BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis
The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA...
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2012
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| Acceso en línea: | http://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepe http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_19326203_v7_n12_p_PerezPepe_oai |
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I28-R145-paper_19326203_v7_n12_p_PerezPepe_oai2020-10-19 Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. 2012 The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al. Fil:Slomiansky, V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Loschi, M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Luchelli, L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Thomas, M.G. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Boccaccio, G.L. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. application/pdf http://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepe info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar PLoS ONE 2012;7(12) focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_19326203_v7_n12_p_PerezPepe_oai |
| institution |
Universidad de Buenos Aires |
| institution_str |
I-28 |
| repository_str |
R-145 |
| collection |
Repositorio Digital de la Universidad de Buenos Aires (UBA) |
| topic |
focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia |
| spellingShingle |
focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| topic_facet |
focal adhesion kinase focal adhesion kinase 56D initiation factor 2alpha messenger RNA phosphoprotein phosphatase 1 transcription factor translation initiation factor 2alpha unclassified drug analytic method article BUHO cell function cell granule cell size cell stimulation cell stress cell structure cellular distribution gene silencing image analysis image processing information processing insect cell mammal cell molecular dynamics molecular imaging processing body protein phosphorylation RNA interference stress granule synapse Algorithms Animals Drosophila melanogaster Image Processing, Computer-Assisted Molecular Imaging Organelles Oxidative Stress RNA Interference RNA, Messenger Software Synapses Time Factors Hexapoda Mammalia |
| description |
The spontaneous and reversible formation of foci and filaments that contain proteins involved in different metabolic processes is common in both the nucleus and the cytoplasm. Stress granules (SGs) and processing bodies (PBs) belong to a novel family of cellular structures collectively known as mRNA silencing foci that harbour repressed mRNAs and their associated proteins. SGs and PBs are highly dynamic and they form upon stress and dissolve thus releasing the repressed mRNAs according to changes in cell physiology. In addition, aggregates containing abnormal proteins are frequent in neurodegenerative disorders. In spite of the growing relevance of these supramolecular aggregates to diverse cellular functions a reliable automated tool for their systematic analysis is lacking. Here we report a MATLAB Script termed BUHO for the high-throughput image analysis of cellular foci. We used BUHO to assess the number, size and distribution of distinct objects with minimal deviation from manually obtained parameters. BUHO successfully addressed the induction of both SGs and PBs in mammalian and insect cells exposed to different stress stimuli. We also used BUHO to assess the dynamics of specific mRNA-silencing foci termed Smaug 1 foci (S-foci) in primary neurons upon synaptic stimulation. Finally, we used BUHO to analyze the role of candidate genes on SG formation in an RNAi-based experiment. We found that FAK56D, GCN2 and PP1 govern SG formation. The role of PP1 is conserved in mammalian cells as judged by the effect of the PP1 inhibitor salubrinal, and involves dephosphorylation of the translation factor eIF2α. All these experiments were analyzed manually and by BUHO and the results differed in less than 5% of the average value. The automated analysis by this user-friendly method will allow high-throughput image processing in short times by providing a robust, flexible and reliable alternative to the laborious and sometimes unfeasible visual scrutiny. © 2012 Perez-Pepe et al. |
| format |
Artículo Artículo publishedVersion |
| author |
Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. |
| author_facet |
Perez-Pepe, M. Slomiansky, V. Loschi, M. Luchelli, L. Neme, M. Thomas, M.G. Boccaccio, G.L. |
| author_sort |
Perez-Pepe, M. |
| title |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| title_short |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| title_full |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| title_fullStr |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| title_full_unstemmed |
BUHO: A MATLAB Script for the Study of Stress Granules and Processing Bodies by High-Throughput Image Analysis |
| title_sort |
buho: a matlab script for the study of stress granules and processing bodies by high-throughput image analysis |
| publishDate |
2012 |
| url |
http://hdl.handle.net/20.500.12110/paper_19326203_v7_n12_p_PerezPepe http://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_19326203_v7_n12_p_PerezPepe_oai |
| work_keys_str_mv |
AT perezpepem buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT slomianskyv buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT loschim buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT luchellil buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT nemem buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT thomasmg buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis AT boccacciogl buhoamatlabscriptforthestudyofstressgranulesandprocessingbodiesbyhighthroughputimageanalysis |
| _version_ |
1766026810400702464 |