Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs

Abstract
Data availability
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Abstract

Transposable elements (TEs) comprise almost half of primate genomes and their aberrant regulation can result in deleterious effects. In pluripotent stem cells, rapidly-evolving KRAB-ZNF genes target TEs for silencing by H3K9me3. To investigate the evolution of TE silencing, we performed H3K9me3 ChIP-seq experiments in induced pluripotent stem cells from ten human and seven chimpanzee individuals. We identified four million orthologous TEs and found the SVA and ERV families to be marked most frequently by H3K9me3. We found little evidence of inter-species differences in TE silencing, with as many as 82% of putatively silenced TEs marked at similar levels in humans and chimpanzees. TEs that are preferentially silenced in one species are a similar age to those silenced in both species, and are not more likely to be associated with expression divergence of nearby orthologous genes. Our data suggest limited species-specificity of TE silencing across six million years of primate evolution.

Data availability

The following data sets were generated

1. Ward MC
(2017) Epigenomic conservation of transposable element silencing
Publicly available at the NCBI Gene Expression Omnibus (accession no: GSE96712).

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96712

The following previously published data sets were used

1. Rosenbloom KR
2. Sloan CA
3. Malladi VS
4. Dreszer TR
5. Learned K
6. Kirkup VM
7. Wong MC
8. Maddren M
9. Fang R
10. Heitner SG
11. Lee BT
12. Barber GP
13. Harte RA
14. Diekhans M
15. Long JC
16. Wilder SP
17. Zweig AS
18. Karolchik D
19. Kuhn RM
20. Haussler D
21. Kent WJ
(2013) ENCODE data in the UCSC Genome Browser
Publicly available at the UCSC Genome Browser.

http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database

Article and author information

Author details

Michelle C Ward

Department of Human Genetics, University of Chicago, Chicago, United States

For correspondence
mcward@uchicago.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-1485-320X
Siming Zhao

Department of Human Genetics, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.
Kaixuan Luo

Department of Human Genetics, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.
Bryan J Pavlovic

Department of Human Genetics, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-7751-5315
Mohammad M Karimi

MRC London Institute of Medical Sciences, Imperial College London, London, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Matthew Stephens

Department of Human Genetics, University of Chicago, Chicago, United States

Competing interests
The authors declare that no competing interests exist.
Yoav Gilad

Department of Human Genetics, University of Chicago, Chicago, United States

For correspondence
gilad@uchicago.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-8284-8926

Funding

National Institute of General Medical Sciences (GM077959)

Yoav Gilad

EMBO Long-Term Fellowship/European Commission Marie Curie Actions (ALTF 751-2014)

Michelle C Ward

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.