scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.

Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. Here, we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium that represent prospective rhombomere r2/r3 (possibly including r1), r4, and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires the resolution of mixed transcription and chromatin states.

Kim YI ，O'Rourke R ，Sagerström CG 《eLife》

scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities.

Kim YI ，O'Rourke R ，Sagerström CG 《-》

scMultiome analysis identifies a single caudal hindbrain compartment in the developing zebrafish nervous system.

Warns J ，Kim YI ，O'Rourke R ，Sagerström CG ... -  《Neural Development》

Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish.

Ghosh P ，Maurer JM ，Sagerström CG 《Neural Development》

vhnf1 integrates global RA patterning and local FGF signals to direct posterior hindbrain development in zebrafish.

Hernandez RE ，Rikhof HA ，Bachmann R ，Moens CB ... -  《DEVELOPMENT》