|
| Status |
Public on Oct 18, 2022 |
| Title |
The RNA Binding Protein Dead End1 Is Differentially Expressed in Male Germ Cells During Late Gestation and Targets Chromatin Modifiers and Translational Machinery |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Other
Third-party reanalysis
|
| Summary |
DND1 is essential to maintain germ cell identity. Loss of Dnd1 function results in trans-differentiation of germ cells to somatic fates in zebrafish or the formation of teratomas in mice. To explore the mechanistic role of DND1, we recently developed a transgenic mouse line in which a functional fusion protein between DND1 and GFP is expressed from the endogenous locus (Dnd1GFP). Surprisingly, we found that this reporter distinguishes two male germ cell populations (MGCs) during late gestation cell cycle arrest (G0). Most MGCs express low levels of DND1-GFP, but 5-12% of the population express high levels of DND1-GFP. An RNA-seq time course during late gestation revealed that Dnd1 transcript levels as well as transcript levels for multiple epigenetic regulators are 5-10-fold higher in DND1-GFP-hi cells. Furthermore, using antibodies against DND1-GFP for RNA immunoprecipitation (RIP) time course sequencing during late gestation, we identified multiple epigenetic and translational regulators that are binding targets of DND1 during G0. Among these targets are DNA methyltransferases (Dnmts), the enzyme Setdb1 that imposes the nuclear lamina associated repressive histone mark (H3K9me3), five Tudor domain proteins (Tdrds), four actin dependent regulators (Smarcs), and a group of ribosomal and Golgi proteins. These data suggest that DND1 binds to transcripts of a group of epigenetic enzymes and gates their translation during MGC G0 arrest in late gestation.
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| Overall design |
Transcriptome time course (E16.5, E18.5) comparing mouse male germ cells with high and low levels of DND1 done in conjunction with a RNA immunoprecipitation sequencing (RIP-seq) time course (E14.5, E16.5, E18.5), to identify transcript targets of DND1 at each timepoint. Findings were initially corroborated against re-analysis of E16.5 scRNA-seq male germ cell data from Law et al. 2019 Nat Comm (GSE124904).
Demultiplexed fastq files of E16.5 male germ cell scRNA-seq data originally published in Law et al. 2019 (GSE124904; GSM3559066-GSM3559068) was downloaded from the Sequence Read Archive (SRA) using the SRA toolkit (n=3: SRR8427519, SRR8427520, SRR8427521) and re-analyzed as following:
The Cell Ranger (v3.1.0) Count pipeline (read alignment, UMI counting) was performed on each biological replicate referenced to the mm10 mouse genome (GRCm38, v3.0.0).
The Cell Ranger Aggregation pipeline was performed on the molecule_h5 files for each biological replicate to generate a single integrated E16.5 dataset for downstream analysis.
Quality control and clustering was performed on the aggregated data using Seurat (v4.0.5)
resulting in the following data files:
Proc_scRNAseq_OatleyE16.5_aggr.cloupe
scRNAseq_Inter_barcodes.tsv.gz
scRNAseq_Inter_features.tsv.gz
scRNAseq_Inter_matrix.mtx.gz
scRNAseq_Supp_scRNA-seq_OatleyE16.5_aggr.RData
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| Web link |
https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1010656
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| |
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| Contributor(s) |
Capel B, Ruthig VA |
| Citation(s) |
36857387 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| F32 GM129956 |
DND1 Mediated Posttranscriptional Regulation in Murine Prospermatogonia During G1/G0 Arrest |
DUKE UNIVERSITY |
Victor A. Ruthig |
| R37 HD039963 |
Opposing Pathways in Mammalian Sex Determination |
DUKE UNIVERSITY |
Blanche Capel |
|
| |
| Submission date |
Feb 28, 2022 |
| Last update date |
Jan 16, 2024 |
| Contact name |
Victor A Ruthig |
| E-mail(s) |
Victor.Ruthig@CUAnschutz.edu
|
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pediatrics, Section of Developmental Biology
|
| Street address |
12800 E 19th Ave
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (34)
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| Relations |
| Reanalysis of |
GSM3559066 |
| Reanalysis of |
GSM3559067 |
| Reanalysis of |
GSM3559068 |
| BioProject |
PRJNA811161 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE197610_DND1seq_Supp_DND1seqFilters.RData.gz |
24.0 Mb |
(ftp)(http) |
RDATA |
| GSE197610_DND1seq_Supp_Dnd1Terseq_Unique.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GCList_Junique.csv.gz |
20.5 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GCList_Lunique.csv.gz |
304.9 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GCList_T_Iunique.csv.gz |
7.3 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GCList_T_T1unique.csv.gz |
18.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0000077_DNAdamage_.csv.gz |
5.9 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0003723_RNAbinding_.csv.gz |
26.4 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0006119_OxidativePhosphorylation_.csv.gz |
3.8 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0006412_Translation_.csv.gz |
29.6 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0007010_CytoOrg_.csv.gz |
60.7 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0007049_CellCycle_.csv.gz |
81.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0016570_HistoneModification_.csv.gz |
19.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0030198_ECMorg_.csv.gz |
12.1 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0033182_HistUbi_.csv.gz |
833 b |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0044391_RibosomalSubunit_.csv.gz |
4.9 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0045786_NegCellCycle_.csv.gz |
20.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0045787_PosCellCycle_.csv.gz |
16.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0048193_Golgi_.csv.gz |
13.8 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0051276_ChroOrg_.csv.gz |
52.4 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0061621_CanonicalGlycolysis_.csv.gz |
1.3 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-0071103_DNAconCha_.csv.gz |
21.0 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_GO-1902275_RchrOrg_.csv.gz |
10.5 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_RIPgeneList.csv.gz |
51.5 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_SomaList_Junique.csv.gz |
26.4 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_SomaList_Sunique.csv.gz |
11.0 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_SomaList_Tunique.csv.gz |
65.7 Kb |
(ftp)(http) |
CSV |
| GSE197610_DND1seq_Supp_lohiGeneList.csv.gz |
61.6 Kb |
(ftp)(http) |
CSV |
| GSE197610_Proc_DND1seq_Filtering.xlsx |
2.2 Mb |
(ftp)(http) |
XLSX |
| GSE197610_Proc_RIPseq_ripRNAseqMaster.xlsx |
12.5 Mb |
(ftp)(http) |
XLSX |
| GSE197610_Proc_hiloRNAseq_hiloRNAseqMaster.xlsx |
16.3 Mb |
(ftp)(http) |
XLSX |
| GSE197610_Proc_scRNAseq_OatleyE16.5_aggr.cloupe.gz |
84.3 Mb |
(ftp)(http) |
CLOUPE |
| GSE197610_RAW.tar |
58.2 Mb |
(http)(custom) |
TAR (of SF) |
| GSE197610_RIPseq_Supp_DND1-GFP_RIP-seq.RData.gz |
74.2 Mb |
(ftp)(http) |
RDATA |
| GSE197610_RIPseq_Supp_MGIBatchReport_RIP.csv.gz |
585.0 Kb |
(ftp)(http) |
CSV |
| GSE197610_Supp_ScriptFull.txt.gz |
21.5 Kb |
(ftp)(http) |
TXT |
| GSE197610_hiloRNAseq_Supp_DND1-GFP_hiloRNA-seq.RData.gz |
118.6 Mb |
(ftp)(http) |
RDATA |
| GSE197610_hiloRNAseq_Supp_MGIBatchReport_hilo.csv.gz |
581.2 Kb |
(ftp)(http) |
CSV |
| GSE197610_scRNAseq_Inter_barcodes.tsv.gz |
24.0 Kb |
(ftp)(http) |
TSV |
| GSE197610_scRNAseq_Inter_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSE197610_scRNAseq_Inter_matrix.mtx.gz |
62.8 Mb |
(ftp)(http) |
MTX |
| GSE197610_scRNAseq_Supp_scRNA-seq_OatleyE16.5_aggr.RData.gz |
1.4 Gb |
(ftp)(http) |
RDATA |
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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