Validation of MGE lineage interneuron-specific splicing regulated by Elavl2
We used network reverse engineering to derive a map of the neuron type-specific AS regulatory landscape of 133 mouse neocortical cell types, predicting splicing programs that drive neuronal diversity. Among these, Elavl2 was identified as a likely regulator of MGE lineage interneuron-specific splicing. We conducted RNAseq on the transcriptomes of ESC-derived MGE- and CGE-lineage interneurons to validate the program. A mouse ESC line was derived containing eGFP downstream of the Lhx6 promoter and tdTomato under the control of an Ai9 reporter allele driven by Cre downstream of the 5ht3a promoter. To encourage neuronal differentiation, an Ascl1 (encoding Mash1) gain-of-function construct driven by Nestin was also incorporated. After knocking out Elavl2 from this parent line, WT and Elavl2 KO ESCs were differentiated into interneurons and ESC-MGE and ESC-CGE cells were collected by FACS sorting for RNA isolation.