated silencing. They depend on PcG proteins, on DNA sequence homology, and on developmental progression. Once long-distance pairing is abolished by removal of the endogenous Fab-7, the derepressed chromatin state induced at the transgene locus can be transmitted through meiosis into a large fraction of the progeny, even after reintroduction of the endogenous Fab-7. Strikingly, meiotic inheritance of the derepressed state involves loss of pairing between endogenous and transgenic Fab-7. This suggests that transmission of nuclear architecture through cell division might contribute to inheritance of chromatin states in eukaryotes.

Meiosis researchers exchange information in the Alps

The 6th European Meiosis Workshop, sponsored by EMBO and organized by Franz Klein of the University of Vienna, met in mid-September. More than 150 participants who have not discovered anything more interesting than sex gathered in a bucolic Alpine valley near the town of Obertraun, Austria, surrounded by granite massifs.

Fine structural cytochemical analysis of homologous chromosome recognition, alignment, and pairing in Guinea pig spermatogonia and spermatocytes

The nuclei of guinea pig spermatogonia and spermatocytes were studied by means of quantitative autoradiography and electron microscopic methods such as high-resolution cytochemistry, immunocytochemistry, and in situ hybridization. Our observations reveal, in the nucleus of spermatogonia type B, small lampbrush structures of extended chromatin not found in nonmeiotic cells. During meiotic interphase, pairs of parallel lampbrush structures become associated by numerous filaments. The formation of the synaptonemal complex is simultaneous with the extension of chromosomal axes in a continuous leptotene-zygotene stage. Some chromosomes do not recognize their homologs before the onset of the leptotene-zygotene stage and undergo classical leptotene and zygotene stages. The immunocytochemical localization of Dmc1 and Rad51 supports the idea that these proteins are not involved in homology search and final pairing. Immunolocalization of DNA, RNA polymerase II, heterogeneous nuclear ribonucleoproteins, small nuclear ribonucleoproteins, and the trimethyl-guanosin cap of small nuclear RNAs suggests that the chromatin of lampbrush structures transcribe hnRNA and that splicing is scarce. The results of quantitative autoradiography after [3H]uridine labeling show an intense transcription accompanied by a very slow export of RNA. In situ hybridization demonstrates the presence of RNA in the regions of homology recognition and pairing. These results lead us to propose that the RNA synthesized in the lampbrush structures is involved in the process of homology searching and recognition.

Segmental allotetraploidy and allelic interactions in buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.) as revealed by genome mapping

Linkage analyses increasingly complement cytological and traditional plant breeding techniques by providing valuable information regarding genome organization and transmission genetics of complex polyploid species. This study reports a genome map of buffelgrass (Pennisetum ciliare (L.) Link syn. Cenchrus ciliaris L.). Maternal and paternal maps were constructed with restriction fragment length polymorphisms (RFLPs) segregating in 87 F1 progeny from an intraspecific cross between two heterozygous genotypes. A survey of 862 heterologous cDNAs and gDNAs from across the Poaceae, as well as 443 buffelgrass cDNAs, yielded 100 and 360 polymorphic probes, respectively. The maternal map included 322 RFLPs, 47 linkage groups, and 3464 cM, whereas the paternal map contained 245 RFLPs, 42 linkage groups, and 2757 cM. Approximately 70 to 80% of the buffelgrass genome was covered, and the average marker spacing was 10.8 and 11.3 cM on the respective maps. Preferential pairing was indicated between many linkage groups, which supports cytological reports that buffelgrass is a segmental allotetraploid. More preferential pairing (disomy) was found in the maternal than paternal parent across linkage groups (55 vs. 38%) and loci (48 vs. 15%). Comparison of interval lengths in 15 allelic bridges indicated significantly less meiotic recombination in paternal gametes. Allelic interactions were detected in four regions of the maternal map and were absent in the paternal map.

Meiosis in the golden hamster: a confocal microscopy and flow cytometric analysis

In this study, confocal microscopy and flow-cytometry were utilized to follow meiosis in hamster spermatogenesis. Confocal microscopy was used as an analytical tool to observe spermatocytes inside the tubules following meiotic progression consecutively at defined spermatogenic stages. To study spermatocyte differentiation, the structure of the synaptonemal complex was studied in detail at various stages of hamster spermatogenesis using the antibody against SC3 (the protein of axial/lateral element). The synaptonemal complex was observed from the leptotene stage until the first meiotic division with maximal staining in mid-pachytene spermatocytes, suggesting a role for SC3 at this postrecombinational stage. In addition, 3-dimensional (3D) images of synaptonemal complex were observed, providing information about spatial distribution of the chromosomes within the nuclei of spermatocytes at different stages of meiosis. Changes in spermatocyte sizes and DNA condensation allowed assessment of meiosis by flow cytometry. Changes in chromatin condensation at different stages of hamster meiosis were followed, revealing decondensation from early to late pachytene stages. The analysis also allowed a comparing of chromatin status of mitotic and meiotic chromosomes, confirming the less compact structure of the latter, possibly connected to increased transcriptional activity during meiosis.

Meiosis, recombination and chromosomes: a review of gene isolation and fluorescent in situ hybridization data in plants

Evidence is now increasing that many functions and processes of meiotic genes are similar in yeast and higher eukaryotes. However, there are significant differences and, most notably, yeast has considerably higher recombination frequencies than higher eukaryotes, different cross-over interference and possibly more than one pathway for recombination, one late and one early. Other significant events are the timing of double-strand breaks (induced by Spo11) that could be either cause or consequence of homologous chromosome synapsis and SC formation depending on the organisms, yeast plants and mammals versus Drosophila melanogaster and Caenorhabditis elegans. Many plant homologues and heterologues to meiotic genes of yeast and other organisms have now been isolated, in particular in Arabidopsis thaliana, showing that overall recombination genes are very conserved while synaptonemal complex and cohesion proteins are not. In addition to the importance of unravelling the meiotic processes by gene discovery, this review discusses the significance of chromatin packaging, genome organization, and distribution of specific repeated DNA sequences for homologous chromosome cognition and pairing, and the distribution of recombination events along the chromosomes.

Chromosome associations in budding yeast caused by integrated tandemly repeated transgenes

The binding of GFP-tagged tetracycline repressor (TetR) molecules to chromosomally integrated tetracycline operator (tetO) sequence repeats has been used as a system to study chromosome behaviour microscopically in vivo. We found that these integrated transgenes influence the architecture of yeast interphase nuclei, as chromosomal loci with tandem repeats of exogenous tetO sequences are frequently associated. These associations occur only if TetR molecules are present. tetO tandem repeats associate regardless of their chromosomal context. When they are present at a proximal and a distal chromosomal position, they perturb the normal polarized Rabl-arrangement of chromosome arms by recruiting chromosome ends to the centromeric pole of the nucleus. Associations are established at G1 and are reduced during S-phase and mitosis. This system may serve as a model for the role of DNA sequence-specific binding proteins in imposing nonrandom distribution of chromosomes within the nucleus.