A fundamental question in developmental and stem cell biology concerns the origin and nature of signals that initiate asymmetry leading to pattern formation and self-organization. Instead of having prominent pre-patterning determinants as present in model organisms (worms, sea urchin, frog), we propose that the mammalian embryo takes advantage of more subtle cues such as compartmentalized intracellular reactions that generate micro-scale inhomogeneity, which is gradually amplified over several cellular generations to drive pattern formation while keeping developmental plasticity. It is therefore possible that by making use of compartmentalized information followed by its amplification, mammalian embryos would follow general principle of development found in other organisms in which the spatial cue is more robustly presented.

Although high-throughput RNA sequencing (RNA-seq) has greatly advanced small non-coding RNA (sncRNA) discovery, the currently widely used complementary DNA library construction protocol generates biased sequencing results. This is partially due to RNA modifications that interfere with adapter ligation and reverse transcription processes, which prevent the detection of sncRNAs bearing these modifications. Here, we present PANDORA-seq (panoramic RNA display by overcoming RNA modification aborted sequencing), employing a combinatorial enzymatic treatment to remove key RNA modifications that block adapter ligation and reverse transcription. PANDORA-seq identified abundant modified sncRNAs-mostly transfer RNA-derived small RNAs (tsRNAs) and ribosomal RNA-derived small RNAs (rsRNAs)-that were previously undetected, exhibiting tissue-specific expression across mouse brain, liver, spleen and sperm, as well as cell-specific expression across embryonic stem cells (ESCs) and HeLa cells. Using PANDORA-seq, we revealed unprecedented landscapes of microRNA, tsRNA and rsRNA dynamics during the generation of induced pluripotent stem cells. Importantly, tsRNAs and rsRNAs that are downregulated during somatic cell reprogramming impact cellular translation in ESCs, suggesting a role in lineage differentiation.

To mark the 15th anniversary of Nature Methods, we asked scientists from across diverse fields of basic biology research for their views on the most exciting and essential methodological challenges that their communities are poised to tackle in the near future.