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

Area of Science:

• Developmental biology
• Neuroscience
• Genomics

Background:

• Neural progenitor specification and positioning are crucial for nervous system development.
• Neuromeres are transient anatomical compartments guiding progenitor positioning along the anteroposterior axis.
• The caudal hindbrain (CHB) organization posterior to rhombomere 6 lacks clear definition due to limited molecular data.

Purpose of the Study:

• To molecularly define and characterize progenitor cells in the caudal hindbrain (CHB) of developing zebrafish.
• To investigate the existence of pseudo-rhombomeres within the CHB.

Main Methods:

• Single-cell Multiome analysis was employed to simultaneously assess gene expression and chromatin state in individual nuclei.
• Zebrafish embryonic central nervous system (CNS) progenitors were identified and characterized.

Main Results:

• CHB progenitors were identified as a transcriptionally distinct population with unique accessible transcription factor binding motifs.
• No molecular evidence for multiple pseudo-rhombomeres within the CHB was found, though it shows dorsoventral subdivision.
• The CHB is closely related to rhombomere 6 early on but diverges over time, regulated by a unique gene regulatory network.

Conclusions:

• The early CHB represents a single neuromere compartment, not divisible into pseudo-rhombomeres.
• The CHB may share an embryonic origin with rhombomere 6, contributing to a refined understanding of hindbrain segmentation.