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Nat Commun. 2019 Jul 18;10(1):3182. doi: 10.1038/s41467-019-11150-8.

Activation of neuronal genes via LINE-1 elements upon global DNA demethylation in human neural progenitors.

Author information

1
Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden.
2
Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, 141 52, Stockholm, Sweden.
3
Division of Molecular Medicine and Gene Therapy, Department of Laboratory Medicine and Lund Stem Cell Center, BMC A12, Lund University, 221 84, Lund, Sweden.
4
Laboratory of Proteomic Hematology, Department of Laboratory Medicine and Lund Stem Cell Center, BMC B12, Lund University, 221 84, Lund, Sweden.
5
Department of Genome Regulation, Max Planck Institute for Molecular Genetics, 14195, Berlin, Germany.
6
Wallenberg Neuroscience Center and Lund Stem Cell Center, Laboratory of Molecular Neurogenetics, Department of Experimental Medical Science, BMC A11, Lund University, 221 84, Lund, Sweden. johan.jakobsson@med.lu.se.

Abstract

DNA methylation contributes to the maintenance of genomic integrity in somatic cells, in part through the silencing of transposable elements. In this study, we use CRISPR-Cas9 technology to delete DNMT1, the DNA methyltransferase key for DNA methylation maintenance, in human neural progenitor cells (hNPCs). We observe that inactivation of DNMT1 in hNPCs results in viable, proliferating cells despite a global loss of DNA CpG-methylation. DNA demethylation leads to specific transcriptional activation and chromatin remodeling of evolutionarily young, hominoid-specific LINE-1 elements (L1s), while older L1s and other classes of transposable elements remain silent. The activated L1s act as alternative promoters for many protein-coding genes involved in neuronal functions, revealing a hominoid-specific L1-based transcriptional network controlled by DNA methylation that influences neuronal protein-coding genes. Our results provide mechanistic insight into the role of DNA methylation in silencing transposable elements in somatic human cells, as well as further implicating L1s in human brain development and disease.

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