Development and Growth of Farm Animals Hw 1

Homework #1

1. Define “Epigenome.”

The epigenome is all of the markers or tags, such as methyl groups, that are added to various parts of the DNA or histones that regulate gene expression without changing the gene sequence. The tags that inhibit or promote gene transcription or expression and result in differentiation between cells, ages, breeds, and individuals are what makes up an epigenome.

1. What argument does Helene Jammes provide for studying epigenetics in livestock?

She says that understanding epigenetics and its process and mechanisms allows us to understand how the environment is affecting our livestock and their performance. If we understand how the environment is affecting the animals, we can make changes in how the livestock animals are raised. Making changes in their environment will then increase good performance and ensure the optimum gene expression and potential of the animals.

1. Genomes and epigenomes

1. What different mechanisms of gene regulation are mentioned in the report that result in different cell types? What are other mechanisms from lecture?

Regulatory proteins that attach to the promoter or regulatory regions of genes upstream of the genes to be transcribed – these control whether the downstream genes are transcribed or not.

Chemical modification of DNA or histones by adding a chemical marker through methylation or acetylation – these can activate or inhibit gene expression.

        Regulation via non-coding RNA – micro RNA that bind to mRNA and block the production of proteins. It suppresses gene expression. There is also the si-RNA that is silencing RNA for micro RNA and creates a knockout gene.

        Regulation can be transcriptional, posttranscriptional, translational, and posttranslational.

        There can also be changes in the gene sequence, but this is different from the regulation of genes.

1. What is epigenetic reprogramming?

A methylation-demethylation process during fertilization and development. The demethylation of epigenetic tags from the parent cells during gamete formation and re-methylation of gamete-specific tags. Then, after fertilization, the demethylation of the gamete-specific tags so that the methylation of the individual’s epigenome over time can occur.

1. How did William Harvey define “epigenesis?”

The progressive appearance of organs during development. (Different fetal stages/development).

1. What different types of epigenetic tags to DNA and histones are known?

DNA methylation adds tags of methyl groups to promoter regions to inhibit expression and coding regions to encourage expression. A recently discovered mechanism of tagging is 5-hydroxymethylation. Histones can also be tagged with methylation, acetylation, phosphorylation, and ubiquitination to condense and inhibit gene expression or open and promote it. Noncoding RNA sequences can also methylate outer structures of DNA or modify the histones to regulate gene expression.

1. What is meant by “epigenetic inheritance?”

When epigenetic tags are transferred from one generation to the next. Usually occurs when the epigenome of a pregnant mother is affected due to changes in the environment. These changes are then passed to the fetus even though they have not been exposed directly to the stimulus of the epigenome tag.

1. What effects following a change in the pattern of epigenetic tags have been described for dairy cows?

Reduced milk production due to chromatin with genes coding for milk proteins becoming more compact if stimulated by mastitis. Reduction in milk production due to a reduced amount of mRNA coding for milk proteins because of hypermethylation if stimulated by once a day milking. Reduced meat tenderness due to stress. Reduction of offspring fertility if dietary needs of mother are not met. Lower milk yield in offspring is mother is milked regularly while pregnant.

1. What is meant by “dietary conditioning” in aquaculture?

Feeding fish certain diets, such as plant-based diets, at early developmental stages, like the alevin stage, so that they can gain the epigenetic tags that allow them to eat and metabolize the same type of food as an adult. This results in more efficient, cheaper, and greener feeding.

1. Broilers

1. What is meant by “thermal conditioning”?

Exposing eggs of the broiler chickens to high temperatures cyclically – 39.5 degrees Celsius 12 hours a day from the seventh to sixteenth day after laying. This applies epigenetic tags and allows the broilers to tolerate higher temperatures after hatching.