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

Virpi Töhönen,Marisa Jaconi,Mona Sheikhi,Sten Linnarsson,Juha Kere,Liselotte Vesterlund,Outi Hovatta,Eeva-Mari Jouhilahti,Shintaro Katayama,Elo Madissoon,Thomas R Bürglin,Giuditta Filippini-Cattaneo,Anna Johnsson

doi:10.1038/ncomms9207

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.

Highlights

Transcriptional program that drives human preimplantation development is largely unknown
We identify alternative promoters for genes using single-cell-tagged reverse transcription (STRT), a multiplex-tagged method for single-cell poly(A)-tailed RNA sequencing[7] that detects the very 50-end of every transcript, here called transcript far 50-ends (TFEs; Supplementary Note 1)
Assuming 5% messenger RNA (mRNA) content in total RNA, the brain sample mRNA input would be B2.5 pg, whereas a single oocyte may have an order of magnitude more mRNA9

Summary

Introduction

Transcriptional program that drives human preimplantation development is largely unknown. 1.91 billion (1,909,944,216) sequenced STRT reads derived from 308 cells representing 131 oocytes or embryos and 23 human brain RNA samples were analysed (Supplementary Table 1a–d).

Results

Conclusion