Genomics

Dataset Information

178

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain


ABSTRACT: Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and gene regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in early-to-mid human fetal brains. We found that early non-CG methylation accumulation at super-enhancers in both fetal brain and organoids marks forthcoming transcriptional repression in the fully developed brain. 74% of 35,627 demethylated regions identified during organoid differentiation overlapped with fetal brain regulatory elements. Interestingly, pericentromeric repeats showed widespread demethylation in multiple types of in vitro human neural differentiation models but not in fetal brain. Our study reveals that organoids recapitulate many epigenomic features of mid-fetal human brain and also identified novel non-CG methylation signatures of brain development. Overall design: MethylC-seq and RNA-seq of Cerebral Organoids differentiation

INSTRUMENT(S): Illumina HiSeq 2500 (Homo sapiens)

SUBMITTER: Joseph R Ecker  

PROVIDER: GSE82022 | GEO | 2016-12-20

SECONDARY ACCESSION(S): PRJNA323702

REPOSITORIES: GEO

altmetric image

Publications

Cerebral Organoids Recapitulate Epigenomic Signatures of the Human Fetal Brain.

Luo Chongyuan C   Lancaster Madeline A MA   Castanon Rosa R   Nery Joseph R JR   Knoblich Juergen A JA   Ecker Joseph R JR  

Cell reports 20161201 12


Organoids derived from human pluripotent stem cells recapitulate the early three-dimensional organization of the human brain, but whether they establish the epigenomic and transcriptional programs essential for brain development is unknown. We compared epigenomic and regulatory features in cerebral organoids and human fetal brain, using genome-wide, base resolution DNA methylome and transcriptome sequencing. Transcriptomic dynamics in organoids faithfully modeled gene expression trajectories in  ...[more]

Similar Datasets

| PRJNA323702 | ENA
| GSE97872 | GEO
2015-12-07 | E-GEOD-75140 | ArrayExpress
| GSE97919 | GEO
| PRJNA304502 | ENA
| GSE80073 | GEO
2019-12-30 | E-MTAB-7552 | ArrayExpress
2019-10-04 | E-MTAB-8234 | ArrayExpress
2019-11-15 | PXD011605 | Pride
| GSE86153 | GEO