Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

RNA-Seq to identify germline stem cell-enriched genes and cystoblast-enriched genes and BMP targeted genes

ABSTRACT: We sequenced the transcriptomes of genetically expanded stem cells that either experience high levels of BMP signalling (expression of constitutively active BMPR, tkvQD.) or low levels (expression of shRNA again the differentiation promoting factor bam). We also sequenced RNA from differentiating daughter cells (cystoblasts) isolated through the expression of bam.GFP. We then performed a differential expression analysis. Our aim was to identify germline stem cell-enriched gene and cystoblast-enriched genes by tkvQD vs bam-GFP. We also wished to identify possible BMP target genes by comparing tkvQD and bam.shRNA. We have subsequently taken a few of the genes identified and validated their roles in germline stem cell self-renewal and differentiation in vivo.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Drosophila melanogaster

SUBMITTER: Ping Wang

PROVIDER: E-MTAB-7063 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Drosophila Ovarian Germline Stem Cell Cytocensor Projections Dynamically Receive and Attenuate BMP Signaling.

Wilcockson Scott G SG Ashe Hilary L HL

Developmental cell 20190606 3

In the Drosophila ovarian germline, Bone Morphogenetic Protein (BMP) signals released by niche cells promote germline stem cell (GSC) maintenance. Although BMP signaling is known to repress expression of a key differentiation factor, it remains unclear whether BMP-responsive transcription also contributes positively to GSC identity. Here, we identify the GSC transcriptome using RNA sequencing (RNA-seq), including the BMP-induced transcriptional network. Based on these data, we provide evidence t ...[more]

PMID: 31178401

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Project description:Both transcription and post-transcriptional processes, such as alternative splicing, play crucial roles in controlling developmental programs in metazoans. Recently emerged RNA-seq method has brought our understanding of eukaryotic transcriptomes to a new level, because it can resolve both gene expression level and alternative splicing events simultaneously. To gain a better understanding of cellular differentiation in gonads, we analyzed mRNA profiles from Drosophila testes and ovaries using RNA-seq. We identified a set of genes that have sex-specific isoforms in wild-type (WT) gonads, including several transcription factors. We found that differentiation of sperms from undifferentiated germ cells induced a dramatic downregulation of RNA splicing factors. Our data confirmed that RNA splicing events are significantly more frequent in the undifferentiated cell-enriched bag of marbles (bam) mutant testis, but downregulated upon differentiation in WT testis. Consistent with this, we showed that genes required for meiosis and terminal differentiation in WT testis were mainly regulated at the transcriptional level, but not by alternative splicing. Unexpectedly, we observed an increase in expression of all families of chromatin remodeling factors and histone modifying enzymes in the undifferentiated cell-enriched bam testis. More interestingly, chromatin regulators and histone modifying enzymes with opposite enzymatic activities are coenriched in undifferentiated cells in testis, suggesting that these cells may possess dynamic chromatin architecture. Finally, our data revealed many new features of the Drosophila gonadal transcriptomes, and will lead to a more comprehensive understanding of how differential gene expression and splicing regulate gametogenesis in Drosophila. Our data provided a foundation for the systematic study of gene expression and alternative splicing in many interesting areas of germ cell biology in Drosophila, such as the molecular basis for sexual dimorphism and the regulation of the proliferation vs terminal differentiation programs in germline stem cell lineages. RNA-Seq experiments for four Drosophila melanogaster samples: (1) bam mutant testes, (2) wild-type testes, (3) bam mutant ovaries, (4) wild-type ovaries

Dataset Information

RNA-Seq to identify germline stem cell-enriched genes and cystoblast-enriched genes and BMP targeted genes

Publications

Drosophila Ovarian Germline Stem Cell Cytocensor Projections Dynamically Receive and Attenuate BMP Signaling.

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