The dark transcriptome mouse organogenesis cell atlas

Single-cell atlases have transformed our understanding of mammalian tissue biology, yet the diverse noncoding "dark transcriptome" remains largely uncharted. Here, we present the Dark Transcriptome Mouse Organogenesis Cell Atlas (DT-MOCA), comprising 276,455 cells across embryonic days 11 to 18 and jointly capturing protein-coding transcripts and five major classes of noncoding RNAs through single-nucleus total RNA sequencing, establishing the first comprehensive catalog of noncoding RNAs across major cell types and developmental lineages. We found that long noncoding RNA and microRNA profiles distinguished major cell types and developmental lineages with resolution comparable to messenger RNA, whereas transfer RNA, small nuclear RNA, and small nucleolar RNA programs were less cell type-discriminative and more broadly shared. We further resolve noncoding RNA expression patterns as lineage-specific, temporally modulated, or coordinately regulated by cell identity and developmental stage. We observed that temporally regulated long noncoding RNAs were evolutionarily younger than those associated with cell identity. We further generate a catalog of the change of noncoding RNAs cross all 11 major developmental trajectories. It revealed lineage-specific coordination between transfer RNA supply and codon demand during musculoskeletal organogenesis as well as dynamic microRNA and small nucleolar RNA programs during the central nervous system development. We observed microRNAs converge on regulators of proliferation and gliogenesis and shared induction of Snord116 defining a developmental window relevant to Prader-Willi syndrome. Together, this atlas provides a comprehensive catalog of the developmental dark transcriptome and reveals how noncoding RNA programs are organized across cell identity, developmental time, and lineage progression.