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. Author manuscript; available in PMC: 2018 Jun 29.
Published in final edited form as: Cell. 2017 Jun 29;170(1):61–71.e11. doi: 10.1016/j.cell.2017.06.013

Figure 1. Stem cells with relaxed epigenetic control of LTR-retrotransposons express sRNA targeting ERVs, including 3′ tRNA-derived fragments (tRFs).

Figure 1

(A) Setdb1 knockout mouse ES cells and TS cells have elevated levels of LTR-retrotransposon (ERV) small RNA and (B) 3′ CCA tRFs which target ERVs. Boxplots represent reads per million total mapped reads (RPM) of biological replicates; for a list of all 33 sRNA libraries refer to Figure S3. Setdb1 knockout induced −/−, uninduced +/+; for details see STAR Methods section. (C) tRF-targeted ERVs (in TS cells) are potentially active and younger than the average genomic ERV copy (avg: average; mdn: median; ± SD). (D) The majority of ERV-K targeted by 3′ tRFs are from the ETn and IAP families which are the most active LTR-retrotransposons in mouse (average RPM values of 4 replicate Setdb1 −/− and 7 replicate TS sRNA libraries). For comparison, relative abundance of ERV-K sequences in the mm9 mouse genome: 9% belong to the IAP family, 1% to the ETn family. See also Figure S1.