Fig. 4: LIM homeobox genes parcellate reticulospinal neurons into spatially and transcriptionally distinct subsets.
From: A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
a, Nuclei from PONS- and MED-enriching dissections were subset and re-embedded (10x data, n = 22,100 nuclei). Left/middle, UMAP of nuclei from PONS- and MED-enriching dissections coloured by ROI and LIM groups, respectively. Right, each LIM group was subset and re-embedded to identify the final types depicted in Fig. 1c. Shown here is the re-embedding of the Lhx2/9 group. b, Dot plot showing expression of Lmx1b, Lhx2, Lhx9, Lhx3, Lhx4, Lhx1 and Lhx5 grouped by the five LIM groups. c, Representative MERFISH sections of ReSN types, each coloured by their respective LIM-defined subclass. d, Anatomical distributions of LIM-defined subclasses summarized using representative coronal reconstructions of Cre-dependent retrogradely labelled nuclei in transgenic lines corresponding to LIM-defined subclasses (from Extended Data Fig. 9). Panel 1: Dbh-Cre, TH-Cre and Phox2b-Cre, coloured as HB Lmx1b Nora subclass. Panel 2: ePet-Cre, coloured as HB Lmx1b Sero subclass. Panel 3: Lhx2-2A-CreER, coloured as HB Lhx2/9 subclass. Panel 4: Chx10-Cre, coloured as HB Lhx3/4 subclass. Panel 5: ChAT-Cre, GlyT2-Cre, and Gcg-iCre, coloured as HB Lhx1/5 subclass. AP, anterior–posterior position (relative to Bregma); B, Barrington’s nucleus; LC, locus coeruleus; LDT, laterodorsal tegmental nucleus; IRN, intermediate reticular nucleus; PARN, parvicellular reticular nucleus; PL, paralemniscal nucleus (Paxinos nomenclature54); PPN, pedunculopontine nucleus; PPY, parapyramidal nucleus; PRNr, pontine reticular nucleus rostral part; RF, reticular formation; RM, nucleus raphe magnus; RO, nucleus raphe obscurus; RPA, nucleus raphe pallidus; SubCD/CV/CA, subcoeruleus nucleus dorsal/ventral/alpha parts (Paxinos).
