Transcriptional program that drives human preimplantation development is largely unknown.

By using single-cell RNA sequencing of 348 oocytes, zygotes and single blastomeres from 2- to 3-day-old embryos, researchers provide a detailed analysis of the human preimplantation transcriptome.

By quantifying transcript far 5′-ends (TFEs), they include in their analysis transcripts that derive from alternative promoters.

Authors 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.

They identify significantly enriched gene regulatory motifs that often overlap with Alu elements.

This 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.