The centenary of Janssens's chiasmatype theory

Meiosis through three centuries

Meiosis is the specialized cellular program that underlies gamete formation for sexual reproduction. It is therefore not only interesting but also a fundamentally important subject for investigation. An especially attractive feature of this program is that many of the processes of special interest involve organized chromosomes, thus providing the possibility to see chromosomes "in action". Analysis of meiosis has also proven to be useful in discovering and understanding processes that are universal to all chromosomal programs. Here we provide an overview of the different historical moments when the gap between observation and understanding of mechanisms and/or roles for the new discovered molecules was bridged. This review reflects also the synergy of thinking and discussion among our three laboratories during the past several decades.

Meiosis: Dances Between Homologs

The raison d'être of meiosis is shuffling of genetic information via Mendelian segregation and, within individual chromosomes, by DNA crossing-over. These outcomes are enabled by a complex cellular program in which interactions between homologous chromosomes play a central role. We first provide a background regarding the basic principles of this program. We then summarize the current understanding of the DNA events of recombination and of three processes that involve whole chromosomes: homolog pairing, crossover interference, and chiasma maturation. All of these processes are implemented by direct physical interaction of recombination complexes with underlying chromosome structures. Finally, we present convergent lines of evidence that the meiotic program may have evolved by coupling of this interaction to late-stage mitotic chromosome morphogenesis.

Evolution of crossover interference enables stable autopolyploidy by ensuring pairwise partner connections in Arabidopsis arenosa

Polyploidy is a major driver of evolutionary change. Autopolyploids, which arise by within-species whole-genome duplication, carry multiple nearly identical copies of each chromosome. This presents an existential challenge to sexual reproduction. Meiotic chromosome segregation requires formation of DNA crossovers (COs) between two homologous chromosomes. How can this outcome be achieved when more than two essentially equivalent partners are available? We addressed this question by comparing diploid, neo-autotetraploid, and established autotetraploid Arabidopsis arenosa using new approaches for analysis of meiotic CO patterns in polyploids. We discover that crossover interference, the classical process responsible for patterning of COs in diploid meiosis, is defective in the neo-autotetraploid but robust in the established autotetraploid. The presented findings suggest that, initially, diploid-like interference fails to act effectively on multivalent pairing and accompanying pre-CO recombination interactions and that stable autopolyploid meiosis can emerge by evolution of a “supercharged” interference process, which can now act effectively on such configurations. Thus, the basic interference mechanism responsible for simplifying CO patterns along chromosomes in diploid meiosis has evolved the capability to also simplify CO patterns among chromosomes in autopolyploids, thereby promoting bivalent formation. We further show that evolution of stable autotetraploidy preadapts meiosis to higher ploidy, which in turn has interesting mechanistic and evolutionary implications.

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In a neo-autotetraploid, aberrant crossover interference confers aberrant meiosis

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In a stable autotetraploid, regular crossover interference confers regular meiosis

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Crossover and synaptic patterns point to evolution of “supercharged” interference

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Accordingly, evolution of stable autotetraploidy preadapts to higher ploidies

Let's get physical - mechanisms of crossover interference

The formation of crossovers between homologous chromosomes is key to sexual reproduction. In most species, crossovers are spaced further apart than would be expected if they formed independently, a phenomenon termed crossover interference. Despite more than a century of study, the molecular mechanisms implementing crossover interference remain a subject of active debate. Recent findings of how signaling proteins control the formation of crossovers and about the interchromosomal interface in which crossovers form offer new insights into this process. In this Review, we present a cell biological and biophysical perspective on crossover interference, summarizing the evidence that links interference to the spatial, dynamic, mechanical and molecular properties of meiotic chromosomes. We synthesize this physical understanding in the context of prevailing mechanistic models that aim to explain how crossover interference is implemented.

A rigorous measure of genome-wide genetic shuffling that takes into account crossover positions and Mendel's second law

Comparative studies in evolutionary genetics rely critically on evaluation of the total amount of genetic shuffling that occurs during gamete production. Such studies have been hampered by the absence of a direct measure of this quantity. Existing measures consider crossing-over by simply counting the average number of crossovers per meiosis. This is qualitatively inadequate, because the positions of crossovers along a chromosome are also critical: a crossover toward the middle of a chromosome causes more shuffling than a crossover toward the tip. Moreover, traditional measures fail to consider shuffling from independent assortment of homologous chromosomes (Mendel's second law). Here, we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations. We define the parameter [Formula: see text] as the probability that the alleles at two randomly chosen loci are shuffled during gamete production. This measure can be decomposed into separate contributions from crossover number and position and from independent assortment. Intrinsic implications of this metric include the fact that [Formula: see text] is larger when crossovers are more evenly spaced, which suggests a selective advantage of crossover interference. Utilization of [Formula: see text] is enabled by powerful emergent methods for determining crossover positions either cytologically or by DNA sequencing. Application of our analysis to such data from human male and female reveals that (i) [Formula: see text] in humans is close to its maximum possible value of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortment, the contribution of which is ∼30 times greater than that of crossovers.

Inheritance of Chromosomes, Sex Determination, and the Human Genome

Who is the determining factor for the sex of the offspring—mother, father, or both parents? This fundamental hypothesis proposes a new model of sex determination, challenging the existing dogma that the male Y chromosome of the father is the sole determinant of the sex of the offspring. According to modern science, the 3 X chromosomes (male XY and female XX) are assumed to be similar, and the sex of the offspring is determined after the zygote is formed. In contrast to this, the new hypothesis based on theoretical research proposes that the 3 X chromosomes can be differentiated, based on the presence of Barr bodies. The first X in female XX chromosomes and X in male XY chromosomes are similar as they lack Barr body and are hereby denoted as ‘X’ and referred to as ancestral chromosomes. The second X chromosome in the female cells which is a Barr body, denoted as X, is different. This X chromosome along with the Y chromosome are referred to as parental chromosomes. Sperm with a Y chromosome can only fuse with an ovum containing the ‘X’ chromosome. Similarly, sperm with the ‘X’ chromosome can only fuse with an ovum containing the X chromosome. Cell biology models of gametogenesis and fertilization were simulated with the new hypothesis model and assessed. Only chromosomes that participated in recombination could unite to form the zygote. This resulted in a paradigm shift in our understanding of sex determination, as both parents were found to be equally responsible for determining the sex of the offspring. The gender of the offspring is determined during the prezygotic stage itself and is dependent on natural selection. A new dimension has been given to inheritance of chromosomes. This new model also presents a new nomenclature for pedigree charts. This work of serendipity may contribute to future research in cell biology, gender studies, genome analysis, and genetic disorders including cancer.

Systematic identification of long non-coding RNAs with cancer-testis expression patterns in 14 cancer types

Cancer-testis (CT) genes are a group of genes that are potential targets of immunotherapy and candidate epi-drivers participating in the development of cancers. Previous studies mainly focused on protein-coding genes, neglecting long non-coding RNAs with the same expression patterns. In this study, we performed a systematic investigation of cancer-testis long non-coding RNAs (CT-lncRNAs) with multiple independent open-access databases.We identified 1,325 extremely highly expressed CT-lncRNAs (EECT-lncRNAs) in 14 cancer types. Functional annotation revealed that CT-lncRNAs reactivated in cancers could promote genome instability and the malignant potential of cancers. We observed a mutually exclusive pattern of EECT-lncRNA activation and mutation in known oncogenes, suggesting their potential role as drivers of cancer that complement known mut-driver genes. Additionally, we provided evidence that testis-specific regulatory elements and promoter hypo-methylation may be EECT-lncRNA activation mechanisms, and EECT-lncRNAs may regulate CT gene reactivation. Taken together, our study puts forth a new hypothesis in the research field of CT genes, whereby CT-lncRNAs/EECT-lncRNAs play important roles in the progression and maintenance of tumorigenesis, expanding candidate CT epi-driver genes from coding genes to non-coding RNAs.

The Evolving Definition of the Term "Gene"

This paper presents a history of the changing meanings of the term "gene," over more than a century, and a discussion of why this word, so crucial to genetics, needs redefinition today. In this account, the first two phases of 20th century genetics are designated the "classical" and the "neoclassical" periods, and the current molecular-genetic era the "modern period." While the first two stages generated increasing clarity about the nature of the gene, the present period features complexity and confusion. Initially, the term "gene" was coined to denote an abstract "unit of inheritance," to which no specific material attributes were assigned. As the classical and neoclassical periods unfolded, the term became more concrete, first as a dimensionless point on a chromosome, then as a linear segment within a chromosome, and finally as a linear segment in the DNA molecule that encodes a polypeptide chain. This last definition, from the early 1960s, remains the one employed today, but developments since the 1970s have undermined its generality. Indeed, they raise questions about both the utility of the concept of a basic "unit of inheritance" and the long implicit belief that genes are autonomous agents. Here, we review findings that have made the classic molecular definition obsolete and propose a new one based on contemporary knowledge.

Robert Heath Lock and his textbook of genetics, 1906

Robert Heath Lock (1879-1915), a Cambridge botanist associated with William Bateson and R. C. Punnett, published his book Recent Progress in the Study of Variation, Heredity, and Evolution in 1906. This was a remarkable textbook of genetics for one appearing so early in the Mendelian era. It covered not only Mendelism but evolution, natural selection, biometry, mutation, and cytology. It ran to five editions but was, despite its success, largely forgotten following Lock's early death in 1915. Nevertheless it was the book that inspired H. J. Muller to do genetics and was remembered by A. H. Sturtevant as the source of the earliest suggestion that linkage might be related to the exchange of parts between homologous chromosomes. Here we also put forward evidence that it had a major influence on the statistician and geneticist R. A. Fisher at the time he was a mathematics student at Cambridge.

Reginald Crundall Punnett: first Arthur Balfour Professor of Genetics, Cambridge, 1912

R. C. Punnett, the codiscoverer of linkage with W. Bateson in 1904, had the good fortune to be invited to be the first Arthur Balfour Professor of Genetics at Cambridge University, United Kingdom, in 1912 when Bateson, for whom it had been intended, declined to leave his new appointment as first Director of the John Innes Horticultural Institute. We here celebrate the centenary of the first professorship dedicated to genetics, outlining Punnett's career and his scientific contributions, with special reference to the discovery of "partial coupling" in the sweet pea (later "linkage") and to the diagram known as Punnett's square. His seeming reluctance as coauthor with Bateson to promote the reduplication hypothesis to explain the statistical evidence for linkage is stressed, as is his relationship with his successor as Arthur Balfour Professor, R. A. Fisher. The background to the establishment of the Professorship is also described.