L4 ENCODE and Negative Selection Flashcards Preview

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Flashcards in L4 ENCODE and Negative Selection Deck (15)
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1
Q

ENCODE Project

A
  • Encyclopedia of DNA elements

- aims to identify all the functional elements of the genome

2
Q

Encode over-interpretation

A
  • Dan Graur said that ENCODE did not consider the evolutionary aspect of genetics
  • over-interpret “biochemical function”
    car hood analogy
3
Q

What is a function?

A
  • if you were to lost it, there would be a fitness cost
  • does the sequence conservation tell us anything about function; if it is conserved, it is likely to have a function
  • sequence conservation reflects function
4
Q

Selective constraint

A

purifying selection/negative selection

Constraint is due to purifying selection - there is a function associated to it

5
Q

How can we tell which proteins have a function related to it?

A

See OneNote

Compare species that are closely related

6
Q

Phylogenetic footprinting

A

See OneNote

Phylogenetic footprinting is a technique used to identify transcription factor binding sites (TFBS) within a non-coding region of DNA of interest by comparing it to the orthologous sequence in different species.

7
Q

DNase1 Footprinting

A

protein modification protection assay

8
Q

Transgenic experiment

A

See OneNote

  • use reporter gene
  • Does our reporter gene show an expression pattern that is consistent with the gene that we are interested in?
9
Q

ApoA

A

See OneNote

10
Q

Extreme levels of conservation

A
  • conserved non-genic sequences (CNG)
  • conserved but not transcribed
  • doesn’t show substitution patterns of coding or ncRNA sequences
11
Q

CNG characteristics

A
  • Has to be at least in 10 different genomes
  • CNG are mutating slowly than protein coding sites
  • many of them but each is unique
  • often clustered
  • often in gene deserts
  • many are near genes that are involved in regulation of transcription or development
  • some overlap with exonic and these are highly enriched for genes involved in RNA binding and splicing regulation
12
Q

Function of non-coding conserved sequences?

A

See OneNote

Regulator modules?
- reporter constructs; Pax6 - eye development

CNG associated with complex genes e.g. genes with alternate splicing

13
Q

Functional conservation without sequence conservation

A

See OneNote

  • even-skipped gene stripe 2 enhancer; regulatory module composed of multiple TF binding sites
  • Limited conservation of stripe 2 enhancer sequence BUT if you place the different stripe 2 enhancer sequence in front of a stripe 2 reporter gene, it still drives the expression of stripe 2
  • expresses at the correct place and rescues to the same extent
    BUT
  • chimeric enhancers don’t recapitulate pattern

The sequences can change over time as long as you keep the same number of bicoid and hunchback sites

14
Q

Some lessons from eve

A
  • enhancer function can be conserved without sequence conservation
  • TF binding sites change relative position over evolutionary time
15
Q

ENCODE debate

A

See OneNote