Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
Qian Yi Lee
Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States; Department of Bioengineering, Stanford University, Stanford, United States
Orly Wapinski
Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States
Rosa Castanon
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Joseph R Nery
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States
Moritz Mall
Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
Michael S Kareta
Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
Sean M Cullen
Stem Cells and Regenerative Medicine Center, Program in Developmental Biology, Baylor College of Medicine, Houston, United States
Center for Personal Dynamic Regulomes, Stanford University, Stanford, United States; Howard Hughes Medical Institute, Stanford University, Stanford, United States
Marius Wernig
Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, United States
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, United States; Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, United States
Direct reprogramming of fibroblasts to neurons induces widespread cellular and transcriptional reconfiguration. Here, we characterized global epigenomic changes during the direct reprogramming of mouse fibroblasts to neurons using whole-genome base-resolution DNA methylation (mC) sequencing. We found that the pioneer transcription factor Ascl1 alone is sufficient for inducing the uniquely neuronal feature of non-CG methylation (mCH), but co-expression of Brn2 and Mytl1 was required to establish a global mCH pattern reminiscent of mature cortical neurons. Ascl1 alone induced promoter CG methylation (mCG) of fibroblast specific genes, while BAM overexpression additionally targets a competing myogenic program and directs a more faithful conversion to neuronal cells. Ascl1 induces local demethylation at its binding sites. Surprisingly, co-expression with Brn2 and Mytl1 inhibited the ability of Ascl1 to induce demethylation, suggesting a contextual regulation of transcription factor - epigenome interaction. Finally, we found that de novo methylation by DNMT3A is required for efficient neuronal reprogramming.
