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Carrick BH, Crittenden SL, Chen F, Linsley M, Woodworth J, Kroll-Conner P, Ferdous AS, Keleş S, Wickens M, Kimble J. PUF partner interactions at a conserved interface shape the RNA-binding landscape and cell fate in Caenorhabditis elegans. Dev Cell 2024; 59:661-675.e7. [PMID: 38290520 PMCID: PMC11253550 DOI: 10.1016/j.devcel.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 11/10/2023] [Accepted: 01/08/2024] [Indexed: 02/01/2024]
Abstract
Protein-RNA regulatory networks underpin much of biology. C. elegans FBF-2, a PUF-RNA-binding protein, binds over 1,000 RNAs to govern stem cells and differentiation. FBF-2 interacts with multiple protein partners via a key tyrosine, Y479. Here, we investigate the in vivo significance of partnerships using a Y479A mutant. Occupancy of the Y479A mutant protein increases or decreases at specific sites across the transcriptome, varying with RNAs. Germline development also changes in a specific fashion: Y479A abolishes one FBF-2 function-the sperm-to-oocyte cell fate switch. Y479A's effects on the regulation of one mRNA, gld-1, are critical to this fate change, though other network changes are also important. FBF-2 switches from repression to activation of gld-1 RNA, likely by distinct FBF-2 partnerships. The role of RNA-binding protein partnerships in governing RNA regulatory networks will likely extend broadly, as such partnerships pervade RNA controls in virtually all metazoan tissues and species.
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Affiliation(s)
- Brian H Carrick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Fan Chen
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - MaryGrace Linsley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jennifer Woodworth
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Peggy Kroll-Conner
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ahlan S Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Sündüz Keleş
- Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Marvin Wickens
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Ferdous AS, Lynch TR, Costa Dos Santos SJ, Kapadia DH, Crittenden SL, Kimble J. LST-1 is a bifunctional regulator that feeds back on Notch-dependent transcription to regulate C. elegans germline stem cells. Proc Natl Acad Sci U S A 2023; 120:e2309964120. [PMID: 37729202 PMCID: PMC10523584 DOI: 10.1073/pnas.2309964120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/15/2023] [Indexed: 09/22/2023] Open
Abstract
Notch signaling regulates stem cells across animal phylogeny. C. elegans Notch signaling activates transcription of two genes, lst-1 and sygl-1, that encode potent regulators of germline stem cells. The LST-1 protein regulates stem cells in two distinct ways: It promotes self-renewal posttranscriptionally and also restricts self-renewal by a poorly understood mechanism. Its self-renewal promoting activity resides in its N-terminal region, while its self-renewal restricting activity resides in its C-terminal region and requires the Zn finger. Here, we report that LST-1 limits self-renewal by down-regulating Notch-dependent transcription. We detect LST-1 in the nucleus, in addition to its previously known cytoplasmic localization. LST-1 lowers nascent transcript levels at both lst-1 and sygl-1 loci but not at let-858, a Notch-independent locus. LST-1 also lowers levels of two key components of the Notch activation complex, the LAG-1 DNA binding protein and Notch intracellular domain (NICD). Genetically, an LST-1 Zn finger mutant increases Notch signaling strength in both gain- and loss-of-function GLP-1/Notch receptor mutants. Biochemically, LST-1 co-immunoprecipitates with LAG-1 from nematode extracts, suggesting a direct effect. LST-1 is thus a bifunctional regulator that coordinates posttranscriptional and transcriptional mechanisms in a single protein. This LST-1 bifunctionality relies on its bipartite protein architecture and is bolstered by generation of two LST-1 isoforms, one specialized for Notch downregulation. A conserved theme from worms to human is the coupling of PUF-mediated RNA repression together with Notch feedback in the same protein.
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Affiliation(s)
- Ahlan S. Ferdous
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Tina R. Lynch
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
- Integrated Program in Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | | | - Deep H. Kapadia
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Sarah L. Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI53706
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Crittenden SL, Seidel HS, Kimble J. Analysis of the C. elegans Germline Stem Cell Pool. Methods Mol Biol 2023; 2677:1-36. [PMID: 37464233 DOI: 10.1007/978-1-0716-3259-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
The Caenorhabditis elegans germline is an excellent model for studying the genetic and molecular regulation of stem cell self-renewal and progression of cells from a stem cell state to a differentiated state. The germline tissue is organized in an assembly line with the germline stem cell (GSC) pool at one end and differentiated gametes at the other. A simple mesenchymal niche caps the GSC pool and maintains GSCs in an undifferentiated state by signaling through the conserved Notch pathway. Notch signaling activates transcription of the key GSC regulators lst-1 and sygl-1 proteins in a gradient through the GSC pool. LST-1 and SYGL-1 proteins work with PUF RNA regulators in a self-renewal hub to maintain the GSC pool. In this chapter, we present methods for characterizing the C. elegans GSC pool and early stages of germ cell differentiation. The methods include examination of germlines in living and fixed worms, cell cycle analysis, and analysis of markers. We also discuss assays to separate mutant phenotypes that affect the stem cell vs. differentiation decision from those that affect germ cell processes more generally.
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Affiliation(s)
- Sarah L Crittenden
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA.
| | - Hannah S Seidel
- Department of Biology, Eastern Michigan University, Ypsilanti, MI, USA
| | - Judith Kimble
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
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Gao Y, Ma X, Lu H, Xu P, Xu C. PLAU is associated with cell migration and invasion and is regulated by transcription factor YY1 in cervical cancer. Oncol Rep 2022; 49:25. [PMID: 36524374 PMCID: PMC9813564 DOI: 10.3892/or.2022.8462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 09/30/2022] [Indexed: 12/14/2022] Open
Abstract
Cervical cancer, one of the most common malignancies, has a poor survival rate. The identification of more biomarkers for cervical cancer diagnosis and therapy is urgently needed. Plasminogen activator urokinase (PLAU) exerts multiple biological effects in various physiological and pathological processes; however the role of PLAU in cervical cancer progression is not fully understood. In the present study, the involvement and transcriptional regulation of PLAU in cervical cancer were explored. The expression of PLAU in cervical cancer was first analyzed, and PLAU was found to be overexpressed. In vitro experiments demonstrated that the migration and invasion of HeLa and HT3 cells were significantly suppressed by PLAU knockdown. Additionally, the core promoter of PLAU was confirmed, and the transcription factor YinYang 1 (YY1) was found to regulate PLAU mRNA expression. Overall, the present study elucidated the direct association between PLAU and cervical cancer, suggesting the YY1/PLAU axis as a potential novel therapeutic target for cervical cancer.
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Affiliation(s)
- Yanjun Gao
- Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Xinmei Ma
- Central Laboratory, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Huanxi Lu
- Department of Gynecology, Dongchangfu People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Pan Xu
- Central Laboratory, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China,Dr Pan Xu, Central Laboratory, Liaocheng People's Hospital, 67 Dongchangxi Road, Liaocheng, Shandong 252000, P.R. China, E-mail:
| | - Chengling Xu
- Clinical Laboratory, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China,Correspondence to: Dr Chengling Xu, Clinical Laboratory, Liaocheng People's Hospital, 67 Dongchangxi Road, Liaocheng, Shandong 252000, P.R. China, E-mail:
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