Genes, Genomes, and transposable elements

Lecture

What is a genome?

the entirety of an organisms hereditary information

All DNA in organism cell

What is the genome of eukaryotes composed of?

coding (islands) and non-coding (open ocean) DNA

What makes the difference in genome size?

the amount of non-coding DNA

What are introns (intragenic genes)?

non-coding DNA

they separate the exons and are spliced out during mRNA processing

What are exons (intergenic genes)?

coding DNA or the Open Reading Frame (ORF) - what starts or stops protein synthesis

What percent of the genome do coding sequences make up?

3%

What is a gene?

the entire nucleic acid sequence that is necessary for the synthesis of a functional product (protein or RNA)

genes are transcribed

Describe the transcription unit - what does it contain?

Region in DNA bounded by an initiation (start site) and termination site, that is transcribed into a single primary transcript

control region: controls how far RNA polymerase goes (how far synthesis goes)

Cap Site

Exons 

Introns 

Poly A site

What does mRNA contain?

contains only the exons regions which are then stuck together

What is the control region?

promoter and cis-regulatory factors

guides transcription factors too

What percentage of the genome does non-coding DNA represent?

42% of the total length in the genome

What are isoforms and how are they formed?

they are formed through alternative splicing which is the way in which genes can be transcribed ( an exon can be missed or not transcribed depending on how far the control region says to transcribe)

isoforms are multiple forms of a protein produced by alternative splicing

what are solitary genes compared to gene families?

solitary genes or single copy genes exist on their own while gene families are a set of related genes formed by a duplication of an original single copy gene

how can the function of a protein be determined?

if they have similar amino acid sequences its likely that they have similar function 

is the actual protein content consistency across species?

yes, the difference in genome size is due to the amount of non-coding DNA and transposable elements 

What is gene duplication?

where new gene copies can either evolve new function or degenerate over time losing their function (pseudogenes)

if after replication, one cell inherits both genes and one inherits nothing, it is likely that the cell that did not inherit anything will die

what is the term orthologs?

same protein in a different species (ie. alpha-tubulin in humans and flies)

What is the term paralogs?

closely related proteins in the same species (ie. alpha tubulin and beta tubulin in humans)

how is mRNA produced? think of splicing of introns

RNA is synthesized

the 3’ poly A tail is added 

introns are removed 

exons are ligated together 

What are simple sequence repeats?

they are repetitive sequences that don’t code for anything 

they show up as minisatellite DNA and microsatellite DNA

What is mini satellite DNA?

repeat units of 14-100bp in length

often found in centromeres and telomeres

(same sequence repeated multiple times)

What is micro satellite DNA?

repeat units of 1-4bp in length

found in transcription units 

if these repeated get expanded it can cause problems like neuromuscular diseases

What is backwards slippage? What neurodegenerative disease can it cause?

if there are many repeats this can occur → a repeat can slip out when DNA polymerase is replicating the repeats and can miss the repeat that slipped out OR it can cause the sequence to be extended by 1 if it slips back in during the second replication

these can lead to diseases like Huntington’s

Since SSR’s are highly variable what can they be used for?

exploiting DNA fingerprinting or paternity determination - amplified by PCR

What are the two types of transposable elements?

transposons and retrotransposons

What are transposable elements?

they are elements that can move within the genome by different mechanisms (with the help of proteins)

can lead to mutations causing disease 

What are DNA transposons?

DNA transposon is cut out of the genome

Target DNA where it needs to be inserted is found

transposon is inserted into new spot

3% of genome

What are retrotransposons?

in this case the genome is not cut

instead the DNA is used as a template to create an RNA intermediate

that is then used to transform the DNA into RNA using reverse transcriptase

then that DNA is inserted into the new spot 

40% of genome

What are the mechanisms of transposition?

DNA transposes which cuts out DNA it makes a blunt end cut in donor DNA → sticks it to DNA with sticky ends → ligates the sticky ends to the donor DNA

results in short duplication of DNA  

What happens if a transposon moves from a region that has replicated to a region that has not been replicated?

the copy number will increase by 1 in one of the daughter chromosomes 

this increased the diversity of the genes

What is an LTR transposon?

long terminal repeats

recognized since ends of the gene have specific repeats and a protein coding region 

What is the protein coding region in LTR composed of?

reverse transcriptase (to covert to RNA) 

integrase (to integrate into genome) 

other proteins 

How does the copy and paste of LTR work?

1. transcribed generating an RNA copy

2. reverse transcriptase to convert that into DNA 

3. tRNA is used as a primer in the process

4. DNA is imported into nucleus with integrase that inserts the DNA into the genome 

What are LINES and SINES? what is their difference?

they are both types of non viral DNA retrotransposons

LINES are rich in AT regions and have 2 proteins coding regions (ORF1 and ORF2 (codes for a reverse transcriptase and nuclease which mediate the insertion))

SINES are shorter elements and not have ORF’s therefore require help from other elements to move - rely on LINES to move

How does the insertion of LINES work?

1. RNA is produced

2. ORF1 and ORF2 are translated and bind the LINE RNA

3. nuclease cuts DNA at AT rich sequence and used DNA ends as primers

4. LINE DNA is incorporated and extended using the RNA primer

5. no transposes or integrase used

6. SINE used ORF1 and ORF2

what does the movement of TE’s lead to?

recombination between repeated elements can shuffle exons and produce new genes with new combinations of the existing exons

What do DNA transposons and LINES carry that LTR’s do not?

they carry flanking sequences which are supporting sequences of the transposons being moved 

example: poly A tail