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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 30, 2024 |
| Title |
Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1 |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Methylation profiling by high throughput sequencing
Other
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| Summary |
Direct neuronal reprogramming is a promising approach to regenerate neurons from local glial cells. However, mechanisms of epigenome remodeling and co-factors facilitating this process are unclear. Here, we combine single-cell multiomics with genome-wide profiling of 3D nuclear architecture and DNA methylation in mouse astrocyte-to-neuron reprogramming mediated by Neurogenin2 (Ngn2) and its phosphorylation-resistant form (PmutNgn2), respectively. We show that Ngn2 drives multilayered chromatin remodelling at dynamic enhancer-gene interaction sites. PmutNgn2 leads to higher reprogramming efficiency and enhances epigenetic remodeling associated with neuronal maturation. However, the differences in binding sites or downstream gene activation cannot fully explain this effect. Instead, we identify Yy1, a transcriptional co-factor, recruited by direct interaction with Ngn2 to its target sites. Upon deletion of Yy1, activation of neuronal enhancers, genes, and ultimately reprogramming are impaired without affecting Ngn2 binding. Thus, our work highlights the key role of interactors of proneural factors in direct neuronal reprogramming.
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| Overall design |
Single cell multiome (scRNA-seeq + scATAC-seq), bulk ATAC-seq, bulk RNA-seq, ChIP-seq, Cut&Run and Methyl-HiC was performed on primary mouse astrocytes (2 days post induction) transduced with doxycycline-inducible lentiviral constructs expressing either GFP, Ngn2 and PmutNgn2 respectively. Since the constructs also expressed GFP, the astrocytes were FACS sorted based on GFP expression. To profile the effect of Yy1 on direct neuronal reprogramming. scRNA-seq and bulk ATAC-seq was performed on Yy1 KO primary mouse astrocytes (2 days post induction) transduced with a doxycycline-inducible lentiviral construct expressing Ngn2.
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| Contributor(s) |
Pereira A, Diwakar J, Masserdotti G, Beşkardeş S, Simon T, So Y, Martín-Loarte L, Bergemann F, Vasan L, Schauer T, Danese A, Bocchi R, Colomé-Tatché M, Schuurmans C, Philpott A, Straub T, Bonev B, Götz M |
| Citation(s) |
38956165 |
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| Submission date |
Jul 21, 2022 |
| Last update date |
Aug 08, 2024 |
| Contact name |
Boyan Bonev |
| E-mail(s) |
boyan.bonev@helmholtz-munich.de
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| Organization name |
Helmholtz Zentrum München
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| Lab |
Bonev Lab
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| Street address |
Ingolstädter Landstr. 1
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| City |
Neuherberg |
| State/province |
Deutschland |
| ZIP/Postal code |
85764 |
| Country |
Germany |
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| Platforms (3) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
| GPL32159 |
NextSeq 1000 (Mus musculus) |
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| Samples (64)
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| Relations |
| BioProject |
PRJNA860940 |
| SRA |
SRP387431 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208742_GFP_ATAC_peaks.bed.gz |
3.3 Mb |
(ftp)(http) |
BED |
| GSE208742_GFP_D2.bw |
567.0 Mb |
(ftp)(http) |
BW |
| GSE208742_Ngn2_ATAC_peaks.bed.gz |
2.9 Mb |
(ftp)(http) |
BED |
| GSE208742_Ngn2_ChIP_peaks.bed.gz |
636.4 Kb |
(ftp)(http) |
BED |
| GSE208742_Ngn2_D2.bw |
575.8 Mb |
(ftp)(http) |
BW |
| GSE208742_Ngn2_chip_D2.bw |
447.3 Mb |
(ftp)(http) |
BW |
| GSE208742_Pereira_et_al_2022_GEO.xlsx |
60.8 Kb |
(ftp)(http) |
XLSX |
| GSE208742_PmutNgn2_ATAC_peaks.bed.gz |
3.4 Mb |
(ftp)(http) |
BED |
| GSE208742_PmutNgn2_D2.bw |
635.5 Mb |
(ftp)(http) |
BW |
| GSE208742_RAW.tar |
26.7 Gb |
(http)(custom) |
TAR (of BED, BEDGRAPH, BW, MTX, NARROWPEAK, TAB, TSV, TXT) |
| GSE208742_Yy1_KO_ATAC_merge.bw |
154.9 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_ATAC_peaks.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
| GSE208742_Yy1_KO_ATAC_rep1.bw |
100.2 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_ATAC_rep2.bw |
81.9 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_Ngn2+_ATAC_merge.bw |
218.6 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_Ngn2+_ATAC_peaks.bed.gz |
2.0 Mb |
(ftp)(http) |
BED |
| GSE208742_Yy1_KO_Ngn2+_ATAC_rep1.bw |
170.6 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_Ngn2+_ATAC_rep2.bw |
79.9 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_KO_Ngn2+_barcodes.tsv.gz |
20.5 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_KO_Ngn2+_features.tsv.gz |
186.8 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_KO_Ngn2+_matrix.mtx.gz |
42.6 Mb |
(ftp)(http) |
MTX |
| GSE208742_Yy1_KO_barcodes.tsv.gz |
20.2 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_KO_features.tsv.gz |
186.8 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_KO_matrix.mtx.gz |
51.5 Mb |
(ftp)(http) |
MTX |
| GSE208742_Yy1_WT_ATAC_merge.bw |
163.7 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_ATAC_peaks.bed.gz |
1.8 Mb |
(ftp)(http) |
BED |
| GSE208742_Yy1_WT_ATAC_rep1.bw |
132.1 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_ATAC_rep2.bw |
62.6 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_Ngn2+_ATAC_merge.bw |
136.2 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_Ngn2+_ATAC_peaks.bed.gz |
1.9 Mb |
(ftp)(http) |
BED |
| GSE208742_Yy1_WT_Ngn2+_ATAC_rep1.bw |
81.3 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_Ngn2+_ATAC_rep2.bw |
76.9 Mb |
(ftp)(http) |
BW |
| GSE208742_Yy1_WT_Ngn2+_barcodes.tsv.gz |
21.9 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_WT_Ngn2+_features.tsv.gz |
186.8 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_WT_Ngn2+_matrix.mtx.gz |
49.1 Mb |
(ftp)(http) |
MTX |
| GSE208742_Yy1_WT_barcodes.tsv.gz |
20.5 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_WT_features.tsv.gz |
186.8 Kb |
(ftp)(http) |
TSV |
| GSE208742_Yy1_WT_matrix.mtx.gz |
50.2 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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