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. Author manuscript; available in PMC: 2015 Jan 31.
Published in final edited form as: Nature. 2014 Jul 23;511(7511):611–615. doi: 10.1038/nature13581

Figure 4. LTR subfamily dynamics are divided into early and late preimplantation phases.

Figure 4

a. Violin plots forthe four LTR families present in human over early development and ESC derivation.

b. Pie charts of LTR family expression calculated as the number of fragments per million (FPM) that align to elements with in the family.

c. Mean methylation of notable ERV1, ERVK, and MalR subfamilies. Three ERV1 subfamilies are included to represent discrete dynamics: gamete/early embryonic hypomethylation (LTR12c), constitutive methylation (HERV9-INT) and rapid demethylation (LTR7). The ERVK subfamily LTR5Hs is also demethylated.

d. Expression dynamics for the same subfamilies in (c). LTR12c is expressed early and downregulated in the blastocyst. Alternatively, LTR7 is expressed throughout, but upregulated in the blastocyst and maintained in hESCs, where it accounts for the majority of ERV1 transcripts. Like LTR7, LTR5Hs is only intermediately methylated during ESC derivation and is embryonically induced. Alternatively, the ERV1 HERV9-INT remains repressed. MLT1H2 is the prevailing MalR transcribed in the oocyte and is lost after fertilization. Expression is the fragments per million that align to subfamily elements, divided by the kb annotated as the subfamily in the genome (FPKM).