Transcriptomic Signatures of Projection Class Neurons for Vocal Control

Author

Stephanie Joy Marcus

Date of Award

2023

Document Type

Thesis

Degree Name

Doctor of Philosophy (PhD)

RU Laboratory

Jarvis Laboratory

Abstract

Vocal learning is the ability to modify acoustic structure and syntax of vocalizations. This rare trait is thought to have independently evolved three times in birds and five times in mammals.Vocal learning species exhibit an underlying convergence in brain circuitry, including a direct, forebrain-to-brainstem projection critical for the motor production of learned vocalizations.The remarkable convergence in fore brain vocal circuitry is associated with convergent molecular specializations.In characterizing specializations for vocal motor control across species, we can expand our knowledge of vocal learning and the evolution of this trait.

In the first section of this thesis, I generated a high-quality reference genome assembly for the common marmoset, anon-human primate that displays flexible vocal communication abilities in complex social settings as well as rudimentary neural circuits for vocal motor control. My findings demonstrate the power of using a trio-binning approach, in combination with long-read sequencing technologies, to produce a diploid genome with the two parental haplotypes assembled independently. This method captures the full range of heterozygous variations at high rates of accuracy between parental alleles in this species that exhibits naturally high levels of chimerism. The genome assembly was annotated and is now the National Center for Biotechnology Information (NCBI)reference assembly for the common marmoset. In the second section of this thesis, I generated and analyzed single nucleus RNA sequencing data sets from vocal motor and locomotor brain regions of marmoset and zebra finch (an avian model of vocal learning) to identify long-range projection classes of neurons, assess transcriptional markers, and make cross-species comparisons. In the marmoset, I identified layer 5extratelencephalic-projecting (L5 ET) excitatory neurons of orofacial and hindlimb primary motor cortex. Compared to L5 ET hindlimb neurons, orofacial L5 ETs showed low fold, though significant, molecular specializations, including rudimentary expression patterns found in projection classes of neurons for vocal learning. In the finch, I identified excitatory neurons unique to the RA song nucleus, showing transcriptional patterns consistent with the direct projection neurons (RA_nXIIts) associated with vocal production and vocal learning behavior. This class of neurons is marked by RBFOX1expression and was annotated, with high confidence, as L5 ET neurons when mapped into a human M1 reference dataset. Cross-species integration of finch, marmoset, and human datasets showed one cluster including human L5 ET, marmoset L5 ET, and finch RA_nXIIts RBFOX1+ neurons. Comparing these groups of neurons across species, I found distinct gene expression patterns of RA_nXIIts neurons related to axonogenesis, calcium homeostasis, rapid firing, and ATP synthesis. This neuronal class also exhibits high expression of L5 ET markers that are primate-specific among mammals. Finally, cross-species genome alignments of RBFOX1promoter regions show high sequence similarities among vocal learning bird species. Together, the data I present here support a hypothesis that certain cell types of the avian vocal learning system evolved to incorporate molecular attributes making them functionally analogous to mammalian cortical layer neurons.

Comments

A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy

Recommended Citation

Marcus, Stephanie Joy, "Transcriptomic Signatures of Projection Class Neurons for Vocal Control" (2023). Student Theses and Dissertations. 767.
https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/767