Transposable Elements

Question 1

class 2 TEs

Answer 1

DNA elements

Question 2

DNA TE’s

Answer 2

cut and paste method

• transposition through DNA intermediate: element excises and reinserts elsewhere in genome
• autonomous elements- code for transposase
• non-autonomous- do not code for transposase
• terminal inverted repeats

Question 3

first DNA TEs recognized

Answer 3

activator (AC) autonomous

dissociation (DS) non autonomous in maize

Question 4

MITEs

Answer 4

minature inverted repeat transposable elements

• small, non-autonomous DNA elements
• found near genes (unlike other transposons)
• very high copy number

Question 5

DNA TE gene mobility

Answer 5

can capture and mobilize genes and gene fragments
sometimes contain gene fragments
many non-functional pseudogenes
- some are expressed and show few signatures of selection
– low ka/ks values, no frameshifts or INDELs
— suggests some are functional

Question 6

class 1 TEs

Answer 6

RNA elements

Question 7

RNA TEs

Answer 7

class 1: retrotransposons
copy and paste
- mRNA is transposon intermediate
- usually high copy number
A: LTR Retrotransposons
- replicative retroposition
- direct orientation terminal repeats
B: NON- LTR retrotransposons

Question 8

LTR retrotransposons

Answer 8

long terminal repeats in DIRECT orientation
- gag and pol coding regions
- gag codes for capsid like proteins
- pol polyprotein codes for RT, protease, RNaseH, integrase
- LOCATION:
Nucleus, RT in cytoplasm, cDNA transport to nucleus

Question 9

Non-LTR retrotransposons

Answer 9

most prevalent type in human genome
- NO terminal repeats
- LINEs ( ORF1, EN, RT ORFs)
- SINEs (short intersperced nuclear elements)
-- no coding regions
- LOCATION:
nucleus, priming and RT at target site

Question 10

LINEs/SINEs

Answer 10

long/short interspersed nuclear elements

• LINES: autonomous
• SINEs: non-autonomous, no coding regions

Question 11

effects of TEs that insert into genes

Answer 11

1. insertional mutagenesis
   - insert into exon
   - insert into enhancer
   - insert into repressor
2. Epigenetic regulation
   - antisense downregulation
   - - inserts into 3’ region and makes antisense RNA to form dsRNA– rna degraded and downregulated
   - epigenetic silencing
   - - metalation of transposon to prevent proliferation
3. Introduction of new information
   - TEs bring new enhancers/ repressors
   - TEs introduce new splice sites
   - TEs bring new promoter or start site
4. Transduction!
   - introduce new exon into gene

Question 12

transduction

Answer 12

intro of new exon into a gene by TEs

• 5’: 5’ end exon of gene incorporated
• 3’
• premature polyadenylation if TE has polyadenylation signal in it
• • premature polyadenylation of protein

Question 13

Nested Retrotransposons

Answer 13

• transposons inserted into other transposons
• each retrotransposon originated later than DNA flanking it
• leads to increased distance btw genes and increased genome size
• diagram ones closest to top newest

Question 14

Dating Transposons

Answer 14

LTR dating

• for non nested transposons
• LTRs are same upon insertion then diverge
• LTR divergence indicates age of insertion

Question 15

families of TEs

Answer 15

phylogenetic analysis of autonomous TEs based on Open Reading frames within TE

Question 16

epigenetic silencing of transposons

Answer 16

transcriptional silencing
- methylation of TE promoters
- chromatin remodeling
post-translational silencing: sequence specific RNA degradation
- double stranded RNA, formed by readthrough transcription from neighboring gene
– inverse of antisense degradation
- siRNAs: target TEs for degradation

Question 17

siRNA

Answer 17

small interfering RNAs

• silence retrotransposons
• dsRNA of retrotransposon triggers Dicer mediated siRNA
• antisense siRNA binds TE mRNA and degrades

Question 18

TE variation and diversity

Answer 18

genome size not related to complexity
More basal= More TE diversity
- most organisms are LINE TE classes

Question 19

Types of TE in human geneome

Answer 19

45% og genome are TEs
most are LINES
except ALU which is a SINE
- only non-LTR TEs are active

Question 20

DNA transposons and human genome

Answer 20

least common - cut and paste method so not as much gene copy numbers

Question 21

TE balance btw expression and repression

Answer 21

expression should be sufficent to promote amplification but not so much that leads to fitness disadvantage for host

Question 22

3 ways TEs can be damaging without transposition

Answer 22

1. TE may interfere with transcriptional processing of host mRNAs if become reactivated
2. TE encoded proteins can induce DNA breaks+ genomic instability
3. accumulate RNA transcripts and extrachromosomal DNA copies derived from TEs may trigger innate immunity response

Question 23

how can TEs add exons to genes

Answer 23

transduction

- cryptic splice sites which can cause alternative splicing

Question 24

How can TEs provide the building blocks of cis-regulatory networks

Answer 24

contain all features of classical gene: integrate multiple inputs, respond to signals and are capable of coordinating regulating gene expression