Transposable elements: insertion pattern and impact on gene expression evolution in hominids

Maria Warnefors, Vini Pereira, Adam Eyre-Walker

University of Sussex, Brighton, United Kingdom

SMBE, Lyon, 2010

Species-specific transposable elements (TEs)

2933 insertions7786 insertions

~95% of these TEs are Alu, L1 or SVA elements

(Mills et al, Am J Hum Genet, 2006)

Images: Wikimedia Commons

Me Me Me Me

TEs can influence gene expression via several mechanisms

TEs provide transcription start sites (TSSs) for 30% of human transcripts (Faulkner et al, Nature Genetics, 2009)

Intronic L1 insertion reduces reporter gene expression in HeLa cells(Han et al, Nature, 2004)

TE silencing downregulates neighbouring genes in Arabidopsis(Hollister and Gaut, Genome Research, 2009)

Have TEs increased expression divergence (ED) between humans and chimpanzees?

Low ED

Have TEs increased expression divergence (ED) between humans and chimpanzees?

Low ED

High ED

Previous studies of TEs and expression divergence

20% of mouse/rat ED is due to TEs (Pereira et al, PLoS ONE, 2009)

Alu elements correlate with mouse/human ED, but the direction depends on the definition of ED (Urrutia et al, Genome Biology, 2008)

Materials and methods

Expression divergence was calculated for ~9000 genes based on expression in five tissues (data from Khaitovich et al, Science, 2005)

Expression divergence is the Euclidean distance between expression levels in one or more tissues

Species-specific TEs (Mills et al, Am J Hum Genet, 2006) were grouped according to insertion site:

UPSTREAM INTRONIC DOWNSTREAM

2 kb10 kb20 kb 2 kb 10 kb 20 kb

Species-specific TEs are associated with an increase in expression divergence

TE

No TE

Combined p = 0.024

Z transformation method (Whitlock, J Evol Biol, 2005)

ED

Do TEs cause the change in expression?

H. sapiens P. troglodytes M. mulatta

SPECIFICContribute to ED

SHAREDDo not contribute to ED

Images: Wikimedia Commons

Shared TEs are also associated with an increase in expression divergence

TE

No TE

SPECIFIC (p = 0.024)

SHARED (p = 0.00003)

ED

ED

Recent TE insertions did not cause an increase in expression divergence

Relative effect =EDSPECIFIC / EDNO SPECIFIC

EDSHARED / EDNO SHARED

Second approach: Human-macaque versus chimp-macaque expression divergence

H. sapiens P. troglodytes M. mulatta

Expression data:~3700 genes in the prefrontal cortex(Somel et al, PNAS, 2009) Images: Wikimedia Commons

Species-specific TEs have not caused increased ED

H/M

C/M

p = 0.32

p = 0.13

Do TEs act to increase transcript diversity?

New TE No new TE p value (M-W)

Human 2.7 2.3 2 x 10-16

Chimp 2.0 1.8 5 x 10-10

Do TEs act to increase transcript diversity?

Expected transcript div.

New TE No new TE p value (M-W)

Human 2.7 2.3 2 x 10-16

Chimp 2.0 1.8 5 x 10-10

No evidence that recently inserted TEs have contributed to hominid transcript diversity

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TE insertions are more common upstream than down-stream of genes

The upstream bias is just significant (p = 0.049).

Summary of ~9000 genes (from the Khaitovich dataset)

561 TEs

496 TEs

TE insertions are more common upstream than down-stream of genes

The upstream bias is just significant (p = 0.049).

TEs may accumulate upstream because they have a role in chromatin regulation. (Huda et al, Gene, 2009)

TEs may preferentially insert upstream (as known for Drosophila P elements)

Summary of ~9000 genes (from the Khaitovich dataset)

561 TEs

496 TEs

Hominid TEs are subject to insertion bias

TE upstream TE downstream

Active in germ line 255 181

Inactive in germ line 306 315

Only germ line expressed genes exhibit upstream bias (p = 0.003, 2test)

The enrichment of TEs in upstream sequences can be explained in terms of insertion bias and does not indicate a role for TEs in gene regulation

Expression state from eGenetics data (Kelso et al, Genome Research, 2003)

Summary

New TEs are correlated with, but not causal to, an increase in expression divergence between human and chimpanzee. (However, TEs may still contribute substantially to within-species variation).

We do not find evidence for a TE-induced increase in transcript diversity.

Excess of upstream insertions can be explained by neutral insertion bias.

To what extent do regulatory regions evolve within TEs, simply because TEs are so abundant?

Acknowledgements

Adam Eyre-Walker

Vini Pereira

John Brookfield