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

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.

New genes from old: asymmetric divergence of gene duplicates and the evolution of development

“…The conundrum was resolved when transcriptome data were published for the earliest stages of human development, before blastocyst formation [64,67], and therefore, earlier than the stages mimicked by hESC. These data revealed that human ARGFX, DPRX, LEUTX, TPRX1 and TPRX2 are specifically expressed from 8-cell to morula in a striking and specific pulse of expression just before cell fates are established [61,63] (figure 5b). These pre-blastocyst embryonic stages are totipotent and will form every tissue of the Figure 4.…”

“…When examining the genomic regions around the Crx-derived mammalian PRD-class genes discussed above, we found much evidence for dynamic gain and loss of genes. For example, a conserved non-coding element associated with the parental and daughter genes is also found in additional copies, with no neighbouring gene, implying that additional Crx-derived genes had been generated, but then lost from all extant lineages [61,63]. In addition, many cases of recent tandem duplication are observed that must have occurred subsequent to the origin of the genes, including additional Tprx loci in tenrec, bat, horse, mouse and rat, and additional Leutx genes in guinea pig and elephant [61,63].…”

“…R. Soc. B 372: 20150480 gene is found in every eutherian species because of gene losses; for example, one gene (Pargfx) found in horse and dog has been lost in humans, and many of the genes are lost in mice and rats [61,63]. In summary, it can be deduced that the Argfx, Dprx, Tprx and Leutx gene families arose by tandem duplication from the Crx gene in the stem lineage of the placental mammals, after their split from marsupials (figure 5a).…”

“…Two indirect approaches have been used. First, Töhönen et al [61] used a bioinformatic approach to identify putative promoter motifs enriched at this stage of development, and showed enrichment in putative binding sites for PRD-class proteins. This suggested transcription factor roles for the divergent PRD-class proteins, and allowed some possible targets to be postulated.…”

SCPattern: A statistical approach to identify and classify expression changes in single cell RNA-seq experiments with ordered conditions

“…Compare to ordered bulk RNA-seq experiments which measure averaged expression over thousands of cells for a given time point or position, ordered scRNA-seq experiments provide unprecedented power to understand how a cell population's expression distribution changes during a biological process. Recent ordered scRNA-seq studies include experiments studying differentiation of human T cells (Buettner et al, 2015), human myoblasts (Trapnell et al, 2014), and human preimplantation development (Yan et al, 2013;Blakeley et al, 2015;Töhönen et al, 2015), to name a few.…”