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

Nat Commun. 2015 Sep 11;6:8207. 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 5' Untranslated Regions
  • Blastocyst / metabolism*
  • Blastomeres / metabolism*
  • Embryonic Development / genetics*
  • Gene Expression Profiling
  • Gene Expression Regulation, Developmental*
  • HEK293 Cells
  • Homeodomain Proteins / genetics*
  • Homeodomain Proteins / metabolism
  • Humans
  • Oocytes / metabolism*
  • RNA, Messenger / metabolism*
  • Retroelements / genetics*
  • Sequence Analysis, RNA
  • Transcription Factors / genetics*
  • Transcription Factors / metabolism
  • Zygote / metabolism*

Substances

  • 5' Untranslated Regions
  • Homeodomain Proteins
  • RNA, Messenger
  • Retroelements
  • Transcription Factors