Repetitive Dna In The Human Genome

Front 1

What is the C-value paradox?

Back 1

- Genome size is not proportional to complexity of organism

- similar organisms (pufferfish and lungfish) may have greatly differing genome sizes

Front 2

What is a possible reason for similar organisms having different genome sizes?

Back 2

- it is mostly due to difference in amount of repetitive DNA

Front 3

Is there any correlation at all between genome size for a class of organisms and complexity?

Back 3

- there is a correlation between minimum genome size and complexity

Front 4

What is project encode?

Back 4

- Identification of all RNAs transcribed from the genome and all functional DNA sequences

Front 5

What are some common types of variations between the genomes of individuals?

Back 5

- single nucleotide polymorphism

- short insertion/deletions (indels)

- copy number variations (CNV)

Front 6

How many gaps are there in the in the human genome project sequence?

Back 6

- almost 300

Front 7

What are the two different types of chromatin?

Back 7

- Heterochromatin

- Euchromatin - expressed DNA

Front 8

What are the two types of euchromatin?

Back 8

- genes

- Intergenic DNA

Front 9

What are the four types of intergenic DNA?

Back 9

- Repetitive DNA

- Pseudogenes

- Structural DNA (telomeres, centromeres)

- other

Front 10

What are the two different types of repetitive DNA?

Back 10

- interspersed repeats

- Tandem repeats

Front 11

What are the two types of genes?

Back 11

- Functional RNA (non-coding)

- Protein coding

Front 12

What are the four types of functional RNA?

Back 12

- tRNA

- rRNA

- Small RNAs snoRNA, snRNA; miRNA, piRNA

- long non-coding RNAs- structural enzymic OR regulatory

Front 13

What percentage do the different types of sequence take in the genome?

Back 13

- Exons - 2.9 (1.2 coding)

- Introns - 36.6

- Intergenic DNA - 60.5

Front 14

What are tandem repeats?

Back 14

- short repetitive sequences present in clusters, each of which contain many copies of the repeat

Front 15

What are the four types of interspersed repeats>

Back 15

- DNA transposons

- LINEs

- SINEs

- endogenous retroviruses

ALSO only LINEs and SINEs are active

Front 16

What are DNA transposons derived from?

Back 16

- derived from transposons that transpose via a DNA intermediate using "cut and paste"

Front 17

What are the LINEs, SINEs and Endogenous viruses derived from?

Back 17

- from transposons that transpose via an RNA intermediate (retrotransposons) using a "copy and paste" mechanism

Front 18

Why are human DNA transposons not transposable?

Back 18

- because all of them have acquired mutations that prevent their transposition = DNA fossils

Front 19

Where are endogenous retroviruses derived from?

Back 19

- retroviruses whose DNA integrated into the genome during infection of a germ line cell

Front 20

How do LINEs transpose?

Back 20

- via an RNA intermediate.

- encode their own reverse transcriptase

- use chromosomal DNA as primer

Front 21

What are the two classes of flanking repeat sequences?

Back 21

- direct repeat - on cis strand

- inverted repeat - on trans strand

Front 22

Talk about the activity of LINEs

Back 22

- almost all including all LINE2 and LINE3 are inactive because LINE elements usually lick DNA from 5'end

- 100 active LINE1 elements

Front 23

When do LINEs show highest activity?

Back 23

- during embryonic activity

Front 24

What percentage of spontaneous mutations is caused by LINE1?

Back 24

- 0.1%

Front 25

What are examples of diseases caused by LINE1 transposition mutations?

Back 25

- muscular dystrophy

- haemophilia - LINE1 into F8

- thalassemia

Front 26

Where are SINEs derived from?

Back 26

- RNAs synthesised by RNA polymerase III

- promoters recognised by RNA polymerase III may be located downstream of the transcription start site: Many SINEs have their own promoter and can be transcribed

Front 27

What is the most important human SINE?

Back 27

- The Alu sequence

- The Alu sequence is the only SINE active in transposition

- Alu transposition may cause genetic disorders e.g. some cases of muscular dystrophy, Tay-Sachs etc

Front 28

How are SINEs transposed?

Back 28

- The same way as LINEs

- SINEs use the endonuclease and reverse transcriptase encoded by LINEs

- Use chromosomal DNA as primers

Front 29

LINEs and SINEs are built in mutagens

Back 29

- deletions can be caused by recombination between two nearby Alu or LINE elements.

- They may arise from unequal crossing over between repeats

Front 30

What are the possible functions of interspersed repeat DNA?

Back 30

- May drive evolutionary change

- may be involved in X inactivation

- may have some role in gene regulation

- genes may derive from heavily mutated repetitive sequences

Front 31

What is possible proof that interspersed repeat DNA may drive evolutionary change?

Back 31

- aproximately 850 kbp have been deleted from human genome BECAUSE of recombination between LINE1 or Alu sequences in the last 6mln years

Front 32

What is possible evidence that interspersed repeat DNA may be involved in X chromosome inactivation?

Back 32

- LINE1 occurs with 2x higher frequency on X chromosome than on autosomes

Front 33

What is possible evidence that interspersed repeat DNA may be involved in gene regulation?

Back 33

- SINEs are more common in gene-rich than in gene-poor regions

Front 34

- What is possible evidence that interspersed repeat DNA may produce new genes?

Back 34

- Mammalian RAG1 recombinase is derived from a DNA transposon