GLP-1 Notch-LAG-1 CSL control of the germline stem cell fate is mediated by transcriptional targets lst-1 and sygl-1
Open Access
- 1 March 2020
- journal article
- research article
- Published by Public Library of Science (PLoS) in PLoS Genetics
- Vol. 16 (3), e1008650
- https://doi.org/10.1371/journal.pgen.1008650
Abstract
Author summary Stem cell systems are central to tissue development, homeostasis and regeneration, where niche to stem cell signaling pathways promote the stem cell fate/self-renewal and inhibit differentiation. The evolutionarily conserved GLP-1 Notch signaling pathway in the C. elegans germline is an experimentally tractable system, allowing dissection of control of the stem cell fate and inhibition of meiotic development. However, as in many systems, the primary molecular targets of the signaling pathway in stem cells is incompletely known, as are secondary molecular targets, and this knowledge is essential for a deep understanding of stem cell systems. Here we focus on the identification of the primary transcriptional targets of the GLP-1 signaling pathway that promotes the stem cell fate, employing unbiased multilevel genomic approaches. 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 also 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. 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.Funding Information
- National Institute of General Medical Sciences (R01 GM-100756)
This publication has 93 references indexed in Scilit:
- Fiji: an open-source platform for biological-image analysisNature Methods, 2012
- In Vivo and Transcriptome-wide Identification of RNA Binding Protein Target SitesMolecular Cell, 2011
- Strategies for Homeostatic Stem Cell Self-Renewal in Adult TissuesCell, 2011
- A quantitative RNA code for mRNA target selection by the germline fate determinant GLD-1The EMBO Journal, 2010
- Metadata matters: access to image data in the real worldThe Journal of cell biology, 2010
- Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell IdentitiesMolecular Cell, 2010
- Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulatorProceedings of the National Academy of Sciences of the United States of America, 2010
- Recombineering: a homologous recombination-based method of genetic engineeringNature Protocols, 2009
- 3′ UTRs Are the Primary Regulators of Gene Expression in the C. elegans GermlineCurrent Biology, 2008
- A conserved RNA-binding protein controls germline stem cells in Caenorhabditis elegansNature, 2002