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PgmNr 304: The ATP-dependent chromatin remodeler CHD7 is critical for neuronal lineage differentiation by changing chromatin accessibility and nascent RNA.

Authors:
D.F. Hannum 1,2; H. Yao 2; S.F. Hill 3; R.D. Albanus 1; W. Lou 2; J.M. Skidmore 2; G.J. Sanchez 2; A. Saiakhova 6; S.L. Bielas 5; P.C. Scacheri 6; M. Ljungman 4; S.C.J. Parker 1,5; D.M. Martin 2,5

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Affiliations:
1) Dept Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI; 2) Dept of Pediatrics, University of Michigan, Ann Arbor, MI; 3) College of Literature, Science and Arts, University of Michigan, Ann Arbor, MI; 4) Dept of Radiation Oncology, University of Michigan, Ann Arbor, MI; 5) Dept of Human Genetics, University of Michigan, Ann Arbor, MI; 6) Dept of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH


Background: CHARGE syndrome, a rare congenital multiple anomaly condition, is caused mainly by haploinsufficiency of the ATP-dependent chromatin remodeling enzyme Chromodomain Helicase DNA binding protein 7 (Chd7). Brain abnormalities and intellectual disability are commonly observed in CHARGE patients. In addition, neuronal differentiation is reduced in CHARGE patient-derived iPSCs and in conditional knockout mouse brains. However, the underlying mechanisms of Chd7 function in nervous system development is not well understood.
Methods: Chd7+/+ and Chd7Gt/Gt (null) embryonic stem cells (ESCs) were derived from sibling blastocysts. Using a previously described protocol, ESCs were differentiated to neural progenitor cells (NPCs) and then further differentiated to neurons and glial cells. Quantitative RT-PCR, cell growth assays, immunostaining, ATAC-sequencing and Bru-sequencing were performed on ESCs and NPCs.
Results: Chd7 expression increased during ESC to NPC and neuronal differentiation, suggesting important roles for Chd7 in NPCs and neuronal differentiation. Interestingly, loss of Chd7 did not affect ESC or NPC identity or proliferation, but significantly reduced TUJ1+ neurons (P = 9.7 x 10-4) and GFAP+ glial cells (P = 5.8 x 10-9). ATAC- and Bru-seq experiments identified transcription factors (Pax3, Tbx3, Nkx6-1, and Zic5) with differentially accessible promoter regions and expression in Chd7Gt/Gt vs wildtype NPCs. These transcription factors are known to play roles in central nervous system development and neural/glial differentiation.
Conclusion: Chd7 loss does not adversely affect ESCs and NPCs but results in a decrease of differentiated neurons and glial cells. CHD7 has a profound effect on the chromatin landscape in NPCs and genome-wide studies indicate mis-regulated transcription factors in Chd7Gt/Gt NPCs. These studies suggest that Chd7 acts preferentially during the transition of NPCs to neurons and glial cells to promote one or more aspects of differentiation and lineage differentiation.