TE content correlates positively with genome size

Transcription

1 TE content correlates positively with genome size Mb 3000 Genomic DNA TE DNA Protein-coding DNA Feschotte & Pritham 2006

2 Transposable elements. 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 CONCLUSIONS and continue to play TEs have played ^ an important role in genome evolution and diversification Can facilitate expansion and contraction of genomes AND gene families

3 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)

4 Repetitive elements are interspersed throughout mammalian genomes Han & Boeke, Bioessays :

5 DNA transposons transposase From Molecular Cell Biol ed 5

6 From Molecular Cell Biol ed 5 Overview of DNA transposition

7 Summary: DNA transposition cis-acting sequences (inverted repeats) recognized by elementencoded 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

8 LTR retrotransposons Retrotransposition: transposition with an RNA intermediate Replication like retroviruses From Molecular Cell Biol ed 5

9 First step in LTR retrotransposition: transcription of an integrated copy From Molecular Cell Biol ed 5

10 Second step in LTR retrotransposition: cdna synthesis From Molecular Cell Biol ed 5

11 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

12 Similarities between DNA transposition and non-ltr retrotransposition transposase integrase From Molecular Cell Biol ed 5

13 Retrotransposition: the non-ltr retrotransposon, L1 Han & Boeke, Bioessays :

14 Non-LTR retrotransposons insert by TPRT Belancio V P et al. Genome Res. 2008;18:

15 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

16 TE composition varies among eukaryotic genomes 100% 80% 60% 40% 20% DNA transposons LTR Retro. Non-LTR Retro. Feschotte & Pritham 2006

17 Major groups of DNA transposons are widespread in eukaryotes

18 TE composition varies among vertebrate genomes

19 Age distribution of interspersed repeats in the mammoth, human, and opossum genomes Zhao F et al. Genome Res. 2009;19:

20 ~45% of the human genome is derived from transposable elements Cordaux & Batzer, 2009, v10,

21 Non-LTR retrotransposons in humans and other eukaryotes Eickbush & Jamburuthugoda, 2009 Kapitonov et al. Gene, 2009

22 Dramatically different LINE amplification in human and fish genomes Furano et al., Trends Genet. 2004, 20:9-14

23 Structure of a typical full-length human L1 element: note subfamily sequence variation Boissinot S et al. Genome Res. 2004;14:

24 Modified from Boissinot, S. et al. Mol Biol Evol : Evolution of L1 in the primate genome OWM, apes, humans humans only all great apes, inc Hs

25 Chromosomal location, activity, allele frequency, and subclass of 82 full-length L1 elements with two intact ORFs Brouha B et al. PNAS 2003;100:

26 L1 activity distribution Brouha B et al. PNAS 2003;100:

27 The frequency distribution of polymorphic Ta1 elements full length truncated Modified from Boissinot S et al. PNAS 2006;103:

28 L1Hs insertions found in various human genomes Ewing A D, Kazazian H H Genome Res. 2010;20: by Cold Spring Harbor Laboratory Press

29 Impact of transposable elements on genomes A source of genetic novelty Alter gene function by insertion Induce chromosomal rearrangements

30 TEs can influence gene expression in many ways Feschotte, C. Nat Rev Genet May; 9(5):

31 Building regulatory systems with transposable elements Feschotte, C. Nat Rev Genet May; 9(5):

32 DNA-binding proteins and transcription factors derived from transposases Feschotte, C. Nat Rev Genet May; 9(5):

33 Mechanisms by which L1 retrotransposition can disrupt genes Han & Boeke, Bioessays :

34 L1 can create novel functional alleles in several ways Han & Boeke, Bioessays :

35 How Retrotransposons Affect the Cell Goodier & Kazazian, Cell, 2008,135:23-35

36 How the Cell Affects Retrotransposons Goodier & Kazazian, Cell, 2008,135:23-35

37 Interspersed repeat-mediated non-allelic homologous recombination Hedges & Deininger, Mutat Res, 616:46-59

38 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?