GEN 7`: Expressing the Genome Flashcards
Observe the learning outcomes of this session

What is gene expression?
- the process by which the information from a gene is used to synthesise a functional gene product
- either a protein or a functional RNA
Label the structure of a protein-coding gene


Fill the missing gaps about gene expression


Define transcription factor
- a sequence-specific DNA binding molecule (typically a protein) that binds at or close to the core promoter and influences the efficiency of transcriptional initiation
What is DNA helicase?
- a subunit of TFIIH that uses energy from the hydrolysis of ATP to open up the DNA double helix, allowing RNA polymerase II to have access to the template strand
What is the transcriptome?
- the total complement of RNA molecules (or transcripts) produced in a specific cell or in a population of cells comprising a tissue
Recap some ways to measure gene expression?

Before RNA polymerase II can be recruited to express a gene, what must happen to chromatin first?
How does that happen?
- the region of chromatin must first become accessible
- this is partly achieved by chromatin-modifying enzymes
- in mammals, the most common DNA modification that contributes to the regulation of transcription is DNA methylation, which occurs at the five carbon position of the cytosine ring, resulting in 5-methylcytosine.

How do methyl groups affect DNA transcription?
- methyl groups distort the DNA double helix, inhibiting transcription

What do CpG sites stand for?
- They stand for 5’—C—phosphate—G—3’, simply referring to a cytosine residue immediately upstream of a guanine.
- The human genome contains ∼30,000 CpG islands (CGIs), which are stretches (0.5–2 kb) of DNA with a greater frequency of CpG dinucleotides than the rest of the genome.
How much of the human genomic DNA is 5-methylcytosine?
- approx. 1.5%
What happens when a CpG island is methylated or unmethylated?
- When a CpG island in the promoter region of a gene is methylated, expression of the gene is usually silenced.
- Conversely, many CGIs occur at gene promoters, and their DNA nearly always remains unmethylated, thus allowing gene expression to occur.
Observe this image of CpG dinucleotides and C-G base-pairs

Compare CGI and non-CGI genomic sequences


Observe this diagram of how CGI methylation affects gene expression


What is genomic imprinting?
- genomic imprinting is a form of epigenetic inheritance
- this is where DNA methylation ensures only one parental allele is expressed
- when the paternal allele is expressed, the maternal copy is silences and vice versa
Describe Prader-Willi Syndrome, a disorder involving genetic imprinting
- is often caused by deletion of a region on chromosome 15 that includes the gene SNRPN.
- This occurs in the paternal chromosome after the maternal SNRPN allele has already been silenced by imprinting, leaving no expression of SNRPN.
- In PWS, patients suffer from extreme feeding problems, including hyperphagia, or extreme, insatiable appetite and obsession with food
- Affected children are also developmentally delayed for motor skills due to decreased muscle tone.

Describe Angelman syndrome
- caused by loss of expression in a region of chromosome 15
- In this case it is usually caused by loss of the maternal allele when the paternal allele has been silenced by imprinting
- In this syndrome, loss of the gene UBE3A results in disorder of the nervous system characterised by developmental disabilities, seizures, speech deficits, and motor oddities.
Look at the diagram of histone H3 and summarise the key modifications on it

- acetylation of lysine 27:
- promotes gene transcription
- methylation of lysine 27:
- or commonly tri-methylation, suppresses transcription and results in large regions of inactive chromatin
- methylation of lysine 9:
- di- or tri-methylation of H3 lysine 9 silences gene promoters and prevents transcription
- methylation of lysine 4:
- tri-methylation of histone H3 lysine 4 results in active promoters and gene expression
What can chromatin folding do?
- it can enhance transcription
Explain the chromatin loop

- part of the chromosomal folding process and allows contact to be made over large genomic distances between regulatory sequences (enhancers) and gene promoters
- tissue-specific enhancers are evolutionary conserved regions (ECRs) that are often located hundreds of kb away from their core promoters
Look at this diagram and explain what TAD is

- they are Topologically Associating Domains (TAD)
- they are self-interacting genomic regions
- the genes within a TAD are brought together in a cell-specific manner to confer specific gene expression patterns that characterise phenotype
- they comprise the majority of characterised enhancer-promoter pairs
- they are conserved among species, cell types and tissues, highlighting their biological relevance
Observe this diagram and explain what chromosomal compartments are

- chromosomes display a non-random organisation within the nucleus, influenced by their gene density and transcriptional status
- the exist in active ‘A’ compartments towards the interior of the nucleus or in inactive ‘B” compartments towards the periphery








