0

500

1000

1500

2000

2500

3000 Genomic DNA

TE DNA

Protein-codingDNA

Mb

Feschotte & Pritham 2006

TE content correlates positively with genome size

Transposable elements ….

•CONCLUSIONS…•TEs have played an important role in genome evolution and diversification

•Can facilitate expansion and contraction of genomes AND gene families

• Variation in gene numbers cannot explain variation in genome size among eukaryotes

• Most variation in genome size is due to variation in the amount of repetitive DNA (mostly derived from TEs)

• TEs accumulate in intergenic and intronic regions

and continue to play

^

Goals for next two class sessions:

1.Distinguish major transposable element classes: • DNA (transposase)• RNA (reverse transcriptase)

• LTR retrotransposon (integrase)• Non-LTR retrotransposon (TPRT)

• Autonomous• Non-autonomous

2.Presently Active Human TEs• LINE – LINE-1 or L1• SINE – Alu• SVA

3.Consequences of TEs• Genetic (individual)• Evolutionary (species)

Repetitive elements are interspersed throughout mammalian genomes

Han & Boeke, Bioessays 2005 27:775-84.

DNA transposons

transposase

From Molecular Cell Biol ed 5

Overview of DNA transposition

From Molecular Cell Biol ed 5

Summary: DNA transposition

•cis-acting sequences (inverted repeats) recognized by element-encoded transposase enzyme (can be supplied in trans)

•transposase leaves a double-strand break upon excision

•similarities to VDJ recombination (e.g., Rag1) which is believed to be an “exapted” transposon

•staggered break in target DNA at the insertion site causes target site duplications (short, direct repeats) to flank the transposon after transposition is complete and the gaps are repaired

LTR retrotransposons

•Retrotransposition: transposition with an RNA intermediate

•Replication like retroviruses

From Molecular Cell Biol ed 5

First step in LTR retrotransposition: transcription of an integrated copy

From Molecular Cell Biol ed 5

Second step in LTR retrotransposition: cDNA synthesis

From Molecular Cell Biol ed 5

Summary: LTR retrotransposition

•transposition begins with transcription

•LTRs (long terminal repeats) are the critical cis-acting sequences (note: these are direct repeats)

•element encodes reverse transcriptase and integrase enzymes, plus additional proteins required for replication

•RNA copied into double-stranded cDNA in cytoplasm, using a cellular tRNA as the first primer

•integrase catalyzes insertion of the ds-cDNA at a staggered break in target DNA, creating a target site duplication as with transposase

Similarities between DNA transposition and non-LTR retrotransposition

From Molecular Cell Biol ed 5

transposase integrase

Han & Boeke, Bioessays 2005 27:775-84.

Retrotransposition: the non-LTR retrotransposon, L1

Belancio V P et al. Genome Res. 2008;18:343-358

Non-LTR retrotransposons insert by TPRT

Summary: non-LTR retrotransposition

• transposition begins with transcription

• requires element-encoded endonuclease and reverse transcriptase

• cDNA synthesis and insertion of the new copy into chromosomal DNA occurs simultaneously, by TPRT (target-primed reverse transcription)

• newly-inserted elements typically have a polyA tail and target-site duplications

20%

40%

60%

80%

100%

DNA transposons

LTR Retro.

Non-LTR Retro.

Feschotte & Pritham 2006

TE composition varies among eukaryotic genomes

Major groups of DNA transposons are widespread in eukaryotes

TE composition varies among vertebrate genomes

Zhao

F e

t al.

Gen

ome

Res

. 200

9;19

:138

4-13

92

Age distribution of interspersed repeats in the mammoth, human, and opossum genomes

~45% of the human genome is derived from transposable elements

Cordaux & Batzer, 2009, v10, 691-703

Non-LTR retrotransposons in humans and other eukaryotes

Eickbush & Jamburuthugoda, 2009

Kapi

tono

v et

al.

Gene

, 200

9

Fura

no e

t al.,

Tre

nds

Gen

et. 2

004,

20:

9-14

Dramatically different LINE amplification in human and fish genomes

Boissinot S et al. Genome Res. 2004;14:1221-1231

Structure of a typical full-length human L1 element: note subfamily sequence variation

Mod

ified

from

Boi

ssin

ot, S

. et a

l. M

ol B

iol E

vol 2

001

18:9

26-9

35.

Evolution of L1 in the primate genome

humans only

all great apes, inc Hs

OWM, apes, humans

Bro

uha

B e

t al.

PN

AS

200

3;10

0:52

80-5

285

Chromosomal location, activity, allele frequency, and subclass of 82 full-length L1 elements with two intact ORFs

Brouha B et al. PNAS 2003;100:5280-5285

L1 activity distribution

Modified from Boissinot S et al. PNAS 2006;103:9590-9594

The frequency distribution of polymorphic Ta1 elements

full lengthtruncated

L1Hs insertions found in various human genomes

Ewing A D , Kazazian H H Genome Res. 2010;20:1262-1270

©2010 by Cold Spring Harbor Laboratory Press

Impact of transposable elements on genomes

•A source of genetic novelty

•Alter gene function by insertion

•Induce chromosomal rearrangements

Feschotte, C. Nat Rev Genet. 2008 May; 9(5): 397–405.

TEs can influence gene expression in many ways

Fesc

hotte

, C. N

at R

ev G

enet

. 200

8 M

ay; 9

(5):

397–

405.

Building regulatory systems with transposable elements

Fesc

hotte

, C. N

at R

ev G

enet

. 200

8 M

ay; 9

(5):

397–

405.

DNA-binding proteins and transcription factors derived from transposases

Mechanisms by which L1 retrotransposition can disrupt genes

Han & Boeke, Bioessays 2005 27:775-84.

L1 can create novel functional alleles in several ways

Han & Boeke, Bioessays 2005 27:775-84.

How Retrotransposons Affect the Cell

Goodier & Kazazian, Cell, 2008,135:23-35

How the Cell Affects Retrotransposons

Goodier & Kazazian, Cell, 2008,135:23-35

Hedges & Deininger, Mutat Res, 616:46-59

Interspersed repeat-mediated non-allelic homologous recombination

Learning Objectives:

Define and discuss the key similarities and differences among DNA transposons, LTR and non-LTR retrotransposons.

Explain how transposable elements can cause variation among individuals within a species or between species? Explain how transposable elements could act to alter phenotypes between humans, including between “identical” twins.

Distinguish autonomous from non-autonomous transposable elements.

Which TEs are currently active in the human genome?