Environment & Gene Expression (HL) (HL IB Biology)

• Epigenesis is the development of differentiation patterns in the cells of multicellular organisms as it develops from a zygote
  • This is determined by the genome and patterns of gene expression in an organism
• Epigenetics is the genetic control by factors other than an individual’s DNA sequence
  • It involves heritable changes in gene function, without changes to the DNA sequence
• In eukaryotic cells, nuclear DNA is wrapped around proteins called histones to form chromatin
• Chromatin can be chemically modified in different ways to alter gene expression
  • Methylation of DNA (chemical addition of a -CH₃ group)
  • Histone modification of of amino acid tails via
    • Acetylation: Acetyl groups are added to histones which allows transcription as it leads to the DNA becoming more loosely packed
    • Methylation: The addition of a -CH₃ group
    • Phosphorylation: the addition of phosphate to an organic compound 
• Such modifications are called epigenetic tags and collectively, all the epigenetic tags in an organism are called the epigenome
• Like the genome, the epigenome is heritable
  • Mounting evidence demonstrates that modifications to the epigenome in one generation can be passed on to the next generation at cellular or whole organism level
• The phenotype of an organism is determined by its genotype
  • Since the DNA sequence is not changed by epigenetic changes, the genotype of an organism will remain the same while the phenotype changes

Differences between the genome, transcriptome and proteome of cells

• The proteome of an organism includes all the proteins synthesised within their cells and is determined by the genome
  
  • Each organism will have a unique proteome due to its unique set of genetic material
  • Different proteins are needed in different cell types, so only the genes responsible for expressing the correct proteins will be "switched on" at any particular time in a cell
  • This avoids energy wastage that would be caused by expressing all the genes in every cell
  • Therefore, the genome of each cell in an organism is the same while the proteome varies
• The range of mRNA transcripts produced within a cell or tissue type is known as its transcriptome
  • This in turn will be determined by the pattern of gene expression in the cell
  • The transcriptome will therefore result in certain proteins being synthesised

Proteome Diagram

The relationship between the genome, transcriptome and proteome in cells

• Nucleosomes are the structural unit of DNA packaging in eukaryotes that facilitate supercoiling
• Within a nucleosome, DNA is wrapped around proteins called histones
• The tails of histones can be chemically modified which can influence whether a gene will be expressed or not
  • One way in which histones may be modified is by adding a methyl group to the amino acids of the protein
  • This can either activate or deactivate genes by making the gene more or less accessible to transcription factors
  • Chemicals (such as methyl or acetyl groups) that regulate gene expression are called epigenetic tags
• Methyl groups can also be directly added to DNA to change the activity of a gene

Methylation of DNA

• DNA methylation commonly involves the direct addition of a methyl group (-CH₃) to cytosine bases of the promoter region which can influence gene expression
• Methylation of DNA suppresses the transcription of the affected gene by inhibiting the binding of transcription factors
• Cells use this mechanism to lock genes in the ‘off’ position
• DNA methylation can be affected by many environmental, lifestyle or age-related factors

Methylation of DNA at the promoter region is an example of how epigenetic tags may regulate gene expression

• When epigenetic tags (such as the methylation of DNA or histone tails) remain in place during mitosis or meiosis, then those modifications are passed on 
  • In the case of mitosis, this results in daughter cells containing the same epigenetic modifications as the parent cells
  • Meiosis will form gametes containing these epigenetic tags which will then be passed on to the offspring that develop when these cells are fertilised
• The inheritance of these epigenetic tags is known as epigenetic inheritance
  • This means that phenotypic changes resulting from epigenetic modifications can be inherited without changes in the nucleotide sequence of DNA occurring
• If epigenetic tags are removed during mitosis or meiosis, then epigenetic inheritance cannot take place