Reporter and Curator: Dr. Sudipta Saha, Ph.D.
Gametogenesis is a biological process by which precursor cells undergo cell division and differentiation to form mature haploid gametes. Human gametogenesis occurs by mitotic division of gametogonia, followed by meiotic division of gametocytes into various gametes. During this process, the gamete genome experiences both programmed and spontaneous changes, among which meiotic recombination shuffles the two haploid somatic genomes to create a unique hybrid haploid genome for each gamete cell, while accumulated replication errors contribute point mutations that may affect the gametes’ functionality. This results in an enormous variety of new genomes being created in the gametes, thereby enabling one’s children to add to the genetic diversity of the human race in a more complex manner than by simply mixing and matching entire parental chromosomes. The genome-wide recombination activity and de novo mutation rate have been directly characterized in many model organisms. However, it has been unclear how an individual human’s genome is edited during gametogenesis. Despite the advances in personal genomics, gamete genome variation within individuals, especially fine-scale personal recombination activity and germline mutation rates, has been as yet generally inaccessible.
An important feature of single molecule multiple displacement amplification (MDA) is its repetitive usage of the originating genuine template molecule. Even if an amplification error happens in the initial stage, there will still be a large fraction of products preserving the correct base information from the original template, and the power of statistics from multiple coverage discriminates these errors from true genomic variation. Using this microfluidic MDA approach, for the first genome-wide single-cell analysis of human sperm was reported. A personal recombination map was created for an individual to measure the rate of de novo mutations in this individual’s germline. The advantage of sampling a large set of meioses from a single individual for fine-scale analysis allowed to uncover individual specific features potentially buried under population data. It was proposed that this partially overlapping feature is also the general pattern in individuals. While some hot spots are dying in some people, new recombination activities evolve to refill the hot spot pool. Support for this theory comes from single-cell analysis. Recombination data from 91 single sperm cells presented a comprehensive landscape of personal recombination activity. Genome-wide meiotic drive and gene conversion were also directly tested. Single-cell whole-genome sequencing further revealed primary information about human sperm genome instability and mutation rate. In this study, microfluidics to single-cell whole genome amplification was applied. This technique not only enabled great parallelization, but also improved amplification performance. MDA is sensitive to environmental contamination, and extensive sample purification is required for traditional bench-top whole genome amplifications.
The data from this study suggested that the germline mutation rate can vary greatly among different individuals, but not among different cells from the same individual. This may explain why the male mutation rate is not always higher than the female. DNA methylation also affects genome instability and C/T point mutation levels but in opposite ways. A fine tuned methylation level is therefore required for high-quality sperm genome. The ability to study a large number of single sperm cells has offered several new insights in meiosis. Studying the germline genome is but one application of single-cell genomics, and it is expected that the method will find applications in many other fields, including cancer, aging, immunology, and developmental biology.
Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm.
Personal Recombination Map from Individual’s Sperm Cell and its Importance