An atlas of small non-coding RNAs in Human Preimplantation Development [Small-Seq]
Our current understanding of the molecular circuitries that govern early embryogenesis remains limited, particularly in the human. Small non-coding RNAs (sncRNAs) regulate gene expression transcriptionally and post-transcriptionally, however, the expression of specific biotypes and their dynamics during preimplantation development remains to be determined. Using Small-seq, we identified the abundance of and dynamic expression of piRNA, rRNA, snoRNA, tRNA, and miRNA in human embryos from day 3 to 7. Among the biotypes, both miRNA and snoRNA displayed distinct associations with developmental time and lineage formation, many of which were  found to target key gene expression programs in pluripotency and lineage establishment. We observed an enrichment of the chromosome 19 miRNA cluster (C19MC) in the trophectoderm (TE), and the chromosome 14 miRNA cluster (C14MC) and MEG8-related snoRNAs in the inner cell mass (ICM). Additionally, isomiR analyses suggested miRNAs are modified differentially during blastulation. Finally, six novel miRNAs and their embryo gene targets we identified. Our analyses provide the first comprehensive measure of sncRNA biotypes and their corresponding dynamics throughout human preimplantation development, providing an extensive resource. Elucidating the functional roles of sncRNAs during preimplantation development will provide insight into the establishment of the blastocyst and exit from pluripotency.  Further, better understanding the miRNA regulatory programs in human embryogenesis will inform strategies to improve embryo development and outcomes of assisted reproductive technologies. We anticipate broad usage of our data as a resource for studies aimed at understanding embryogenesis, optimising stem cell-based models, assisted reproductive technology, and stem cell biology. Overall design: We utilized Small-seq in parallel with Co-seq on single-cells derived from human embryos spanning embryonic day (E) 3 to E7.