Transposons contribute to the acquisition of cell type-specific cis-elements in the brain

Mammalian brains have evolved in stages over a long history to acquire higher functions. Recently, several transposable element (TE) families have been shown to evolve into cis-regulatory elements of brain-specific genes. However, it is not fully understood how TEs are important for gene regulatory networks. Here, we performed a single-cell level analysis using public data of scATAC-seq to discover TE-derived cis-elements that are important for specific cell types. Our results suggest that DNA elements derived from TEs, MER130 and MamRep434, can function as transcription factor-binding sites based on their internal motifs for Neurod2 and Lhx2, respectively, especially in glutamatergic neuronal progenitors. Furthermore, MER130- and MamRep434-derived cis-elements were amplified in the ancestors of Amniota and Eutheria, respectively. These results suggest that the acquisition of cis-elements with TEs occurred in different stages during evolution and may contribute to the acquisition of different functions or morphologies in the brain. A public dataset of scATAC-seq is analyzed to identify transposable element-derived cis-elements specific to certain cell types, possibly contributing to different functions or morphologies in the brain.

Automated summary

A single-cell level analysis of public data from scATAC-seq reveals the importance of transposable element-derived cis-elements in specific cell types for gene regulatory networks. DNA elements derived from TEs, MER130 and MamRep434, are found to function as transcription factor-binding sites in glutamatergic neuronal progenitors. The amplification of MER130- and MamRep434-derived cis-elements occurred in the ancestors of Amniota and Eutheria, respectively, suggesting their contribution to different functions or morphologies in the brain.