Lecture 10- Non-coding DNA evolution, transposable elements, endogenous viruses, and other mobile DNA

Question 1

what is the c-value paradox

Answer 1

uncertainty over why genome size (c value) and gene number don’t seem to correlate much

Question 2

4 possible explanations for why non coding DNA exists

Answer 2

-has essential functions, such as regulation
-is just linked with functional genes
-has a structural function
-‘parasitic’- carried by genomes at their own expense

Question 3

what features is genome size correlated with

Answer 3

nucleus size, duration of mitosis/meiosis, metabolic rate, plant seed size

Question 4

what may explain these correlations other than causation

Answer 4

body/cell size as the third variable?

Question 5

issue with nucleoskeletal function arguments

Answer 5

it has been found in some groups- nucleomorph algae- that nuclear size and DNA content don’t actually correlate

Question 6

evidence for genome sizes being non-adaptive ‘junk’

Answer 6

simply not high enough effective pop size for junk to be removed from eukaryotic populations
not really any proper evidence of this idea once you correct numbers for common ancestry

Question 7

satellite dna

Answer 7

100s of kb long highly repetitive tandem repeats, often in heterochromatin

Question 8

minisattelite

Answer 8

moderately repetitive tandem repeats, with many VNTR loci

Question 9

microsattelite

Answer 9

dispersed and either moderately or highly repetitive, 2-5bp repeats

Question 10

what type of satellite has the highest mutation rate

Answer 10

microsatellite, 10ish mutations per gamete per generation

Question 11

what is a transposable element

Answer 11

‘selfish’ dna elements which increase their copy number and jump around the genome

Question 12

class I transposable element

Answer 12

retroelements which use an RNA intermediate, use/encode reverse transcriptase, e.g. LINEs (encode) and SINEs (use)

Question 13

class II transposable elements

Answer 13

transposases and Ac-like elements- these are DNA elements and have terminal repeats at either side

Question 14

another TE example

Answer 14

MITEs- rely on proteins they dont encode, made up of a few short repeats w terminal repeats

Question 15

by how much can TE copy number increase in a single generation

Answer 15

20-100 copies

Question 16

trait that can vary in different organisms which could help solve the c value paradox

Answer 16

different effectiveness of removal of TEs, e.g. drosophila seem to be better at it than mammals

Question 17

impact of endogenous retroviruses on genomes

Answer 17

segmental duplication of genome, can become inserted into host genome

Question 18

2 mechanisms of ERV host integration

Answer 18

co-option- host using viral genes for its own purposes, e.g. salivary amylase gene
recombination- viral genes can be involved in chromosomal recombination

Question 19

what is ectopic exchange

Answer 19

crossing over of homologous dna sequences at non-allelic locations

Question 20

how might levels of ectopic exchange be significant

Answer 20

may lead to pressure against TEs and recombination in general- some correlation between TE density and recomb rates in Drosophila and humans

Question 21

how much of the (human) genome is estimated to be conserved and functional

Answer 21

5%, with 1.5% actually being genes

Question 22

what are HARs

Answer 22

human accelerated regions, which are conserved in most mammals but diverge a lot in humans- e.g. HAR1 which is involved in cerebral cortex development

Question 23

how much of the genome is functional according to ENCODE

Answer 23

80%, as 75% is transcribed and other parts are found in open chromatin, has TF binding sites etc- this implies function kinda