Transposable Elements Flashcards
class 2 TEs
DNA elements
DNA TE’s
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
first DNA TEs recognized
activator (AC) autonomous
dissociation (DS) non autonomous in maize
MITEs
minature inverted repeat transposable elements
- small, non-autonomous DNA elements
- found near genes (unlike other transposons)
- very high copy number
DNA TE gene mobility
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
class 1 TEs
RNA elements
RNA TEs
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
LTR retrotransposons
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
Non-LTR retrotransposons
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
LINEs/SINEs
long/short interspersed nuclear elements
- LINES: autonomous
- SINEs: non-autonomous, no coding regions
effects of TEs that insert into genes
- insertional mutagenesis
- insert into exon
- insert into enhancer
- insert into repressor - 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 - Introduction of new information
- TEs bring new enhancers/ repressors
- TEs introduce new splice sites
- TEs bring new promoter or start site - Transduction!
- introduce new exon into gene
transduction
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
Nested Retrotransposons
- 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
Dating Transposons
LTR dating
- for non nested transposons
- LTRs are same upon insertion then diverge
- LTR divergence indicates age of insertion
families of TEs
phylogenetic analysis of autonomous TEs based on Open Reading frames within TE
epigenetic silencing of transposons
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
siRNA
small interfering RNAs
- silence retrotransposons
- dsRNA of retrotransposon triggers Dicer mediated siRNA
- antisense siRNA binds TE mRNA and degrades
TE variation and diversity
genome size not related to complexity
More basal= More TE diversity
- most organisms are LINE TE classes
Types of TE in human geneome
45% og genome are TEs
most are LINES
except ALU which is a SINE
- only non-LTR TEs are active
DNA transposons and human genome
least common - cut and paste method so not as much gene copy numbers
TE balance btw expression and repression
expression should be sufficent to promote amplification but not so much that leads to fitness disadvantage for host
3 ways TEs can be damaging without transposition
- TE may interfere with transcriptional processing of host mRNAs if become reactivated
- TE encoded proteins can induce DNA breaks+ genomic instability
- accumulate RNA transcripts and extrachromosomal DNA copies derived from TEs may trigger innate immunity response
how can TEs add exons to genes
transduction
- cryptic splice sites which can cause alternative splicing
How can TEs provide the building blocks of cis-regulatory networks
contain all features of classical gene: integrate multiple inputs, respond to signals and are capable of coordinating regulating gene expression
