Meiotic crossing-over in lily and mouse

Is RNA the working genome in eukaryotes ? The 60 year evolution of a conceptual challenge

About 80 years ago, in 1943, after a century of biochemical and genetic research, DNA was established as the carrier of genetic information. At the onset of Molecular Biology around 1960, the genome of living organisms embodied 3 basic, still unknown paradigms: its composition, organisation and expression. Between 1980 and 1990, its replication was understood, and ideas about its 3D-organisation were suggested and finally confirmed by 2010. The basic mechanisms of gene expression in higher organisms, the synthesis of precursor RNAs and their processing into functional RNAs, were also discovered about 60 years ago in 1961/62. However, some aspects were then, and are still now debated, although the latest results in post-genomic research have confirmed the basic principles. When my history-essay was published in 2003, describing the discovery of RNA processing 40 years earlier, the main facts were not yet generally confirmed or acknowledged. The processing of pre-rRNA to 28 S and 18 S rRNA was clearly demonstrated, confirmed by others and generally accepted as a fact. However, the "giant" size of pre-mRNA 10-100 kb-long and pervasive DNA transcription were still to be confirmed by post-genomic methods. It was found, surprisingly, that up to 90% of DNA is transcribed in the life cycle of eukaryotic organisms thus showing that pervasive transcription was the general rule. In this essay, we shall take a journey through the 60-year history of evolving paradigms of gene expression which followed the emergence of Molecular Biology, and we will also evoke some of the "folklore" in research throughout this period. Most important was the growing recognition that although the genome is encoded in DNA, the Working Genome in eukaryotic organisms is RNA.

Information theory, gene expression, and combinatorial regulation: a quantitative analysis

According to a functional definition of the term "gene", a protein-coding gene corresponds to a polypeptide and, hence, a coding sequence. It is therefore as such not yet present at the DNA level, but assembled from possibly heterogeneous pieces in the course of RNA processing. Assembly and regulation of genes require, thus, information about when and in which quantity specific polypeptides are to be produced. To assess this, we draw upon precise biochemical data. On the basis of our conceptual framework, we also develop formal models for the coordinated expression of specific sets of genes through the interaction of transcripts and mRNAs and with proteins via a precise putative regulatory code. Thus, the nucleotides in transcripts and mRNA are not only arranged into amino acid-coding triplets, but at the same time may participate in regulatory oligomotifs that provide binding sites for specific proteins. We can then quantify and compare product and regulatory information involved in gene expression and regulation.

Two X family DNA polymerases, λ and μ, in meiotic tissues of the basidiomycete, Coprinus cinereus

The X family DNA polymerases lambda (CcPollambda) and mu (CcPolmu) were shown to be expressed during meiotic prophase in the basidiomycete, Coprinus cinereus. These two polymerases are the only members of the X family in the C. cinereus genome. The open reading frame of CcPollambda encoded a predicted product of 800 amino acid residues and that of CcPolmicro of 621 amino acid residues. Both CcPollambda and CcPolmicro required Mn(2+) ions for activity, and both were strongly inhibited by dideoxythymidine triphosphate. Unlike their mammalian counterparts, CcPollambda and CcPolmicro had no terminal deoxynucleotidyl transferase activity. Immunostaining analysis revealed that CcPollambda was present at meiotic prophase nuclei in zygotene and pachytene cells, which is the period when homologous chromosomes pair and recombine. CcPolmicro was present in a slightly wider range of cell stages, zygotene to diplotene. In analyses using D-loop recombination intermediate substrates, we found that both CcPollambda and CcPolmicro could promote primer extension of an invading strand in a D-loop structure. Moreover, both polymerases could fully extend the primer in the D-loop substrate, suggesting that D-loop extension is an activity intrinsic to CcPollambda and CcPolmicro. Based on these data, we discuss the possible roles of these polymerases in meiosis.

Meiosis and small ubiquitin-related modifier (SUMO)-conjugating enzyme, Ubc9

In this review, we describe the role of a small ubiquitin-like protein modifier (SUMO)-conjugating protein, Ubc9, in synaptonemal complex formation during meiosis in a basidiomycete, Coprinus cinereus. Because its meiotic cell cycle is long and naturally synchronous, it is suitable for molecular biological, biochemical and genetic studies of meiotic prophase events. In yeast two-hybrid screening using the meiotic-specific cDNA library of C. cinereus, we found that the meiotic RecA homolog CcLim15 interacted with CcUbc9, CcTopII and CcPCNA. Moreover, both TopII and PCNA homologs were known as Ubc9 interactors and the targets of sumoylation. Immunocytochemistry demonstrates that CcUbc9, CcTopII and CcPCNA localize with CcLim15 in meiotic nuclei during leptotene to zygotene when synaptonemal complex is formed and when homologous chromosomes pair. We discuss the relationships between Lim15/Dmc1 (CcLim15), TopII (CcTopII), PCNA (CcPCNA) and CcUbc9, and subsequently, the role of sumoylation in the stages. We speculate that CcLim15 and CcTopII work in cohesion between homologous chromatins initially and then, in the process of the zygotene events, CcUbc9 works with factors including CcLim15 and CcTopII as an inhibitor of ubiquitin-mediated degradation and as a metabolic switch in the meiotic prophase cell cycle. After CcLim15-CcTopII dissociation, CcLim15 remains on the zygotene DNA and recruits CcUbc9, Rad54B, CcUbc9, Swi5-Sfr1, CcUbc9 and then CcPCNA in rotation on the C-terminus. Finally during zygotene, CcPCNA replaces CcLim15 on the DNA and the free-CcLim15 is probably ubiquitinated and disappears. CcPCNA may recruit the polymerase. The idea that CcUbc9 intervenes in every step by protecting CcLim15 and by switching several factors at the C-terminus of CcLim15 is likely. At the boundary of the zygotene and pachytene stages, CcPCNA would be sumoylated. CcUbc9 may also be involved with CcPCNA in the switch from the replicative polymerase being recruited at zygotene to the repair-type DNA polymerases being recruited at pachytene.

Localization of the glucocorticoid receptor in testis and accessory sexual organs of male rat

Localization of glucocorticoid receptor-like immunoreactivity (GR-LI) was studied in adult rat testis, epididymis, ejaculatory duct, seminal vesicle and prostate by light and electron microscopic immunocytochemistry. In the interstitium of the testis GR-LI was seen in the nuclei of Leydig cells, macrophages, fibroblasts, smooth muscle cells and endothelial cells of blood vessels. Furthermore, GR-LI was observed in zygotene and early pachytene primary spermatocytes of some seminiferous tubules during stages XIII-XIV and I-III of the spermatogenic cycle. Other spermatogenic cells and Sertoli cells were devoid of staining. GR-LI was also found in peritubular myoid cells, fibroblasts and basal cells of the epididymis, vas deferens and prostate. Localization of GR-LI in primary spermatocytes and Leydig cells suggests that glucocorticoids directly affect spermato- and steroidogenesis in the testis. The absence of GR-LI from functional, stromal cells of the male accessory sexual organs suggests that they are not targets for glucocorticoid hormones.

Synaptic interrelationships between the segments of the heteromorphic bivalent in double heterozygotes for paracentric inversions in chromosome 1 of the house mouse

Electron microscopic analysis of synaptonemal complexes in double heterozygotes for the partially overlapping inversions In(1)1Rk and In(1)12Rk in chromosome 1 of the house mouse was carried out. A great variety of synaptic configurations with complicated combinations of homologously and non-homologously paired segments was observed. Analysis of these configurations revealed at least five independent pairing regions in chromosome 1. Interrelationships between these regions with respect to their pairing ability were estimated. Pairings in the distal non-inverted segment and in inversions inhibit each other, while pairing in either inverted segment facilitates synapsis in the other. In other words, pairing initiations in different parts of the same bivalent are not independent events.

A model for effective pairing and recombination at meiosis based on early replicating sites (R-bands) along chromosomes

A model for meiotic pairing is proposed in which early replicating sites (R-band equivalent) along chromosomes are envisaged as sites for synaptic initiation. Only within such sites will "effective" pairing for recombination be established. Pairing in later replicating (G- and C-band equivalent) regions will be "ineffective" and will not provide for the stringent requirements of the crossover process. Exchange events might be predetermined at S-phase, and possibly at junctions between early and later replicating sequences, these being seen as vulnerable sites for breakage. Temporal shifts in replication from early to late S, are postulated to produce localized pairing disruption and lowering of crossover values as regions of chromatin shift from being effectively to ineffectively paired.

Meiosis-specific transcripts of a DNA component replicated during chromosome pairing: homology across the phylogenetic spectrum

In meiotic cells of Lilium, a group of single or low copy number DNA sequences that constitute about 0.1-0.2% of the genome do not replicate during the premeiotic S-phase but do so at zygotene in coordination with chromosome pairing. An appreciable fraction of these sequences has now been found to be transcribed into poly(A)+ RNA when chromosomes initiate the pairing process. This "zygRNA" has not been detected in nonmeiotic tissues. Even within the meiocytes, zygRNA is not detectable prior to leptotene or beyond midpachytene. S1 nuclease digestion of mouse spermatocyte nuclei selectively released zygDNA, which hybridizes with lily zygRNA. zygRNA has not been detected in mouse somatic tissues. The profile of zygRNA formation and disappearance in mouse spermatocytes is very similar to that of zygRNA in lily meiocytes.

Hyperrecombination at a specific DNA sequence in pneumococcal transformation

In pneumococcal transformation, recombination frequency between point mutations is usually proportional to physical distances. We have identified an aberrant marker belonging to the amiA locus that appeared to markedly enhance recombination frequency when crossed with any other markers of this gene. This mutation results from the C-to-A transversion in the sequence A-T-T-C-A-T----A-T-T-A-A-T. This effect is especially apparent for short distances as small as 27 base pairs. The hyperrecombination does not require the wild-type function of the pneumococcal gene for an ATP-dependent DNase (which is homologous to the product of the Escherichia coli recBC genes) or of the hex genes, which correct certain mismatched bases in transformation. The hyperrecombination is affected by the presence of nearby mismatched bases that trigger an excision-repair system. It is proposed that the mutation that shows hyperrecombination is sometimes converted to the wild-type allele at the heteroduplex stage of transformation.

Hybrid dysgenesis in Drosophila: the mechanism of T-007-induced male recombination

The term "hybrid dysgenesis" describes a syndrome of genetic effects which sometimes results when Drosophila melanogaster from wild populations are outcrossed; this syndrome often includes male recombination as well as enhanced rates of genic and chromosomal mutation, sterility, and transmission ratio distortion. In this study, we have examined the mechanism of T-007-induced male recombination by genetically characterizing third chromosomes generated by an exchange in a well-marked euchromatic region. Most recombinant chromosomes were sequentially normal, and no recessive lethal events at the point of exchange were recovered. The results demonstrate that although some recombinants may be generated by nonhomologous chromosome (or chromatid) breakage and reunion, the predominant effect of T-007 is through an enhanced rate of normal mitotic exchange. The rate of mitotic exchange is also increased by ionizing radiation and chemical mutagens; we suggest that the common factor in all three cases is the induction of single strand breaks.

Small nuclear RNA molecules that regulate nuclease accessibility in specific chromatin regions of meiotic cells

One of the factors regulating the accessibility of specific DNA sequences to endonuclease nicking during meiosis is a group of small nuclear RNA molecules, 125 nucleotides in length and transcribed by RNA polymerase III. These molecules (referred to as PsnRNA) are synthesized during meiotic prophase, when chromosomes are undergoing homologous pairing or are already paired. Accessibility to the meiotically active DNA sequences (P DNA) depends on an as-yet-undefined alteration in chromatin structure. PsnRNA is a critical factor in the alteration; it cannot be replaced by other forms of RNA. The specificity of the chromatin sites altered by PsnRNA appears to be a function of sequence complementarity between it and P DNA. Under in vivo conditions the effective action of PsnRNA depends on homologous chromosome pairing. Chromatin sites housing P-DNA sequences in nuclei isolated from cells lacking homologous pairing are not affected by meiotic endonuclease or DNAse II. Accessibility to these sites can be effected by incubation of the nuclei with PsnRNA, but only if the nuclei are from zygotene-pachytene cells. Analyses of pachytene nuclei preincubated with PsnRNA indicate that PsnRNA renders chromatin accessible to at least two endonucleases, meiotic endonuclease and DNAase II, and that it also limits such accessibility to regions housing the complementary P-DNA sequences.

The effect of dephosphorylation on the properties of a helix-destabilizing protein from meiotic cells and its partial reversal by a protein kinase

Properties of the helix-destabilizing protein from Lilium meiotic cells, 'R-protein', have been examined after treating it either with alkaline phosphatase or with two types of protein kinase. Dephosphorylation with the phosphatase increases binding capacity for single-strand DNA, but abolishes specificity of binding. Dephosphorylated R-protein binds equally to single and double-strand DNA. The capacity to facilitate denaturation or renaturation of DNA is also abolished by the treatment, but cooperativity characteristics are unaffected. The consequences of protein kinase treatment of native or dephosphorylated R-protein depend upon the origin of the kinase. Heterologous cyclic-AMP-dependent protein kinase cannot reverse the effects of dephosphorylation. However, it abolishes the binding affinity of either native or dephosphorylated R-protein for DNA. A protein kinase isolated from meiotic cells has no effect on the native protein, but it does restore all native properties tested to the dephosphorylated form after phosphorylating approximately two residues/molecule of protein.

Satellite DNA and heterochromatin variants: the case for unequal mitotic crossing over

Variations of constitutive heterochromatin (heteromorphisms) appear to be a general feature of eucaryotes. A variety of molecular and cytogenetic evidence supports the hypothesis that heteromorphisms result from unequal double-strand exchanges during mitotic DNA replication. Constitutive heterochromatin consists of highly repeated DNA sequences that are not transcribed. Thus, heteromorphisms are tolerated without overt phenotypic effect. Several of the highly repeated DNAs that comprise constitutive heterochromatin have been shown to contain site-specific endonuclease recognition sequences interspersed at regular intervals dependent upon nucleosome structure. These interspersed short repeated sequences could mediate unequal crossovers, resulting in quantitative variability of constitutive heterochromatin and satellite DNA. De novo variations of constitutive heterochromatin may be useful as markers of exposure to mutagens and/or carcinogens.

Side-by-side pairing of the XY bivalent in spermatocytes and the ubiquity of the H-Y locus

The pairing mechanism of the XY bivalent, the possibility of crossing-over between X and Y chromosomes during meiotic prophase, and the location of the H-Y locus are of interest with regard to genetic control mechanisms, male gametogenesis, and testicular organization. A whole-mount electron microscope technique has permitted the study of a large number of mouse and hamster spermatocytes to evaluate the spatial relationship of sex chromosomes and autosomes. X and Y chromosomes showed a transient, extensive side-by-side pairing segment along most of the length of the Y chromosome. This extensive pairing segment may cause genetic exchange between X and Y chromosomes. The finding of a small unpaired paracentromeric region of the Y chromosome could be related to a locus of totally sex-linked gene(s) that determine the development of the testis from the undifferentiated embryonic gonad.

Absence of satellite DNA synthesis during meiotic prophase in mouse and human spermatocytes

Mouse spermatocytes were labelled in situ with 3H-thymidine at successive stages of meiosis. Isolated mouse as well as human spermatocytes were similarly labelled under in vitro conditions. DNA synthesis was followed either by tracking radioactivities in Cs2SO4 gradients or by measuring reassociation kinetics. Mouse satellite DNA and the 3 satellites of human DNA are labelled during S-phase but not during pachytene. In the mouse genome, there is a preferential labelling of regions containing foldbacks (human spermatocytes were not analyzed in this respect). The absence of detectable pachytene synthesis in satellite DNA is consistent with genetic evidence on the absence of crossing-over in constitutive heterochromatin.