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Large-scale, quantitative proteomics reveals key proteins required for planarian regeneration initiation

ABSTRACT: Large-scale, quantitative proteomics reveals key proteins required for planarian regeneration initiation

PROVIDER: PRJNA974382 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR24657774_1.fastq.gz	Fastqsanger.gz
	SRR24657774_2.fastq.gz	Fastqsanger.gz
	SRR24657775_1.fastq.gz	Fastqsanger.gz
	SRR24657775_2.fastq.gz	Fastqsanger.gz
	SRR24657776_1.fastq.gz	Fastqsanger.gz

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Large-scale, quantitative proteomics reveals key proteins required for planarian regeneration initiation

Project description:Multi-omics studies are increasingly used to decipher the mechanisms underlying tissue regeneration. However, the use of proteomics for such studies has been limited due to the high cost and relatively low throughput and reproducibility. The genes required for planarian regeneration have primarily been identified based on changes in mRNA transcripts; previous studies have not addressed the possibility of protein upregulation prior to detectable increases in transcript abundance during the early stages of planarian regeneration. Here, we used in-depth high-throughput proteomics approaches to analyze the model planarian Schmidtea mediterranea during regeneration and discovered 13 proteins that are essential regulators of key regeneration steps. Two of these proteins, Troponin T and MRPL18, are key regulators of regeneration initiation and showed increases in protein abundance prior to upregulation at the mRNA level. Extensive comparisons between proteomic and transcriptomic datasets suggested the critical mechanisms beyond the transcriptional level, such as the translational and post-translational levels. In summary, this study revealed key regulators of regeneration in a model organism; furthermore, it established an adaptable spectral library and comprehensive proteomics datasets, enabling future in-depth and multi-omics analyses of planarian biology.

2025-05-18 | GSE232894 | GEO

The head-regeneration transcriptome of the planarian Schmidtea mediterranea

Project description:The head-regeneration transcriptome of the planarian Schmidtea mediterranea

2011-07-15 | E-MTAB-607 | biostudies-arrayexpress

equinox is a planarian wound epidermis gene required for the initiation of regeneration

Project description:equinox is a planarian wound epidermis gene required for the initiation of regeneration

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neuroendocrine control of planarian regeneration

Project description:Effective tissue regeneration requires cells to perceive the surrounding context and make internal state adaptations that enable context-dependent fate changes in time and space, but the mechanisms underlying this complex process remain unclear. Here, transcriptom sequencing was used for study neuroendocrine control of planarian regneration

2024-12-31 | GSE210686 | GEO

iTRAQ-Based Quantitative Proteomic Analysis of the Initiation of Head Regeneration in Planarians

Project description:The planarian Dugesia japonica has amazing ability to regenerate a head from the anterior ends of the amputated stump with maintenance of the original anterior-posterior polarity. Although planarians present an attractive system for molecular investigation of regeneration and research has focused on clarifying the molecular mechanism of regeneration initiation in planarians, but proteomic studies are still in the early stages. Here, a global proteomics analysis of regenerating head fragments in planarians at 0h, 2h and 6h after amputation was performed using isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomics coupled with LC-MS/MS strategy. Then the significantly changed proteins were identified. The correlation betwwen protein expression profiles and signaling pathways/biological processes was analyzed by bioinformatics and systems biology.

2015-07-07 | PXD002100 | Pride

neuroendocrine control of planarian regeneration

Project description:neuroendocrine control of planarian regeneration

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m6A Modification Promotes Planarian Regeneration

Project description:m6A Modification Promotes Planarian Regeneration

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in vivo mRNA display: Large-scale Proteomics by Next Generation Sequencing

Project description:We introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem.

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m6A Modification Regulates Planarian Regeneration [scRNA-seq]

Project description:Regeneration is the regrowth of damaged tissues or organs, a vital mechanism in response to damages from primitive organisms to higher mammals. Planarian possesses active whole-body regenerative capability owning to its vast reservoir of adult stem cells, neoblasts, providing an ideal model to delineate the underlying mechanisms for regeneration. RNA N6-methyladenosine (m6A) modification participates in many biological processes, including stem cell self-renewal and differentiation, in particular the regeneration of hematopoietic stem cells and axons. However, how m6A controls regeneration at the whole-organism level remains largely unknown. Here, we demonstrate that the depletion of m6A methyltransferase regulatory subunit wtap abolishes planarian regeneration, potentially through regulating genes related to cell-cell communication and cell cycle. Single-cell RNA-seq (scRNA-seq) analysis unveils that the wtap knockdown induces a unique type of neural progenitor-like cells (NP-like cells), characterized by specific expression of the cell-cell communication ligand grn. Intriguingly, the depletion of m6A-modified transcripts grn/cdk9 (or cdk7) axis rescues the defective regeneration of planarian caused by wtap knockdown. Overall, our study reveals an indispensable role of m6A modification in regulating whole-organism regeneration.

2023-04-28 | GSE202928 | GEO

m6A Modification Regulates Planarian Regeneration [MeRIP-seq]

Project description:The fundamental of regeneration process of invertebrates involves the renewal, differentiation and reprogramming of stem cell in an orchestrated manner. It has been known that N6-methyladenosine (m6A) regulates stem cell renewal and differentiation. It is still unclear if m6A is crucial for the regeneration at whole-organism level. Here, we demonstrate that wtap knockdown mediated m6A depletion impairs planarian regeneration upon amputation. The cell cycle related genes displayed decreased m6A while increased expression levels in response to wtap knockdown. The m6A depletion induced phenotypes can be rescued by double-knocking down these genes together with wtap, suggesting that m6A-mediated cell cycle controls planarian regeneration. Further analysis combining the single-cell sequencing unveils a unique neuronal progenitor-like cell type, named NCC and characterized by specific expression of grn, which is indispensable for neuroregeneration. Overall, our study uncovered an essential role of wtap-mediated m6A modification in regulating stem cell population dynamics and homeostasis in terms of general-body regeneration.

2023-04-28 | GSE171249 | GEO

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