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
http://www.genomeweb.com//node/1108291?hq_e=el&hq_m=1311723&hq_l=2&hq_v=e1df6f3681
Entire Genetic Sequence of Individual Human Sperm Determined
http://www.sciencedaily.com/releases/2012/07/120719132855.htm
We Are All Mutants: First Direct Whole-Genome Measure of Human Mutation Predicts 60 New Mutations in Each of Us
http://www.sciencedaily.com/releases/2011/06/110613012758.htm
First Whole Genome Sequencing of Family of Four Reveals New Genetic Power
http://www.sciencedaily.com/releases/2010/03/100310185541.htm
Sequencing Genome of Entire Family Reveals Parents Give Kids Fewer Gene Mutations Than Was Thought
http://www.sciencedaily.com/releases/2010/03/100310175141.htm
Epigenetics May Be The Underlying Cause For Male Infertility
http://www.sciencedaily.com/releases/2007/12/071212202006.htm
Genetic Alteration Linked With Human Male Infertility
http://www.sciencedaily.com/releases/2010/09/100930142713.htm
Dr. Saha, Thank you for this fascinating post on new directions in finding explanation for infertility in some cases when genetic factors are the cause.
Please connect this post with the linkedIn Groups. If I do it for you it shows your name But the attention is on me since my picture will show.
I do not wish to gain credit from work of others, I myself have posts which our team need to rate and comment on.
I am extremely impressed with your writing skills and also with the
layout on your blog. Is this a paid theme or did you modify it yourself?
Anyway keep up the excellent quality writing,
it’s rare to see a great blog like this one today.
Thank you for the comment above.
Indeed, Dr. Saha writes very well. This is a Scientific WebSIte in a NEW market niche, DBA, Scientific Web SIte (SWS). We are carving a new wide niche for ourselves on the spectrum between Open Scientific Journals and On-Line Scientific Publishing. We are better than both offering the PUBLIC and our Scientific Team the following advantages:
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My initial reaction was: Each of the sperm from the same man have to be different otherwise all his children wood be carbon copies as if cloned! Recombination offers the route to provide variations which help in evolution. Unfortunately, the same events can also usher in mutations. Of course these can affect fertility rate. I am, however, more worried about the “epimutation rates” which can be detrimental to the embryo or the new individual. The man may remain fertile with selected sperm but produce offspring with congenital defects! Epimutations can be a real problem during embryogenesis, even more than mutations which will get weeded out after selection of healthy sperm. The idea of reproduction is not limited to fertility alone but encompasses the production of a healthy, viable offspring. Otherwise, fertility is of no use! So, can this research also indicate the presence or absence of epimutations during the selection procedure for healthy sperm? Dr manjeet sharma (retired scientist/NIRRH, Mumbai, India)
Dr. Sharma,
Thank you for the insightful observations made in your comment above.
To great extend, one may assume that such research will facilitate and indicate the presence or absence of epimutations during the selection procedure for healthy sperm.
If, so, in reality, that very privileged “lab screening” of sperm per criteria od “wellness” prior to insemination is available only for couples or females subjected to the artificial insemination procedure in a Fertility Lab controlled environment.
All the Billions of mating individuals contribute to the large number of intercourses creating RANDOM and PoIson Processes of Exposure Events of embryogenesis.
Each event of one/more then one embryogenesis represents a statistically independent event as well as one conditional probabilistical EVENT with an EVENT Probability for the occurance of one/more than one Epimutation(s). Statistically speaking in large populations with great diversity, the probability of congenital defects is known, usually pretty low.
However, with increased longevity and exposure to environmental factors, mutations of genes occur during the ENTIRE life span, rather than just at birth, as a result of embryogenesis dysfunctional processes. Thus, gene related diseases are a fact of life and their prevalence increases every year while in most populations the incidence of epimutations is in decline.
This is indeed a very interesting report on a topic of great interest. It is not of limited interest because of the potential link to studying biological diversity.
Dr. Saha,
may be you wish to research and provide some statistics found in the literature to the points I made in my comment to Dr. Sharma. Edify us on this topic which brought wide readers and traffic to our website.
Thank you
Larrybhen, Thanks for the response. Still I have the following concerns:
During recombination, genetic material is exchanged in species-specific, fixed number of chiasmata. Genetic aberrations do occur at this time. Mutations can be introduced. Existing transgenerational epimutations can also be inherited at this time! Genome is no doubt important but epigenome is even more important in determining the fate of an embryo. Imprinting errors also get incorporated into the sperm epigenome, but at a later period. These make each sperm different. The accumulated epimutations produce effects in the embryo. If these are acquired by the embryo during development, consequent to drug exposure, these will also produce effects. All these epigenetic problems arise due to differential methylation pattern of the genome. So many dseases/disorders are known to occur due to imprinted gene defects. Exposure to bisphenol A has been shown to alter the methylation of agouti gene which gets permanently turned on and expresses the agouti peptide which acts on the skin cells and eventually lead to agouti skin color instead of the normal brown. Even if this epimutation is induced during embryogenesis, it is invariably inherited at the time of recombination. This would apply to many other potentially harmful epimutations since we are exposed to so many such environmental chemicals. It would thus be unwise to write these off as of low incidence! If the method can weed these out, it would be ideal for screening sperm of subfertile males.
Case history: I remember a weird divorce case between a german couple from my doctorate days in Europe. The couple produced a “black baby” instaed of a white one! Husband sued his wife for divorce on grounds of infidelity. Poor lady was not involved with anyone else. But the facts were going against her! I left for India but the case was still on. I dont know what was the end of it. Today, I am reminded of this case and am wondering if the real culprit could be the “epigenome” as has been seen in the case of agouti mice? Dr manjeet sharma
Dr. Sharma,
Thank you for your participation in the discussion following the post by Dr. Saha.
2012pharmaceutical is the ID of Aviva Lev-Ari, PhD, RN, Please read the ABOUT for this web site.
I have responded above earlier in the discussion.
While genomic information is uniform in the different cells of complex organisms, the epigenome controls the differential expression of genes in specific cells. The programming of gene expression profiles is therefore dependent on the epigenome. The epigenome is composed of two modules, a component that is part of the covalent structure of DNA, methylated cytosines located in the dinucleotide sequence CG and a noncovalent module. Our understanding of the noncovalent module of the epigenome the chromatin and its associated chromatin modifying and remodeling activities is rapidly expanding in recent years (Strahl and Allis, 2000). It is now becoming clear that modifications of histones and their tails by acetylation, phosphorylation, and methylation plays an important role in determining the positioning of nucleosomes on DNA and the compactness of chromatin. Chromatin structure determines the state of activity of genes by gating the access of the transcription machinery to transcriptional regulatory regions. Chromatin structure plays a role in other genomic activities such as recombination and repai. Changes in chromatin structure play an important role in the silencing of certain genes in cancer and histone deacetylase inhibitors have demonstrated anticancer effect.
Some researchers have devised affinity-based methods to detect hydroxy-methylation, but the problems with those approaches are that they generally can’t precisely pinpoint which base is hydroxymethylated, nor can they pinpoint how much hydroxy-methylation there is, Hon says. These methods are also prone to sequence bias.
To address these problems, Hon, along with his UCSD colleagues, and their collaborators at the University of Chicago and Emory University devised a new method based on bisulfite sequencing that is able to tell the difference between methylation and hydroxymethylation. They described their method, called TAB-seq, in Cell in May. In bisulfite sequencing, says Chicago’s Chuan He, 5-methyl-cytosine is distinguished from regular cytosine through the process of deamination, which turns all un-methylated cytosine into uracil.
TAB-seq protects the hydroxyl group with a sugar residue and then performs an oxidation step, so that all methyl-cytosine is converted to carboxylcytosine. This way, he adds, when deamination is performed, the newly converted carboxyl-cytosine is turned into uracil like the other cytosine, and all that is left is 5-hydroxymethyl-cytosine. “What the method provides is a way to carefully examine whether this is really methyl-C or hydroxymethyl-C, because they may have different implications for disease and treatment,” He says. “The method is general. You can do it on the whole genome, or more likely people will use it in a loci-specific manner.”
Hon adds that two groups of researchers — both those studying hydroxy-methylation and methylation — will be able to use TAB-seq: the first group to understand hydroxymethylation and the second group to make sure the purported methylation they are studying isn’t also mixed in with hydroxymethylation. ”This is the missing link we’ve needed to not only further dissect the function of 5-hydroxy-methylation but also to correctly interpret what we previously thought was DNA methylation,” he adds.
http://www.linkedin.com/groups/Researchers-Develop-Method-Tell-Methylation-4346921%2ES%2E137693234?qid=d99bbe86-a032-4ee4-a801-f476579fbf6d&trk=group_items_see_more-0-b-ttl
“It tells us that treating cancer will be far more complex than we imagined, as it will first involve understanding and reversing epigenetic change.”
The findings are timely in that they coincide with very recent events and publications that have brought the concepts of the ‘epigenome’ and ‘epigenetics’ into world focus. In January 2010 the International Human Epigenome Consortium (IHEC) was launched in Paris (with Professor Clark on the interim steering Committee). Time magazine ran a feature on epigenetics in January, and Nature published two articles on the subject this month: one addressing the importance of IHEC and the urgency of pooling international mind power and resources; the other describing the infinite complexity of the project – orders of magnitude more challenging than the Human Genome Project.
The ultimate aim of IHEC is to produce a map of the human epigenome. The initial intention is to map 1,000 epigenomes within a decade. This will provide a healthy tissue base against which to compare the epigenomes of diseased tissue.
The Human Genome Project, completed in March 2000, found that the human genome contains around 25,000 genes. It took 3 billion US dollars to map them.
We do not yet know how many variations the human epigenome is likely to contain – certainly millions – as a single person could have many epigenomes in a lifetime, or even in a day. The technological advances and computational power necessary to map the epigenome, therefore, remain incalculable.
The project at Garvan involved an initial bioinformatics phase; a comparative tissue analysis phase; and a data analysis phase.
http://www.news-medical.net/news/20100224/Gene-expression-in-prostate-cancer-cell-more-complex-than-ever-imagined.aspx
Regarding the Black baby of the German couple — I believe that it is not
epigenetics but that an ancestry or either the husband or the wife who had an encounter in the past that was interracial in nature.
Thanks for the long and elaborate explanations. I am glad that efforts are on to map the human epigenome or epigenpomes, as you have rightly put. In fact, it brings to my mind the title of a recent article that I came across and liked” THERE IS A GENIE IN YOUR GENES”. There has to be a genie to have so may variations of the epigenome. The important think to remember is that, at least here in Indi as also in other parts of the world, people are exposed to many toxic chemicals from plastics bottles and polluted water etc which can activate this genie! Which means that screening of the sperm becomes all the more important. Dr manjeet sharma
While I do agree about the importance of “screening sperms” — I am at the same time in full rejection of the concept of supporting a revival of Eugenics.
The First International Eugenics Congress (1912)
http://en.wikipedia.org/wiki/International_Eugenics_Conference
Thank you for your informative, educative and exhaustive considered response. I am glad the epigenome mapping is being undertaken. But there are many epigenomes to a single genome! Genie sure knows its job!
Some time back I got this literature from ACTIVE MOTIF which I hope can be useful towards this aim. I too would like to know what is the significance of hydroxymethylation of cytosines. Would these be more permanent marks which cannot be removed and serve as landmarks since there are a whole lot of rogue jumping genes in there? In that case this mechanism would be helpful in reducing the occurrence of mutations? Or maybe there is another explanation and that there are some binding molecules which need this type of conformation to sit on DNA. I will wait for this epigenetic mystery to be solved. This can be very important for cancers, as you say. And if sperm can carry it across to the next generation (transgenerational) it needs to be understood.
ACTIVE MOTIF
Hydroxymethyl Collector™
biotin-based enrichment of 5-hydroxymethylcytosine
The Hydroxymethyl Collector™ Kit is designed to detect and capture DNA fragments containing 5-hydroxymethylcytosine (5-hmC) DNA methylation*. The Hydroxymethyl Collector kit utilizes a β-glucosyltransferase enzyme to transfer a modified glucose moiety to 5-hydroxymethylcytosine residues in double-stranded DNA. This modified glucose is then used to chemically attach a biotin conjugate for capture and enrichment with streptavidin magnetic beads. Enriched DNA can be used in the analysis of individual genes by PCR, or in combination with microarrays and sequencing for geome-wide analysis of 5-hydroxymethylcytosine.
By utilizing chemical labeling of 5-hmC residues, the Hydroxymethyl Collector Kit is extremely specific in its capture of hydroxymethylated DNA fragments. The biotin-streptavidin binding reaction also allows for stringent binding and wash conditions to reduce any non-specific background. The technique is sensitive enough to enrich DNA fragments containing two or more 5-hmC residues.
Advantages
No cross-reactivity with 5-mC
Detection of non-CpG methylation
Stingent binding ensures lower background
No antibody variability concerns
Procedure completed in under 4 hours
* Song, C.X., et al., Nature Biotechnology. 29, 68-72 (2011).
Patent pending
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May I request Dr. Larry Bernstein to address last comment by Dr. Sharma.
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