GSE106956
In vivo nuclear capture and molecular profiling identifies Gmeb1 as a transcriptional regulator essential for dopamine neuron function
Midbrain dopamine (mDA) neurons play a central role in reward signaling and are widely implicated in psychiatric and neurodegenerative disorders. To understand how mDA neurons perform these functions, it is important to understand how mDA-specific genes are regulated. However, cellular heterogeneity in the mammalian brain presents a major challenge to obtaining this understanding. To this end, we developed a virus-based approach to label and capture mDA nuclei for transcriptome (RNA-Seq), and low-input chromatin accessibility (liDNase-Seq) profiling, followed by predictive modeling to identify putative transcriptional regulators of mDA neurons. Using this method, we identified Gmeb1, a transcription factor predicted to regulate expression of Th and Dat, genes critical for dopamine synthesis and reuptake, respectively. Gmeb1 knockdown in mDA neurons resulted in downregulation of Th and Dat, as well as in severe motor deficits. This study thus identifies Gmeb1 as a master regulator of mDA gene expression and function, and provides a general method for identifying cell type-specific transcriptional regulators.. Overall design: mDA neurons were targeted by injection of an AAV-DIO-KASH-HA (KASH-HA) virus into the midbrain of dopamine transporter (DAT)-Cre heterozygous (het) mice. mDA KASH-HA tagged nuclei were FANS sotred for transcriptome (RNA-Seq), and low-input chromatin accessibility (liDNase-Seq) profiling. To study the transcriptional effects of Gmeb1 knockdown in mDA neurons, we generated RNA-Seq profiles of mDA neurons  from (DAT)-Cre het mice injected with shGmeb1 or shScrambled virus.