Novel PRD-like homeodomain transcription factors and retrotransposon elements in early human development

Virpi Töhönen, Shintaro Katayama, Liselotte Vesterlund, Eeva-Mari Jouhilahti, Mona Sheikhi, Elo Madissoon, Giuditta Filippini-Cattaneo, Marisa Jaconi, Anna Johnsson, Thomas R. Bürglin, Sten Linnarsson, Outi Hovatta and Juha Kere ()
Additional contact information
Virpi Töhönen: Karolinska Institutet
Shintaro Katayama: Karolinska Institutet
Liselotte Vesterlund: Karolinska Institutet
Eeva-Mari Jouhilahti: Karolinska Institutet
Mona Sheikhi: Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge
Elo Madissoon: Karolinska Institutet
Giuditta Filippini-Cattaneo: ProCreaLab SA
Marisa Jaconi: Faculty of Medicine, Geneva University
Anna Johnsson: Karolinska Institutet
Thomas R. Bürglin: Karolinska Institutet
Sten Linnarsson: Karolinska Institutet
Outi Hovatta: Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge
Juha Kere: Karolinska Institutet

Nature Communications, 2015, vol. 6, issue 1, 1-9

Abstract: Abstract Transcriptional program that drives human preimplantation development is largely unknown. Here, by using single-cell RNA sequencing of 348 oocytes, zygotes and single blastomeres from 2- to 3-day-old embryos, we provide a detailed analysis of the human preimplantation transcriptome. By quantifying transcript far 5′-ends (TFEs), we include in our analysis transcripts that derive from alternative promoters. We show that 32 and 129 genes are transcribed during the transition from oocyte to four-cell stage and from four- to eight-cell stage, respectively. A number of identified transcripts originates from previously unannotated genes that include the PRD-like homeobox genes ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB and LEUTX. Employing de novo promoter motif extraction on sequences surrounding TFEs, we identify significantly enriched gene regulatory motifs that often overlap with Alu elements. Our high-resolution analysis of the human transcriptome during preimplantation development may have important implications on future studies of human pluripotent stem cells and cell reprograming.

Date: 2015
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DOI: 10.1038/ncomms9207

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