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 10 human and 7 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 6 million years of primate evolution.
Highlights
Over half of primate genomes are annotated as transposable elements (TEs) (Jurka, 2000; de Koning et al, 2011)
The potential for TEs to participate in the regulation of gene expression has received increasing attention as genomic technologies to study these elements advance (Davidson and Britten, 1979; Jordan et al, 2003; Feschotte, 2008; Goke and Ng, 2016)
The role of TEs can be paradoxical. They can serve as regulatory sequence when they are bound by transcription factors, or localize in regions of open chromatin
Summary
Over half of primate genomes are annotated as transposable elements (TEs) (Jurka, 2000; de Koning et al, 2011). A fraction of evolutionarily recent TEs are active in the human genome, including HERV-K ERVs (Tonjes et al, 1996; Medstrand and Mager, 1998; Fuchs et al, 2013; Klawitter et al, 2016; Wildschutte et al, 2016), members of the Alu (Batzer and Deininger, 1991; Batzer et al, 1991), L1 (Kazazian et al, 1988, Brouha et al, 2003), and SVA (Wang et al, 2005; Ostertag et al, 2003) families. Most studies on mammalian TEs have focused on humans and mice, with a handful that describe the ERV and L1 TE families in chimpanzees (Yohn et al, 2005; Mun et al, 2014; Marchetto et al, 2013)
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