Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.

Humans Argonaute Proteins / genetics Transcriptome Proteomics MicroRNAs / genetics HEK293 Cells Cell Line, Tumor Gene Expression Profiling

Journal

Scientific data
ISSN: 2052-4463
Titre abrégé: Sci Data
Pays: England
ID NLM: 101640192

Informations de publication

Date de publication:
12 Jun 2024
Historique:
received: 14 03 2024
accepted: 03 06 2024
medline: 13 6 2024
pubmed: 13 6 2024
entrez: 12 6 2024
Statut: epublish

Résumé

In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.

Identifiants

DOI: 10.1038/s41597-024-03465-z PMID: 38866801
pubmed: 38866801
doi: 10.1038/s41597-024-03465-z
pii: 10.1038/s41597-024-03465-z
doi:

Substances chimiques

Argonaute Proteins 0
MicroRNAs 0
AGO2 protein, human 0

Types de publication

Dataset Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

617

Subventions

Organisme : Vetenskapsrådet (Swedish Research Council)
ID : 2019-01855
Organisme : Svenska Sällskapet för Medicinsk Forskning (Swedish Society for Medical Research)
ID : S19-0019
Organisme : Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)
ID : PAR 2020/228

Informations de copyright

© 2024. The Author(s).

Références

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Auteurs

Vivian Lobo (V)

Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.

Evgeniia Shcherbinina (E)

Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.

Jakub O Westholm (JO)

Department of Biochemistry and Biophysics, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Stockholm University, Box 1031, SE, 17121, Solna, Sweden.

Iwona Nowak (I)

Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.

Hsiang-Chi Huang (HC)

Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.

Davide Angeletti (D)

SciLifeLab, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden.
ORCID: 0000-0002-5256-1972

Dimitrios G Anastasakis (DG)

RNA Molecular Biology Laboratory, National Institute for Arthritis and Musculoskeletal and Skin Disease, Bethesda, MD, 20892, USA.

Aishe A Sarshad (AA)

Department of Medical Biochemistry and Cell biology, Institute of Biomedicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden. aishe.sarshad@gu.se.
Wallenberg Centre for Molecular and Translational Medicine, University of Gothenburg, SE, 40530, Gothenburg, Sweden. aishe.sarshad@gu.se.
ORCID: 0000-0001-7153-5959

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Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Acides aminés, peptides et protéines › Protéines › Nucléoprotéines › Protéines de liaison à l'ARN › Ribonucléoprotéines › Complexe réprimant l'expression de l'ARN › Protéines Argonaute › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Transcriptome › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Disciplines des sciences naturelles › Chimie › Biochimie › Protéomique › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › ARN non traduit › Petit ARN non traduit › microARN › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Cellules › Cellules épithéliales › Cellules HEK293 › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Cellules › Cellules cultivées › Cellules cancéreuses en culture › Lignée cellulaire tumorale › Integrative transcriptomic and proteomic...
questionsmedicales.fr › Techniques d'investigation › Techniques génétiques › Analyse de profil d'expression de gènes › Integrative transcriptomic and proteomic...