Posts Tagged ‘recombination’

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.

Source References:

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


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Reporter and Curator: Dr. Sudipta Saha, Ph.D.

Researchers have mapped out the entire genomes of 91 separate sperm cells donated by a 40 year old man. The results will allow scientists a closer view of the recombination process. Following single cell amplification of DNA in the sperm cells, the researchers genotyped each with the Illumina Omni1S Bead Array. Amplified DNA from eight more individual sperm cells was sequenced using the Illumina GAII or HiSeq 2000 to look at de novo mutation rates. At the genome level, recombination patterns in the sperm cells matched those predicted previously from Caucasian population and pedigrees and studies using cytology-based sperm testing, researchers reported, with each sperm cell showing almost 23 recombination events, on average. Likewise, recombination at the chromosome level, it was found that patterns similar to those described in the past, including an over-representation of recombination sites in telomeric chromosome regions and a dearth of recombination around chromosome centromeres. On the genome stability side, 7 percent of the sperm cells tested showed some signs of genome instability, including some sperm cells that were missing complete or partial chromosomes. Recombination is important because it means children develop completely new genetic codes and add to the diversity of the human race, which would not be the case if they inherited entire chromosomes from their parents. But problems in the process can result in sperm missing certain portions of genetic code or even entire chromosomes, potentially leading to infertility. Until now, such issues have been hard to diagnose. According to Prof Stephen Quake, who led the study published in the Cell journal, people have difficulty conceiving children due to reproductive disorders, and this will provide a very effective way to analyse when there are problems with their sperm. Examining individual sperm cells can reveal how often the blending of DNA has happened in each cell, and how the rate of recombination differs between people. Previous studies have only been able to estimate the rate of recombination at the level of whole populations, and could not reveal how often the process occurs in individuals. For the first time, it was possible to generate an individual recombination map and mutation rate for each of several sperm from one person. It may now be possible to look at a particular individual’s cells and comment about what they would likely contribute genetically to an embryo and perhaps even diagnose or detect potential problems. Further technological advances could allow the technique to be used to routinely screen men for reproductive problems, and to improve the success rate of fertility treatments. It is very interesting that what happens in one person’s body mirrors the population average. A futuristic idea would be to associate and correlate many such features to harmlessly identify healthy sperm for use in IVF. The DNA is the raw material that ultimately defines a sperm’s potential. The current sequencing technique involves the destruction of the sperm, but catching the cells just as they divide from one another could allow healthy cells to be identified without being killed. Researchers would then sequence the genome of one cell – destroying it in the process – but the results would enable them to determine the exact genetic properties of its “mirror” cell while allowing it to remain intact.

Resources that may be reviewed:

Stanford-led Team Produces Personal Recombination Map from Individual’s Sperm Cells


Entire Genetic Sequence of Individual Human Sperm Determined


We Are All Mutants: First Direct Whole-Genome Measure of Human Mutation Predicts 60 New Mutations in Each of Us


First Whole Genome Sequencing of Family of Four Reveals New Genetic Power


Sequencing Genome of Entire Family Reveals Parents Give Kids Fewer Gene Mutations Than Was Thought


Epigenetics May Be The Underlying Cause For Male Infertility


Genetic Alteration Linked With Human Male Infertility


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