Supplementary Figure 6: Further characterization of the relationship between transcription levels at HERV-H elements and regular genes and formation of TAD boundaries. | Nature Genetics

Supplementary Figure 6: Further characterization of the relationship between transcription levels at HERV-H elements and regular genes and formation of TAD boundaries.

From: Transcriptionally active HERV-H retrotransposons demarcate topologically associating domains in human pluripotent stem cells

Supplementary Figure 6

(a) Aggregated DI score profiles of the TAD-boundary associated with HERV-Hs in multiple H1 ESC derived lineages and iPSCs. ESC: embryonic stem cell; MES: mesendoderm. MSC: mesenchymal stem cell; NPC: neural progenitor cell; TRO: trophoblast-like cell; iPSC: induced pluripotent stem cell. Interestingly, in human mesendoderm cells (an early human embryonic state that gives rise to mesoderm and endoderm cells), both the expression of these HERV-Hs and their corresponding TAD boundary strength were approximately half the levels compared to those observed in hESCs. There might be some un-differentiated cells in this population. (b) Heatmaps showing the aggregated DI score profile centered on the TSSs of genes (ranked by expression levels from high to low; every 1000 genes were segregated into bins, and separated by whether or not having a CTCF peak within 20kb of TSS). The DI score profile of top 50 HERV-H is shown at the bottom and the distribution of the HERV-H’s rank is shown on the right.

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