Machine learning reveals bilateral distribution of somatic L1 insertions in human neurons and glia

• Published in: Nature neuroscience 2021-02, Vol.24 (2), p.186-196
• Main Authors: Zhu, Xiaowei, Zhou, Bo, Pattni, Reenal, Gleason, Kelly, Tan, Chunfeng, Kalinowski, Agnieszka, Sloan, Steven, Fiston-Lavier, Anna-Sophie, Mariani, Jessica, Petrov, Dmitri, Barres, Ben A., Duncan, Laramie, Abyzov, Alexej, Vogel, Hannes, Moran, John V., Vaccarino, Flora M., Tamminga, Carol A., Levinson, Douglas F., Urban, Alexander E.
• Format: Article
• Language: English
• Subjects: 13/106; 13/109; 13/31; 14; 38; 38/35; 45/22; 45/23; 45/29; 45/77; 631/114/1305; 631/208/366; 631/378/1689/1799; 631/378/2571/1696; 631/378/2571/219; Adaptor Proteins, Signal Transducing - genetics; Adult; Animal Genetics and Genomics; Behavioral Sciences; Biological Techniques; Biomedical and Life Sciences; Biomedicine; Brain; Cation Transport Proteins - genetics; Embryogenesis; Embryonic Development - genetics; Embryonic growth stage; Female; Gene expression; Gene sequencing; Genome - genetics; Genomes; HeLa Cells; Hemispheres; High-Throughput Nucleotide Sequencing; Humans; Introns; Learning algorithms; Long Interspersed Nucleotide Elements; Machine Learning; Mental disorders; Mental Disorders - genetics; Mutagenesis, Insertional - genetics; Nervous system; Neurobiology; Neuroglia; Neuronal-glial interactions; Neurons; Neurosciences; Pathological effects; Pregnancy; Retroelements; Retrotransposition; Schizophrenia; Schizophrenia - genetics; Whole genome sequencing
• ISSN: 1097-6256; 1546-1726
• DOI: 10.1038/s41593-020-00767-4

Retrotransposons can cause somatic genome variation in the human nervous system, which is hypothesized to have relevance to brain development and neuropsychiatric disease. However, the detection of individual somatic mobile element insertions presents a difficult signal-to-noise problem. Using a machine-learning method (RetroSom) and deep whole-genome sequencing, we analyzed L1 and Alu retrotransposition in sorted neurons and glia from human brains. We characterized two brain-specific L1 insertions in neurons and glia from a donor with schizophrenia. There was anatomical distribution of the L1 insertions in neurons and glia across both hemispheres, indicating retrotransposition occurred during early embryogenesis. Both insertions were within the introns of genes ( CNNM2 and FRMD4A ) inside genomic loci associated with neuropsychiatric disorders. Proof-of-principle experiments revealed these L1 insertions significantly reduced gene expression. These results demonstrate that RetroSom has broad applications for studies of brain development and may provide insight into the possible pathological effects of somatic retrotransposition. Zhu et al. discover that in human brain there is widespread anatomic distribution of low-frequency somatic, mosaic L1 insertions, using deep whole-genome sequencing of neuronal and glial fractions and machine-learning analysis.