Annotation

Question 1

what does annotation mean in genomics?

Answer 1

to make sense of the assembly, characterizing functional elements

Question 2

2 ideas about what a gene is

what is their main difference?

Answer 2

johannsen 1905 - the word gene is completely free from any hypothesis, many characteristics of the organism are conditioned by special, separable, and therefore self-existent fundamentals that occur in the gametes. (gene is defined by effect on characteristics of an org).

gene model - region of the genome to be transcribed into RNA and then protein. (no link to characteristics of an org)

Question 3

what is an ORF

Answer 3

region of DNA which starts with ATG and ends in stop codon

Question 4

difference btw PK and EK genes

Answer 4

PK - 1 gene is a contiguous region of DNA (no introns), intergene spaces are small. genome of smaller, fewer genes.
EK - exons separated by introns (removed from mRNA before translation).

Question 5

what is key about alternative splicing?

Answer 5

it can increase genome complexity without increasing genome size.

in humans, 75% genes have an alternative isoform

Question 6

2 approaches to identify gene models

Answer 6

1. A prior/ab initio: look for sequence patterns. Protein-coding regions have distinctive patterns of codon statistics.
2. Evidence based: Recognises regions corresponding to
   previously identified gene models. uses similarity of translated AA seq to known proteins in other species.

Question 7

Which is better approach to identify gene models?

Answer 7

A priori less biased but as more genomes are annotated, evidence based annotation becomes more reliable. however error propagation is a big issue.

Question 8

what features of a gene does A priori look for?

Answer 8

ATG - start
TATA box - promoter region (30bp upstream of ATG. binding site of RNA pol)
Stop codon
Splice sites on codons
Poly adenylation sequence

these features are versatile, which presents a difficulty for A priori.

Question 9

example of 2 protein domains

Answer 9

kinase domains - signal transduction

LRR leucine rich repeats - involved in protein protein interaction.

Question 10

what is domain shuffling

Answer 10

gene segments coding for functional domains are shuffled between different genes in evolution.

Question 11

what causes complexity when using evidence based method of gene model prediction?

Answer 11

Codon usage preference

Different orgs may prefer to have different codons for he same AA over other codons.

Question 12

what is Pfam

Answer 12

a database which makes predictions about domains of proteins based an AA seq.

Question 13

How much of human genome codes for proteins?

Answer 13

1.3%

23000

Question 14

what is different about sub telomeric regions?

Answer 14

low in protein encoding genes.

Question 15

what causes huge variation in gene length amongst protein encoding genes?

Answer 15

variation in intron size

exon size stays fairly constant, around 200bp.

Question 16

example of a very long gene

Answer 16

dystrophin gene - 2400kb

Question 17

how can distribution of genes across a chromosome vary?

Answer 17

Less in the centre and at very end (subtelomeric region)
in centre, more repetitive (LTR).
Recombination rate is higher near ends of chromosome.

Question 18

how many RNA coding genes in human genome? (not mRNA)

Answer 18

3000
code tRNA and siRNAs eg
usually involved in control of gene expression

Question 19

what is a pseudogene?

Answer 19

degenerated genes that have mutated so far from their original sequences that the polypeptide sequence they encode will no longer be functional

Question 20

what is a processed pseudogene?

How do they act?

Answer 20

picked up by viruses from mRNA, and reverse transcribed.
Introns and promoters have been lost.not expressed as the original protein but sometimes transcribed and can regulate gene function by competing with miRNA for binding to messenger

Question 21

what is a non processed pseudogene?

Answer 21

derived from gene duplication and located on the same chr as the parental gene

Question 22

what is a unitary pseudogene?

Answer 22

derived from mutations of the parental genes, which are lost.

Question 23

What is an enhancer?

Answer 23

short 50-1500bp region, binds to proteins to increase transcription.
can be up to 1Mb away from associated gene

Question 24

How much of out genome is repetitive elements?

Answer 24

80-90%

Question 25

4 types of repetitive elements in human genome

Answer 25

LINE long interspersed elements. 21% of genome
SINE short.. 13% genome
Micro satellites
mini satellites - together 15%. 10,000-100,000 copies

Question 26

who discovered transposable elements?

Answer 26

Barbara McClintock 1940s

Studied maize pigments

Question 27

How do transposable elements work in corn kernels to give color variation?

Answer 27

dark color - anthocyanin
yellow - transposable element disrupts anthocyanin gene expression.
Transposition occurs rapidly in kernel development.
Chr 9 more prone to breakage in some cultivars. breaks caused by transposable element, named Dissociation element (Ds). Ds depends on presence of Activator element (Ac), unlinked.
Heterozygous for colorless (c), lord of Chr 9 part = yellow.

Question 28

when does a mottled or striped kernel phenotype occur?

Answer 28

If Ds inserts directly into C gene. - yellow
if Ac is present, Ds can jump out of c gene and reactivate C. - purple.
Causes spots as all cells derived from this cell are purple.
Size of spot indicates at what stage in kernel development transposition occurred.

Question 29

where else in nature can we see effect of transposable elements.

Answer 29

Rose

grape colour

Question 30

Names of 2 types of TEs

Answer 30

Class 1 - Retrotransposons.

Class 2 - DNA transposons

Question 31

Describe Retrotransposons?

Answer 31

usually degenerated retroviruses.
require an RNA intermediate to replicate.
in mammals - LINE SINE
LINE - encodes reverse transcriptase and can replicate autonomously.
SINE too short to encode own reverse transcriptase, depend on LINES for replication.
Often have LTRs at the end.

Question 32

Describe DNA transposons

Answer 32

Do not require RNA intermediate.
Encode transposes enzyme., recognizes seq in transposon itself, cuts it out and inserts somewhere else. Often leaves mutation at original site.
Contain terminal inverted repeats at the ends, targets of excision machinery.

Question 33

How are inserted transposable elements flanked by repeats?

Answer 33

Transposase cuts DNA leaving sticky ends.

TE inserts, and sticky ends filled in.

Question 34

Biological functions of transposable elements

Answer 34

1. Altering properties of genes - insertion can cause knock out phenotype. insertion into promoter region can alter expression patterns/splicing of near by genes.
2. Gene evolution by gene fusion or exon shuffling. Eg, rapidly evolving virulence effectors in fungal plant pathogens are preferably located in repeat-rich regions of the genome.

Question 35

How do TEs control grape colour?

Answer 35

insertion of Gret1 LTR into allele Vvmyb1A in black grapes caused loss of function = white grapes.
Rearrangement of Gret1 = red coloured.

Question 36

How have TE driven evolution of peppered moths?

Answer 36

replacement of pale form by black form, driven by predation and pollution.
black due to insertion of large tandemly repeated TE into first intron of cortex gene. increased expression of cortex.

Question 37

what do TEs partially explain?

Answer 37

C value paradox.

differences in repeat content

Question 38

What is ENCODE

Answer 38

Encyclopedia of DNA elements
international collaboration or research groups funded by the National Human Genome Research Institute (NHGRI).
trying to compile a list of all functional elements in human genome, and regulatory elements.
2012 published biochmical functions for 80% of genome, but is highly debated.

Question 39

What is BUSCO

Answer 39

Benchmarking Universal Single-Copy Orthologs

defined a set of universal single-copy genes that occur in all organisms, used to assess completedness of assembly and annotation.