Question

Read the article below and answer the questions (article should be 1 page, 11-point font). The article is provided via the link below

https://web.natur.cuni.cz/zoologie/biodiversity/prednasky/EvolucniGenetika/clanky_2016/Transgenerational-epig-inheritance-Science-2016.pdf

Primary Paper HW assignment guideline

Your primary paper consists of three parts:

1. In your own words, state the essential take-home message of the paper assigned.

--Here you should briefly mention what was known about this topic before this paper was published

--Then state what the aim/goal/purpose of this published study was. In other words, what did the authors set out to do?

--Also describe why this research is important (if you think it is important)/ what are the researchers hoping to contribute to the existing knowledge.

2. State how the authors demonstrated the essential point of the paper: what experiments and what methods they used to prove the point

--In this section, you should link how a particular approach/method was used to obtain a particular result and why it would be important/relevant. For example:

--Authors used method A to get/show result B. Result B is important because (it supports their original hypothesis in the following way/describe how/ or it provides novel findings regarding mechanism X

--Continue the bulleted list to correlate specific method with the specific result and how it supports the claims made in the paper.

3. Discuss the strengths and significance of the paper and also the weaknesses and indicate additional lines of investigation that you think would be worth pursuing that were opened up by the paper.

--Here I want you to critique the experimental approach and author’s conclusions, not their writing style or format of the paper. Also, keep in mind that these are primary research articles published in scientific journals, so they are intended for a scientific, not general audience. Hence the language could be a bit dense.

--I want you to be very specific here. Do not write general and vague statements. Instead, refer to specific data in the paper (in figure X, or table Y) and indicate any possible flaws or limitations of the experiment.

--Propose possible future directions or follow up studies. You can look up papers that cited this research or follow up on the last author’s subsequent research.

--Explain if this paper contributed anything new to the field and if it enables a better understanding of the subject.

Answer 1

1. In your own words, state the essential take-home message of the paper assigned.

Epigenetic changes are also inherited just like genetics (or genes) are inherited, from the parents(in this study –paternal). And that a consequence (or consequences) of a change in the epigenetic make up induced in the parent can be seen in offsprings across many generations.

--Here you should briefly mention what was known about this topic before this paper was published

It was known that transmission of environmentally induced phenotypic traits is through epigenetic modification of the genome like histone medications, DNA methylation etc. These traits are associated with altered gene expression and tissue functions in first and second offspring which is known as trans or inter generational inheritance

--Then state what the aim/goal/purpose of this published study was. In other words, what did the authors set out to do?

Authors wanted to know the mechanism underlying the transmission of paternal epigenetics.

--Also describe why this research is important (if you think it is important)/ what are the researchers hoping to contribute to the existing knowledge.

The researchers were trying to pin point the exact molecular mechanism through which epigenetically induced phenotypic traits were transmitted across generations, paternally.

2. State how the authors demonstrated the essential point of the paper: what experiments and what methods they used to prove the point

They created a transgenic male mouse with over expressed KDM1A gene.

Human KDM1A histone lysine 4 demethylase gene was over expressed during mouse spermatogenesis which resulted in spermatozoa containing reduced dimethylation in histone H3 (H3K4me2) which is detrimental for the development and survival of the offspring.

Then they generated heterozygous transgeneic TG and non transgenic non TG brothers by mating the transgenic mice with C57BL/6 female mice. The TG and non TG brothers were mated with C57BL/6 female mice and the offsprings were tested for inter and transgenerational effects.

KDM1A overexpression in one generation was detrimental and it resulted in impairment of development and survival of the offspring. This effect lasted for 2 generation in non TG mice (transgeneration) and one generation in TG mice(intergeneration) which proved that an epigenetic change( here impairment of histone methylation) is carried onto offspring from father and an absence of this modification resulted in a mouse phenotype that is defective in development and survival, which appeared in inter and transgeneration offsprings.

3. Discuss the strengths and significance of the paper and also the weaknesses and indicate additional lines of investigation that you think would be worth pursuing that were opened up by the paper.

The authors were able to prove the transmission of epigenetic modification (that is responsible for a particular set of phenotypic traits) from father to offspring and to further generation. But it appears difficult to understand what exactly is the author’s definition of transgeneration and intergeneration. It is not clear whether TG and non TG offsprings all had developmental defects, if they had that is understandable since an absence of methylation in father’s genome means an absence of methylation in half of offspring’s genome. The effect should be more in TG offsprings because they are also carrying the transgene KDM1A.

It is also unclear that what kind of developmental defects are seen in the offsprings due to absence of H3Kme2 and since there was reduced survival then what was the survival rate?

The author's claim histone methylation as the potential underlying mechanism for paternal epigenetic inheritance. But they have tested only histone methylation in this study and concluding this is the mechanism underlying this inheritance does not make sense since they have not tested the paternal inheritance of other epigenetic modifications like DNA methylation, histone acetylation, phosphorylation etc across several generation.

--Propose possible future directions or follow up studies. You can look up papers that cited this research or follow up on the last author’s subsequent research.

It would have been easier to measure a non lethal phenotype that has been affected by epigenetic modification of its gene.

They can check for the H3Kme2 methylation levels in the offsprings across the generation and see how that is affected and inherited.