Florian Noack, Silvia Vangelisti, Gerald Raffl, Madalena Carido, Jeisimhan Diwakar et al.
How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.
Florian Noack, Silvia Vangelisti, Gerald Raffl, Madalena Carido, Jeisimhan Diwakar, Faye Chong, Boyan Bonev. Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler. 2022-02-07. https://doi.org/10.1038/s41593-021-01002-4
The in vivo MPRA pool was delivered by in utero electroporation at E13.5, and fixed electroporated cells were immunostained for Eomes and isolated by FACS at E15.5 to enrich intermediate progenitor cells. DNA/RNA barcode counts are provided for two biological replicates over the shared enhancer and motif-mutant library.
An in vivo episomal MPRA pool was delivered by in utero electroporation at E13.5 and recovered 48 h later from mScarlet-I-positive E15.5 somatosensory cortex cells. The library contains wild-type enhancer classes, scrambled controls, and transcription-factor motif-mutant constructs, with DNA/RNA barcode counts from two biological replicates.
The in vivo MPRA pool was delivered by in utero electroporation at E13.5, and fixed electroporated cells were immunostained for TUBB3 and isolated by FACS at E15.5 to enrich projection neurons. DNA/RNA barcode counts are provided for two biological replicates over the shared enhancer and motif-mutant library.
The in vivo MPRA pool was delivered by in utero electroporation at E13.5, and fixed electroporated cells were immunostained for Pax6 and isolated by FACS at E15.5 to enrich neural stem cells. DNA/RNA barcode counts are provided for two biological replicates over the shared enhancer and motif-mutant library.
Original supplemental and deposited inputs retained for this study. Download files individually or together as a ZIP; nested folders are preserved. Source reuse terms apply, and sequencing reads may be omitted.
Download all 11 files (ZIP)GSE155677_family.soft.gzGSE155677_supplementary_filelist.txtGSM5583719_CRE_BC_association.pickle.gzGSM5583719_design.fa.gzGSM5583719_labels.tsv.gzGSM5583720_MPRA_pool_rep1_rep2.tar.gzGSM5583722_MPRA_PAX6_rep1_rep2.tar.gzGSM5583724_MPRA_EOMES_rep1_rep2.tar.gzGSM5583726_MPRA_TUBB3_rep1_rep2.tar.gzSupplementary_Data_10_primers.xlsxSupplementary_Data_1_assay_QC.xlsx