Abstract
Stem cell systems are essential for the development and maintenance of polarized tissues. Intercellular signaling pathways control stem cell systems, where niche cells signal stem cells to maintain the stem cell fate/self-renewal and inhibit differentiation. In the C. elegans germline, GLP-1 Notch signaling specifies the stem cell fate, employing the sequence-specific DNA binding protein LAG-1 to implement the transcriptional response. We undertook a comprehensive genome-wide approach to identify transcriptional targets of GLP-1 signaling. We expected primary response target genes to be evident at the intersection of genes identified as directly bound by LAG-1, from ChIP-seq experiments, with genes identified as requiring GLP-1 signaling for RNA accumulation, from RNA-seq analysis. Furthermore, we performed a time-course transcriptomics analysis following auxin inducible degradation of LAG-1 to distinguish between genes whose RNA level was a primary or secondary response of GLP-1 signaling. Surprisingly, only lst-1 and sygl-1, the two known target genes of GLP-1 in the germline, fulfilled these criteria, indicating that these two genes are the primary response targets of GLP-1 Notch and may be the sole germline GLP-1 signaling protein-coding transcriptional targets for mediating the stem cell fate. In addition, three secondary response genes were identified based on their timing following loss of LAG-1, their lack of a LAG-1 ChIP-seq peak and that their glp-1 dependent mRNA accumulation could be explained by a requirement for lst-1 and sygl-1 activity. Moreover, our analysis also suggests that the function of the primary response genes lst-1 and sygl-1 can account for the glp-1 dependent peak protein accumulation of FBF-2, which promotes the stem cell fate and, in part, for the spatial restriction of elevated LAG-1 accumulation to the stem cell region.
Highlights
Stem cell systems are required for the development and maintenance of polarized tissues, controlling the position, number and timing of differentiated cell type production
We identify only lst-1 and sygl-1, two of a number of previously reported targets, as likely the sole primary mRNA transcriptional targets of GLP-1 signaling that promote the germline stem cell fate
We identify secondary GLP-1 signaling RNA and protein targets, whose expression shows dependence on lst-1 and sygl-1, where the protein targets reinforce the importance of posttranscriptional regulation in control of the stem cell fate
Summary
Stem cell systems are required for the development and maintenance of polarized tissues, controlling the position, number and timing of differentiated cell type production. A deep understanding of how a stem cell system works requires knowledge of the full repertoire of genes that are the primary targets of the signaling pathway, as well as secondary response gene products. The DTC expresses two Notch pathway DSL (for Delta, Serate, LAG-2) ligands, LAG-2 and APX-1 [8,9,10]. GLP-1 is expressed in progenitor zone germ cells and continuously required to promote the germline stem cell fate. The current model is that when the DTC presenting LAG-2 and APX-1 interacts with GLP-1 expressed in germ cells, ligand dependent cleavage of the receptor generates the GLP-1 intracellular domain, GLP-1(ICD), which translocates to the nucleus and associates with the sequence specific DNA binding protein LAG-1 to activate primary target gene transcription
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