This is a very interesting threat but from the OP until know it seems the discussion is only on epigenetics and not all of the different types of mutations. I will keep on the topic of epigenetics since the research I conduct is closely related to epigenetics, and I am interested in many aspects of non-Mendelian inheritance. So, I thought I would add an real example of an epigenetic phenomenon to help clarify any misunderstandings on epigenetics.
Methylation and histone modification are not the only sources of epigenetic effects. Some unicellular
eukaryotic organisms called
ciliates have a cool way of regulating DNA expression through epigenetic phenomenon. I will define epigenetics as reversible, heritable changes in gene regulation that do not change the genotype or the organism. What this means is that gene regulation is modified by some affect outside of the genome and this regulation can be passed on to other generations.
The ciliate
Paramecium like all ciliates contain at least two nuclei. Remember the nucleus is where the genetic information of the organism is stored so you can say that ciliates have more than one genome. There is the germ-line nucleus where the genome goes through meiosis and mitosis during sexual reproduction and there is the somatic nucleus that is transcriptionally active.
Paramecium can only multiply through asexual reproduction, but during stressful environments, such as starvation,
Paramecium will go through sexual conjugation with another
Paramecium. It is thought this occurs so recombination can take place and genetic variation will increase thus allowing the organism more chance to survive in the stressful environment.
Paramecium have two mating types. A mating type can be thought of sexes and only opposite mating types can mate with each other. So, as humans have females and males,
Paramecium has O and E mating type. During this sexual reproduction the transcriptionally inactive germ-line nucleus goes through meiosis. Meiosis is a process in which a diploid nucleus is divided into a haploid nucleus. So now there are 2 haploid germ-line nuclei. Conjugation of O and E
Paramecium cells take place and one haploid germ-line nuclei is exchanged with the other cell. Now each
Paramecium cell has one native haploid germ-line nucleus and one foreign germ-line nucleus. These haploid germ-line nuclei fuse creating a new germ-line nucleus. Notice that both conjugating cells have the exact same genotype in the germ-line nucleus now.
So what goes on during the somatic nucleus during sexual conjugation? This is a very important question as it is the somatic nucleus that creates the phenotype since it is the only transcriptionally active nucleus in the organism. This is the nucleus that produces has its genome transcribed (mRNA is produced), and translated (proteins are produced).
After sexual conjugation and the formation of a new germ-line nucleus, the germ-line nucleus goes through mitosis, a process in which the diploid nucleus is duplicated. Now there are two germ-line nuclei and one somatic nucleus. The somatic nucleus is then degraded one of the germ-line nuclei goes through genome processing to become a somatic nucleus. During this processing the chromosomes in the genome are broken apart into pieces, there is deletion of specific sequences in the genome, and each new pieces of the chromosomes are amplified to a certain number. Sexual reproduction is complete as there is a new germ-line and somatic nucleus.
The cell can then go through asexual reproduction to form two daughter cells. It was expected that after sexual conjugation of O and E mating types that the cells should now produce the same mating type daughter cells after asexual reproduction, but this is not what was found by observation. What was found was that O mating type only produced O mating type daughter cells and E mating type only produced E daughter cells. So this mating type is not inherited Mendelianly.
It was found that mating type was determined by two differential states of the somatic nucleus. Mating type E is caused by a gene being present in the somatic nucleus, while O mating type is caused by the absence of the mating type E gene.
Saving you from the methods but you can read in Meyer 2002 (link below) it was found that during there are epigenetic affects during the development of the somatic nucleus from the germ-line nucleus. During this development the entire genome of the germ-line nucleus is transcribed into RNA, which is then transported into the old somatic nucleus. Remember that the somatic nucleus is made from the germ-line nucleus except that it has many copies of broken up chromosomes, and that these chromosomes are missing pieces that are found in the germ-line nucleus. These RNA molecules then bind in a sequence specific manner to complementary DNA in the old somatic nucleus. RNA that binds is degraded and the RNA that does not bind (since the old somatic nucleus is missing DNA that the germ-line nucleus has) is transported to the new developing somatic nucleus. The left over RNA binds to complementary DNA in the developing somatic nucleus and any DNA it binds to is deleted.
This deletion step is why there are two mating types in
Paramecium. A O mating type
Paramecium could have an epigenetic mutation in which the deleting RNA molecule base sequence is not exactly complementary to the E mating type gene that is found in the developing somatic nucleus and not delete it from the somatic nucleus genome. This lack of deletion will cause the E mating type gene to be present in the somatic nucleus and thus expression of the E mating type gene causing the E mating type phenotype. The reverse could happen to create the the O mating type from the original E mating type genome.
So in summary the mating types of
Paramecium is affected by epigenetics. The underlining genotype of the germ-line nucleus has not changed but the expression of the genome has.
I hope this helps others to understand epigenetics without having to understand methylation and histone modification, things that I am not to familiar with and that put me to sleep. If clarification is needed let me know and I can post some pictures from the below sources.
I'm feeling a thread devoted to epigenetics and its role in evolution should be started as this is a very actively pursued research topic in evolutionary biology.
Sources:
Meyer 2002 may need academic institution to access, email me for a copy. This is a 33 page review.
Mochizuki and Gorovsky same epigenetic action in another ciliate
Paper I wrote on this subject in a graduate course on Non-Mendelian inheritance
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